Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c109' (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/6725360-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64 Version: 0.70 PID: 24164 Logging PID: 24165 Task: {'appstream': False, 'background': True, 'build_id': 6725360, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '407595c3674c409d9ec8f4abc4d662e71fc4fe3a', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83/openbabel', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'openbabel', 'package_version': '3.1.1-21', 'project_dirname': 'boost-1.83', 'project_name': 'boost-1.83', 'project_owner': 'ppalka', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ppalka/boost-1.83/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}], 'sandbox': 'ppalka/boost-1.83--ppalka', 'source_json': {}, 'source_type': None, 'submitter': 'ppalka', 'tags': [], 'task_id': '6725360-fedora-rawhide-x86_64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83/openbabel /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ppalka/boost-1.83/openbabel', '/var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel'... Running: git checkout 407595c3674c409d9ec8f4abc4d662e71fc4fe3a -- cmd: ['git', 'checkout', '407595c3674c409d9ec8f4abc4d662e71fc4fe3a', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel rc: 0 stdout: stderr: Note: switching to '407595c3674c409d9ec8f4abc4d662e71fc4fe3a'. 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 407595c automatic import of openbabel Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading openbabel-openbabel-3-1-1.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o openbabel-openbabel-3-1-1.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/ppalka/boost-1.83/openbabel/openbabel-openbabel-3-1-1.tar.gz/md5/7efb864d2ba5593b286ddc49d70aa851/openbabel-openbabel-3-1-1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 100 34.9M 100 34.9M 0 0 41.0M 0 --:--:-- --:--:-- --:--:-- 41.0M INFO: Reading stdout from command: md5sum openbabel-openbabel-3-1-1.tar.gz Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel/openbabel.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1701768643.660671 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 5.2 starting (python version = 3.11.3, NVR = mock-5.2-1.fc38), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel/openbabel.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1701768643.660671 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel/openbabel.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Mock Version: 5.2 INFO: Mock Version: 5.2 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1701768643.660671/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1701768643.660671/root INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/6b84d969583eab0c41f489d3b55e82f78ada08ef1320e9fb113e0d98a3d2c934/merged INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/6b84d969583eab0c41f489d3b55e82f78ada08ef1320e9fb113e0d98a3d2c934/merged) with podman image umount INFO: Package manager dnf detected and used (fallback) INFO: Bootstrap image not marked ready Start(bootstrap): installing dnf tooling No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 8.4 MB/s | 7.2 MB 00:00 fedora 22 MB/s | 72 MB 00:03 Last metadata expiration check: 0:00:01 ago on Tue Dec 5 09:30:50 2023. Package python3-dnf-4.18.1-2.fc40.noarch is already installed. Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: python3-dnf-plugins-core noarch 4.4.3-1.fc40 fedora 317 k Installing dependencies: dbus-libs x86_64 1:1.14.10-1.fc40 fedora 155 k python3-dateutil noarch 1:2.8.2-11.fc40 fedora 356 k python3-dbus x86_64 1.3.2-4.fc39 fedora 157 k python3-distro noarch 1.8.0-6.fc39 fedora 49 k python3-six noarch 1.16.0-12.fc39 fedora 41 k python3-systemd x86_64 235-5.fc39 fedora 107 k Transaction Summary ================================================================================ Install 7 Packages Total download size: 1.2 M Installed size: 3.6 M Downloading Packages: (1/7): dbus-libs-1.14.10-1.fc40.x86_64.rpm 299 kB/s | 155 kB 00:00 (2/7): python3-dbus-1.3.2-4.fc39.x86_64.rpm 274 kB/s | 157 kB 00:00 (3/7): python3-distro-1.8.0-6.fc39.noarch.rpm 465 kB/s | 49 kB 00:00 (4/7): python3-dateutil-2.8.2-11.fc40.noarch.rp 511 kB/s | 356 kB 00:00 (5/7): python3-six-1.16.0-12.fc39.noarch.rpm 476 kB/s | 41 kB 00:00 (6/7): python3-systemd-235-5.fc39.x86_64.rpm 1.2 MB/s | 107 kB 00:00 (7/7): python3-dnf-plugins-core-4.4.3-1.fc40.no 1.4 MB/s | 317 kB 00:00 -------------------------------------------------------------------------------- Total 1.4 MB/s | 1.2 MB 00:00 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : python3-systemd-235-5.fc39.x86_64 1/7 Installing : python3-six-1.16.0-12.fc39.noarch 2/7 Installing : python3-dateutil-1:2.8.2-11.fc40.noarch 3/7 Installing : python3-distro-1.8.0-6.fc39.noarch 4/7 Installing : dbus-libs-1:1.14.10-1.fc40.x86_64 5/7 Installing : python3-dbus-1.3.2-4.fc39.x86_64 6/7 Installing : python3-dnf-plugins-core-4.4.3-1.fc40.noarch 7/7 Running scriptlet: python3-dnf-plugins-core-4.4.3-1.fc40.noarch 7/7 Installed: dbus-libs-1:1.14.10-1.fc40.x86_64 python3-dateutil-1:2.8.2-11.fc40.noarch python3-dbus-1.3.2-4.fc39.x86_64 python3-distro-1.8.0-6.fc39.noarch python3-dnf-plugins-core-4.4.3-1.fc40.noarch python3-six-1.16.0-12.fc39.noarch python3-systemd-235-5.fc39.x86_64 Complete! Finish(bootstrap): installing dnf tooling Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1701768643.660671/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 dnf detected and used (direct choice) Start: installing minimal buildroot with dnf No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 37 kB/s | 1.5 kB 00:00 Copr repository 24 MB/s | 7.2 MB 00:00 fedora 855 kB/s | 24 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.21-2.fc40 fedora 1.8 M bzip2 x86_64 1.0.8-16.fc39 fedora 52 k coreutils x86_64 9.4-1.fc40 fedora 1.1 M cpio x86_64 2.14-5.fc40 fedora 280 k diffutils x86_64 3.10-3.fc39 fedora 398 k fedora-release-common noarch 40-0.20 fedora 20 k findutils x86_64 1:4.9.0-6.fc40 fedora 492 k gawk x86_64 5.2.2-2.fc39 fedora 1.1 M glibc-minimal-langpack x86_64 2.38.9000-26.fc40 fedora 85 k grep x86_64 3.11-5.fc40 fedora 298 k gzip x86_64 1.12-6.fc39 fedora 166 k info x86_64 7.1-1.fc40 fedora 184 k patch x86_64 2.7.6-22.fc39 fedora 125 k redhat-rpm-config noarch 271-1.fc40 fedora 81 k rpm-build x86_64 4.19.0-3.fc40 fedora 79 k sed x86_64 4.8-14.fc39 fedora 306 k shadow-utils x86_64 2:4.14.0-2.fc40 fedora 1.3 M tar x86_64 2:1.35-2.fc40 fedora 864 k unzip x86_64 6.0-62.fc39 fedora 184 k util-linux x86_64 2.39.2-1.fc40 fedora 1.2 M which x86_64 2.21-40.fc39 fedora 42 k xz x86_64 5.4.5-1.fc40 fedora 557 k Installing dependencies: alternatives x86_64 1.25-1.fc39 fedora 39 k ansible-srpm-macros noarch 1-11.fc39 fedora 21 k audit-libs x86_64 3.1.2-5.fc40 fedora 117 k authselect x86_64 1.4.3-1.fc40 fedora 149 k authselect-libs x86_64 1.4.3-1.fc40 fedora 249 k basesystem noarch 11-18.fc39 fedora 7.2 k binutils x86_64 2.41-15.fc40 fedora 6.3 M binutils-gold x86_64 2.41-15.fc40 fedora 797 k bzip2-libs x86_64 1.0.8-16.fc39 fedora 41 k ca-certificates noarch 2023.2.62_v7.0.401-4.fc40 fedora 863 k coreutils-common x86_64 9.4-1.fc40 fedora 2.1 M cracklib x86_64 2.9.11-2.fc39 fedora 94 k crypto-policies noarch 20231113-1.gitb402e82.fc40 fedora 99 k curl x86_64 8.4.0-1.fc40 fedora 362 k cyrus-sasl-lib x86_64 2.1.28-11.fc39 fedora 793 k debugedit x86_64 5.0-11.fc40 fedora 77 k dwz x86_64 0.15-3.fc39 fedora 134 k ed x86_64 1.19-4.fc39 fedora 79 k efi-srpm-macros noarch 5-9.fc39 fedora 22 k elfutils x86_64 0.190-4.fc40 fedora 550 k elfutils-debuginfod-client x86_64 0.190-4.fc40 fedora 38 k elfutils-default-yama-scope noarch 0.190-4.fc40 fedora 13 k elfutils-libelf x86_64 0.190-4.fc40 fedora 194 k elfutils-libs x86_64 0.190-4.fc40 fedora 259 k fedora-gpg-keys noarch 40-0.2 fedora 130 k fedora-release noarch 40-0.20 fedora 9.3 k fedora-release-identity-basic noarch 40-0.20 fedora 10 k fedora-repos noarch 40-0.2 fedora 9.3 k fedora-repos-rawhide noarch 40-0.2 fedora 8.9 k file x86_64 5.45-1.fc40 fedora 49 k file-libs x86_64 5.45-1.fc40 fedora 763 k filesystem x86_64 3.18-6.fc39 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-12.fc39 fedora 26 k forge-srpm-macros noarch 0.1.0-1.fc40 fedora 18 k fpc-srpm-macros noarch 1.3-8.fc39 fedora 7.4 k gdb-minimal x86_64 13.2-12.fc40 fedora 4.2 M gdbm x86_64 1:1.23-4.fc39 fedora 155 k gdbm-libs x86_64 1:1.23-4.fc39 fedora 56 k ghc-srpm-macros noarch 1.6.1-3.fc40 fedora 8.1 k glibc x86_64 2.38.9000-26.fc40 fedora 2.2 M glibc-common x86_64 2.38.9000-26.fc40 fedora 367 k glibc-gconv-extra x86_64 2.38.9000-26.fc40 fedora 1.7 M gmp x86_64 1:6.2.1-5.fc39 fedora 313 k gnat-srpm-macros noarch 6-3.fc39 fedora 8.8 k go-srpm-macros noarch 3.3.1-1.fc40 fedora 28 k jansson x86_64 2.13.1-7.fc39 fedora 44 k kernel-srpm-macros noarch 1.0-20.fc39 fedora 10 k keyutils-libs x86_64 1.6.1-7.fc39 fedora 31 k krb5-libs x86_64 1.21.2-2.fc40 fedora 765 k libacl x86_64 2.3.1-11.fc40 fedora 24 k libarchive x86_64 3.7.2-1.fc40 fedora 408 k libattr x86_64 2.5.1-9.fc40 fedora 18 k libblkid x86_64 2.39.2-1.fc40 fedora 116 k libbrotli x86_64 1.1.0-1.fc40 fedora 336 k libcap x86_64 2.69-1.fc40 fedora 83 k libcap-ng x86_64 0.8.3-8.fc40 fedora 32 k libcom_err x86_64 1.47.0-2.fc39 fedora 26 k libcurl x86_64 8.4.0-1.fc40 fedora 343 k libeconf x86_64 0.5.2-1.fc40 fedora 30 k libevent x86_64 2.1.12-9.fc39 fedora 258 k libfdisk x86_64 2.39.2-1.fc40 fedora 162 k libffi x86_64 3.4.4-4.fc39 fedora 40 k libgcc x86_64 13.2.1-5.fc40 fedora 112 k libgomp x86_64 13.2.1-5.fc40 fedora 321 k libidn2 x86_64 2.3.4-3.fc39 fedora 117 k libmount x86_64 2.39.2-1.fc40 fedora 154 k libnghttp2 x86_64 1.58.0-1.fc40 fedora 76 k libnsl2 x86_64 2.0.0-6.fc39 fedora 30 k libpkgconf x86_64 1.9.5-2.fc39 fedora 38 k libpsl x86_64 0.21.2-4.fc39 fedora 63 k libpwquality x86_64 1.4.5-6.fc39 fedora 120 k libselinux x86_64 3.6-0.rc2.1.fc40 fedora 88 k libsemanage x86_64 3.6-0.rc2.1.fc40 fedora 116 k libsepol x86_64 3.6-0.rc2.1.fc40 fedora 340 k libsigsegv x86_64 2.14-5.fc39 fedora 27 k libsmartcols x86_64 2.39.2-1.fc40 fedora 67 k libssh x86_64 0.10.5-2.fc39 fedora 211 k libssh-config noarch 0.10.5-2.fc39 fedora 9.2 k libstdc++ x86_64 13.2.1-5.fc40 fedora 864 k libtasn1 x86_64 4.19.0-3.fc39 fedora 74 k libtirpc x86_64 1.3.4-0.fc40 fedora 94 k libunistring x86_64 1.1-5.fc40 fedora 543 k libutempter x86_64 1.2.1-10.fc39 fedora 26 k libuuid x86_64 2.39.2-1.fc40 fedora 28 k libverto x86_64 0.3.2-6.fc39 fedora 20 k libxcrypt x86_64 4.4.36-2.fc39 fedora 119 k libxml2 x86_64 2.12.1-1.fc40 fedora 699 k libzstd x86_64 1.5.5-4.fc39 fedora 309 k lua-libs x86_64 5.4.6-3.fc39 fedora 133 k lua-srpm-macros noarch 1-9.fc39 fedora 8.6 k lz4-libs x86_64 1.9.4-4.fc39 fedora 67 k mpfr x86_64 4.2.1-1.fc40 fedora 343 k ncurses-base noarch 6.4-8.20231001.fc40 fedora 88 k ncurses-libs x86_64 6.4-8.20231001.fc40 fedora 338 k ocaml-srpm-macros noarch 9-1.fc40 fedora 9.0 k openblas-srpm-macros noarch 2-14.fc39 fedora 7.5 k openldap x86_64 2.6.6-1.fc39 fedora 255 k openssl-libs x86_64 1:3.1.4-1.fc40 fedora 2.2 M p11-kit x86_64 0.25.3-1.fc40 fedora 522 k p11-kit-trust x86_64 0.25.3-1.fc40 fedora 142 k package-notes-srpm-macros noarch 0.5-9.fc39 fedora 11 k pam x86_64 1.5.3-8.fc40 fedora 547 k pam-libs x86_64 1.5.3-8.fc40 fedora 57 k pcre2 x86_64 10.42-2.fc40 fedora 233 k pcre2-syntax noarch 10.42-2.fc40 fedora 143 k perl-srpm-macros noarch 1-51.fc39 fedora 8.0 k pkgconf x86_64 1.9.5-2.fc39 fedora 42 k pkgconf-m4 noarch 1.9.5-2.fc39 fedora 14 k pkgconf-pkg-config x86_64 1.9.5-2.fc39 fedora 9.6 k popt x86_64 1.19-3.fc39 fedora 66 k publicsuffix-list-dafsa noarch 20230812-1.fc40 fedora 57 k pyproject-srpm-macros noarch 1.10.0-1.fc40 fedora 14 k python-srpm-macros noarch 3.12-4.fc40 fedora 25 k qt5-srpm-macros noarch 5.15.11-1.fc40 fedora 8.3 k qt6-srpm-macros noarch 6.6.1-1.fc40 fedora 8.6 k readline x86_64 8.2-4.fc39 fedora 213 k rpm x86_64 4.19.0-3.fc40 fedora 537 k rpm-build-libs x86_64 4.19.0-3.fc40 fedora 96 k rpm-libs x86_64 4.19.0-3.fc40 fedora 313 k rpm-sequoia x86_64 1.5.0-2.fc40 fedora 879 k rust-srpm-macros noarch 25.2-2.fc40 fedora 13 k setup noarch 2.14.5-1.fc40 fedora 155 k sqlite-libs x86_64 3.44.1-1.fc40 fedora 693 k systemd-libs x86_64 255~rc4-3.fc40 fedora 702 k util-linux-core x86_64 2.39.2-1.fc40 fedora 493 k xxhash-libs x86_64 0.8.2-1.fc39 fedora 37 k xz-libs x86_64 5.4.5-1.fc40 fedora 108 k zip x86_64 3.0-39.fc40 fedora 266 k zlib x86_64 1.2.13-5.fc40 fedora 94 k zstd x86_64 1.5.5-4.fc39 fedora 482 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 152 Packages Total size: 52 M Installed size: 180 M Downloading Packages: [SKIPPED] alternatives-1.25-1.fc39.x86_64.rpm: Already downloaded [SKIPPED] ansible-srpm-macros-1-11.fc39.noarch.rpm: Already downloaded [SKIPPED] audit-libs-3.1.2-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] authselect-1.4.3-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] authselect-libs-1.4.3-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-18.fc39.noarch.rpm: Already downloaded [SKIPPED] bash-5.2.21-2.fc40.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.41-15.fc40.x86_64.rpm: Already downloaded [SKIPPED] binutils-gold-2.41-15.fc40.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.8-16.fc39.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.8-16.fc39.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch.rpm: Already downloaded [SKIPPED] coreutils-9.4-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] coreutils-common-9.4-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cpio-2.14-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] cracklib-2.9.11-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] crypto-policies-20231113-1.gitb402e82.fc40.noarch.rpm: Already downloaded [SKIPPED] curl-8.4.0-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] cyrus-sasl-lib-2.1.28-11.fc39.x86_64.rpm: Already downloaded [SKIPPED] debugedit-5.0-11.fc40.x86_64.rpm: Already downloaded [SKIPPED] diffutils-3.10-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] dwz-0.15-3.fc39.x86_64.rpm: Already downloaded [SKIPPED] ed-1.19-4.fc39.x86_64.rpm: Already downloaded [SKIPPED] efi-srpm-macros-5-9.fc39.noarch.rpm: Already downloaded [SKIPPED] elfutils-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-debuginfod-client-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-default-yama-scope-0.190-4.fc40.noarch.rpm: Already downloaded [SKIPPED] elfutils-libelf-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] elfutils-libs-0.190-4.fc40.x86_64.rpm: Already downloaded [SKIPPED] fedora-gpg-keys-40-0.2.noarch.rpm: Already downloaded [SKIPPED] fedora-release-40-0.20.noarch.rpm: Already downloaded [SKIPPED] fedora-release-common-40-0.20.noarch.rpm: Already downloaded [SKIPPED] fedora-release-identity-basic-40-0.20.noarch.rpm: Already 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/usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-40-primary (0xA15B79CC) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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Installing : gawk-5.2.2-2.fc39.x86_64 102/152 Installing : libverto-0.3.2-6.fc39.x86_64 103/152 Installing : xxhash-libs-0.8.2-1.fc39.x86_64 104/152 Installing : libssh-config-0.10.5-2.fc39.noarch 105/152 Installing : kernel-srpm-macros-1.0-20.fc39.noarch 106/152 Installing : gnat-srpm-macros-6-3.fc39.noarch 107/152 Installing : ghc-srpm-macros-1.6.1-3.fc40.noarch 108/152 Installing : fpc-srpm-macros-1.3-8.fc39.noarch 109/152 Installing : coreutils-common-9.4-1.fc40.x86_64 110/152 Installing : openssl-libs-1:3.1.4-1.fc40.x86_64 111/152 Installing : coreutils-9.4-1.fc40.x86_64 112/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/152 Installing : ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 113/152 Installing : krb5-libs-1.21.2-2.fc40.x86_64 114/152 Installing : libtirpc-1.3.4-0.fc40.x86_64 115/152 Running scriptlet: authselect-libs-1.4.3-1.fc40.x86_64 116/152 Installing : authselect-libs-1.4.3-1.fc40.x86_64 116/152 Installing : gzip-1.12-6.fc39.x86_64 117/152 Installing : cracklib-2.9.11-2.fc39.x86_64 118/152 Installing : libpwquality-1.4.5-6.fc39.x86_64 119/152 Installing : authselect-1.4.3-1.fc40.x86_64 120/152 Installing : libnsl2-2.0.0-6.fc39.x86_64 121/152 Installing : pam-1.5.3-8.fc40.x86_64 122/152 Installing : libssh-0.10.5-2.fc39.x86_64 123/152 Installing : libarchive-3.7.2-1.fc40.x86_64 124/152 Installing : libevent-2.1.12-9.fc39.x86_64 125/152 Installing : openldap-2.6.6-1.fc39.x86_64 126/152 Installing : libcurl-8.4.0-1.fc40.x86_64 127/152 Installing : elfutils-libs-0.190-4.fc40.x86_64 128/152 Installing : elfutils-debuginfod-client-0.190-4.fc40.x86_64 129/152 Installing : binutils-gold-2.41-15.fc40.x86_64 130/152 Running scriptlet: binutils-gold-2.41-15.fc40.x86_64 130/152 Installing : binutils-2.41-15.fc40.x86_64 131/152 Running scriptlet: binutils-2.41-15.fc40.x86_64 131/152 Installing : elfutils-0.190-4.fc40.x86_64 132/152 Installing : gdb-minimal-13.2-12.fc40.x86_64 133/152 Installing : debugedit-5.0-11.fc40.x86_64 134/152 Installing : curl-8.4.0-1.fc40.x86_64 135/152 Installing : rpm-sequoia-1.5.0-2.fc40.x86_64 136/152 Installing : rpm-libs-4.19.0-3.fc40.x86_64 137/152 Running scriptlet: rpm-4.19.0-3.fc40.x86_64 138/152 Installing : rpm-4.19.0-3.fc40.x86_64 138/152 Installing : efi-srpm-macros-5-9.fc39.noarch 139/152 Installing : lua-srpm-macros-1-9.fc39.noarch 140/152 Installing : rpm-build-libs-4.19.0-3.fc40.x86_64 141/152 Installing : ansible-srpm-macros-1-11.fc39.noarch 142/152 Installing : fonts-srpm-macros-1:2.0.5-12.fc39.noarch 143/152 Installing : forge-srpm-macros-0.1.0-1.fc40.noarch 144/152 Installing : go-srpm-macros-3.3.1-1.fc40.noarch 145/152 Installing : python-srpm-macros-3.12-4.fc40.noarch 146/152 Installing : redhat-rpm-config-271-1.fc40.noarch 147/152 Installing : rpm-build-4.19.0-3.fc40.x86_64 148/152 Installing : pyproject-srpm-macros-1.10.0-1.fc40.noarch 149/152 Installing : util-linux-2.39.2-1.fc40.x86_64 150/152 Installing : which-2.21-40.fc39.x86_64 151/152 Installing : info-7.1-1.fc40.x86_64 152/152 Running scriptlet: filesystem-3.18-6.fc39.x86_64 152/152 Running scriptlet: ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch 152/152 Running scriptlet: authselect-libs-1.4.3-1.fc40.x86_64 152/152 Running scriptlet: rpm-4.19.0-3.fc40.x86_64 152/152 Running scriptlet: info-7.1-1.fc40.x86_64 152/152 Installed: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc40.x86_64 authselect-1.4.3-1.fc40.x86_64 authselect-libs-1.4.3-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.x86_64 binutils-2.41-15.fc40.x86_64 binutils-gold-2.41-15.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-1.fc40.x86_64 coreutils-common-9.4-1.fc40.x86_64 cpio-2.14-5.fc40.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231113-1.gitb402e82.fc40.noarch curl-8.4.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-11.fc40.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.x86_64 elfutils-debuginfod-client-0.190-4.fc40.x86_64 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.x86_64 elfutils-libs-0.190-4.fc40.x86_64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.20.noarch fedora-release-common-40-0.20.noarch fedora-release-identity-basic-40-0.20.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-1:4.9.0-6.fc40.x86_64 fonts-srpm-macros-1:2.0.5-12.fc39.noarch forge-srpm-macros-0.1.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-13.2-12.fc40.x86_64 gdbm-1:1.23-4.fc39.x86_64 gdbm-libs-1:1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-26.fc40.x86_64 glibc-common-2.38.9000-26.fc40.x86_64 glibc-gconv-extra-2.38.9000-26.fc40.x86_64 glibc-minimal-langpack-2.38.9000-26.fc40.x86_64 gmp-1:6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.1-1.fc40.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc40.x86_64 libacl-2.3.1-11.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.1-9.fc40.x86_64 libblkid-2.39.2-1.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.69-1.fc40.x86_64 libcap-ng-0.8.3-8.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.4.0-1.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc40.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-5.fc40.x86_64 libgomp-13.2.1-5.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.58.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.6-0.rc2.1.fc40.x86_64 libsemanage-3.6-0.rc2.1.fc40.x86_64 libsepol-3.6-0.rc2.1.fc40.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc40.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-5.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc40.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.12.1-1.fc40.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.1-1.fc40.x86_64 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-1:3.1.4-1.fc40.x86_64 p11-kit-0.25.3-1.fc40.x86_64 p11-kit-trust-0.25.3-1.fc40.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-8.fc40.x86_64 pam-libs-1.5.3-8.fc40.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-2.fc40.x86_64 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.10.0-1.fc40.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.11-1.fc40.noarch qt6-srpm-macros-6.6.1-1.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-271-1.fc40.noarch rpm-4.19.0-3.fc40.x86_64 rpm-build-4.19.0-3.fc40.x86_64 rpm-build-libs-4.19.0-3.fc40.x86_64 rpm-libs-4.19.0-3.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.5-1.fc40.noarch shadow-utils-2:4.14.0-2.fc40.x86_64 sqlite-libs-3.44.1-1.fc40.x86_64 systemd-libs-255~rc4-3.fc40.x86_64 tar-2:1.35-2.fc40.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc40.x86_64 util-linux-core-2.39.2-1.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.5-1.fc40.x86_64 xz-libs-5.4.5-1.fc40.x86_64 zip-3.0-39.fc40.x86_64 zlib-1.2.13-5.fc40.x86_64 zstd-1.5.5-4.fc39.x86_64 Complete! Finish: installing minimal buildroot with dnf Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: alternatives-1.25-1.fc39.x86_64 ansible-srpm-macros-1-11.fc39.noarch audit-libs-3.1.2-5.fc40.x86_64 authselect-1.4.3-1.fc40.x86_64 authselect-libs-1.4.3-1.fc40.x86_64 basesystem-11-18.fc39.noarch bash-5.2.21-2.fc40.x86_64 binutils-2.41-15.fc40.x86_64 binutils-gold-2.41-15.fc40.x86_64 bzip2-1.0.8-16.fc39.x86_64 bzip2-libs-1.0.8-16.fc39.x86_64 ca-certificates-2023.2.62_v7.0.401-4.fc40.noarch coreutils-9.4-1.fc40.x86_64 coreutils-common-9.4-1.fc40.x86_64 cpio-2.14-5.fc40.x86_64 cracklib-2.9.11-2.fc39.x86_64 crypto-policies-20231113-1.gitb402e82.fc40.noarch curl-8.4.0-1.fc40.x86_64 cyrus-sasl-lib-2.1.28-11.fc39.x86_64 debugedit-5.0-11.fc40.x86_64 diffutils-3.10-3.fc39.x86_64 dwz-0.15-3.fc39.x86_64 ed-1.19-4.fc39.x86_64 efi-srpm-macros-5-9.fc39.noarch elfutils-0.190-4.fc40.x86_64 elfutils-debuginfod-client-0.190-4.fc40.x86_64 elfutils-default-yama-scope-0.190-4.fc40.noarch elfutils-libelf-0.190-4.fc40.x86_64 elfutils-libs-0.190-4.fc40.x86_64 fedora-gpg-keys-40-0.2.noarch fedora-release-40-0.20.noarch fedora-release-common-40-0.20.noarch fedora-release-identity-basic-40-0.20.noarch fedora-repos-40-0.2.noarch fedora-repos-rawhide-40-0.2.noarch file-5.45-1.fc40.x86_64 file-libs-5.45-1.fc40.x86_64 filesystem-3.18-6.fc39.x86_64 findutils-4.9.0-6.fc40.x86_64 fonts-srpm-macros-2.0.5-12.fc39.noarch forge-srpm-macros-0.1.0-1.fc40.noarch fpc-srpm-macros-1.3-8.fc39.noarch gawk-5.2.2-2.fc39.x86_64 gdb-minimal-13.2-12.fc40.x86_64 gdbm-1.23-4.fc39.x86_64 gdbm-libs-1.23-4.fc39.x86_64 ghc-srpm-macros-1.6.1-3.fc40.noarch glibc-2.38.9000-26.fc40.x86_64 glibc-common-2.38.9000-26.fc40.x86_64 glibc-gconv-extra-2.38.9000-26.fc40.x86_64 glibc-minimal-langpack-2.38.9000-26.fc40.x86_64 gmp-6.2.1-5.fc39.x86_64 gnat-srpm-macros-6-3.fc39.noarch go-srpm-macros-3.3.1-1.fc40.noarch gpg-pubkey-18b8e74c-62f2920f gpg-pubkey-a15b79cc-63d04c2c grep-3.11-5.fc40.x86_64 gzip-1.12-6.fc39.x86_64 info-7.1-1.fc40.x86_64 jansson-2.13.1-7.fc39.x86_64 kernel-srpm-macros-1.0-20.fc39.noarch keyutils-libs-1.6.1-7.fc39.x86_64 krb5-libs-1.21.2-2.fc40.x86_64 libacl-2.3.1-11.fc40.x86_64 libarchive-3.7.2-1.fc40.x86_64 libattr-2.5.1-9.fc40.x86_64 libblkid-2.39.2-1.fc40.x86_64 libbrotli-1.1.0-1.fc40.x86_64 libcap-2.69-1.fc40.x86_64 libcap-ng-0.8.3-8.fc40.x86_64 libcom_err-1.47.0-2.fc39.x86_64 libcurl-8.4.0-1.fc40.x86_64 libeconf-0.5.2-1.fc40.x86_64 libevent-2.1.12-9.fc39.x86_64 libfdisk-2.39.2-1.fc40.x86_64 libffi-3.4.4-4.fc39.x86_64 libgcc-13.2.1-5.fc40.x86_64 libgomp-13.2.1-5.fc40.x86_64 libidn2-2.3.4-3.fc39.x86_64 libmount-2.39.2-1.fc40.x86_64 libnghttp2-1.58.0-1.fc40.x86_64 libnsl2-2.0.0-6.fc39.x86_64 libpkgconf-1.9.5-2.fc39.x86_64 libpsl-0.21.2-4.fc39.x86_64 libpwquality-1.4.5-6.fc39.x86_64 libselinux-3.6-0.rc2.1.fc40.x86_64 libsemanage-3.6-0.rc2.1.fc40.x86_64 libsepol-3.6-0.rc2.1.fc40.x86_64 libsigsegv-2.14-5.fc39.x86_64 libsmartcols-2.39.2-1.fc40.x86_64 libssh-0.10.5-2.fc39.x86_64 libssh-config-0.10.5-2.fc39.noarch libstdc++-13.2.1-5.fc40.x86_64 libtasn1-4.19.0-3.fc39.x86_64 libtirpc-1.3.4-0.fc40.x86_64 libunistring-1.1-5.fc40.x86_64 libutempter-1.2.1-10.fc39.x86_64 libuuid-2.39.2-1.fc40.x86_64 libverto-0.3.2-6.fc39.x86_64 libxcrypt-4.4.36-2.fc39.x86_64 libxml2-2.12.1-1.fc40.x86_64 libzstd-1.5.5-4.fc39.x86_64 lua-libs-5.4.6-3.fc39.x86_64 lua-srpm-macros-1-9.fc39.noarch lz4-libs-1.9.4-4.fc39.x86_64 mpfr-4.2.1-1.fc40.x86_64 ncurses-base-6.4-8.20231001.fc40.noarch ncurses-libs-6.4-8.20231001.fc40.x86_64 ocaml-srpm-macros-9-1.fc40.noarch openblas-srpm-macros-2-14.fc39.noarch openldap-2.6.6-1.fc39.x86_64 openssl-libs-3.1.4-1.fc40.x86_64 p11-kit-0.25.3-1.fc40.x86_64 p11-kit-trust-0.25.3-1.fc40.x86_64 package-notes-srpm-macros-0.5-9.fc39.noarch pam-1.5.3-8.fc40.x86_64 pam-libs-1.5.3-8.fc40.x86_64 patch-2.7.6-22.fc39.x86_64 pcre2-10.42-2.fc40.x86_64 pcre2-syntax-10.42-2.fc40.noarch perl-srpm-macros-1-51.fc39.noarch pkgconf-1.9.5-2.fc39.x86_64 pkgconf-m4-1.9.5-2.fc39.noarch pkgconf-pkg-config-1.9.5-2.fc39.x86_64 popt-1.19-3.fc39.x86_64 publicsuffix-list-dafsa-20230812-1.fc40.noarch pyproject-srpm-macros-1.10.0-1.fc40.noarch python-srpm-macros-3.12-4.fc40.noarch qt5-srpm-macros-5.15.11-1.fc40.noarch qt6-srpm-macros-6.6.1-1.fc40.noarch readline-8.2-4.fc39.x86_64 redhat-rpm-config-271-1.fc40.noarch rpm-4.19.0-3.fc40.x86_64 rpm-build-4.19.0-3.fc40.x86_64 rpm-build-libs-4.19.0-3.fc40.x86_64 rpm-libs-4.19.0-3.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 rust-srpm-macros-25.2-2.fc40.noarch sed-4.8-14.fc39.x86_64 setup-2.14.5-1.fc40.noarch shadow-utils-4.14.0-2.fc40.x86_64 sqlite-libs-3.44.1-1.fc40.x86_64 systemd-libs-255~rc4-3.fc40.x86_64 tar-1.35-2.fc40.x86_64 unzip-6.0-62.fc39.x86_64 util-linux-2.39.2-1.fc40.x86_64 util-linux-core-2.39.2-1.fc40.x86_64 which-2.21-40.fc39.x86_64 xxhash-libs-0.8.2-1.fc39.x86_64 xz-5.4.5-1.fc40.x86_64 xz-libs-5.4.5-1.fc40.x86_64 zip-3.0-39.fc40.x86_64 zlib-1.2.13-5.fc40.x86_64 zstd-1.5.5-4.fc39.x86_64 Start: buildsrpm Start: rpmbuild -bs sh: line 1: perl: command not found warning: %patchN is deprecated (9 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/openbabel-3.1.1-21.fc40.src.rpm RPM build warnings: %patchN is deprecated (9 usages found), use %patch N (or %patch -P N) Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1701768643.660671/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1701768643.660671/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1701768643.660671/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-v07p19m8/openbabel/openbabel.spec) Config(child) 0 minutes 51 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/openbabel-3.1.1-21.fc40.src.rpm) Config(fedora-rawhide-x86_64) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1701768643.660671/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1701768643.660671/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1701768643.660671/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 Finish: chroot init INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-4.19.0-3.fc40.x86_64 rpm-sequoia-1.5.0-2.fc40.x86_64 python3-dnf-4.18.1-2.fc40.noarch python3-dnf-plugins-core-4.4.3-1.fc40.noarch yum-4.18.1-2.fc40.noarch Start: build phase for openbabel-3.1.1-21.fc40.src.rpm Start: build setup for openbabel-3.1.1-21.fc40.src.rpm sh: line 1: perl: command not found warning: %patchN is deprecated (9 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Wrote: /builddir/build/SRPMS/openbabel-3.1.1-21.fc40.src.rpm RPM build warnings: %patchN is deprecated (9 usages found), use %patch N (or %patch -P N) No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 42 kB/s | 1.5 kB 00:00 Copr repository 38 MB/s | 7.2 MB 00:00 fedora 650 kB/s | 24 kB 00:00 Last metadata expiration check: 0:00:01 ago on Tue Dec 5 09:31:42 2023. Dependencies resolved. ================================================================================================ Package Arch Version Repo Size ================================================================================================ Installing: ImageMagick x86_64 1:7.1.1.15-1.fc40 fedora 82 k boost-devel x86_64 1.83.0-0.fc40 copr_base 12 M cmake x86_64 3.27.7-1.fc40 fedora 8.0 M desktop-file-utils x86_64 0.26-9.fc39 fedora 72 k dos2unix x86_64 7.5.1-1.fc40 fedora 298 k eigen3-devel noarch 3.4.0-12.fc39 fedora 1.2 M gcc-c++ x86_64 13.2.1-5.fc40 fedora 13 M inchi-devel x86_64 1.0.6-7.fc39 fedora 24 k libxml2-devel x86_64 2.12.1-1.fc40 fedora 524 k make x86_64 1:4.4.1-2.fc39 fedora 589 k perl-devel x86_64 4:5.38.2-503.fc40 fedora 757 k perl-generators noarch 1.16-3.fc39 fedora 16 k python3-devel x86_64 3.12.0-2.fc40 fedora 311 k python3-setuptools noarch 68.2.2-1.fc40 fedora 1.5 M rapidjson-devel x86_64 1.1.0-23.fc39 fedora 117 k ruby-devel x86_64 3.2.2-183.fc40 fedora 458 k swig x86_64 4.1.1-12.fc40 copr_base 1.5 M wxGTK-devel x86_64 3.2.4-1.fc40 fedora 33 k Installing dependencies: ImageMagick-libs x86_64 1:7.1.1.15-1.fc40 fedora 2.5 M LibRaw x86_64 0.21.1-7.fc40 fedora 416 k SDL2 x86_64 2.28.5-1.fc40 fedora 692 k abattis-cantarell-vf-fonts noarch 0.301-10.fc39 fedora 121 k adobe-mappings-cmap noarch 20230622-1.fc39 fedora 2.1 M adobe-mappings-cmap-deprecated noarch 20230622-1.fc39 fedora 113 k adobe-mappings-pdf noarch 20190401-5.fc39 fedora 698 k adwaita-cursor-theme noarch 45.0-1.fc40 fedora 678 k adwaita-icon-theme noarch 45.0-1.fc40 fedora 407 k alsa-lib x86_64 1.2.10-3.fc40 fedora 522 k annobin-docs noarch 12.32-1.fc40 fedora 92 k annobin-plugin-gcc x86_64 12.32-1.fc40 fedora 959 k at-spi2-atk x86_64 2.50.0-1.fc40 fedora 86 k at-spi2-atk-devel x86_64 2.50.0-1.fc40 fedora 10 k at-spi2-core x86_64 2.50.0-1.fc40 fedora 371 k at-spi2-core-devel x86_64 2.50.0-1.fc40 fedora 315 k atk x86_64 2.50.0-1.fc40 fedora 81 k atk-devel x86_64 2.50.0-1.fc40 fedora 432 k avahi-libs x86_64 0.8-24.fc39 fedora 67 k boost x86_64 1.83.0-0.fc40 copr_base 14 k boost-atomic x86_64 1.83.0-0.fc40 copr_base 20 k boost-chrono x86_64 1.83.0-0.fc40 copr_base 26 k boost-container x86_64 1.83.0-0.fc40 copr_base 40 k boost-context x86_64 1.83.0-0.fc40 copr_base 17 k boost-contract x86_64 1.83.0-0.fc40 copr_base 46 k boost-coroutine x86_64 1.83.0-0.fc40 copr_base 20 k boost-date-time x86_64 1.83.0-0.fc40 copr_base 16 k boost-fiber x86_64 1.83.0-0.fc40 copr_base 42 k boost-filesystem x86_64 1.83.0-0.fc40 copr_base 68 k boost-graph x86_64 1.83.0-0.fc40 copr_base 152 k boost-iostreams x86_64 1.83.0-0.fc40 copr_base 42 k boost-json x86_64 1.83.0-0.fc40 copr_base 143 k boost-locale x86_64 1.83.0-0.fc40 copr_base 212 k boost-log x86_64 1.83.0-0.fc40 copr_base 493 k boost-math x86_64 1.83.0-0.fc40 copr_base 218 k boost-nowide x86_64 1.83.0-0.fc40 copr_base 21 k boost-numpy3 x86_64 1.83.0-0.fc40 copr_base 30 k boost-program-options x86_64 1.83.0-0.fc40 copr_base 110 k boost-python3 x86_64 1.83.0-0.fc40 copr_base 97 k boost-random x86_64 1.83.0-0.fc40 copr_base 24 k boost-regex x86_64 1.83.0-0.fc40 copr_base 112 k boost-serialization x86_64 1.83.0-0.fc40 copr_base 135 k boost-stacktrace x86_64 1.83.0-0.fc40 copr_base 30 k boost-system x86_64 1.83.0-0.fc40 copr_base 16 k boost-test x86_64 1.83.0-0.fc40 copr_base 240 k boost-thread x86_64 1.83.0-0.fc40 copr_base 62 k boost-timer x86_64 1.83.0-0.fc40 copr_base 22 k boost-type_erasure x86_64 1.83.0-0.fc40 copr_base 34 k boost-wave x86_64 1.83.0-0.fc40 copr_base 225 k brotli x86_64 1.1.0-1.fc40 fedora 20 k brotli-devel x86_64 1.1.0-1.fc40 fedora 34 k bubblewrap x86_64 0.8.0-1.fc40 fedora 60 k bzip2-devel x86_64 1.0.8-16.fc39 fedora 214 k cairo x86_64 1.18.0-1.fc40 fedora 710 k cairo-devel x86_64 1.18.0-1.fc40 fedora 193 k cairo-gobject x86_64 1.18.0-1.fc40 fedora 19 k cairo-gobject-devel x86_64 1.18.0-1.fc40 fedora 11 k cdparanoia-libs x86_64 10.2-42.fc39 fedora 54 k cmake-data noarch 3.27.7-1.fc40 fedora 2.2 M cmake-filesystem x86_64 3.27.7-1.fc40 fedora 19 k cmake-rpm-macros noarch 3.27.7-1.fc40 fedora 19 k colord-libs x86_64 1.4.6-6.fc40 fedora 233 k cpp x86_64 13.2.1-5.fc40 fedora 11 M crypto-policies-scripts noarch 20231113-1.gitb402e82.fc40 fedora 117 k cups-libs x86_64 1:2.4.7-3.fc40 fedora 267 k dbus x86_64 1:1.14.10-1.fc40 fedora 8.1 k dbus-broker x86_64 33-2.fc39 fedora 173 k dbus-common noarch 1:1.14.10-1.fc40 fedora 15 k dbus-devel x86_64 1:1.14.10-1.fc40 fedora 40 k dbus-libs x86_64 1:1.14.10-1.fc40 fedora 155 k default-fonts-core-sans noarch 4.0-9.fc40 fedora 32 k emacs-filesystem noarch 1:29.1-14.fc40 fedora 7.4 k enchant2 x86_64 2.6.3-1.fc40 fedora 63 k expat x86_64 2.5.0-3.fc39 fedora 110 k fftw-libs-double x86_64 3.3.10-7.fc39 fedora 1.2 M flexiblas x86_64 3.3.1-5.fc39 fedora 33 k flexiblas-netlib x86_64 3.3.1-5.fc39 fedora 3.1 M flexiblas-openblas-openmp x86_64 3.3.1-5.fc39 fedora 17 k fontconfig x86_64 2.14.2-5.fc40 fedora 297 k fontconfig-devel x86_64 2.14.2-5.fc40 fedora 165 k fonts-filesystem noarch 1:2.0.5-12.fc39 fedora 8.2 k freetype x86_64 2.13.1-2.fc39 fedora 414 k freetype-devel x86_64 2.13.1-2.fc39 fedora 950 k fribidi x86_64 1.0.13-2.fc39 fedora 91 k fribidi-devel x86_64 1.0.13-2.fc39 fedora 30 k gc x86_64 8.2.2-4.fc39 fedora 110 k gcc x86_64 13.2.1-5.fc40 fedora 34 M gcc-plugin-annobin x86_64 13.2.1-5.fc40 fedora 49 k gd x86_64 2.3.3-12.fc39 fedora 139 k gdk-pixbuf2 x86_64 2.42.10-5.fc39 fedora 484 k gdk-pixbuf2-devel x86_64 2.42.10-5.fc39 fedora 366 k gdk-pixbuf2-modules x86_64 2.42.10-5.fc39 fedora 85 k gettext x86_64 0.22-2.fc39 fedora 1.1 M gettext-envsubst x86_64 0.22-2.fc39 fedora 36 k gettext-libs x86_64 0.22-2.fc39 fedora 328 k gettext-runtime x86_64 0.22-2.fc39 fedora 120 k gl-manpages noarch 1.1-29.20190306.fc40 fedora 1.2 M glib2 x86_64 2.78.1-1.fc40 fedora 2.8 M glib2-devel x86_64 2.78.1-1.fc40 fedora 596 k glibc-devel x86_64 2.38.9000-26.fc40 fedora 100 k glibc-headers-x86 noarch 2.38.9000-26.fc40 fedora 585 k gnutls x86_64 3.8.2-2.fc40 fedora 1.1 M google-droid-sans-fonts noarch 20200215-17.fc40 fedora 2.7 M google-noto-fonts-common noarch 20230801-4.fc40 fedora 17 k google-noto-sans-vf-fonts noarch 20230801-4.fc40 fedora 583 k graphene x86_64 1.10.6-6.fc39 fedora 61 k graphite2 x86_64 1.3.14-13.fc40 fedora 95 k graphite2-devel x86_64 1.3.14-13.fc40 fedora 21 k graphviz x86_64 9.0.0-3.fc40 fedora 5.0 M groff-base x86_64 1.23.0-3.fc40 fedora 1.1 M gssdp x86_64 1.6.3-1.fc40 fedora 58 k gstreamer1 x86_64 1.22.7-2.fc40 fedora 1.4 M gstreamer1-plugins-bad-free-libs x86_64 1.22.7-2.fc40 fedora 765 k gstreamer1-plugins-base x86_64 1.22.7-1.fc40 fedora 2.2 M gtk-update-icon-cache x86_64 3.24.38-3.fc39 fedora 34 k gtk3 x86_64 3.24.38-3.fc39 fedora 4.9 M gtk3-devel x86_64 3.24.38-3.fc39 fedora 4.2 M gts x86_64 0.7.6-46.20121130.fc39 fedora 240 k guile22 x86_64 2.2.7-9.fc39 fedora 6.5 M gupnp x86_64 1.6.6-2.fc40 fedora 107 k gupnp-igd x86_64 1.6.0-2.fc39 fedora 34 k harfbuzz x86_64 8.3.0-2.fc40 fedora 995 k harfbuzz-devel x86_64 8.3.0-2.fc40 fedora 450 k harfbuzz-icu x86_64 8.3.0-2.fc40 fedora 16 k hicolor-icon-theme noarch 0.17-16.fc39 fedora 66 k highway x86_64 1.0.7-1.fc40 fedora 481 k hunspell x86_64 1.7.2-5.fc39 fedora 472 k hunspell-en-US noarch 0.20201207-7.fc39 fedora 181 k hunspell-filesystem x86_64 1.7.2-5.fc39 fedora 9.2 k hwdata noarch 0.376-1.fc40 fedora 1.6 M hyphen x86_64 2.8.8-21.fc39 fedora 29 k imath x86_64 3.1.9-3.fc40 copr_base 97 k inchi-libs x86_64 1.0.6-7.fc39 fedora 682 k iso-codes noarch 4.15.0-2.fc39 fedora 3.5 M jasper-libs x86_64 4.1.0-1.fc40 fedora 162 k javascriptcoregtk4.1 x86_64 2.43.1-2.fc40 fedora 8.3 M jbig2dec-libs x86_64 0.20-1.fc40 fedora 73 k jbigkit-libs x86_64 2.1-27.fc40 fedora 53 k json-glib x86_64 1.8.0-1.fc40 fedora 166 k jsoncpp x86_64 1.9.5-5.fc39 fedora 99 k kernel-headers x86_64 6.7.0-0.rc3.git0.1.fc40 fedora 1.6 M lasi x86_64 1.1.3-11.fc39 fedora 54 k lcms2 x86_64 2.15-2.fc39 fedora 177 k libICE x86_64 1.1.1-1.fc40 fedora 74 k libSM x86_64 1.2.4-1.fc40 fedora 43 k libX11 x86_64 1.8.7-1.fc40 fedora 647 k libX11-common noarch 1.8.7-1.fc40 fedora 176 k libX11-devel x86_64 1.8.7-1.fc40 fedora 1.0 M libX11-xcb x86_64 1.8.7-1.fc40 fedora 12 k libXau x86_64 1.0.11-4.fc40 fedora 31 k libXau-devel x86_64 1.0.11-4.fc40 fedora 14 k libXcomposite x86_64 0.4.6-1.fc40 fedora 24 k libXcomposite-devel x86_64 0.4.6-1.fc40 fedora 16 k libXcursor x86_64 1.2.1-5.fc40 fedora 30 k libXcursor-devel x86_64 1.2.1-5.fc40 fedora 40 k libXdamage x86_64 1.1.6-1.fc40 fedora 23 k libXdamage-devel x86_64 1.1.6-1.fc40 fedora 9.4 k libXext x86_64 1.3.5-4.fc40 fedora 39 k libXext-devel x86_64 1.3.5-4.fc40 fedora 86 k libXfixes x86_64 6.0.1-1.fc40 fedora 19 k libXfixes-devel x86_64 6.0.1-1.fc40 fedora 12 k libXft x86_64 2.3.8-4.fc40 fedora 72 k libXft-devel x86_64 2.3.8-4.fc40 fedora 50 k libXi x86_64 1.8.1-3.fc40 fedora 40 k libXi-devel x86_64 1.8.1-3.fc40 fedora 116 k libXinerama x86_64 1.1.5-4.fc40 fedora 14 k libXinerama-devel x86_64 1.1.5-4.fc40 fedora 13 k libXpm x86_64 3.5.17-1.fc40 fedora 65 k libXrandr x86_64 1.5.4-1.fc40 fedora 27 k libXrandr-devel x86_64 1.5.4-1.fc40 fedora 19 k libXrender x86_64 0.9.11-4.fc40 fedora 27 k libXrender-devel x86_64 0.9.11-4.fc40 fedora 19 k libXt x86_64 1.3.0-1.fc40 fedora 179 k libXtst x86_64 1.2.4-4.fc40 fedora 20 k libXtst-devel x86_64 1.2.4-4.fc40 fedora 16 k libXv x86_64 1.0.12-1.fc40 fedora 18 k libXxf86vm x86_64 1.1.5-4.fc40 fedora 18 k libaom x86_64 3.7.1-1.fc40 fedora 1.8 M libatomic x86_64 13.2.1-5.fc40 fedora 37 k libavif x86_64 0.11.1-11.fc39 fedora 84 k libb2 x86_64 0.98.1-9.fc39 fedora 25 k libblkid-devel x86_64 2.39.2-1.fc40 fedora 18 k libcloudproviders x86_64 0.3.5-1.fc40 fedora 47 k libcloudproviders-devel x86_64 0.3.5-1.fc40 fedora 49 k libdatrie x86_64 0.2.13-7.fc39 fedora 32 k libdatrie-devel x86_64 0.2.13-7.fc39 fedora 148 k libdav1d x86_64 1.2.1-2.fc39 fedora 618 k libdecor x86_64 0.2.1-1.fc40 fedora 58 k libdrm x86_64 2.4.117-1.fc40 fedora 156 k libepoxy x86_64 1.5.10-4.fc39 fedora 234 k libepoxy-devel x86_64 1.5.10-4.fc39 fedora 133 k libevdev x86_64 1.13.1-2.fc39 fedora 44 k libffi-devel x86_64 3.4.4-4.fc39 fedora 29 k libgcrypt x86_64 1.10.3-1.fc40 fedora 507 k libgfortran x86_64 13.2.1-5.fc40 fedora 906 k libglvnd x86_64 1:1.7.0-1.fc40 fedora 133 k libglvnd-core-devel x86_64 1:1.7.0-1.fc40 fedora 17 k libglvnd-devel x86_64 1:1.7.0-1.fc40 fedora 162 k libglvnd-egl x86_64 1:1.7.0-1.fc40 fedora 36 k libglvnd-gles x86_64 1:1.7.0-1.fc40 fedora 31 k libglvnd-glx x86_64 1:1.7.0-1.fc40 fedora 142 k libglvnd-opengl x86_64 1:1.7.0-1.fc40 fedora 42 k libgpg-error x86_64 1.47-2.fc39 fedora 230 k libgs x86_64 10.02.1-4.fc40 fedora 3.4 M libgudev x86_64 238-2.fc39 fedora 35 k libgusb x86_64 0.4.8-1.fc40 fedora 65 k libheif x86_64 1.16.2-2.fc40 fedora 298 k libicu x86_64 73.2-2.fc39 fedora 11 M libicu-devel x86_64 73.2-2.fc39 fedora 924 k libijs x86_64 0.35-19.fc39 fedora 29 k libimagequant x86_64 4.0.3-1.fc40 fedora 321 k libjpeg-turbo x86_64 2.1.4-3.fc39 fedora 183 k libjpeg-turbo-devel x86_64 2.1.4-3.fc39 fedora 98 k libjxl x86_64 1:0.8.2-3.fc40 fedora 1.2 M liblerc x86_64 4.0.0-4.fc39 fedora 201 k liblqr-1 x86_64 0.4.2-22.fc39 fedora 49 k libmanette x86_64 0.2.6-7.fc39 fedora 49 k libmount-devel x86_64 2.39.2-1.fc40 fedora 18 k libmpc x86_64 1.3.1-3.fc39 fedora 70 k libmspack x86_64 0.10.1-0.10.alpha.fc39 fedora 70 k libnice x86_64 0.1.21-4.fc39 fedora 200 k libogg x86_64 2:1.3.5-6.fc39 fedora 33 k libpaper x86_64 1:2.1.1-1.fc39 fedora 27 k libpciaccess x86_64 0.16-9.fc39 fedora 26 k libpng x86_64 2:1.6.40-1.fc40 fedora 119 k libpng-devel x86_64 2:1.6.40-1.fc40 fedora 291 k libquadmath x86_64 13.2.1-5.fc40 fedora 197 k libquadmath-devel x86_64 13.2.1-5.fc40 fedora 39 k libraqm x86_64 0.8.0-5.fc39 fedora 20 k librsvg2 x86_64 2.57.0-3.fc40 fedora 1.6 M libseccomp x86_64 2.5.3-6.fc39 fedora 71 k libsecret x86_64 0.21.1-1.fc40 fedora 192 k libselinux-devel x86_64 3.6-0.rc2.1.fc40 fedora 151 k libsepol-devel x86_64 3.6-0.rc2.1.fc40 fedora 49 k libsoup3 x86_64 3.4.4-1.fc40 fedora 389 k libstdc++-devel x86_64 13.2.1-5.fc40 fedora 2.6 M libstemmer x86_64 2.2.0-7.fc39 fedora 171 k libthai x86_64 0.1.29-6.fc39 fedora 213 k libthai-devel x86_64 0.1.29-6.fc39 fedora 139 k libtheora x86_64 1:1.1.1-34.fc39 fedora 166 k libtiff x86_64 4.5.0-3.fc40 fedora 305 k libtiff-devel x86_64 4.5.0-3.fc40 fedora 251 k libtool-ltdl x86_64 2.4.7-8.fc40 fedora 36 k libtracker-sparql x86_64 3.6.0-1.fc40 fedora 374 k libunwind x86_64 1.7.2-1.fc40 fedora 70 k libusb1 x86_64 1.0.26-4.fc40 fedora 74 k libuv x86_64 1:1.47.0-3.fc40 fedora 250 k libva x86_64 2.20.0-1.fc40 fedora 105 k libvisual x86_64 1:0.4.1-2.fc39 fedora 151 k libvmaf x86_64 2.3.0-6.fc39 fedora 180 k libvorbis x86_64 1:1.3.7-8.fc39 fedora 195 k libwayland-client x86_64 1.22.0-2.fc39 fedora 34 k libwayland-cursor x86_64 1.22.0-2.fc39 fedora 19 k libwayland-egl x86_64 1.22.0-2.fc39 fedora 13 k libwayland-server x86_64 1.22.0-2.fc39 fedora 42 k libwebp x86_64 1.3.2-2.fc40 fedora 284 k libwebp-devel x86_64 1.3.2-2.fc40 fedora 39 k libwmf-lite x86_64 0.2.13-2.fc39 fedora 73 k libwpe x86_64 1.15.1-2.fc39 fedora 29 k libxcb x86_64 1.16-2.fc40 fedora 238 k libxcb-devel x86_64 1.16-2.fc40 fedora 1.4 M libxcrypt-devel x86_64 4.4.36-2.fc39 fedora 30 k libxkbcommon x86_64 1.6.0-1.fc40 fedora 142 k libxkbcommon-devel x86_64 1.6.0-1.fc40 fedora 66 k libxshmfence x86_64 1.3.2-1.fc40 fedora 12 k libxslt x86_64 1.1.39-1.fc40 fedora 187 k libyaml x86_64 0.2.5-12.fc39 fedora 59 k libzip x86_64 1.10.1-1.fc40 fedora 67 k libzstd-devel x86_64 1.5.5-4.fc39 fedora 51 k mesa-filesystem x86_64 23.3.0-1.fc40 fedora 18 k mesa-libEGL x86_64 23.3.0-1.fc40 fedora 133 k mesa-libGL x86_64 23.3.0-1.fc40 fedora 175 k mesa-libGLU x86_64 9.0.3-1.fc39 fedora 160 k mesa-libGLU-devel x86_64 9.0.3-1.fc39 fedora 12 k mesa-libgbm x86_64 23.3.0-1.fc40 fedora 45 k mesa-libglapi x86_64 23.3.0-1.fc40 fedora 52 k mpdecimal x86_64 2.5.1-7.fc39 fedora 89 k ncurses x86_64 6.4-8.20231001.fc40 fedora 418 k netpbm x86_64 11.02.00-3.fc40 fedora 184 k nettle x86_64 3.9.1-2.fc39 fedora 425 k nspr x86_64 4.35.0-16.fc40 fedora 138 k nss x86_64 3.95.0-1.fc40 fedora 695 k nss-softokn x86_64 3.95.0-1.fc40 fedora 414 k nss-softokn-freebl x86_64 3.95.0-1.fc40 fedora 351 k nss-sysinit x86_64 3.95.0-1.fc40 fedora 18 k nss-util x86_64 3.95.0-1.fc40 fedora 87 k openblas x86_64 0.3.25-1.fc40 fedora 38 k openblas-openmp x86_64 0.3.25-1.fc40 fedora 5.0 M openexr-libs x86_64 3.1.10-2.fc39 fedora 1.1 M openjpeg2 x86_64 2.5.0-5.fc40 fedora 178 k opus x86_64 1.4-1.fc40 fedora 212 k orc x86_64 0.4.33-3.fc39 fedora 202 k pango x86_64 1.51.0-1.fc40 fedora 343 k pango-devel x86_64 1.51.0-1.fc40 fedora 161 k pcre2-devel x86_64 10.42-2.fc40 fedora 505 k pcre2-utf16 x86_64 10.42-2.fc40 fedora 213 k pcre2-utf32 x86_64 10.42-2.fc40 fedora 200 k perl-AutoLoader noarch 5.74-503.fc40 fedora 21 k perl-AutoSplit noarch 5.74-503.fc40 fedora 22 k perl-B x86_64 1.88-503.fc40 fedora 177 k perl-Benchmark noarch 1.24-503.fc40 fedora 27 k perl-Carp noarch 1.54-500.fc39 fedora 29 k perl-Class-Struct noarch 0.68-503.fc40 fedora 22 k perl-Data-Dumper x86_64 2.188-501.fc39 fedora 56 k perl-Devel-PPPort x86_64 3.71-501.fc39 fedora 218 k perl-Digest noarch 1.20-500.fc39 fedora 25 k perl-Digest-MD5 x86_64 2.58-501.fc40 fedora 35 k perl-DynaLoader x86_64 1.54-503.fc40 fedora 26 k perl-Encode x86_64 4:3.20-501.fc40 fedora 1.7 M perl-Errno x86_64 1.37-503.fc40 fedora 15 k perl-Exporter noarch 5.77-500.fc39 fedora 31 k perl-ExtUtils-Command noarch 2:7.70-501.fc39 fedora 14 k perl-ExtUtils-Constant noarch 0.25-503.fc40 fedora 44 k perl-ExtUtils-Install noarch 2.22-500.fc39 fedora 43 k perl-ExtUtils-MakeMaker noarch 2:7.70-501.fc39 fedora 292 k perl-ExtUtils-Manifest noarch 1:1.75-3.fc39 fedora 34 k perl-ExtUtils-ParseXS noarch 1:3.51-501.fc40 fedora 187 k perl-Fcntl x86_64 1.15-503.fc40 fedora 21 k perl-Fedora-VSP noarch 0.001-32.fc39 fedora 23 k perl-File-Basename noarch 2.86-503.fc40 fedora 17 k perl-File-Compare noarch 1.100.700-503.fc40 fedora 13 k perl-File-Copy noarch 2.41-503.fc40 fedora 20 k perl-File-Find noarch 1.43-503.fc40 fedora 26 k perl-File-Path noarch 2.18-501.fc40 fedora 35 k perl-File-Temp noarch 1:0.231.100-501.fc40 fedora 59 k perl-File-stat noarch 1.13-503.fc40 fedora 17 k perl-FileHandle noarch 2.05-503.fc40 fedora 16 k perl-Getopt-Long noarch 1:2.57-1.fc40 fedora 63 k perl-Getopt-Std noarch 1.13-503.fc40 fedora 16 k perl-HTTP-Tiny noarch 0.088-3.fc39 fedora 56 k perl-IO x86_64 1.52-503.fc40 fedora 82 k perl-IO-Socket-IP noarch 0.42-1.fc39 fedora 42 k perl-IO-Socket-SSL noarch 2.084-1.fc40 fedora 225 k perl-IPC-Open3 noarch 1.22-503.fc40 fedora 22 k perl-MIME-Base64 x86_64 3.16-501.fc40 fedora 29 k perl-Mozilla-CA noarch 20230821-1.fc40 fedora 13 k perl-Net-SSLeay x86_64 1.92-10.fc39 fedora 360 k perl-POSIX x86_64 2.13-503.fc40 fedora 97 k perl-PathTools x86_64 3.89-500.fc39 fedora 87 k perl-Pod-Escapes noarch 1:1.07-501.fc40 fedora 19 k perl-Pod-Perldoc noarch 3.28.01-501.fc39 fedora 86 k perl-Pod-Simple noarch 1:3.45-4.fc39 fedora 218 k perl-Pod-Usage noarch 4:2.03-500.fc39 fedora 39 k perl-Scalar-List-Utils x86_64 5:1.63-500.fc39 fedora 72 k perl-SelectSaver noarch 1.02-503.fc40 fedora 12 k perl-Socket x86_64 4:2.037-3.fc39 fedora 55 k perl-Storable x86_64 1:3.32-500.fc39 fedora 99 k perl-Symbol noarch 1.09-503.fc40 fedora 14 k perl-Term-ANSIColor noarch 5.01-502.fc40 fedora 47 k perl-Term-Cap noarch 1.18-500.fc39 fedora 22 k perl-Test-Harness noarch 1:3.48-1.fc40 fedora 275 k perl-Text-ParseWords noarch 3.31-500.fc39 fedora 16 k perl-Text-Tabs+Wrap noarch 2023.0511-3.fc39 fedora 22 k perl-Time-Local noarch 2:1.350-3.fc39 fedora 34 k perl-URI noarch 5.21-1.fc40 fedora 125 k perl-base noarch 2.27-503.fc40 fedora 16 k perl-constant noarch 1.33-501.fc39 fedora 22 k perl-if noarch 0.61.000-503.fc40 fedora 14 k perl-interpreter x86_64 4:5.38.2-503.fc40 fedora 72 k perl-lib x86_64 0.65-503.fc40 fedora 15 k perl-libnet noarch 3.15-501.fc39 fedora 129 k perl-libs x86_64 4:5.38.2-503.fc40 fedora 2.3 M perl-locale noarch 1.10-503.fc40 fedora 14 k perl-macros noarch 4:5.38.2-503.fc40 fedora 13 k perl-mro x86_64 1.28-503.fc40 fedora 29 k perl-overload noarch 1.37-503.fc40 fedora 46 k perl-overloading noarch 0.02-503.fc40 fedora 13 k perl-parent noarch 1:0.241-500.fc39 fedora 14 k perl-podlators noarch 1:5.01-500.fc39 fedora 125 k perl-vars noarch 1.05-503.fc40 fedora 13 k perl-version x86_64 8:0.99.30-1.fc40 fedora 62 k pixman x86_64 0.42.2-2.fc39 fedora 288 k pixman-devel x86_64 0.42.2-2.fc39 fedora 17 k poppler x86_64 23.08.0-1.fc40 copr_base 1.2 M poppler-data noarch 0.4.11-5.fc39 fedora 2.0 M poppler-glib x86_64 23.08.0-1.fc40 copr_base 185 k pyproject-rpm-macros noarch 1.10.0-1.fc40 fedora 41 k python-pip-wheel noarch 23.2.1-1.fc39 fedora 1.5 M python-rpm-macros noarch 3.12-4.fc40 fedora 19 k python3 x86_64 3.12.0-2.fc40 fedora 26 k python3-libs x86_64 3.12.0-2.fc40 fedora 9.2 M python3-numpy x86_64 1:1.26.0-2.fc40 fedora 7.5 M python3-packaging noarch 23.2-2.fc40 fedora 125 k python3-pyparsing noarch 3.0.9-11.fc39 fedora 254 k python3-rpm-generators noarch 14-8.fc40 fedora 30 k python3-rpm-macros noarch 3.12-4.fc40 fedora 14 k rav1e-libs x86_64 0.6.6-3.fc40 fedora 1.0 M rhash x86_64 1.4.3-3.fc39 fedora 194 k rsvg-pixbuf-loader x86_64 2.57.0-3.fc40 fedora 16 k ruby x86_64 3.2.2-183.fc40 fedora 41 k ruby-default-gems noarch 3.2.2-183.fc40 fedora 42 k ruby-libs x86_64 3.2.2-183.fc40 fedora 4.0 M rubygem-io-console x86_64 0.6.0-183.fc40 fedora 25 k rubygem-psych x86_64 5.0.1-183.fc40 fedora 59 k rubygems noarch 3.4.10-183.fc40 fedora 288 k rubypick noarch 1.1.1-19.fc39 fedora 9.9 k shared-mime-info x86_64 2.3-1.fc40 fedora 391 k svt-av1-libs x86_64 1.4.1-3.fc39 fedora 2.0 M sysprof-capture-devel x86_64 45.1-1.fc40 fedora 53 k systemtap-sdt-devel x86_64 5.0~pre16958465gca71442b-1.fc40 fedora 74 k tzdata noarch 2023c-4.fc40 fedora 717 k urw-base35-bookman-fonts noarch 20200910-18.fc39 fedora 847 k urw-base35-c059-fonts noarch 20200910-18.fc39 fedora 874 k urw-base35-d050000l-fonts noarch 20200910-18.fc39 fedora 76 k urw-base35-fonts noarch 20200910-18.fc39 fedora 10 k urw-base35-fonts-common noarch 20200910-18.fc39 fedora 21 k urw-base35-gothic-fonts noarch 20200910-18.fc39 fedora 643 k urw-base35-nimbus-mono-ps-fonts noarch 20200910-18.fc39 fedora 795 k urw-base35-nimbus-roman-fonts noarch 20200910-18.fc39 fedora 856 k urw-base35-nimbus-sans-fonts noarch 20200910-18.fc39 fedora 1.3 M urw-base35-p052-fonts noarch 20200910-18.fc39 fedora 974 k urw-base35-standard-symbols-ps-fonts noarch 20200910-18.fc39 fedora 42 k urw-base35-z003-fonts noarch 20200910-18.fc39 fedora 276 k vim-filesystem noarch 2:9.0.2120-1.fc40 fedora 18 k vulkan-loader x86_64 1.3.268.0-1.fc40 fedora 148 k wayland-devel x86_64 1.22.0-2.fc39 fedora 148 k webkit2gtk4.1 x86_64 2.43.1-2.fc40 fedora 24 M woff2 x86_64 1.0.2-18.fc39 fedora 61 k wpebackend-fdo x86_64 1.14.2-2.fc39 fedora 46 k wxBase x86_64 3.2.4-1.fc40 fedora 1.0 M wxBase-devel x86_64 3.2.4-1.fc40 fedora 1.3 M wxGTK x86_64 3.2.4-1.fc40 fedora 4.8 M wxGTK-gl x86_64 3.2.4-1.fc40 fedora 40 k wxGTK-i18n noarch 3.2.4-1.fc40 fedora 490 k wxGTK-media x86_64 3.2.4-1.fc40 fedora 54 k wxGTK-webview x86_64 3.2.4-1.fc40 fedora 75 k xdg-dbus-proxy x86_64 0.1.5-1.fc39 fedora 43 k xkeyboard-config noarch 2.40-2.fc40 fedora 972 k xml-common noarch 0.6.3-62.fc40 fedora 31 k xorg-x11-proto-devel noarch 2023.2-3.fc40 fedora 298 k xprop x86_64 1.2.5-4.fc39 fedora 35 k xz-devel x86_64 5.4.5-1.fc40 fedora 67 k zlib-devel x86_64 1.2.13-5.fc40 fedora 45 k Transaction Summary ================================================================================================ Install 451 Packages Total size: 297 M Total download size: 104 M Installed size: 1.2 G Downloading Packages: [SKIPPED] boost-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] boost-atomic-1.83.0-0.fc40.x86_64.rpm: Already downloaded [SKIPPED] 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gcc-13.2.1-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] gcc-c++-13.2.1-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] gcc-plugin-annobin-13.2.1-5.fc40.x86_64.rpm: Already downloaded [SKIPPED] gdk-pixbuf2-2.42.10-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] gdk-pixbuf2-modules-2.42.10-5.fc39.x86_64.rpm: Already downloaded [SKIPPED] gettext-0.22-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] gettext-envsubst-0.22-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] gettext-libs-0.22-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] gettext-runtime-0.22-2.fc39.x86_64.rpm: Already downloaded [SKIPPED] gl-manpages-1.1-29.20190306.fc40.noarch.rpm: Already downloaded [SKIPPED] glib2-2.78.1-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] glib2-devel-2.78.1-1.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-devel-2.38.9000-26.fc40.x86_64.rpm: Already downloaded [SKIPPED] glibc-headers-x86-2.38.9000-26.fc40.noarch.rpm: Already downloaded [SKIPPED] gnutls-3.8.2-2.fc40.x86_64.rpm: Already 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adobe-mappings-cmap-deprecated-20230622-1.fc39.noarch adobe-mappings-pdf-20190401-5.fc39.noarch adwaita-cursor-theme-45.0-1.fc40.noarch adwaita-icon-theme-45.0-1.fc40.noarch alsa-lib-1.2.10-3.fc40.x86_64 annobin-docs-12.32-1.fc40.noarch annobin-plugin-gcc-12.32-1.fc40.x86_64 at-spi2-atk-2.50.0-1.fc40.x86_64 at-spi2-atk-devel-2.50.0-1.fc40.x86_64 at-spi2-core-2.50.0-1.fc40.x86_64 at-spi2-core-devel-2.50.0-1.fc40.x86_64 atk-2.50.0-1.fc40.x86_64 atk-devel-2.50.0-1.fc40.x86_64 avahi-libs-0.8-24.fc39.x86_64 boost-1.83.0-0.fc40.x86_64 boost-atomic-1.83.0-0.fc40.x86_64 boost-chrono-1.83.0-0.fc40.x86_64 boost-container-1.83.0-0.fc40.x86_64 boost-context-1.83.0-0.fc40.x86_64 boost-contract-1.83.0-0.fc40.x86_64 boost-coroutine-1.83.0-0.fc40.x86_64 boost-date-time-1.83.0-0.fc40.x86_64 boost-devel-1.83.0-0.fc40.x86_64 boost-fiber-1.83.0-0.fc40.x86_64 boost-filesystem-1.83.0-0.fc40.x86_64 boost-graph-1.83.0-0.fc40.x86_64 boost-iostreams-1.83.0-0.fc40.x86_64 boost-json-1.83.0-0.fc40.x86_64 boost-locale-1.83.0-0.fc40.x86_64 boost-log-1.83.0-0.fc40.x86_64 boost-math-1.83.0-0.fc40.x86_64 boost-nowide-1.83.0-0.fc40.x86_64 boost-numpy3-1.83.0-0.fc40.x86_64 boost-program-options-1.83.0-0.fc40.x86_64 boost-python3-1.83.0-0.fc40.x86_64 boost-random-1.83.0-0.fc40.x86_64 boost-regex-1.83.0-0.fc40.x86_64 boost-serialization-1.83.0-0.fc40.x86_64 boost-stacktrace-1.83.0-0.fc40.x86_64 boost-system-1.83.0-0.fc40.x86_64 boost-test-1.83.0-0.fc40.x86_64 boost-thread-1.83.0-0.fc40.x86_64 boost-timer-1.83.0-0.fc40.x86_64 boost-type_erasure-1.83.0-0.fc40.x86_64 boost-wave-1.83.0-0.fc40.x86_64 brotli-1.1.0-1.fc40.x86_64 brotli-devel-1.1.0-1.fc40.x86_64 bubblewrap-0.8.0-1.fc40.x86_64 bzip2-devel-1.0.8-16.fc39.x86_64 cairo-1.18.0-1.fc40.x86_64 cairo-devel-1.18.0-1.fc40.x86_64 cairo-gobject-1.18.0-1.fc40.x86_64 cairo-gobject-devel-1.18.0-1.fc40.x86_64 cdparanoia-libs-10.2-42.fc39.x86_64 cmake-3.27.7-1.fc40.x86_64 cmake-data-3.27.7-1.fc40.noarch cmake-filesystem-3.27.7-1.fc40.x86_64 cmake-rpm-macros-3.27.7-1.fc40.noarch colord-libs-1.4.6-6.fc40.x86_64 cpp-13.2.1-5.fc40.x86_64 crypto-policies-scripts-20231113-1.gitb402e82.fc40.noarch cups-libs-1:2.4.7-3.fc40.x86_64 dbus-1:1.14.10-1.fc40.x86_64 dbus-broker-33-2.fc39.x86_64 dbus-common-1:1.14.10-1.fc40.noarch dbus-devel-1:1.14.10-1.fc40.x86_64 dbus-libs-1:1.14.10-1.fc40.x86_64 default-fonts-core-sans-4.0-9.fc40.noarch desktop-file-utils-0.26-9.fc39.x86_64 dos2unix-7.5.1-1.fc40.x86_64 eigen3-devel-3.4.0-12.fc39.noarch emacs-filesystem-1:29.1-14.fc40.noarch enchant2-2.6.3-1.fc40.x86_64 expat-2.5.0-3.fc39.x86_64 fftw-libs-double-3.3.10-7.fc39.x86_64 flexiblas-3.3.1-5.fc39.x86_64 flexiblas-netlib-3.3.1-5.fc39.x86_64 flexiblas-openblas-openmp-3.3.1-5.fc39.x86_64 fontconfig-2.14.2-5.fc40.x86_64 fontconfig-devel-2.14.2-5.fc40.x86_64 fonts-filesystem-1:2.0.5-12.fc39.noarch freetype-2.13.1-2.fc39.x86_64 freetype-devel-2.13.1-2.fc39.x86_64 fribidi-1.0.13-2.fc39.x86_64 fribidi-devel-1.0.13-2.fc39.x86_64 gc-8.2.2-4.fc39.x86_64 gcc-13.2.1-5.fc40.x86_64 gcc-c++-13.2.1-5.fc40.x86_64 gcc-plugin-annobin-13.2.1-5.fc40.x86_64 gd-2.3.3-12.fc39.x86_64 gdk-pixbuf2-2.42.10-5.fc39.x86_64 gdk-pixbuf2-devel-2.42.10-5.fc39.x86_64 gdk-pixbuf2-modules-2.42.10-5.fc39.x86_64 gettext-0.22-2.fc39.x86_64 gettext-envsubst-0.22-2.fc39.x86_64 gettext-libs-0.22-2.fc39.x86_64 gettext-runtime-0.22-2.fc39.x86_64 gl-manpages-1.1-29.20190306.fc40.noarch glib2-2.78.1-1.fc40.x86_64 glib2-devel-2.78.1-1.fc40.x86_64 glibc-devel-2.38.9000-26.fc40.x86_64 glibc-headers-x86-2.38.9000-26.fc40.noarch gnutls-3.8.2-2.fc40.x86_64 google-droid-sans-fonts-20200215-17.fc40.noarch google-noto-fonts-common-20230801-4.fc40.noarch google-noto-sans-vf-fonts-20230801-4.fc40.noarch graphene-1.10.6-6.fc39.x86_64 graphite2-1.3.14-13.fc40.x86_64 graphite2-devel-1.3.14-13.fc40.x86_64 graphviz-9.0.0-3.fc40.x86_64 groff-base-1.23.0-3.fc40.x86_64 gssdp-1.6.3-1.fc40.x86_64 gstreamer1-1.22.7-2.fc40.x86_64 gstreamer1-plugins-bad-free-libs-1.22.7-2.fc40.x86_64 gstreamer1-plugins-base-1.22.7-1.fc40.x86_64 gtk-update-icon-cache-3.24.38-3.fc39.x86_64 gtk3-3.24.38-3.fc39.x86_64 gtk3-devel-3.24.38-3.fc39.x86_64 gts-0.7.6-46.20121130.fc39.x86_64 guile22-2.2.7-9.fc39.x86_64 gupnp-1.6.6-2.fc40.x86_64 gupnp-igd-1.6.0-2.fc39.x86_64 harfbuzz-8.3.0-2.fc40.x86_64 harfbuzz-devel-8.3.0-2.fc40.x86_64 harfbuzz-icu-8.3.0-2.fc40.x86_64 hicolor-icon-theme-0.17-16.fc39.noarch highway-1.0.7-1.fc40.x86_64 hunspell-1.7.2-5.fc39.x86_64 hunspell-en-US-0.20201207-7.fc39.noarch hunspell-filesystem-1.7.2-5.fc39.x86_64 hwdata-0.376-1.fc40.noarch hyphen-2.8.8-21.fc39.x86_64 imath-3.1.9-3.fc40.x86_64 inchi-devel-1.0.6-7.fc39.x86_64 inchi-libs-1.0.6-7.fc39.x86_64 iso-codes-4.15.0-2.fc39.noarch jasper-libs-4.1.0-1.fc40.x86_64 javascriptcoregtk4.1-2.43.1-2.fc40.x86_64 jbig2dec-libs-0.20-1.fc40.x86_64 jbigkit-libs-2.1-27.fc40.x86_64 json-glib-1.8.0-1.fc40.x86_64 jsoncpp-1.9.5-5.fc39.x86_64 kernel-headers-6.7.0-0.rc3.git0.1.fc40.x86_64 lasi-1.1.3-11.fc39.x86_64 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libxml2-devel-2.12.1-1.fc40.x86_64 libxshmfence-1.3.2-1.fc40.x86_64 libxslt-1.1.39-1.fc40.x86_64 libyaml-0.2.5-12.fc39.x86_64 libzip-1.10.1-1.fc40.x86_64 libzstd-devel-1.5.5-4.fc39.x86_64 make-1:4.4.1-2.fc39.x86_64 mesa-filesystem-23.3.0-1.fc40.x86_64 mesa-libEGL-23.3.0-1.fc40.x86_64 mesa-libGL-23.3.0-1.fc40.x86_64 mesa-libGLU-9.0.3-1.fc39.x86_64 mesa-libGLU-devel-9.0.3-1.fc39.x86_64 mesa-libgbm-23.3.0-1.fc40.x86_64 mesa-libglapi-23.3.0-1.fc40.x86_64 mpdecimal-2.5.1-7.fc39.x86_64 ncurses-6.4-8.20231001.fc40.x86_64 netpbm-11.02.00-3.fc40.x86_64 nettle-3.9.1-2.fc39.x86_64 nspr-4.35.0-16.fc40.x86_64 nss-3.95.0-1.fc40.x86_64 nss-softokn-3.95.0-1.fc40.x86_64 nss-softokn-freebl-3.95.0-1.fc40.x86_64 nss-sysinit-3.95.0-1.fc40.x86_64 nss-util-3.95.0-1.fc40.x86_64 openblas-0.3.25-1.fc40.x86_64 openblas-openmp-0.3.25-1.fc40.x86_64 openexr-libs-3.1.10-2.fc39.x86_64 openjpeg2-2.5.0-5.fc40.x86_64 opus-1.4-1.fc40.x86_64 orc-0.4.33-3.fc39.x86_64 pango-1.51.0-1.fc40.x86_64 pango-devel-1.51.0-1.fc40.x86_64 pcre2-devel-10.42-2.fc40.x86_64 pcre2-utf16-10.42-2.fc40.x86_64 pcre2-utf32-10.42-2.fc40.x86_64 perl-AutoLoader-5.74-503.fc40.noarch perl-AutoSplit-5.74-503.fc40.noarch perl-B-1.88-503.fc40.x86_64 perl-Benchmark-1.24-503.fc40.noarch perl-Carp-1.54-500.fc39.noarch perl-Class-Struct-0.68-503.fc40.noarch perl-Data-Dumper-2.188-501.fc39.x86_64 perl-Devel-PPPort-3.71-501.fc39.x86_64 perl-Digest-1.20-500.fc39.noarch perl-Digest-MD5-2.58-501.fc40.x86_64 perl-DynaLoader-1.54-503.fc40.x86_64 perl-Encode-4:3.20-501.fc40.x86_64 perl-Errno-1.37-503.fc40.x86_64 perl-Exporter-5.77-500.fc39.noarch perl-ExtUtils-Command-2:7.70-501.fc39.noarch perl-ExtUtils-Constant-0.25-503.fc40.noarch perl-ExtUtils-Install-2.22-500.fc39.noarch perl-ExtUtils-MakeMaker-2:7.70-501.fc39.noarch perl-ExtUtils-Manifest-1:1.75-3.fc39.noarch perl-ExtUtils-ParseXS-1:3.51-501.fc40.noarch perl-Fcntl-1.15-503.fc40.x86_64 perl-Fedora-VSP-0.001-32.fc39.noarch perl-File-Basename-2.86-503.fc40.noarch perl-File-Compare-1.100.700-503.fc40.noarch perl-File-Copy-2.41-503.fc40.noarch perl-File-Find-1.43-503.fc40.noarch perl-File-Path-2.18-501.fc40.noarch perl-File-Temp-1:0.231.100-501.fc40.noarch perl-File-stat-1.13-503.fc40.noarch perl-FileHandle-2.05-503.fc40.noarch perl-Getopt-Long-1:2.57-1.fc40.noarch perl-Getopt-Std-1.13-503.fc40.noarch perl-HTTP-Tiny-0.088-3.fc39.noarch perl-IO-1.52-503.fc40.x86_64 perl-IO-Socket-IP-0.42-1.fc39.noarch perl-IO-Socket-SSL-2.084-1.fc40.noarch perl-IPC-Open3-1.22-503.fc40.noarch perl-MIME-Base64-3.16-501.fc40.x86_64 perl-Mozilla-CA-20230821-1.fc40.noarch perl-Net-SSLeay-1.92-10.fc39.x86_64 perl-POSIX-2.13-503.fc40.x86_64 perl-PathTools-3.89-500.fc39.x86_64 perl-Pod-Escapes-1:1.07-501.fc40.noarch perl-Pod-Perldoc-3.28.01-501.fc39.noarch perl-Pod-Simple-1:3.45-4.fc39.noarch perl-Pod-Usage-4:2.03-500.fc39.noarch perl-Scalar-List-Utils-5:1.63-500.fc39.x86_64 perl-SelectSaver-1.02-503.fc40.noarch perl-Socket-4:2.037-3.fc39.x86_64 perl-Storable-1:3.32-500.fc39.x86_64 perl-Symbol-1.09-503.fc40.noarch perl-Term-ANSIColor-5.01-502.fc40.noarch perl-Term-Cap-1.18-500.fc39.noarch perl-Test-Harness-1:3.48-1.fc40.noarch perl-Text-ParseWords-3.31-500.fc39.noarch perl-Text-Tabs+Wrap-2023.0511-3.fc39.noarch perl-Time-Local-2:1.350-3.fc39.noarch perl-URI-5.21-1.fc40.noarch perl-base-2.27-503.fc40.noarch perl-constant-1.33-501.fc39.noarch perl-devel-4:5.38.2-503.fc40.x86_64 perl-generators-1.16-3.fc39.noarch perl-if-0.61.000-503.fc40.noarch perl-interpreter-4:5.38.2-503.fc40.x86_64 perl-lib-0.65-503.fc40.x86_64 perl-libnet-3.15-501.fc39.noarch perl-libs-4:5.38.2-503.fc40.x86_64 perl-locale-1.10-503.fc40.noarch perl-macros-4:5.38.2-503.fc40.noarch perl-mro-1.28-503.fc40.x86_64 perl-overload-1.37-503.fc40.noarch perl-overloading-0.02-503.fc40.noarch perl-parent-1:0.241-500.fc39.noarch perl-podlators-1:5.01-500.fc39.noarch perl-vars-1.05-503.fc40.noarch perl-version-8:0.99.30-1.fc40.x86_64 pixman-0.42.2-2.fc39.x86_64 pixman-devel-0.42.2-2.fc39.x86_64 poppler-23.08.0-1.fc40.x86_64 poppler-data-0.4.11-5.fc39.noarch poppler-glib-23.08.0-1.fc40.x86_64 pyproject-rpm-macros-1.10.0-1.fc40.noarch python-pip-wheel-23.2.1-1.fc39.noarch python-rpm-macros-3.12-4.fc40.noarch python3-3.12.0-2.fc40.x86_64 python3-devel-3.12.0-2.fc40.x86_64 python3-libs-3.12.0-2.fc40.x86_64 python3-numpy-1:1.26.0-2.fc40.x86_64 python3-packaging-23.2-2.fc40.noarch python3-pyparsing-3.0.9-11.fc39.noarch python3-rpm-generators-14-8.fc40.noarch python3-rpm-macros-3.12-4.fc40.noarch python3-setuptools-68.2.2-1.fc40.noarch rapidjson-devel-1.1.0-23.fc39.x86_64 rav1e-libs-0.6.6-3.fc40.x86_64 rhash-1.4.3-3.fc39.x86_64 rsvg-pixbuf-loader-2.57.0-3.fc40.x86_64 ruby-3.2.2-183.fc40.x86_64 ruby-default-gems-3.2.2-183.fc40.noarch ruby-devel-3.2.2-183.fc40.x86_64 ruby-libs-3.2.2-183.fc40.x86_64 rubygem-io-console-0.6.0-183.fc40.x86_64 rubygem-psych-5.0.1-183.fc40.x86_64 rubygems-3.4.10-183.fc40.noarch rubypick-1.1.1-19.fc39.noarch shared-mime-info-2.3-1.fc40.x86_64 svt-av1-libs-1.4.1-3.fc39.x86_64 swig-4.1.1-12.fc40.x86_64 sysprof-capture-devel-45.1-1.fc40.x86_64 systemtap-sdt-devel-5.0~pre16958465gca71442b-1.fc40.x86_64 tzdata-2023c-4.fc40.noarch urw-base35-bookman-fonts-20200910-18.fc39.noarch urw-base35-c059-fonts-20200910-18.fc39.noarch urw-base35-d050000l-fonts-20200910-18.fc39.noarch urw-base35-fonts-20200910-18.fc39.noarch urw-base35-fonts-common-20200910-18.fc39.noarch urw-base35-gothic-fonts-20200910-18.fc39.noarch urw-base35-nimbus-mono-ps-fonts-20200910-18.fc39.noarch urw-base35-nimbus-roman-fonts-20200910-18.fc39.noarch urw-base35-nimbus-sans-fonts-20200910-18.fc39.noarch urw-base35-p052-fonts-20200910-18.fc39.noarch urw-base35-standard-symbols-ps-fonts-20200910-18.fc39.noarch urw-base35-z003-fonts-20200910-18.fc39.noarch vim-filesystem-2:9.0.2120-1.fc40.noarch vulkan-loader-1.3.268.0-1.fc40.x86_64 wayland-devel-1.22.0-2.fc39.x86_64 webkit2gtk4.1-2.43.1-2.fc40.x86_64 woff2-1.0.2-18.fc39.x86_64 wpebackend-fdo-1.14.2-2.fc39.x86_64 wxBase-3.2.4-1.fc40.x86_64 wxBase-devel-3.2.4-1.fc40.x86_64 wxGTK-3.2.4-1.fc40.x86_64 wxGTK-devel-3.2.4-1.fc40.x86_64 wxGTK-gl-3.2.4-1.fc40.x86_64 wxGTK-i18n-3.2.4-1.fc40.noarch wxGTK-media-3.2.4-1.fc40.x86_64 wxGTK-webview-3.2.4-1.fc40.x86_64 xdg-dbus-proxy-0.1.5-1.fc39.x86_64 xkeyboard-config-2.40-2.fc40.noarch xml-common-0.6.3-62.fc40.noarch xorg-x11-proto-devel-2023.2-3.fc40.noarch xprop-1.2.5-4.fc39.x86_64 xz-devel-5.4.5-1.fc40.x86_64 zlib-devel-1.2.13-5.fc40.x86_64 Complete! Finish: build setup for openbabel-3.1.1-21.fc40.src.rpm Start: rpmbuild openbabel-3.1.1-21.fc40.src.rpm warning: %patchN is deprecated (9 usages found), use %patch N (or %patch -P N) Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1689811200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.hUsB4V + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf openbabel-openbabel-3-1-1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/openbabel-openbabel-3-1-1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd openbabel-openbabel-3-1-1 + rm -rf /builddir/build/BUILD/openbabel-openbabel-3-1-1-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/openbabel-openbabel-3-1-1-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (openbabel-perl.patch):' Patch #0 (openbabel-perl.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .perl_path --fuzz=0 patching file scripts/CMakeLists.txt Hunk #1 succeeded at 367 (offset 31 lines). + echo 'Patch #1 (openbabel-plugindir.patch):' Patch #1 (openbabel-plugindir.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .plugindir --fuzz=0 patching file CMakeLists.txt patching file OpenBabel3Config.cmake.in + echo 'Patch #2 (openbabel-noswig-rubymethod.patch):' Patch #2 (openbabel-noswig-rubymethod.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .noswig_ruby --fuzz=0 patching file scripts/CMakeLists.txt Hunk #1 succeeded at 416 (offset 42 lines). + echo 'Patch #3 (openbabel-ruby19-vendorarch.patch):' Patch #3 (openbabel-ruby19-vendorarch.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .ruby_vendor --fuzz=0 patching file scripts/CMakeLists.txt Hunk #1 succeeded at 447 (offset 47 lines). + echo 'Patch #5 (openbabel-fix-libdir-in-pkgconfig.patch):' Patch #5 (openbabel-fix-libdir-in-pkgconfig.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .s390x --fuzz=0 patching file openbabel-3.pc.cmake + echo 'Patch #7 (openbabel-3.1.1-fix_bug2223.patch):' Patch #7 (openbabel-3.1.1-fix_bug2223.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file src/forcefields/forcefielduff.cpp + echo 'Patch #8 (openbabel-3.1.1-fix_bug2217.patch):' Patch #8 (openbabel-3.1.1-fix_bug2217.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file test/testdistgeom.py + echo 'Patch #9 (openbabel-3.1.1-bug2378.patch):' Patch #9 (openbabel-3.1.1-bug2378.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file scripts/CMakeLists.txt Hunk #1 succeeded at 102 (offset -4 lines). + echo 'Patch #10 (openbabel-3.1.1-bug2493.patch):' Patch #10 (openbabel-3.1.1-bug2493.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .backup --fuzz=0 patching file src/config.h.cmake + rm -rf src/formats/libinchi + dos2unix -k data/chemdrawcdx.h include/openbabel/tautomer.h include/openbabel/math/align.h src/math/align.cpp test/testsmartssym.py dos2unix: converting file data/chemdrawcdx.h to Unix format... dos2unix: converting file include/openbabel/tautomer.h to Unix format... dos2unix: converting file include/openbabel/math/align.h to Unix format... dos2unix: converting file src/math/align.cpp to Unix format... dos2unix: converting file test/testsmartssym.py to Unix format... + convert src/GUI/babel.xpm -transparent white babel.png + pushd doc ~/build/BUILD/openbabel-openbabel-3-1-1/doc ~/build/BUILD/openbabel-openbabel-3-1-1 + for man in *.1 ++ basename obabel.1 .1 + html=obabel.html + '[' -f obabel.html ']' + rm obabel.html + for man in *.1 ++ basename obchiral.1 .1 + html=obchiral.html + '[' -f obchiral.html ']' + rm obchiral.html + for man in *.1 ++ basename obconformer.1 .1 + html=obconformer.html + '[' -f obconformer.html ']' + rm obconformer.html + for man in *.1 ++ basename obdistgen.1 .1 + html=obdistgen.html + '[' -f obdistgen.html ']' + for man in *.1 ++ basename obenergy.1 .1 + html=obenergy.html + '[' -f obenergy.html ']' + rm obenergy.html + for man in *.1 ++ basename obfit.1 .1 + html=obfit.html + '[' -f obfit.html ']' + rm obfit.html + for man in *.1 ++ basename obgen.1 .1 + html=obgen.html + '[' -f obgen.html ']' + rm obgen.html + for man in *.1 ++ basename obgrep.1 .1 + html=obgrep.html + '[' -f obgrep.html ']' + rm obgrep.html + for man in *.1 ++ basename obgui.1 .1 + html=obgui.html + '[' -f obgui.html ']' + rm obgui.html + for man in *.1 ++ basename obminimize.1 .1 + html=obminimize.html + '[' -f obminimize.html ']' + rm obminimize.html + for man in *.1 ++ basename obprobe.1 .1 + html=obprobe.html + '[' -f obprobe.html ']' + rm obprobe.html + for man in *.1 ++ basename obprop.1 .1 + html=obprop.html + '[' -f obprop.html ']' + rm obprop.html + for man in *.1 ++ basename obrms.1 .1 + html=obrms.html + '[' -f obrms.html ']' + for man in *.1 ++ basename obrotamer.1 .1 + html=obrotamer.html + '[' -f obrotamer.html ']' + rm obrotamer.html + for man in *.1 ++ basename obrotate.1 .1 + html=obrotate.html + '[' -f obrotate.html ']' + rm obrotate.html + for man in *.1 ++ basename obspectrophore.1 .1 + html=obspectrophore.html + '[' -f obspectrophore.html ']' + rm obspectrophore.html + for man in *.1 ++ basename obsym.1 .1 + html=obsym.html + '[' -f obsym.html ']' + for man in *.1 ++ basename obtautomer.1 .1 + html=obtautomer.html + '[' -f obtautomer.html ']' + for man in *.1 ++ basename obthermo.1 .1 + html=obthermo.html + '[' -f obthermo.html ']' + for man in *.1 ++ basename roundtrip.1 .1 + html=roundtrip.html + '[' -f roundtrip.html ']' + popd ~/build/BUILD/openbabel-openbabel-3-1-1 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.vU0wcj + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd openbabel-openbabel-3-1-1 + mkdir -p x86_64-redhat-linux-gnu + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Werror=implicit-function-declaration -Werror=implicit-int -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-Wl,-z,relro -Clink-arg=-Wl,-z,now -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /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 -B x86_64-redhat-linux-gnu -Wno-dev -DCMAKE_SKIP_RPATH:BOOL=ON -DBUILD_GUI:BOOL=ON -DPYTHON_BINDINGS:BOOL=ON -DPYTHON_EXECUTABLE=/usr/bin/python3 -DPERL_BINDINGS:BOOL=ON -DRUBY_BINDINGS:BOOL=ON -DWITH_MAEPARSER:BOOL=OFF -DWITH_COORDGEN:BOOL=OFF -DOB_PLUGIN_INSTALL_DIR:PATH=lib64/openbabel3 -DOPENBABEL_USE_SYSTEM_INCHI=true -DENABLE_VERSIONED_FORMATS=false -DRUN_SWIG=true -DENABLE_TESTS:BOOL=ON -DOPTIMIZE_NATIVE=OFF -DGLIBC_24_COMPATIBLE:BOOL=OFF -- The C compiler identification is GNU 13.2.1 -- The CXX compiler identification is GNU 13.2.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found INCHI: /usr/lib64/libinchi.so -- Found LibXml2: /usr/lib64/libxml2.so (found version "2.12.1") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.13") -- Found wxWidgets: -pthread;;;-lwx_baseu-3.2;-lwx_gtk3u_core-3.2 (found version "3.2.4") -- Looking for conio.h -- Looking for conio.h - not found -- Looking for sys/time.h -- Looking for sys/time.h - found -- Looking for time.h -- Looking for time.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for rpc/xdr.h -- Looking for rpc/xdr.h - not found -- Looking for regex.h -- Looking for regex.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Looking for rint -- Looking for rint - not found -- Looking for snprintf -- Looking for snprintf - found -- Looking for sranddev -- Looking for sranddev - not found -- Looking for strcasecmp -- Looking for strcasecmp - found -- Looking for strncasecmp -- Looking for strncasecmp - found -- Looking for dlopen in dl -- Looking for dlopen in dl - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of clock_t -- Check size of clock_t - done -- Performing Test SCANDIR_NEEDS_CONST -- Performing Test SCANDIR_NEEDS_CONST - Failed -- Performing Test HAVE_GCC_VISIBILITY -- Performing Test HAVE_GCC_VISIBILITY - Success -- Checking available shared pointer... -- Performing Test HAVE_STD_SHARED_PTR -- Performing Test HAVE_STD_SHARED_PTR - Success -- Performing Test HAVE_STD_TR1_SHARED_PTR -- Performing Test HAVE_STD_TR1_SHARED_PTR - Failed -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER -- Performing Test HAVE_STD_TR1_SHARED_PTR_IN_TR1_HEADER - Success -- Use std::shared_ptr in memory -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: program_options iostreams -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: filesystem iostreams unit_test_framework -- Maestro formats will NOT be supported. Please install Boost to enable Maestro formats. -- Coordinate generation with Coordgen will NOT be supported. Please install Boost to enable Maestro formats. -- Found PkgConfig: /usr/bin/pkg-config (found version "1.9.5") -- Found RapidJSON: /usr/include (found suitable version "1.1.0", minimum required is "1.1.0") -- JSON formats will be supported. Using RapidJSON 1.1.0 at /usr/include -- Checking for module 'cairo' -- Found cairo, version 1.18.0 -- Found Cairo: /usr/lib64/libcairo.so -- Cairo found. PNG output will be supported. -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found suitable version "1.83.0", minimum required is "1.45.0") found components: system -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found Boost: /usr/lib64/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") found components: program_options iostreams -- Looking for getopt -- Looking for getopt - found -- Attempting to build the GUI -- wxWidgets found => GUI will be built -- Found PythonInterp: /usr/bin/python3 (found version "3.12") -- Found SWIG: /usr/bin/swig (found version "4.1.1") -- Found SWIG: /usr/bin/swig (found suitable version "4.1.1", minimum required is "2.0") -- Found PythonLibs: /usr/lib64/libpython3.12.so (found version "3.12.0") -- Python bindings will be compiled -- Found Perl: /usr/bin/perl (found version "5.38.2") -- Found PerlLibs: /usr/lib64/libperl.so (found version "5.38.2") -- Perl bindings will be compiled -- Found Ruby: /usr/bin/ruby (found suitable version "3.2.2", minimum required is "1.8.0") -- Ruby bindings will be compiled -- Configuring done (7.0s) -- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP INCLUDE_INSTALL_DIR SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu + /usr/bin/make -O -j2 V=1 VERBOSE=1 -C x86_64-redhat-linux-gnu make: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/cmake -S/builddir/build/BUILD/openbabel-openbabel-3-1-1 -B/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/CMakeFiles /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu//CMakeFiles/progress.marks make: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/openbabel.dir/build.make src/CMakeFiles/openbabel.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/CMakeFiles/openbabel.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/openbabel.dir/build.make src/CMakeFiles/openbabel.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/atom.cpp.o -MF CMakeFiles/openbabel.dir/atom.cpp.o.d -o CMakeFiles/openbabel.dir/atom.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/atom.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/alias.cpp.o -MF CMakeFiles/openbabel.dir/alias.cpp.o.d -o CMakeFiles/openbabel.dir/alias.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/alias.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/alias.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/alias.cpp:16: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/openbabel.dir/base.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/base.cpp.o -MF CMakeFiles/openbabel.dir/base.cpp.o.d -o CMakeFiles/openbabel.dir/base.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/base.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/openbabel.dir/bitvec.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/bitvec.cpp.o -MF CMakeFiles/openbabel.dir/bitvec.cpp.o.d -o CMakeFiles/openbabel.dir/bitvec.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/bitvec.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/bond.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/bond.cpp.o -MF CMakeFiles/openbabel.dir/bond.cpp.o.d -o CMakeFiles/openbabel.dir/bond.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/bond.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/bondtyper.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/bondtyper.cpp.o -MF CMakeFiles/openbabel.dir/bondtyper.cpp.o.d -o CMakeFiles/openbabel.dir/bondtyper.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/bondtyper.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/builder.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL 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/builddir/build/BUILD/openbabel-openbabel-3-1-1/src/builder.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/builder.cpp:31: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/builder.h:23, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/builder.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/canon.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/canon.cpp.o -MF CMakeFiles/openbabel.dir/canon.cpp.o.d -o CMakeFiles/openbabel.dir/canon.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/canon.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/chargemodel.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL 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-c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/chargemodel.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/chargemodel.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory 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-m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/chains.cpp.o -MF CMakeFiles/openbabel.dir/chains.cpp.o.d -o CMakeFiles/openbabel.dir/chains.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/chains.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/data_utilities.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/data_utilities.cpp.o -MF CMakeFiles/openbabel.dir/data_utilities.cpp.o.d -o CMakeFiles/openbabel.dir/data_utilities.cpp.o -c 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-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/data.cpp.o -MF CMakeFiles/openbabel.dir/data.cpp.o.d -o CMakeFiles/openbabel.dir/data.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/data.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/descriptor.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 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CMakeFiles/openbabel.dir/descriptor.cpp.o.d -o CMakeFiles/openbabel.dir/descriptor.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptor.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptor.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptor.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 2%] Building CXX object src/CMakeFiles/openbabel.dir/elements.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 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cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer 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binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/format.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/format.cpp.o -MF CMakeFiles/openbabel.dir/format.cpp.o.d -o CMakeFiles/openbabel.dir/format.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/format.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/format.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/generic.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include 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'/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/forcefield.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/forcefield.cpp.o -MF CMakeFiles/openbabel.dir/forcefield.cpp.o.d -o CMakeFiles/openbabel.dir/forcefield.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void Init(OBMol &box); | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 123 | void Init(OBMol &box,double spacing, double pad=0.0); | ^~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:48, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:26: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:228:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 228 | virtual const std::string &GetValue() const | ^~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 76 | double GetValue (vector3 pos) const; | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:391:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 391 | if (_ignoreAtom == a) | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:393:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 393 | if (_ignoreAtom == b) | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:403:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 403 | if (_ignoreAtom == b) | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:413:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 413 | if (_ignoreAtom == d) | ~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintType(int) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:665:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 665 | if (index >= _constraints.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘double OpenBabel::OBFFConstraints::GetConstraintValue(int) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:673:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 673 | if (index >= _constraints.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomA(int) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:681:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 681 | if (index >= _constraints.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomB(int) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:689:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 689 | if (index >= _constraints.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomC(int) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:697:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 697 | if (index >= _constraints.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomD(int) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:705:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 705 | if (index >= _constraints.size()) | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1353:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1353 | num_permutations = factorial[num_rotors_to_permute]; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1357:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1357 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1370 | for (int i=0; i >&, std::vector, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1571:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 1571 | if (j == rotorKey[i]) /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1590:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} [-Wsign-compare] 1590 | if (j == rotorKey[i]) In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:624:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:620:20: note: ‘constraint’ declared here 620 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:624:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:620:20: note: ‘constraint’ declared here 620 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:660:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:652:20: note: ‘constraint’ declared here 652 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:660:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:652:20: note: ‘constraint’ declared here 652 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘stmake[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' d::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:635:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:629:20: note: ‘constraint’ declared here 629 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:635:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:629:20: note: ‘constraint’ declared here 629 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:647:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:640:20: note: ‘constraint’ declared here 640 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:647:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:640:20: note: ‘constraint’ declared here 640 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddIgnore(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:580:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM [(double *)&constraint + 16B]’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddIgnore(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:577:20: note: ‘constraint’ declared here 577 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:591:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:587:20: note: ‘constraint’ declared here 587 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:591:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:587:20: note: ‘constraint’ declared here 587 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:602:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:598:20: note: ‘constraint’ declared here 598 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:602:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:598:20: note: ‘constraint’ declared here 598 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:613:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rab0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:609:20: note: ‘constraint’ declared here 609 | OBFFConstraint constraint; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFConstraint::OBFFConstraint(OpenBabel::OBFFConstraint const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFConstraint*, OpenBabel::OBFFConstraint const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFConstraint const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:613:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:233:16: warning: ‘MEM[(const struct OBFFConstraint &)&constraint].rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 233 | class OBFPRT OBFFConstraint | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:609:20: note: ‘constraint’ declared here 609 | OBFFConstraint constraint; | ^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp: In member function ‘OpenBabel::OBForceField::FastRotorSearch(bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1393:29: warning: ‘minj’ may be used uninitialized [-Wmaybe-uninitialized] 1393 | rotorKey[idx + 1] = minj; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1319:21: note: ‘minj’ was declared here 1319 | unsigned int j, minj; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1410:11: warning: ‘minE’ may be used uninitialized [-Wmaybe-uninitialized] 1410 | if (minE < best_minE) { | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefield.cpp:1320:22: note: ‘minE’ was declared here 1320 | double currentE, minE, best_minE; | ^~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/grid.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/grid.cpp.o -MF CMakeFiles/openbabel.dir/grid.cpp.o.d -o CMakeFiles/openbabel.dir/grid.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/grid.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/grid.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void Init(OBMol &box); | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 123 | void Init(OBMol &box,double spacing, double pad=0.0); | ^~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 3%] Building CXX object src/CMakeFiles/openbabel.dir/graphsym.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ 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Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/griddata.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/griddata.cpp.o -MF CMakeFiles/openbabel.dir/griddata.cpp.o.d -o CMakeFiles/openbabel.dir/griddata.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/griddata.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/generic.h:31, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/griddata.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/griddata.cpp:25: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:228:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 228 | virtual const std::string &GetValue() const | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 76 | double GetValue (vector3 pos) const; | ^~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/griddata.cpp:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 55 | virtual void Init(OBMol &box); | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 123 | void Init(OBMol &box,double spacing, double pad=0.0); | ^~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory 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-specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/kekulize.cpp.o -MF CMakeFiles/openbabel.dir/kekulize.cpp.o.d -o CMakeFiles/openbabel.dir/kekulize.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/kekulize.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/kekulize.cpp: In function ‘bool OpenBabel::NeedsDoubleBond(OBAtom*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/kekulize.cpp:94:15: warning: unused variable ‘nbr’ [-Wunused-variable] 94 | OBAtom *nbr = bond->GetNbrAtom(atom); | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 4%] Building CXX object src/CMakeFiles/openbabel.dir/locale.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection 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make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/mol.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/mol.cpp.o -MF CMakeFiles/openbabel.dir/mol.cpp.o.d -o CMakeFiles/openbabel.dir/mol.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mol.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mol.cpp: In member function ‘unsigned int OpenBabel::OBMol::NumHvyAtoms()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mol.cpp:809:30: warning: unnecessary parentheses in declaration of ‘i’ [-Wparentheses] 809 | vector::iterator(i); | ^~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mol.cpp:809:30: note: remove parentheses 809 | vector::iterator(i); | ^~~ | - - /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mol.cpp: In member function ‘unsigned int OpenBabel::OBMol::GetTotalSpinMultiplicity()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mol.cpp:1221:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1221 | if (chg % 2 != unpaired_electrons %2) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/mcdlutil.cpp.o -MF CMakeFiles/openbabel.dir/mcdlutil.cpp.o.d -o CMakeFiles/openbabel.dir/mcdlutil.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:423:5: warning: multi-line comment [-Wcomment] 423 | // / \ | ^ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘bool OpenBabel::TSimpleMolecule::threeBondResolve(int, int, double&, double&, OpenBabel::neighbourlist*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:968:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 968 | for (i=0; i&, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:1471:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1471 | for (j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1478 | } while (k&, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&, std::vector&, std::vector&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:2009:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2009 | for (j=0; j0) atDef=atDef+1; | ~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:2019:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2019 | if (cN>=0) if (maxAtDef==atomCycle[cN].size()) { | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:2034:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2034 | for (j=1; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2040 | for (j=0;currNumDef < atomClean && j&, std::vector, std::vector&, std::vector >&, std::vector&, std::vector&, std::vector&, std::vector&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:2107:98: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2107 | if (baseCycle>0) for (i=0; i, std::vector, int, int&, int, int, int, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:2238:67: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2238 | for (j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2240 | for (k=0; k::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2264 | for (j=1; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2575 | if ((nb + i) > dsATN.size()) nb=dsATN.size()-i; // Check added to avoid segfault below, see issue #1851 | ~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘void OpenBabel::TSimpleMolecule::flipSmall(int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:2985:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2985 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3024 | for (i=0; i, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3103 | if (bond->at[0]==dblbond->bstereo_refs[ref_atom1] || bond->at[1]==dblbond->bstereo_refs[ref_atom1]) /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3103:75: warning: comparison of integer expressions of different signedness: ‘short int’ and ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3103 | if (bond->at[0]==dblbond->bstereo_refs[ref_atom1] || bond->at[1]==dblbond->bstereo_refs[ref_atom1]) /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3105:26: warning: comparison of integer expressions of different signedness: ‘short int’ and ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3105 | if (bond->at[0]==dblbond->bstereo_refs[ref_atom2] || bond->at[1]==dblbond->bstereo_refs[ref_atom2]) /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3105:75: warning: comparison of integer expressions of different signedness: ‘short int’ and ‘__gnu_cxx::__alloc_traits, long unsigned int>::value_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3105 | if (bond->at[0]==dblbond->bstereo_refs[ref_atom2] || bond->at[1]==dblbond->bstereo_refs[ref_atom2]) /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In function ‘bool OpenBabel::compareAtoms(int, int, std::vector*>)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3127:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3127 | if ((a1 < 0) || (a2 < 0) || (a1 >= aeqList.size()) || (a2 >= aeqList.size())) return result; | ~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3127:63: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3127 | if ((a1 < 0) || (a2 < 0) || (a1 >= aeqList.size()) || (a2 >= aeqList.size())) return result; | ~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘void OpenBabel::TSimpleMolecule::makeEquivalentList(std::vector&, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3291:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3291 | for (j=0; jsize(); j++) (*lL)[i]=0; | ~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3299:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3299 | for (i=0; i*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3309 | for (int i=0; i&, std::vector)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3325:13: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const __gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘const int’} [-Wsign-compare] 3325 | if (l <= maxValues[i]) { /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘int OpenBabel::TSimpleMolecule::correctOverlapped()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3374:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3374 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3427 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3437 | for (i=0; i*, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:3540:44: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3540 | for (i=0; isize(); i++) if (i != index) { | ~~^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘void OpenBabel::TEditedMolecule::addAsTemplate(OpenBabel::TEditedMolecule&, int, int, int, int, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4216:19: warning: variable ‘nBondsOld’ set but not used [-Wunused-but-set-variable] 4216 | int nAtomsOld,nBondsOld,naDef1,naDef,i; | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4217:10: warning: variable ‘test’ set but not used [-Wunused-but-set-variable] 4217 | bool test,test1,test2; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4217:15: warning: variable ‘test1’ set but not used [-Wunused-but-set-variable] 4217 | bool test,test1,test2; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4217:21: warning: variable ‘test2’ set but not used [-Wunused-but-set-variable] 4217 | bool test,test1,test2; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4219:40: warning: variable ‘xCenter’ set but not used [-Wunused-but-set-variable] 4219 | double r,scale,xOld,yOld,xNew,yNew,xCenter,yCenter; | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4219:48: warning: variable ‘yCenter’ set but not used [-Wunused-but-set-variable] 4219 | double r,scale,xOld,yOld,xNew,yNew,xCenter,yCenter; | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘OpenBabel::TEditedMolecule* OpenBabel::TEditedMolecule::extractFragment(int, std::vector*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4410:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4410 | if (list.size()>1) for (i=0; i<(list.size()-1); i++) for (j=i+1; jlist[j]) { | ~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4410:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4410 | if (list.size()>1) for (i=0; i<(list.size()-1); i++) for (j=i+1; jlist[j]) { | ~^~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4415:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4415 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4418 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4591 | for (j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4596 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4601 | for (i=0; i*, std::vector*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4636:31: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 4636 | if (qEnumerator->size() != nAtoms()) qEnumerator->resize(nAtoms()); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4637:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4637 | for (i=0; isize(); i++) (*qEnumerator)[i]=i; | ~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4666:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4666 | for (j=0; jsize(); j++) { | ~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘bool OpenBabel::TEditedMolecule::fragmentSearch(OpenBabel::TEditedMolecule*, std::vector*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4853:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4853 | if (molecule1->listarSize()>aSTested.size()) aSTested.resize(molecule1->listarSize()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4854:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4854 | if (molecule1->listarSize()>bSTested.size()) bSTested.resize(molecule1->listarSize()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4855:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4855 | if (molecule1->listarSize()>queryQHydr.size()) queryQHydr.resize(molecule1->listarSize()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4856:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4856 | if (molecule1->listarSize()>queryAQTested.size()) queryAQTested.resize(molecule1->listarSize()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4857:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4857 | if (molecule1->listarSize()>queryBQTested.size()) queryBQTested.resize(molecule1->listarSize()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4858:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4858 | if (molecule1->listarSize()>queryCurrentAssignment.size()) queryCurrentAssignment.resize(molecule1->listarSize()); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4859:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 4859 | if (this->listarSize()>queryAQTested.size()) queryAQTested.resize(this->listarSize()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5036:10: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 5036 | if (test2) for (j=0; jnBonds(); j++) if (bSTested[j]>=0) (*bondLabel)[j]=1; else (*bondLabel)[j]=0; | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4840:9: warning: variable ‘cycleNumber’ set but not used [-Wunused-but-set-variable] 4840 | int cycleNumber; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘bool OpenBabel::TemplateRedraw::loadTemplates()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5115:24: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 5115 | } catch (exception ex) { | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘bool OpenBabel::TemplateRedraw::internalBondsPresent(OpenBabel::TEditedMolecule*, OpenBabel::TSimpleMolecule*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5205:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 5205 | for (i=0; inAtoms(); i++) aList[mQuery->queryAQTested[i]]=1; | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5206:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 5206 | for (i=0; inBonds(); i++) bList[mQuery->queryBQTested[i]]=1; | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘void OpenBabel::TemplateRedraw::rotateBondVertically(OpenBabel::TSimpleMolecule*, std::vector, int, double, double, double&, double&, double&, double&, double&, double&, int&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5236:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5236 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5281 | for (i=0; i*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5315:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5315 | for (i=0; isize(); i++) { | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5332 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5362 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5372 | for (i=0; i*, OpenBabel::PartFragmentDefinition&, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5403:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5403 | for (i=0; isize(); i++) { | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5416:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5416 | for (i=0; isize(); i++) { | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5432:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5432 | for (i=0; isize(); i++) { | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘int OpenBabel::TemplateRedraw::coordinatesPrepare(OpenBabel::TEditedMolecule&, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5671:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5671 | for (i=kk; ifragmentSearch(&sm,nullptr)) { | ~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:5719:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5719 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5722 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5730 | for (j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5802 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5832 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5898 | for (j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5910 | for (frCount=0; frCount::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5926 | for (frCount=0; frCount::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5949 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 5964 | for (frCount=0; frCount::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6004 | for (i=0;i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6011 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6030 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6038 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6039 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6040 | for (i=0; i::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 6362 | if (result == string::npos) result=-1; | ~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6363:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6363 | if (result >= instring.length()) result=-1; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In function ‘std::string OpenBabel::getAtomMCDL(OBMol*, int, std::vector, std::vector, std::vector, std::vector)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6550:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6550 | for (j=0; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6595 | if (anumStereo.size() > 1) for (i=0; i<(anumStereo.size()-1); i++) if (anumStereo[i] >= 0) { | ~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6597:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6597 | for (j=i+1; j= 0) && (anumStereo[j] >= 0)) if (eqList[anumStereo[i]] == eqList[anumStereo[j]]) n++; | ~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6603:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6603 | for (j=i+1; j= 0) && (anumStereo[j] >= 0)) if (eqList[anumStereo[i]] == eqList[anumStereo[j]]) { | ~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6613:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6613 | for (j=i+1; j= 0) && (anumStereo[j] >= 0)) if (eqList[anumStereo[i]] == eqList[anumStereo[j]]) anumStereo[j]=-1; | ~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6616:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6616 | for (j=i+1; j= 0) && (anumStereo[j] >= 0)) if (eqList[anumStereo[i]] == eqList[anumStereo[j]]) anumStereo[j]=-2; | ~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6627:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6627 | if (k == 1) for (i=0; i >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6636 | if (v.size() > 1) for (i=0; i<(v.size() - 1); i++) for (j=i+1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6636 | if (v.size() > 1) for (i=0; i<(v.size() - 1); i++) for (j=i+1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6646 | for (i=0; i < v.size(); i++) { | ~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In function ‘std::string OpenBabel::getBondMCDL(OBMol*, int, int, std::vector, std::vector, int (*)[4], std::vector, std::vector)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6847:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6847 | if (anumStereo.size() > 1) for (i=0; i<(anumStereo.size()-1); i++) if (anumStereo[i] >= 0) { | ~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6849:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6849 | for (j=i+1; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6854 | for (j=i+1; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6868 | for (j=i+1; j::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6876 | for (j=i+1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6881 | if (v.size() > 1) for (i=0; i<(v.size() - 1); i++) for (j=i+1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6881 | if (v.size() > 1) for (i=0; i<(v.size() - 1); i++) for (j=i+1; j >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6891 | for (i=0; i < v.size(); i++) { | ~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6684:26: warning: variable ‘n4’ set but not used [-Wunused-but-set-variable] 6684 | int i,j,n,m,n1,n2,n3,n4,an1,an2,an3,an4,k; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In function ‘void OpenBabel::implementAtomStereo(std::vector&, std::vector&, std::vector&, std::vector, std::vector, int, int, std::string)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:6964:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 6964 | if (n1 < (astereo.length()-1)) astereo=astereo.substr(n1+1); else astereo=""; | ~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In function ‘void OpenBabel::implementBondStereo(std::vector, std::vector, std::vector&, std::vector&, int, int, std::string)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7028:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7028 | if (n1 < (bstereo.length()-1)) bstereo=bstereo.substr(n1+1); else bstereo=""; | ~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7071:34: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 7071 | } catch (exception ex) { | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7085:34: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=] 7085 | } catch (exception ex) { | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In function ‘int OpenBabel::groupRedraw(OBMol*, int, int, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7163:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7163 | for (i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7171 | for (int i=0; i&, int&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7213:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7213 | if (n='0') && (value.at(n)<='9')) { | ~^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7216:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7216 | while ((n2<(value.length()-1)) && (value.at(n2)>='0') && (value.at(n2)<='9')) n2++; | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7237:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7237 | if (n='0') && (value.at(n)<='9')) { | ~^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:7240:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 7240 | while ((n2<(value.length()-1)) && (value.at(n2)>='0') && (value.at(n2)<='9')) n2++; | ~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp: In member function ‘OpenBabel::TEditedMolecule::addAsTemplate(OpenBabel::TEditedMolecule&, int, int, int, int, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4333:16: warning: ‘r1’ may be used uninitialized [-Wmaybe-uninitialized] 4333 | xNew=r1*scale*xu1+this->getAtom(thisAN)->rx; | ~~^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/mcdlutil.cpp:4220:12: note: ‘r1’ was declared here 4220 | double r1; | ^~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/oberror.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON 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-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/obfunctions.cpp.o -MF CMakeFiles/openbabel.dir/obfunctions.cpp.o.d -o CMakeFiles/openbabel.dir/obfunctions.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obfunctions.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 5%] Building CXX object src/CMakeFiles/openbabel.dir/obconversion.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/obconversion.cpp.o -MF CMakeFiles/openbabel.dir/obconversion.cpp.o.d -o CMakeFiles/openbabel.dir/obconversion.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obconversion.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obconversion.cpp:48: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obconversion.cpp:37: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/obutil.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/obutil.cpp.o -MF CMakeFiles/openbabel.dir/obutil.cpp.o.d -o CMakeFiles/openbabel.dir/obutil.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obutil.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 6%] Building CXX object src/CMakeFiles/openbabel.dir/op.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection 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-specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/obiter.cpp.o -MF CMakeFiles/openbabel.dir/obiter.cpp.o.d -o CMakeFiles/openbabel.dir/obiter.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obiter.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/patty.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL 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/builddir/build/BUILD/openbabel-openbabel-3-1-1/src/patty.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/parsmart.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/parsmart.cpp.o -MF CMakeFiles/openbabel.dir/parsmart.cpp.o.d -o CMakeFiles/openbabel.dir/parsmart.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp: In function ‘int OpenBabel::CreateAtom(Pattern*, AtomExpr*, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp:446:15: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 446 | int index,size; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp: In function ‘int OpenBabel::CreateBond(Pattern*, BondExpr*, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp:478:15: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 478 | int index,size; | ^~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/plugin.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/plugin.cpp.o -MF CMakeFiles/openbabel.dir/plugin.cpp.o.d -o CMakeFiles/openbabel.dir/plugin.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/plugin.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/plugin.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/phmodel.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/phmodel.cpp.o -MF CMakeFiles/openbabel.dir/phmodel.cpp.o.d -o CMakeFiles/openbabel.dir/phmodel.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/phmodel.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/query.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/query.cpp.o -MF CMakeFiles/openbabel.dir/query.cpp.o.d -o CMakeFiles/openbabel.dir/query.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/query.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/query.cpp:29: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/bond.h:31, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/query.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/query.cpp:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 7%] Building CXX object src/CMakeFiles/openbabel.dir/pointgroup.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/pointgroup.cpp.o -MF CMakeFiles/openbabel.dir/pointgroup.cpp.o.d -o CMakeFiles/openbabel.dir/pointgroup.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp: In member function ‘int OpenBabel::PointGroupPrivate::establish_pairs(SYMMETRY_ELEMENT*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:267:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 267 | if( elem->transform[i] >= _mol->NumAtoms() ){ /* No symmetric atom yet */ | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp: In member function ‘int OpenBabel::PointGroupPrivate::check_transform_order(SYMMETRY_ELEMENT*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:311:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 311 | if( elem->transform[i] == i ) /* Identity transform is Ok for any order */ | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:315:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 315 | if( elem->transform[j] == i ) | ~~~~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp: In member function ‘int OpenBabel::PointGroupPrivate::same_transform(SYMMETRY_ELEMENT*, SYMMETRY_ELEMENT*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:358:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 358 | if( b->transform[j] != i ) | ~~~~~~~~~~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp: In member function ‘OpenBabel::OBPointGroup::Symbol OpenBabel::OBPointGroup::IdentifyPointGroupSymbol(double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:1958:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1958 | || d->NormalAxesCounts[2] >= maxAxis) { // Are there the perpendicular C2 axes? | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:1961:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1961 | if (d->PlanesCount >= maxAxis + 1) { // Likely Dnh | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:1986:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1986 | else if (d->PlanesCount == maxAxis) { // Likely Dnd | ~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:2088:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2088 | else if (d->PlanesCount >= maxAxis) { // Cnv | ~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp: In member function ‘void OpenBabel::OBPointGroup::Symmetrize(OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:2175:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2175 | for (unsigned int i = 0; i < d->PlanesCount; i++) | ~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:2182:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2182 | for (unsigned int i = 0; i < d->NormalAxesCount; i++) | ~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/pointgroup.cpp:2189:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2189 | for (unsigned int i = 0; i < d->ImproperAxesCount; i++) | ~~^~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/rand.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/rand.cpp.o -MF CMakeFiles/openbabel.dir/rand.cpp.o.d -o CMakeFiles/openbabel.dir/rand.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rand.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rand.cpp:428:15: warning: ‘void OpenBabel::GenerateSequence(unsigned int, unsigned int, unsigned int, unsigned int)’ defined but not used [-Wunused-function] 428 | static void GenerateSequence( unsigned int p, unsigned int m, | ^~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/reactionfacade.cpp.o -MF CMakeFiles/openbabel.dir/reactionfacade.cpp.o.d -o CMakeFiles/openbabel.dir/reactionfacade.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/reactionfacade.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/reactionfacade.cpp: In member function ‘void OpenBabel::OBReactionFacadePrivate::FindComponents()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/reactionfacade.cpp:122:15: warning: unused variable ‘atm’ [-Wunused-variable] 122 | OBAtom* atm = &*atom; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/residue.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/residue.cpp.o -MF CMakeFiles/openbabel.dir/residue.cpp.o.d -o CMakeFiles/openbabel.dir/residue.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/residue.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 8%] Building CXX object src/CMakeFiles/openbabel.dir/ring.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/ring.cpp.o -MF CMakeFiles/openbabel.dir/ring.cpp.o.d -o CMakeFiles/openbabel.dir/ring.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ring.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/rotamer.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/rotamer.cpp.o -MF CMakeFiles/openbabel.dir/rotamer.cpp.o.d -o CMakeFiles/openbabel.dir/rotamer.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp: In member function ‘void OpenBabel::OBRotamerList::AddRotamer(std::vector)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp:410:11: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 410 | while (angle < 0.0) | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp:412:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 412 | while (angle > 360.0) | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp: In member function ‘bool OpenBabel::OBRotamerList::SetCurrentCoordinates(OpenBabel::OBMol&, std::vector)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp:543:11: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 543 | while (angle < 0.0) | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotamer.cpp:545:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 545 | while (angle > 360.0) | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/rotor.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/rotor.cpp.o -MF CMakeFiles/openbabel.dir/rotor.cpp.o.d -o CMakeFiles/openbabel.dir/rotor.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/rotor.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/tautomer.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/tautomer.cpp.o -MF CMakeFiles/openbabel.dir/tautomer.cpp.o.d -o CMakeFiles/openbabel.dir/tautomer.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/tautomer.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/tautomer.cpp:26: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/tautomer.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/tautomer.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/spectrophore.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/spectrophore.cpp.o -MF CMakeFiles/openbabel.dir/spectrophore.cpp.o.d -o CMakeFiles/openbabel.dir/spectrophore.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/spectrophore.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 9%] Building CXX object src/CMakeFiles/openbabel.dir/tokenst.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/tokenst.cpp.o -MF CMakeFiles/openbabel.dir/tokenst.cpp.o.d -o CMakeFiles/openbabel.dir/tokenst.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/tokenst.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/transform.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/transform.cpp.o -MF CMakeFiles/openbabel.dir/transform.cpp.o.d -o CMakeFiles/openbabel.dir/transform.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/transform.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/transform.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/transform.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/typer.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/typer.cpp.o -MF CMakeFiles/openbabel.dir/typer.cpp.o.d -o CMakeFiles/openbabel.dir/typer.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/typer.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/obmolecformat.cpp.o -MF CMakeFiles/openbabel.dir/obmolecformat.cpp.o.d -o CMakeFiles/openbabel.dir/obmolecformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obmolecformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obmolecformat.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:48, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obmolecformat.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:286:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 286 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} | ^~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/obmolecformat.cpp:22: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/reaction.h:99:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 99 | std::string GetTitle() const { return _title; } | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:287:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 287 | virtual void SetTitle(const char *) {} | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/reaction.h:101:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 101 | void SetTitle(const std::string& title) { _title=title; } | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/confsearch.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/confsearch.cpp.o -MF CMakeFiles/openbabel.dir/confsearch.cpp.o.d -o CMakeFiles/openbabel.dir/confsearch.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/atom.h:30, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp: In constructor ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp:134:66: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 134 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less(), (cutoff + 0.1) )), vec.end()); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp:189:14: warning: unused variable ‘min_rmsd’ [-Wunused-variable] 189 | double min_rmsd = DBL_MAX; | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp: In member function ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/confsearch.cpp:444:77: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = plus; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 444 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(std::plus(), energy_offset)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 10%] Building CXX object src/CMakeFiles/openbabel.dir/conformersearch.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/conformersearch.cpp.o -MF CMakeFiles/openbabel.dir/conformersearch.cpp.o.d -o CMakeFiles/openbabel.dir/conformersearch.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:22: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/conformersearch.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:250:12: warning: unused variable ‘score’ [-Wunused-variable] 250 | double score = ff->Energy(false); // no gradients | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘bool OpenBabel::OBConformerSearch::Setup(const OpenBabel::OBMol&, int, int, int, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:352:23: warning: variable ‘end_it’ set but not used [-Wunused-but-set-variable] 352 | OBRotorIterator end_it = m_rotorList.EndRotors(); | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::local_opt()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:790:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 790 | for (i = 1; i <= m_rotorList.Size(); ++i, rotor = m_rotorList.NextRotor(ri)) | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::reproduce(OpenBabel::RotorKey&, OpenBabel::RotorKey&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:851:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 851 | if (iniche > -1) | ~~~~~~~^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::share_fitness()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1006:37: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1006 | if ((dynamic_niches.size () < nb_niches) && (dynamic_niches.size () %2)) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1021:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1021 | if (dist < min_dist ) | ~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1034:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 1034 | if (imax == -1) | ~~~~~^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1051:40: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1051 | if (dynamic_niches.size () < nb_niches) | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:977:10: warning: unused variable ‘flag_niched’ [-Wunused-variable] 977 | bool flag_niched = false; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::sharing_generation()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1140:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1140 | while (ninsert < ((half_pop * 2) / 3)) | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1149:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1149 | if (iround < imax) | ~~~~~~~^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1157:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1157 | if (ninsert >= half_pop) | ~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1182:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1182 | while (ninsert < half_pop) | ~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1106:23: warning: unused variable ‘lowest’ [-Wunused-variable] 1106 | double sum = 0.0, lowest = 0.0, highest = 0.0; | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:1106:37: warning: unused variable ‘highest’ [-Wunused-variable] 1106 | double sum = 0.0, lowest = 0.0, highest = 0.0; | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp: In member function ‘OpenBabel::OBConformerSearch::MakeSelection()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/conformersearch.cpp:550:31: warning: ‘highest’ may be used uninitialized [-Wmaybe-uninitialized] 550 | double sum = 0.0, lowest, highest; | ^~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER 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CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/dlhandler_unix.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/depict/depict.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/depict/depict.cpp.o -MF CMakeFiles/openbabel.dir/depict/depict.cpp.o.d -o CMakeFiles/openbabel.dir/depict/depict.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp: In function ‘unsigned int OpenBabel::GetAtomSymClass(OBAtom*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:284:11: warning: unused variable ‘nclasses’ [-Wunused-variable] 284 | int nclasses = end_pos - copy_sym.begin(); | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtomLabel(const std::string&, int, const OpenBabel::vector3&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:1024:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 1024 | OBFontMetrics metrics = painter->GetFontMetrics(str); | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:1029:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 1029 | OBFontMetrics metrics = painter->GetFontMetrics(subscript); | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp: In member function ‘void OpenBabel::OBDepictPrivateBallAndStick::DrawAromaticRingBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, const OpenBabel::vector3&, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:1238:99: warning: expression does not compute the number of elements in this array; element type is ‘const float’, not ‘double’ [-Wsizeof-array-div] 1238 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:1238:100: note: add parentheses around ‘sizeof (double)’ to silence this warning 1238 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); | ^~~~~~~~~~~~~~ | ( ) /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:1237:24: note: array ‘dashpattern’ declared here 1237 | static const float dashpattern[] = {5., 5.}; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp: In member function ‘OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:462:22: warning: ‘min_x’ may be used uninitialized [-Wmaybe-uninitialized] 462 | width = max_x - min_x + 2*margin; | ~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:435:14: note: ‘min_x’ was declared here 435 | double min_x, max_x; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:462:22: warning: ‘max_x’ may be used uninitialized [-Wmaybe-uninitialized] 462 | width = max_x - min_x + 2*margin; | ~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:435:21: note: ‘max_x’ was declared here 435 | double min_x, max_x; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:463:22: warning: ‘min_y’ may be used uninitialized [-Wmaybe-uninitialized] 463 | height = max_y - min_y + 2*margin; | ~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:436:14: note: ‘min_y’ was declared here 436 | double min_y, max_y; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:463:22: warning: ‘max_y’ may be used uninitialized [-Wmaybe-uninitialized] 463 | height = max_y - min_y + 2*margin; | ~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:436:21: note: ‘max_y’ was declared here 436 | double min_y, max_y; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:465:25: warning: ‘min_z’ may be used uninitialized [-Wmaybe-uninitialized] 465 | d->zScale = max_z - min_z; | ~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:437:14: note: ‘min_z’ was declared here 437 | double min_z, max_z; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:465:25: warning: ‘max_z’ may be used uninitialized [-Wmaybe-uninitialized] 465 | d->zScale = max_z - min_z; | ~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/depict.cpp:437:21: note: ‘max_z’ was declared here 437 | double min_z, max_z; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o -MF CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o.d -o CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/svgpainter.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/svgpainter.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/depict/svgpainter.h: In constructor ‘OpenBabel::SVGPainter::SVGPainter(std::ostream&, std::set >*, bool, double, double)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/depict/svgpainter.h:77:11: warning: ‘OpenBabel::SVGPainter::m_fontPointSize’ will be initialized after [-Wreorder] 77 | int m_fontPointSize; | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/depict/svgpainter.h:75:12: warning: ‘bool OpenBabel::SVGPainter::m_isFillcolor’ [-Wreorder] 75 | bool m_isFillcolor; | ^~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, | ^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/depict/svgpainter.h:75:12: warning: ‘OpenBabel::SVGPainter::m_isFillcolor’ will be initialized after [-Wreorder] 75 | bool m_isFillcolor; | ^~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/depict/svgpainter.h:74:32: warning: ‘std::set >* OpenBabel::SVGPainter::m_Gradients’ [-Wreorder] 74 | std::set *m_Gradients; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, | ^~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem 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Building CXX object src/CMakeFiles/openbabel.dir/math/spacegroup.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables 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-I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/math/transform3d.cpp.o -MF CMakeFiles/openbabel.dir/math/transform3d.cpp.o.d -o CMakeFiles/openbabel.dir/math/transform3d.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/math/transform3d.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/vector3.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/math/vector3.cpp.o -MF CMakeFiles/openbabel.dir/math/vector3.cpp.o.d -o CMakeFiles/openbabel.dir/math/vector3.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/math/vector3.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 11%] Building CXX object src/CMakeFiles/openbabel.dir/distgeom.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/distgeom.cpp.o -MF CMakeFiles/openbabel.dir/distgeom.cpp.o.d -o CMakeFiles/openbabel.dir/distgeom.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:54: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 54 | #pragma warning(disable : 4244) // warning C4244: '=' : conversion from 'double' to 'float', possible loss of data | /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:55: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 55 | #pragma warning(disable : 4305) // warning C4305: '*=' : truncation from 'double' to 'float' | /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:619:3: warning: multi-line comment [-Wcomment] 619 | // \ | ^ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:38: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/distgeom.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp: In member function ‘bool OpenBabel::OBDistanceGeometry::generateInitialCoords()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1089:16: warning: unused variable ‘lb’ [-Wunused-variable] 1089 | double lb = _d->GetLowerBounds(i, j); | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1090:16: warning: unused variable ‘ub’ [-Wunused-variable] 1090 | double ub = _d->GetUpperBounds(i, j); | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp: In member function ‘bool OpenBabel::OBDistanceGeometry::firstMinimization()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1136:16: warning: unused variable ‘lb’ [-Wunused-variable] 1136 | double lb = _d->GetLowerBounds(i, j); | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1137:16: warning: unused variable ‘ub’ [-Wunused-variable] 1137 | double ub = _d->GetUpperBounds(i, j); | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1115:9: warning: unused variable ‘niter’ [-Wunused-variable] 1115 | int niter = solver.minimize(fun, _coord, fx); | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp: In member function ‘bool OpenBabel::OBDistanceGeometry::minimizeFourthDimension()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1160:9: warning: unused variable ‘niter’ [-Wunused-variable] 1160 | int niter = solver.minimize(fun, _coord, fx); | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp: In member function ‘double OpenBabel::DistGeomFunc::operator()(const Eigen::VectorXd&, Eigen::VectorXd&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/distgeom.cpp:1325:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 1325 | for (size_t i=0; i::run, -1, -1, false> const, -1, -1, false> const>, Eigen::Transpose, Eigen::CwiseNullaryOp, Eigen::Matrix const> const, Eigen::Transpose, -1, -1, false> const, -1, 1, true> const, -1, 1, false> const> const> const>, Eigen::Transpose, 1, -1, true>, 1, -1, false> > >(Eigen::Transpose, -1, -1, false> const, -1, -1, false> const> const&, Eigen::Transpose, Eigen::CwiseNullaryOp, Eigen::Matrix const> const, Eigen::Transpose, -1, -1, false> const, -1, 1, true> const, -1, 1, false> const> const> const> const&, Eigen::Transpose, 1, -1, true>, 1, -1, false> >&, Eigen::Transpose, 1, -1, true>, 1, -1, false> >::Scalar const&)void [clone .isra.0]’: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result_48’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double *’ to ‘Eigen::internal::triangular_matrix_vector_product::run(long, long, double const*, long, double const*, long, double*, long, double const&) [clone .constprop.0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:337: /usr/include/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector.h: In function ‘Eigen::internal::selfmake[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' adjoint_product_impl, -1, -1, false>, 17, false, Eigen::CwiseBinaryOp, Eigen::CwiseNullaryOp, Eigen::Matrix const> const, Eigen::Block, -1, 1, true>, -1, 1, false> const>, 0, true>::run, -1, 1, false> >(Eigen::Block, -1, 1, false>&, Eigen::Block, -1, -1, false> const&, Eigen::CwiseBinaryOp, Eigen::CwiseNullaryOp, Eigen::Matrix const> const, Eigen::Block, -1, 1, true>, -1, 1, false> const> const&, double const&)void [clone .isra.0]’: /usr/include/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector.h:229:7: warning: ‘result_66’ may be used uninitialized [-Wmaybe-uninitialized] 227 | internal::selfadjoint_matrix_vector_product::Flags&RowMajorBit) ? RowMajor : ColMajor, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 228 | int(LhsUpLo), bool(LhsBlasTraits::NeedToConjugate), bool(RhsBlasTraits::NeedToConjugate)>::run | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 229 | ( | ^ 230 | lhs.rows(), // size | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 231 | &lhs.coeffRef(0,0), lhs.outerStride(), // lhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 232 | actualRhsPtr, // rhs info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 233 | actualDestPtr, // result info | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 234 | actualAlpha // scale factor | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 235 | ); | ~ /usr/include/eigen3/Eigen/src/Core/products/SelfadjointMatrixVector.h:41:6: note: by argument 4 of type ‘const double *’ to ‘Eigen::internal::selfadjoint_matrix_vector_product::run(long, double const*, long, double const*, double*, double)’ declared here 41 | void selfadjoint_matrix_vector_product::run( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/stereo/stereo.cpp.o -MF CMakeFiles/openbabel.dir/stereo/stereo.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/stereo.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/stereo.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 12%] Building CXX object src/CMakeFiles/openbabel.dir/math/align.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/math/align.cpp.o -MF CMakeFiles/openbabel.dir/math/align.cpp.o.d -o CMakeFiles/openbabel.dir/math/align.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/math/align.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include 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'/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o -MF CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/tetraplanar.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON 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CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/squareplanar.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 13%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem 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Building CXX object src/CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables 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-I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/stereo/facade.cpp.o -MF CMakeFiles/openbabel.dir/stereo/facade.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/facade.cpp.o -c 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-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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o -MF CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.cpp:29: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/gen3dstereohelper.cpp:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 14%] Building CXX object src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMAKE_OBDLL -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/openbabel.dir/stereo/perception.cpp.o -MF CMakeFiles/openbabel.dir/stereo/perception.cpp.o.d -o CMakeFiles/openbabel.dir/stereo/perception.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp: In function ‘bool OpenBabel::TetStereoToWedgeHash(OBMol&, std::map&, std::map&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:2795:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 2795 | for (std::vector::iterator data = vdata.begin(); data != vdata.end(); ++data) | ^~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:2951:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 2951 | return true; | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp: In function ‘void OpenBabel::StereoRefToImplicit(OBMol&, OBStereo::Ref)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:2973:16: warning: ‘template class std::binder1st’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2973 | const std::binder1st > equal_to_atomId = std::bind1st (equal_to(), atomId); | ^~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438, from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/stereo/stereo.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/stereo/tetranonplanar.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/stereo/tetrahedral.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:26: /usr/include/c++/13/backward/binders.h:108:11: note: declared here 108 | class binder1st | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:2973:88: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 2973 | const std::binder1st > equal_to_atomId = std::bind1st (equal_to(), atomId); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp: In function ‘void OpenBabel::ImplicitRefToStereo(OBMol&, OBStereo::Ref, OBStereo::Ref)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:3005:16: warning: ‘template class std::binder1st’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 3005 | const std::binder1st > equal_to_implicitRef = std::bind1st (equal_to(), (OBStereo::Ref) OBStereo::ImplicitRef); | ^~~~~~~~~ /usr/include/c++/13/backward/binders.h:108:11: note: declared here 108 | class binder1st | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/stereo/perception.cpp:3005:93: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = equal_to; _Tp = long unsigned int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 3005 | const std::binder1st > equal_to_implicitRef = std::bind1st (equal_to(), (OBStereo::Ref) OBStereo::ImplicitRef); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 14%] Linking CXX shared library ../lib64/libopenbabel.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/openbabel.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -Wl,-soname,libopenbabel.so.7 -o ../lib64/libopenbabel.so.7.0.0 CMakeFiles/openbabel.dir/alias.cpp.o CMakeFiles/openbabel.dir/atom.cpp.o CMakeFiles/openbabel.dir/base.cpp.o CMakeFiles/openbabel.dir/bitvec.cpp.o CMakeFiles/openbabel.dir/bond.cpp.o CMakeFiles/openbabel.dir/bondtyper.cpp.o CMakeFiles/openbabel.dir/builder.cpp.o CMakeFiles/openbabel.dir/canon.cpp.o CMakeFiles/openbabel.dir/chains.cpp.o CMakeFiles/openbabel.dir/chargemodel.cpp.o CMakeFiles/openbabel.dir/data.cpp.o CMakeFiles/openbabel.dir/data_utilities.cpp.o CMakeFiles/openbabel.dir/descriptor.cpp.o CMakeFiles/openbabel.dir/elements.cpp.o CMakeFiles/openbabel.dir/fingerprint.cpp.o CMakeFiles/openbabel.dir/forcefield.cpp.o CMakeFiles/openbabel.dir/format.cpp.o CMakeFiles/openbabel.dir/generic.cpp.o CMakeFiles/openbabel.dir/graphsym.cpp.o CMakeFiles/openbabel.dir/grid.cpp.o CMakeFiles/openbabel.dir/griddata.cpp.o CMakeFiles/openbabel.dir/isomorphism.cpp.o CMakeFiles/openbabel.dir/kekulize.cpp.o CMakeFiles/openbabel.dir/locale.cpp.o CMakeFiles/openbabel.dir/matrix.cpp.o CMakeFiles/openbabel.dir/mcdlutil.cpp.o CMakeFiles/openbabel.dir/molchrg.cpp.o CMakeFiles/openbabel.dir/mol.cpp.o CMakeFiles/openbabel.dir/obconversion.cpp.o CMakeFiles/openbabel.dir/oberror.cpp.o CMakeFiles/openbabel.dir/obfunctions.cpp.o CMakeFiles/openbabel.dir/obiter.cpp.o CMakeFiles/openbabel.dir/obutil.cpp.o CMakeFiles/openbabel.dir/op.cpp.o CMakeFiles/openbabel.dir/parsmart.cpp.o CMakeFiles/openbabel.dir/patty.cpp.o CMakeFiles/openbabel.dir/phmodel.cpp.o CMakeFiles/openbabel.dir/plugin.cpp.o CMakeFiles/openbabel.dir/pointgroup.cpp.o CMakeFiles/openbabel.dir/query.cpp.o CMakeFiles/openbabel.dir/rand.cpp.o CMakeFiles/openbabel.dir/reactionfacade.cpp.o CMakeFiles/openbabel.dir/residue.cpp.o CMakeFiles/openbabel.dir/ring.cpp.o CMakeFiles/openbabel.dir/rotamer.cpp.o CMakeFiles/openbabel.dir/rotor.cpp.o CMakeFiles/openbabel.dir/spectrophore.cpp.o CMakeFiles/openbabel.dir/tautomer.cpp.o CMakeFiles/openbabel.dir/tokenst.cpp.o CMakeFiles/openbabel.dir/transform.cpp.o CMakeFiles/openbabel.dir/typer.cpp.o CMakeFiles/openbabel.dir/obmolecformat.cpp.o CMakeFiles/openbabel.dir/conformersearch.cpp.o CMakeFiles/openbabel.dir/confsearch.cpp.o CMakeFiles/openbabel.dir/distgeom.cpp.o CMakeFiles/openbabel.dir/dlhandler_unix.cpp.o CMakeFiles/openbabel.dir/depict/depict.cpp.o CMakeFiles/openbabel.dir/depict/svgpainter.cpp.o CMakeFiles/openbabel.dir/math/matrix3x3.cpp.o CMakeFiles/openbabel.dir/math/spacegroup.cpp.o CMakeFiles/openbabel.dir/math/transform3d.cpp.o CMakeFiles/openbabel.dir/math/vector3.cpp.o CMakeFiles/openbabel.dir/math/align.cpp.o CMakeFiles/openbabel.dir/stereo/stereo.cpp.o CMakeFiles/openbabel.dir/stereo/tetranonplanar.cpp.o CMakeFiles/openbabel.dir/stereo/tetraplanar.cpp.o CMakeFiles/openbabel.dir/stereo/squareplanar.cpp.o CMakeFiles/openbabel.dir/stereo/cistrans.cpp.o CMakeFiles/openbabel.dir/stereo/tetrahedral.cpp.o CMakeFiles/openbabel.dir/stereo/perception.cpp.o CMakeFiles/openbabel.dir/stereo/facade.cpp.o CMakeFiles/openbabel.dir/stereo/gen3dstereohelper.cpp.o -lm -ldl -lz cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library ../lib64/libopenbabel.so.7.0.0 ../lib64/libopenbabel.so.7 ../lib64/libopenbabel.so /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp: In function ‘CreateAtom’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp:457:53: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 457 | AtomSpec *tmp = new AtomSpec[pat->aalloc]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/parsmart.cpp:463:47: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 463 | pat->atom = new AtomSpec[pat->aalloc]; | ^ /usr/include/c++/13/new:128:26: note: in a call to allocation function ‘operator new []’ declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 14%] Built target openbabel make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_descriptors.dir/build.make src/CMakeFiles/plugin_descriptors.dir/depend /usr/bin/make -f src/CMakeFiles/plugin_fingerprints.dir/build.make src/CMakeFiles/plugin_fingerprints.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/CMakeFiles/plugin_descriptors.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_descriptors.dir/build.make src/CMakeFiles/plugin_descriptors.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/CMakeFiles/plugin_fingerprints.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_fingerprints.dir/build.make src/CMakeFiles/plugin_fingerprints.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 14%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/cansmidescriptor.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/cansmidescriptor.cpp:22: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/cansmidescriptor.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 15%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/cmpdfilter.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/cmpdfilter.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/cmpdfilter.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 15%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_fingerprints_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o -MF CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o.d -o CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger2.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/fingerprint.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger2.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger2.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/groupcontrib.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/groupcontrib.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/groupcontrib.cpp:33: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/groupcontrib.cpp:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_fingerprints_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o -MF CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o.d -o CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/fingerprint.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp:27: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp: In member function ‘virtual bool OpenBabel::PatternFP::GetFingerprint(OpenBabel::OBBase*, std::vector&, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp:109:13: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 109 | while(n < _bitcount) | ~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp: In member function ‘virtual std::string OpenBabel::PatternFP::DescribeBits(std::vector, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp:258:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 258 | ngrp = (num + div -1)/div--; //rounds up | ~~~^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/finger3.cpp:258:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/filters.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/filters.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/inchidescriptor.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/inchidescriptor.cpp:22: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/inchidescriptor.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/inchidescriptor.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:134:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 134 | : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h: In member function ‘bool OpenBabel::InChIFormat::InchiLess::operator()(const std::string&, const std::string&) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:149:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 149 | while(p1!=s1.end() && isdigit(*p1++)); --p1; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:149:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 149 | while(p1!=s1.end() && isdigit(*p1++)); --p1; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:154:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 154 | while(p2!=s2.end() && isdigit(*p2++)); --p2; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:154:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 154 | while(p2!=s2.end() && isdigit(*p2++)); --p2; | ^~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_fingerprints_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o -MF CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o.d -o CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/fingerecfp.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/fingerprint.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/fingerecfp.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/fingerprints/fingerecfp.cpp:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_descriptors_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o -MF CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o.d -o CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/smartsdescriptors.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/descriptor.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/smartsdescriptors.cpp:22: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/oberror.h:26, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/descriptors/smartsdescriptors.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Linking CXX shared module ../lib64/plugin_descriptors.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/plugin_descriptors.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../lib64/plugin_descriptors.so CMakeFiles/plugin_descriptors.dir/descriptors/cansmidescriptor.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/cmpdfilter.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/groupcontrib.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/filters.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/inchidescriptor.cpp.o CMakeFiles/plugin_descriptors.dir/descriptors/smartsdescriptors.cpp.o -lm -ldl -lz ../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Built target plugin_descriptors make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_forcefields.dir/build.make src/CMakeFiles/plugin_forcefields.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/CMakeFiles/plugin_forcefields.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_forcefields.dir/build.make src/CMakeFiles/plugin_forcefields.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Linking CXX shared module ../lib64/plugin_fingerprints.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/plugin_fingerprints.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../lib64/plugin_fingerprints.so CMakeFiles/plugin_fingerprints.dir/fingerprints/finger2.cpp.o CMakeFiles/plugin_fingerprints.dir/fingerprints/finger3.cpp.o CMakeFiles/plugin_fingerprints.dir/fingerprints/fingerecfp.cpp.o -lm -ldl -lz ../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Built target plugin_fingerprints make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_ops.dir/build.make src/CMakeFiles/plugin_ops.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/CMakeFiles/plugin_ops.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_ops.dir/build.make src/CMakeFiles/plugin_ops.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addfilename.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addfilename.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addfilename.cpp:18: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 17%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addinindex.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addinindex.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addinindex.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 17%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addpolarh.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addpolarh.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addpolarh.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 17%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addnonpolarh.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addnonpolarh.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/addnonpolarh.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 17%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/canonical.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/canonical.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 17%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/changecell.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/changecell.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/changecell.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/changecell.cpp: In member function ‘virtual bool OpenBabel::OpChangeCell::Do(OpenBabel::OBBase*, const char*, OpenBabel::OBOp::OpMap*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/changecell.cpp:88:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 88 | for(int i = 0; i < vcvs.size(); i++) | ~~^~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/changecell.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 119 | for(int i = 0; i < vcvs.size(); i++) | ~~^~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 16%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:29: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:572:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:572:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:572:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:572:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9: warning: ‘bondcalc’ may be used uninitialized [-Wmaybe-uninitialized] 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:587:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:587:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:587:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:587:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9: warning: ‘MEM[(const struct OBFFBondCalculationGaff &)&bondcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(OpenBabel::OBFFBondCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGaff*, OpenBabel::OBFFBondCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:587:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:31:9: warning: ‘MEM[(const struct OBFFBondCalculationGaff &)&bondcalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 31 | class OBFFBondCalculationGaff : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:535:29: note: ‘bondcalc’ declared here 535 | OBFFBondCalculationGaff bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:637:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:637:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:637:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:637:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&anglecalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:637:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9: warning: ‘MEM[(const struct OBFFAngleCalculationGaff &)&anglecalc].theta’ may be used uninitialized [-Wmaybe-uninitialized] 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:637:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9: warning: ‘MEM[(const struct OBFFAngleCalculationGaff &)&anglecalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:653:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:653:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:653:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:653:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&anglecalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:653:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9: warning: ‘MEM[(const struct OBFFAngleCalculationGaff &)&anglecalc].theta’ may be used uninitialized [-Wmaybe-uninitialized] 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(OpenBabel::OBFFAngleCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGaff*, OpenBabel::OBFFAngleCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:653:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:39:9: warning: ‘MEM[(const struct OBFFAngleCalculationGaff &)&anglecalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 39 | class OBFFAngleCalculationGaff : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:596:30: note: ‘anglecalc’ declared here 596 | OBFFAngleCalculationGaff anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:707:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:707:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:707:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:707:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&torsioncalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:707:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16: warning: ‘MEM[(const struct OBFFCalculation4 &)&torsioncalc].force_d’ may be used uninitialized [-Wmaybe-uninitialized] 199 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:707:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9: warning: ‘MEM[(const struct OBFFTorsionCalculationGaff &)&torsioncalc].tor’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class OBFFTorsionCalculationGaff : public OBFFCalculation4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:724:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:724:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vectomake[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' r.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:724:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:724:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&torsioncalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’, inlined from ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:724:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16: warning: ‘MEM[(const struct OBFFCalculation4 &)&torsioncalc].force_d’ may be used uninitialized [-Wmaybe-uninitialized] 199 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(OpenBabel::OBFFTorsionCalculationGaff const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGaff*, OpenBabel::OBFFTorsionCalculationGaff const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGaff const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:724:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.h:47:9: warning: ‘MEM[(const struct OBFFTorsionCalculationGaff &)&torsioncalc].tor’ may be used uninitialized [-Wmaybe-uninitialized] 47 | class OBFFTorsionCalculationGaff : public OBFFCalculation4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp: In member function ‘OpenBabel::OBForceFieldGaff::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldgaff.cpp:662:32: note: ‘torsioncalc’ declared here 662 | OBFFTorsionCalculationGaff torsioncalc; | ^~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 18%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/delpolarh.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/delpolarh.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/delpolarh.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 19%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/delnonpolarh.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/delnonpolarh.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/delnonpolarh.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 19%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/gen2D.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/gen2D.cpp:22: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/gen2D.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 19%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/fillUC.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/fillUC.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 19%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/forcefield.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/forcefield.cpp:31: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/forcefield.cpp:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/forcefield.cpp: In member function ‘virtual bool OpenBabel::OpMinimize::Do(OpenBabel::OBBase*, const char*, OpenBabel::OBOp::OpMap*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/forcefield.cpp:265:10: warning: unused variable ‘done’ [-Wunused-variable] 265 | bool done = true; | ^~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 19%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:23, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:20: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:477:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:477:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:477:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:477:40: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9: warning: ‘bondcalc’ may be used uninitialized [-Wmaybe-uninitialized] 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:492:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:492:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:492:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:492:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9: warning: ‘MEM[(const struct OBFFBondCalculationGhemical &)&bondcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(OpenBabel::OBFFBondCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationGhemical*, OpenBabel::OBFFBondCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:492:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:29:9: warning: ‘MEM[(const struct OBFFBondCalculationGhemical &)&bondcalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 29 | class OBFFBondCalculationGhemical : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:435:33: note: ‘bondcalc’ declared here 435 | OBFFBondCalculationGhemical bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:542:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:542:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:542:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:542:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&anglecalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:542:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9: warning: ‘MEM[(const struct OBFFAngleCalculationGhemical &)&anglecalc].theta’ may be used uninitialized [-Wmaybe-uninitialized] 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:542:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9: warning: ‘MEM[(const struct OBFFAngleCalculationGhemical &)&anglecalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:558:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:558:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:558:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:558:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&anglecalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:558:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9: warning: ‘MEM[(const struct OBFFAngleCalculationGhemical &)&anglecalc].theta’ may be used uninitialized [-Wmaybe-uninitialized] 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(OpenBabel::OBFFAngleCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationGhemical*, OpenBabel::OBFFAngleCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:558:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:38:9: warning: ‘MEM[(const struct OBFFAngleCalculationGhemical &)&anglecalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 38 | class OBFFAngleCalculationGhemical : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:501:34: note: ‘anglecalc’ declared here 501 | OBFFAngleCalculationGhemical anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:46:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:674:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:567:36: note: ‘torsioncalc’ declared here 567 | OBFFTorsionCalculationGhemical torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:46:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:674:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:567:36: note: ‘torsioncalc’ declared here 567 | OBFFTorsionCalculationGhemical torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:46:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:674:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:567:36: note: ‘torsioncalc’ declared here 567 | OBFFTorsionCalculationGhemical torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:46:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:674:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&torsioncalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:567:36: note: ‘torsioncalc’ declared here 567 | OBFFTorsionCalculationGhemical torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’, inlined from ‘OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:46:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:674:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16: warning: ‘MEM[(const struct OBFFCalculation4 &)&torsioncalc].force_d’ may be used uninitialized [-Wmaybe-uninitialized] 199 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:567:36: note: ‘torsioncalc’ declared here 567 | OBFFTorsionCalculationGhemical torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(OpenBabel::OBFFTorsionCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationGhemical*, OpenBabel::OBFFTorsionCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:674:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:46:9: warning: ‘MEM[(const struct OBFFTorsionCalculationGhemical &)&torsioncalc].tor’ may be used uninitialized [-Wmaybe-uninitialized] 46 | class OBFFTorsionCalculationGhemical : public OBFFCalculation4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:567:36: note: ‘torsioncalc’ declared here 567 | OBFFTorsionCalculationGhemical torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:56:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:778:33: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&vdwcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:683:32: note: ‘vdwcalc’ declared here 683 | OBFFVDWCalculationGhemical vdwcalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:56:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:778:33: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&vdwcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:683:32: note: ‘vdwcalc’ declared here 683 | OBFFVDWCalculationGhemical vdwcalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:56:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:778:33: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&vdwcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:683:32: note: ‘vdwcalc’ declared here 683 | OBFFVDWCalculationGhemical vdwcalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(OpenBabel::OBFFVDWCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:778:33: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc’ may be used uninitialized [-Wmaybe-uninitialized] 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:683:32: note: ‘vdwcalc’ declared here 683 | OBFFVDWCalculationGhemical vdwcalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(OpenBabel::OBFFVDWCalculationGhemical const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFVDWCalculationGhemical*, OpenBabel::OBFFVDWCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFVDWCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:778:33: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:56:9: warning: ‘MEM[(const struct OBFFVDWCalculationGhemical &)&vdwcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:683:32: note: ‘vdwcalc’ declared here 683 | OBFFVDWCalculationGhemical vdwcalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(OpenBabel::OBFFElectrostaticCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:71:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationGhemical*, OpenBabel::OBFFElectrostaticCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationGhemical*, OpenBabel::OBFFElectrostaticCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:829:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculamake[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' tion2 &)&elecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:787:42: note: ‘elecalc’ declared here 787 | OBFFElectrostaticCalculationGhemical elecalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(OpenBabel::OBFFElectrostaticCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:71:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationGhemical*, OpenBabel::OBFFElectrostaticCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationGhemical*, OpenBabel::OBFFElectrostaticCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:829:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&elecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:787:42: note: ‘elecalc’ declared here 787 | OBFFElectrostaticCalculationGhemical elecalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(OpenBabel::OBFFElectrostaticCalculationGhemical const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.h:71:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationGhemical*, OpenBabel::OBFFElectrostaticCalculationGhemical const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationGhemical*, OpenBabel::OBFFElectrostaticCalculationGhemical const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationGhemical const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:829:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&elecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp: In member function ‘OpenBabel::OBForceFieldGhemical::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldghemical.cpp:787:42: note: ‘elecalc’ declared here 787 | OBFFElectrostaticCalculationGhemical elecalc; | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/gen3d.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/gen3d.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/largest.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/largest.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/largest.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/largest.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/largest.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/largest.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/loader.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/loader.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/loader.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/loader.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/loader.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/loader.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/loader.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/neutralize.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/neutralize.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opsplit.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opsplit.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opsplit.cpp: In member function ‘virtual bool OpenBabel::OpSplit::Do(OpenBabel::OBBase*, const char*, OpenBabel::OBOp::OpMap*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opsplit.cpp:92:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 92 | if(!pConv) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opsplit.cpp:95:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 95 | if(pConv->IsFirstInput()) | ^~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 20%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:31: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2798:32: warning: variable ‘bondtype1’ set but not used [-Wunused-but-set-variable] 2798 | int angletype, strbndtype, bondtype1, bondtype2; | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2798:43: warning: variable ‘bondtype2’ set but not used [-Wunused-but-set-variable] 2798 | int angletype, strbndtype, bondtype1, bondtype2; | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:289:40: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:148:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 148 | for (int i = 0; i < _bondcalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:289:58: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:148:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:295:41: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:263:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 263 | for (int i = 0; i < _anglecalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:295:60: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:263:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:301:42: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:376:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 376 | for (int i = 0; i < _strbndcalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:301:62: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:376:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:307:43: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:512:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 512 | for (int i = 0; i < _torsioncalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:307:64: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:512:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:313:39: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:610:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 610 | for (int i = 0; i < _oopcalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:313:56: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:610:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:319:39: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:707:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 707 | for (int i = 0; i < _vdwcalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:319:56: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:707:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:325:49: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:793:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 793 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:325:76: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:793:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::PerceiveAromatic()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:1451:30: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 1451 | ringbond = _mol.GetBond(first_rj, index); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:1388:12: note: ‘index’ was declared here 1388 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:1451:30: warning: ‘first_rj’ may be used uninitialized [-Wmaybe-uninitialized] 1451 | ringbond = _mol.GetBond(first_rj, index); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:1388:29: note: ‘first_rj’ was declared here 1388 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; | ^~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:44: In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2765:38: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2765:38: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2765:38: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2765:38: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9: warning: ‘MEM[(const struct OBFFBondCalculationMMFF94 &)&bondcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2765:38: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9: warning: ‘MEM[(const struct OBFFBondCalculationMMFF94 &)&bondcalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2775:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2775:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2775:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2775:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9: warning: ‘MEM[(const struct OBFFBondCalculationMMFF94 &)&bondcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(OpenBabel::OBFFBondCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationMMFF94*, OpenBabel::OBFFBondCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2775:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:30:9: warning: ‘MEM[(const struct OBFFBondCalculationMMFF94 &)&bondcalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 30 | class OBFFBondCalculationMMFF94 : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2707:31: note: ‘bondcalc’ declared here 2707 | OBFFBondCalculationMMFF94 bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2931:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2796:32: note: ‘anglecalc’ declared here 2796 | OBFFAngleCalculationMMFF94 anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2931:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2796:32: note: ‘anglecalc’ declared here 2796 | OBFFAngleCalculationMMFF94 anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2931:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&anglecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2796:32: note: ‘anglecalc’ declared here 2796 | OBFFAngleCalculationMMFF94 anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:39:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2931:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&anglecalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2796:32: note: ‘anglecalc’ declared here 2796 | OBFFAngleCalculationMMFF94 anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(OpenBabel::OBFFAngleCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2931:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:39:9: warning: ‘MEM[(const struct OBFFAngleCalculationMMFF94 &)&anglecalc].theta’ may be used uninitialized [-Wmaybe-uninitialized] 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2796:32: note: ‘anglecalc’ declared here 2796 | OBFFAngleCalculationMMFF94 anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(OpenBabel::OBFFAngleCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFAngleCalculationMMFF94*, OpenBabel::OBFFAngleCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFAngleCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2931:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:39:9: warning: ‘MEM[(const struct OBFFAngleCalculationMMFF94 &)&anglecalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2796:32: note: ‘anglecalc’ declared here 2796 | OBFFAngleCalculationMMFF94 anglecalc; | ^~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&strbndcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&strbndcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&strbndcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&strbndcalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].delta_theta’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].delta_rab’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].delta_rbc’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].theta’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].rbc’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFStrBndCalculationMMFF94*, OpenBabel::OBFFStrBndCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFStrBndCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3074:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:49:9: warning: ‘MEM[(const struct OBFFStrBndCalculationMMFF94 &)&strbndcalc].force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:2797:33: note: ‘strbndcalc’ declared here 2797 | OBFFStrBndCalculationMMFF94 strbndcalc; | ^~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:61:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3350:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3093:34: note: ‘torsioncalc’ declared here 3093 | OBFFTorsionCalculationMMFF94 torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:61:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3350:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3093:34: note: ‘torsioncalc’ declared here 3093 | OBFFTorsionCalculationMMFF94 torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:61:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3350:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&torsioncalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3093:34: note: ‘torsioncalc’ declared here 3093 | OBFFTorsionCalculationMMFF94 torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation3::OBFFCalculation3(OpenBabel::OBFFCalculation3 const&)’, inlined from ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16, inlined from ‘OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:61:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3350:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:168:16: warning: ‘MEM[(const struct OBFFCalculation3 &)&torsioncalc].force_c’ may be used uninitialized [-Wmaybe-uninitialized] 168 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3093:34: note: ‘torsioncalc’ declared here 3093 | OBFFTorsionCalculationMMFF94 torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFCalculation4::OBFFCalculation4(OpenBabel::OBFFCalculation4 const&)’, inlined from ‘OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:61:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3350:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:199:16: warning: ‘MEM[(const struct OBFFCalculation4 &)&torsioncalc].force_d’ may be used uninitialized [-Wmaybe-uninitialized] 199 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3093:34: note: ‘torsioncalc’ declared here 3093 | OBFFTorsionCalculationMMFF94 torsioncalc; | ^~~~~~~~~~~ In member function ‘OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFTorsionCalculationMMFF94*, OpenBabel::OBFFTorsionCalculationMMFF94 const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFTorsionCalculationMMFF94 const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3350:37: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.h:61:9: warning: ‘MEM[(const struct OBFFTorsionCalculationMMFF94 &)&torsioncalc].cosine’ may be used uninitialized [-Wmaybe-uninitialized] 61 | class OBFFTorsionCalculationMMFF94 : public OBFFCalculation4 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:3093:34: note: ‘torsioncalc’ declared here 3093 | OBFFTorsionCalculationMMFF94 torsioncalc; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp: In member function ‘OpenBabel::OBForceFieldMMFF94::Validate()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4329:13: warning: ‘etot’ may be used uninitialized [-Wmaybe-uninitialized] 4329 | delta = (Energy() - etot); | ~~~~~~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:12: note: ‘etot’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4300:13: warning: ‘ebond’ may be used uninitialized [-Wmaybe-uninitialized] 4300 | delta = (E_Bond() - ebond); | ~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:18: note: ‘ebond’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4304:13: warning: ‘eangle’ may be used uninitialized [-Wmaybe-uninitialized] 4304 | delta = (E_Angle() - eangle); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:25: note: ‘eangle’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4312:13: warning: ‘eoop’ may be used uninitialized [-Wmaybe-uninitialized] 4312 | delta = (E_OOP() - eoop); | ~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:33: note: ‘eoop’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4308:13: warning: ‘estbn’ may be used uninitialized [-Wmaybe-uninitialized] 4308 | delta = (E_StrBnd() - estbn); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:39: note: ‘estbn’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4316:13: warning: ‘etor’ may be used uninitialized [-Wmaybe-uninitialized] 4316 | delta = (E_Torsion() - etor); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:46: note: ‘etor’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4320:13: warning: ‘evdw’ may be used uninitialized [-Wmaybe-uninitialized] 4320 | delta = (E_VDW() - evdw); | ~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:52: note: ‘evdw’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4324:13: warning: ‘eeq’ may be used uninitialized [-Wmaybe-uninitialized] 4324 | delta = (E_Electrostatic() - eeq); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefieldmmff94.cpp:4002:58: note: ‘eeq’ was declared here 4002 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; | ^~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/optransform.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/optransform.h:21, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/optransform.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/parsmart.h:23, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/phmodel.h:23, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/optransform.h:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/partialcharges.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/partialcharges.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/readconformers.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/readconformers.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/sort.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/sort.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/sort.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/sort.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/sort.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/sort.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/sort.cpp:32:28: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 32 | struct Order : public std::binary_function, std::pair, bool> | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Building CXX object src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_forcefields_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o -MF CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o.d -o CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:28, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:32: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = true]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:478:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = true]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:193:37: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:431:14: warning: unused variable ‘ab’ [-Wunused-variable] 431 | double ab[3]; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = false]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:478:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:193:54: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:431:14: warning: unused variable ‘ab’ [-Wunused-variable] In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:82:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1585:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&elecalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1534:37: note: ‘elecalc’ declared here 1534 | OBFFElectrostaticCalculationUFF elecalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:82:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1585:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&elecalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1534:37: note: ‘elecalc’ declared here 1534 | OBFFElectrostaticCalculationUFF elecalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:82:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1585:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&elecalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1534:37: note: ‘elecalc’ declared here 1534 | OBFFElectrostaticCalculationUFF elecalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(OpenBabel::OBFFElectrostaticCalculationUFF const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFElectrostaticCalculationUFF*, OpenBabel::OBFFElectrostaticCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFElectrostaticCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1585:45: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:82:9: warning: ‘MEM[(const struct OBFFElectrostaticCalculationUFF &)&elecalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 82 | class OBFFElectrostaticCalculationUFF : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:1534:37: note: ‘elecalc’ declared here 1534 | OBFFElectrostaticCalculationUFF elecalc; | ^~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(OpenBabel::OBFFBondCalculationUFF const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:969:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].energy’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:745:28: note: ‘bondcalc’ declared here 745 | OBFFBondCalculationUFF bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(OpenBabel::OBFFBondCalculationUFF const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:969:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_a’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:745:28: note: ‘bondcalc’ declared here 745 | OBFFBondCalculationUFF bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFCalculation2::OBFFCalculation2(OpenBabel::OBFFCalculation2 const&)’, inlined from ‘OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(OpenBabel::OBFFBondCalculationUFF const&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:30:9, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:969:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/forcefield.h:137:16: warning: ‘MEM[(const struct OBFFCalculation2 &)&bondcalc].force_b’ may be used uninitialized [-Wmaybe-uninitialized] 137 | class OBFPRT OBFFCalculation2 | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:745:28: note: ‘bondcalc’ declared here 745 | OBFFBondCalculationUFF bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(OpenBabel::OBFFBondCalculationUFF const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:969:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:30:9: warning: ‘MEM[(const struct OBFFBondCalculationUFF &)&bondcalc].rab’ may be used uninitialized [-Wmaybe-uninitialized] 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:745:28: note: ‘bondcalc’ declared here 745 | OBFFBondCalculationUFF bondcalc; | ^~~~~~~~ In member function ‘OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(OpenBabel::OBFFBondCalculationUFF const&)’, inlined from ‘std::__new_allocator::construct(OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/new_allocator.h:191:4, inlined from ‘std::allocator_traits >::construct(std::allocator&, OpenBabel::OBFFBondCalculationUFF*, OpenBabel::OBFFBondCalculationUFF const&)void’ at /usr/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘std::vector >::push_back(OpenBabel::OBFFBondCalculationUFF const&)’ at /usr/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:969:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.h:30:9: warning: ‘MEM[(const struct OBFFBondCalculationUFF &)&bondcalc].delta’ may be used uninitialized [-Wmaybe-uninitialized] 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 | ^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp: In member function ‘OpenBabel::OBForceFieldUFF::SetupCalculations()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/forcefields/forcefielduff.cpp:745:28: note: ‘bondcalc’ declared here 745 | OBFFBondCalculationUFF bondcalc; | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opisomorph.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opisomorph.h:15, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opisomorph.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/parsmart.h:23, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opisomorph.cpp:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opisomorph.cpp: In member function ‘virtual bool OpenBabel::OpNewS::Do(OpenBabel::OBBase*, const char*, OpenBabel::OBOp::OpMap*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opisomorph.cpp:303:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 303 | if(pmol->NumHvyAtoms() != nPatternAtoms) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/ophighlight.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/ophighlight.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/parsmart.h:23, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/ophighlight.cpp:16: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/xout.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/xout.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/xout.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/xout.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/xout.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/conformer.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/conformer.cpp:32: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/conformer.cpp:29: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/conformer.cpp: In member function ‘virtual bool OpenBabel::OpConformer::Do(OpenBabel::OBBase*, const char*, OpenBabel::OBOp::OpMap*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/conformer.cpp:287:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 287 | if (p1>pmol->NumAtoms() || p2>pmol->NumAtoms()){ | ~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/conformer.cpp:287:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 287 | if (p1>pmol->NumAtoms() || p2>pmol->NumAtoms()){ | ~~^~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opalign.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opalign.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opalign.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 22%] Building CXX object src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_ops_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o -MF CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o.d -o CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opconfab.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opconfab.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opconfab.cpp:22: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opconfab.cpp: In member function ‘void OpenBabel::OpConfab::Run(OpenBabel::OBConversion*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/opconfab.cpp:167:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 167 | for (; c < mol.NumConformers(); ++c) { | ~~^~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 21%] Linking CXX shared module ../lib64/plugin_forcefields.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/plugin_forcefields.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../lib64/plugin_forcefields.so CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldgaff.cpp.o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldghemical.cpp.o CMakeFiles/plugin_forcefields.dir/forcefields/forcefieldmmff94.cpp.o CMakeFiles/plugin_forcefields.dir/forcefields/forcefielduff.cpp.o -lm -ldl -lz ../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 23%] Built target plugin_forcefields make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_charges.dir/build.make src/CMakeFiles/plugin_charges.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/CMakeFiles/plugin_charges.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/CMakeFiles/plugin_charges.dir/build.make src/CMakeFiles/plugin_charges.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 23%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/eem.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/eem.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/eem.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/eem.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/eem.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/eem.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/eem.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 23%] Linking CXX shared module ../lib64/plugin_ops.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/plugin_ops.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../lib64/plugin_ops.so CMakeFiles/plugin_ops.dir/ops/addfilename.cpp.o CMakeFiles/plugin_ops.dir/ops/addinindex.cpp.o CMakeFiles/plugin_ops.dir/ops/addpolarh.cpp.o CMakeFiles/plugin_ops.dir/ops/addnonpolarh.cpp.o CMakeFiles/plugin_ops.dir/ops/canonical.cpp.o CMakeFiles/plugin_ops.dir/ops/changecell.cpp.o CMakeFiles/plugin_ops.dir/ops/delpolarh.cpp.o CMakeFiles/plugin_ops.dir/ops/delnonpolarh.cpp.o CMakeFiles/plugin_ops.dir/ops/gen2D.cpp.o CMakeFiles/plugin_ops.dir/ops/fillUC.cpp.o CMakeFiles/plugin_ops.dir/ops/forcefield.cpp.o CMakeFiles/plugin_ops.dir/ops/gen3d.cpp.o CMakeFiles/plugin_ops.dir/ops/largest.cpp.o CMakeFiles/plugin_ops.dir/ops/loader.cpp.o CMakeFiles/plugin_ops.dir/ops/neutralize.cpp.o CMakeFiles/plugin_ops.dir/ops/opsplit.cpp.o CMakeFiles/plugin_ops.dir/ops/optransform.cpp.o CMakeFiles/plugin_ops.dir/ops/partialcharges.cpp.o CMakeFiles/plugin_ops.dir/ops/readconformers.cpp.o CMakeFiles/plugin_ops.dir/ops/sort.cpp.o CMakeFiles/plugin_ops.dir/ops/opisomorph.cpp.o CMakeFiles/plugin_ops.dir/ops/ophighlight.cpp.o CMakeFiles/plugin_ops.dir/ops/xout.cpp.o CMakeFiles/plugin_ops.dir/ops/conformer.cpp.o CMakeFiles/plugin_ops.dir/ops/opalign.cpp.o CMakeFiles/plugin_ops.dir/ops/opconfab.cpp.o -lm -ldl -lz ../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Built target plugin_ops make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/smilesformat.dir/build.make src/formats/CMakeFiles/smilesformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/smilesformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/smilesformat.dir/build.make src/formats/CMakeFiles/smilesformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/gasteiger.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/gasteiger.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/gasteiger.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/none.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/none.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/none.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/none.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/none.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/none.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/mmff94.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/mmff94.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/mmff94.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/fromfile.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/fromfile.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/fromfile.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/fromfile.cpp: In member function ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/fromfile.cpp:102:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 102 | for ( int i = 1; i <= mol.NumAtoms(); i++) | ~~^~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/formats/CMakeFiles/smilesformat.dir/smilesformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsmilesformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/smilesformat.dir/smilesformat.cpp.o -MF CMakeFiles/smilesformat.dir/smilesformat.cpp.o.d -o CMakeFiles/smilesformat.dir/smilesformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In constructor ‘OpenBabel::OBSmilesParser::OBSmilesParser(bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:291:10: warning: ‘OpenBabel::OBSmilesParser::_preserve_aromaticity’ will be initialized after [-Wreorder] 291 | bool _preserve_aromaticity; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:289:9: warning: ‘int OpenBabel::OBSmilesParser::_rxnrole’ [-Wreorder] 289 | int _rxnrole; | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:318:5: warning: when initialized here [-Wreorder] 318 | OBSmilesParser(bool preserve_aromaticity=false): _preserve_aromaticity(preserve_aromaticity), _rxnrole(1) { } | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘bool OpenBabel::OBSmilesParser::ParseSmiles(OpenBabel::OBMol&, const std::string&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:655:15: warning: variable ‘atom’ set but not used [-Wunused-but-set-variable] 655 | OBAtom* atom; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘int OpenBabel::OBSmilesParser::NumConnections(OpenBabel::OBAtom*, bool)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2200:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 2200 | if (idx-1 < _hcount.size() && _hcount[idx-1] > 0) | ~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘bool OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector&, std::vector&, std::string&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2685:10: warning: variable ‘symbol’ set but not used [-Wunused-but-set-variable] 2685 | char symbol[10]; | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2689:10: warning: unused variable ‘normalValence’ [-Wunused-variable] 2689 | bool normalValence = true; | ^~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2690:10: warning: unused variable ‘writeExplicitHydrogen’ [-Wunused-variable] 2690 | bool writeExplicitHydrogen = false; | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘bool OpenBabel::OBMol2Cansmi::BuildCanonTree(OpenBabel::OBMol&, OpenBabel::OBBitVec&, std::vector&, OpenBabel::OBCanSmiNode*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:3139:22: warning: unused variable ‘bond_order’ [-Wunused-variable] 3139 | unsigned int bond_order = bond->GetBondOrder(); | ^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:3134:20: warning: unused variable ‘nbr_bond_order’ [-Wunused-variable] 3134 | unsigned int nbr_bond_order = nbr_bond->GetBondOrder(); | ^~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘std::vector OpenBabel::OBMol2Cansmi::GetCanonClosureDigits(OpenBabel::OBAtom*, OpenBabel::OBBitVec&, std::vector&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:3286:11: warning: unused variable ‘bo’ [-Wunused-variable] 3286 | int bo = (bond1->IsAromatic())? 1 : bond1->GetBondOrder(); // CJ: why was this line added? bo is never used? | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘void OpenBabel::OBMol2Cansmi::CreateFragCansmiString(OpenBabel::OBMol&, OpenBabel::OBBitVec&, std::string&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:3899:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3899 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 3905 | for (int i=0; i >&, std::vector >&, std::__cxx11::basic_string, std::allocator >&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2865:35: warning: ‘__snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 2865 | snprintf(tcount, 10, "%d", hcount); | ^ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54: In function ‘snprintf’, inlined from ‘OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector >&, std::vector >&, std::__cxx11::basic_string, std::allocator >&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2865:19: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 2 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' ~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp: In member function ‘OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector >&, std::vector >&, std::__cxx11::basic_string, std::allocator >&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2857:35: warning: ‘__snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 2857 | snprintf(tcount, 10, "%d", i); | ^ In function ‘snprintf’, inlined from ‘OpenBabel::OBMol2Cansmi::GetSmilesElement(OpenBabel::OBCanSmiNode*, std::vector >&, std::vector >&, std::__cxx11::basic_string, std::allocator >&)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smilesformat.cpp:2857:19: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 2 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Linking CXX shared module ../../lib64/smilesformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/smilesformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/smilesformat.so CMakeFiles/smilesformat.dir/smilesformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Built target smilesformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/mdlformat.dir/build.make src/formats/CMakeFiles/mdlformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/mdlformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/mdlformat.dir/build.make src/formats/CMakeFiles/mdlformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/eqeq.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/eqeq.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/eqeq.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/eqeq.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 24%] Building CXX object src/formats/CMakeFiles/mdlformat.dir/mdlformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmdlformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mdlformat.dir/mdlformat.cpp.o -MF CMakeFiles/mdlformat.dir/mdlformat.cpp.o.d -o CMakeFiles/mdlformat.dir/mdlformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:35: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:26: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:43: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h: In function ‘unsigned int MDLValence(unsigned int, int, unsigned int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:51:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 51 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:51:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 51 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:64:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 64 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:64:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 64 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:77:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 77 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:77:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 77 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:90:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 90 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:90:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 90 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:103:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 103 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:103:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 103 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:116:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 116 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:116:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 116 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:119:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 119 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:119:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 119 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:121:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 121 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:121:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 121 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:134:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 134 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:134:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 134 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:137:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 137 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:137:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 137 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:139:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 139 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:139:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 139 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:152:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 152 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:152:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 152 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:155:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 155 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:155:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 155 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:157:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 157 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:157:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 157 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:170:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 170 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:170:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 170 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:173:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 173 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:173:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 173 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:175:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 175 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:175:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 175 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:188:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 188 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:188:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 188 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:191:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 191 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:191:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 191 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:193:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 193 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:193:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 193 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:206:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 206 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:206:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 206 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:209:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 209 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:209:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 209 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:211:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 211 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:211:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 211 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:223:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 223 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:223:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 223 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:226:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 226 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:226:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 226 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:228:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 228 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:228:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 228 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:240:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 240 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:240:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 240 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:243:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 243 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:243:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 243 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:245:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 245 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:245:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 245 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:257:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 257 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:257:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 257 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:260:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 260 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:260:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 260 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:262:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 262 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:262:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 262 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:274:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 274 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:274:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 274 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:277:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 277 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:277:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 277 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:279:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 279 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:279:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 279 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:291:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 291 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:291:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 291 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:294:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 294 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:294:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 294 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:296:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 296 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:296:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 296 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:298:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 298 | if (val <= 4) return 4; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:298:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 298 | if (val <= 4) return 4; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:310:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 310 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:310:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 310 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:313:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 313 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:313:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 313 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:315:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 315 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:315:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 315 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:317:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 317 | if (val <= 4) return 4; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:317:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 317 | if (val <= 4) return 4; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:329:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 329 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:329:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 329 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:332:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 332 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:332:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 332 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:334:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 334 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:334:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 334 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:336:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 336 | if (val <= 4) return 4; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:336:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 336 | if (val <= 4) return 4; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:348:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 348 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:348:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 348 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:351:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 351 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:351:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 351 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:353:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 353 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:353:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 353 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:355:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 355 | if (val <= 4) return 4; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:355:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 355 | if (val <= 4) return 4; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:367:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 367 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:367:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 367 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:370:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 370 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:370:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 370 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:372:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 372 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:372:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 372 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:374:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 374 | if (val <= 4) return 4; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:374:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 374 | if (val <= 4) return 4; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:385:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 385 | if (val <= 7) return 7; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:385:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 385 | if (val <= 7) return 7; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:388:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 388 | if (val <= 6) return 6; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:388:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 388 | if (val <= 6) return 6; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:390:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 390 | if (val <= 5) return 5; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:390:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 390 | if (val <= 5) return 5; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:392:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 392 | if (val <= 4) return 4; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:392:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 392 | if (val <= 4) return 4; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:394:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 394 | if (val <= 3) return 3; break; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:394:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 394 | if (val <= 3) return 3; break; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h: In function ‘unsigned int HYDValence(unsigned int, int, unsigned int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlvalence.h:416:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 416 | if (val > impval) { | ~~~~^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadAtomBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:1488:10: warning: unused variable ‘chiralWatch’ [-Wunused-variable] 1488 | bool chiralWatch=false; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp: In member function ‘OpenBabel::MDLFormat::GetTimeDate[abi:cxx11]()’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:1709:27: warning: ‘%02d’ directive output may be truncated writing between 2 and 11 bytes into a region of size between 0 and 9 [-Wformat-truncation=] 1709 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:1709:22: note: directive argument in the range [-2147483648, 2147483547] 1709 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/iomanip:42, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:27: In function ‘snprintf’, inlined from ‘OpenBabel::MDLFormat::GetTimeDate[abi:cxx11]()’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:1709:13: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 11 and 56 bytes into a destination of size 11 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp: In member function ‘OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map, std::allocator > >*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:2022:7: warning: ‘a1_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2022 | if (a1_stereo == a2_stereo) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:1987:31: note: ‘a1_stereo’ was declared here 1987 | OBStereo::BondDirection a1_stereo, a2_stereo; | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:2022:7: warning: ‘a2_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2022 | if (a1_stereo == a2_stereo) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mdlformat.cpp:1987:42: note: ‘a2_stereo’ was declared here 1987 | OBStereo::BondDirection a1_stereo, a2_stereo; | ^~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 25%] Linking CXX shared module ../../lib64/mdlformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/mdlformat.so CMakeFiles/mdlformat.dir/mdlformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 25%] Built target mdlformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/mol2format.dir/build.make src/formats/CMakeFiles/mol2format.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/mol2format.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/mol2format.dir/build.make src/formats/CMakeFiles/mol2format.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 25%] Building CXX object src/formats/CMakeFiles/mol2format.dir/mol2format.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmol2format_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mol2format.dir/mol2format.cpp.o -MF CMakeFiles/mol2format.dir/mol2format.cpp.o.d -o CMakeFiles/mol2format.dir/mol2format.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp:422:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 422 | if(aid <= mol.NumAtoms()) | ~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp: In member function ‘virtual int OpenBabel::MOL2Format::SkipObjects(int, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp:785:10: warning: unused variable ‘ch’ [-Wunused-variable] 785 | char ch = ifs.peek(); | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp: At global scope: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mol2format.cpp:86:15: warning: ‘bool OpenBabel::IsThiocarboxylSulfur(OBAtom*)’ defined but not used [-Wunused-function] 86 | static bool IsThiocarboxylSulfur(OBAtom* queryatom) | ^~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 25%] Linking CXX shared module ../../lib64/mol2format.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/mol2format.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/mol2format.so CMakeFiles/mol2format.dir/mol2format.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 25%] Built target mol2format make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/pdbformat.dir/build.make src/formats/CMakeFiles/pdbformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/pdbformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/pdbformat.dir/build.make src/formats/CMakeFiles/pdbformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 26%] Building CXX object src/formats/CMakeFiles/pdbformat.dir/pdbformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpdbformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pdbformat.dir/pdbformat.cpp.o -MF CMakeFiles/pdbformat.dir/pdbformat.cpp.o.d -o CMakeFiles/pdbformat.dir/pdbformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:615:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] 615 | if (origin == pUC->GetSpaceGroup()->HEXAGONAL_ORIGIN) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:684:58: warning: ‘__snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 684 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); | ^ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54: In function ‘snprintf’, inlined from ‘OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:684:21: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp: In member function ‘OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:702:70: warning: ‘__snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 702 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); | ^ In function ‘snprintf’, inlined from ‘OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:702:29: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp: In member function ‘OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:739:35: warning: ‘%+d’ directive output may be truncated writing between 2 and 6 bytes into a region of size 3 [-Wformat-truncation=] 739 | snprintf(scharge, 3, "%+d", charge); | ^~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:739:34: note: directive argument in the range [-32768, 32767] 739 | snprintf(scharge, 3, "%+d", charge); | ^~~~~ In function ‘snprintf’, inlined from ‘OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbformat.cpp:739:21: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 3 and 7 bytes into a destination of size 3 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 26%] Linking CXX shared module ../../lib64/pdbformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdbformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/pdbformat.so CMakeFiles/pdbformat.dir/pdbformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 26%] Built target pdbformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/inchiformat.dir/build.make src/formats/CMakeFiles/inchiformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/inchiformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/inchiformat.dir/build.make src/formats/CMakeFiles/inchiformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 26%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/inchiformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dinchiformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/inchiformat.dir/inchiformat.cpp.o -MF CMakeFiles/inchiformat.dir/inchiformat.cpp.o.d -o CMakeFiles/inchiformat.dir/inchiformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp:19: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp:32: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:134:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 134 | : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h: In member function ‘bool OpenBabel::InChIFormat::InchiLess::operator()(const std::string&, const std::string&) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:149:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 149 | while(p1!=s1.end() && isdigit(*p1++)); --p1; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:149:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 149 | while(p1!=s1.end() && isdigit(*p1++)); --p1; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:154:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 154 | while(p2!=s2.end() && isdigit(*p2++)); --p2; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:154:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 154 | while(p2!=s2.end() && isdigit(*p2++)); --p2; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp: In member function ‘virtual bool OpenBabel::InChIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp:193:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘AT_NUM’ {aka ‘short int’} [-Wsign-compare] 193 | if ( !(a->GetId() == ct->end || a->GetId() == stereo.neighbor[0] ) ) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/inchiformat.cpp:199:54: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘AT_NUM’ {aka ‘short int’} [-Wsign-compare] 199 | if ( !(b->GetId() == ct->begin || b->GetId() == stereo.neighbor[3] ) ) { | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 25%] Building CXX object src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src && /usr/bin/g++ -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dplugin_charges_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o -MF CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o.d -o CMakeFiles/plugin_charges.dir/charges/qeq.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/qeq.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/chargemodel.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/qeq.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/qeq.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/dlhandler.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/LU:11, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/charges/qeq.h:29: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘Eigen::internal::trmv_selector<6, 1>::run, -1, -1, false> const, -1, -1, false> const>, Eigen::Transpose, Eigen::CwiseNullaryOp, Eigen::Matrix const> const, Eigen::Transpose, -1, -1, false> const, -1, 1, true> const, -1, 1, false> const> const> const>, Eigen::Transpose, 1, -1, true>, 1, -1, false> > >(Eigen::Transpose, -1, -1, false> const, -1, -1, false> const> const&, Eigen::Transpose, Eigen::CwiseNullaryOp, Eigen::Matrix const> const, Eigen::Transpose, -1, -1, false> const, -1, 1, true> const, -1, 1, false> const> const> const> const&, Eigen::Transpose, 1, -1, true>, 1, -1, false> >&, Eigen::Transpose, 1, -1, true>, 1, -1, false> >::Scalar const&)void [clone .isra.0]’: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result_48’ may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double *’ to ‘Eigen::internal::triangular_matrix_vector_product::run(long, long, double const*, long, double const*, long, double*, long, double const&) [clone .constprop.0]’ declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 27%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dinchiformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/inchiformat.dir/getinchi.cpp.o -MF CMakeFiles/inchiformat.dir/getinchi.cpp.o.d -o CMakeFiles/inchiformat.dir/getinchi.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/getinchi.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 27%] Building CXX object src/formats/CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dinchiformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o -MF CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o.d -o CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/unique.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:25, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/unique.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/op.h:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/ops/unique.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:134:19: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 134 | : public std::binary_function | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h: In member function ‘bool OpenBabel::InChIFormat::InchiLess::operator()(const std::string&, const std::string&) const’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:149:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 149 | while(p1!=s1.end() && isdigit(*p1++)); --p1; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:149:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 149 | while(p1!=s1.end() && isdigit(*p1++)); --p1; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:154:13: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 154 | while(p2!=s2.end() && isdigit(*p2++)); --p2; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/inchiformat.h:154:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 154 | while(p2!=s2.end() && isdigit(*p2++)); --p2; | ^~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 27%] Linking CXX shared module ../../lib64/inchiformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/inchiformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/inchiformat.so CMakeFiles/inchiformat.dir/inchiformat.cpp.o CMakeFiles/inchiformat.dir/getinchi.cpp.o CMakeFiles/inchiformat.dir/__/ops/unique.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 27%] Built target inchiformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/asciiformat.dir/build.make src/formats/CMakeFiles/asciiformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/asciiformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/asciiformat.dir/build.make src/formats/CMakeFiles/asciiformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 28%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dasciiformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/asciiformat.dir/asciiformat.cpp.o -MF CMakeFiles/asciiformat.dir/asciiformat.cpp.o.d -o CMakeFiles/asciiformat.dir/asciiformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/asciiformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/asciiformat.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 28%] Building CXX object src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dasciiformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -MF CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o.d -o CMakeFiles/asciiformat.dir/__/depict/asciipainter.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/asciipainter.cpp /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawText(double, double, const std::string&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/depict/asciipainter.cpp:118:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 118 | for (int i=0; i> buf; cout << buf << endl; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:871:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 871 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:884:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 884 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:884:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 884 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:906:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 906 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:906:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 906 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:921:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 921 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:921:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 921 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:936:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 936 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/adfformat.cpp:936:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 936 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; | ^~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 35%] Building CXX object src/formats/CMakeFiles/castepformat.dir/castepformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcastepformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/castepformat.dir/castepformat.cpp.o -MF CMakeFiles/castepformat.dir/castepformat.cpp.o.d -o CMakeFiles/castepformat.dir/castepformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/castepformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/castepformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54: In function ‘snprintf’, inlined from ‘OpenBabel::CASTEPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/castepformat.cpp:211:17: /usr/include/bits/stdio2.h:54:35: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/castepformat.cpp: In member function ‘OpenBabel::CASTEPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/castepformat.cpp:94:30: note: ‘enthalpy’ was declared here 94 | double pressure, volume, enthalpy; | ^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Linking CXX shared module ../../lib64/castepformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/castepformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/castepformat.so CMakeFiles/castepformat.dir/castepformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Built target castepformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/crystal09format.dir/build.make src/formats/CMakeFiles/crystal09format.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/crystal09format.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/crystal09format.dir/build.make src/formats/CMakeFiles/crystal09format.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 35%] Linking CXX shared module ../../lib64/adfformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/adfformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/adfformat.so CMakeFiles/adfformat.dir/adfformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Built target adfformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/daltonformat.dir/build.make src/formats/CMakeFiles/daltonformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/daltonformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/daltonformat.dir/build.make src/formats/CMakeFiles/daltonformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Building CXX object src/formats/CMakeFiles/daltonformat.dir/daltonformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Ddaltonformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/daltonformat.dir/daltonformat.cpp.o -MF CMakeFiles/daltonformat.dir/daltonformat.cpp.o.d -o CMakeFiles/daltonformat.dir/daltonformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp:15: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp:148:9: warning: variable ‘atomcount’ set but not used [-Wunused-but-set-variable] 148 | int atomcount = 0; // for each atom type | ^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp:312:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 312 | if(atom->GetAtomicNum() != atomtype) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/daltonformat.cpp:332:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 332 | if(atom->GetAtomicNum() != atomtype) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Linking CXX shared module ../../lib64/daltonformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/daltonformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/daltonformat.so CMakeFiles/daltonformat.dir/daltonformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Built target daltonformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/dmolformat.dir/build.make src/formats/CMakeFiles/dmolformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/dmolformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/dmolformat.dir/build.make src/formats/CMakeFiles/dmolformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Building CXX object src/formats/CMakeFiles/crystal09format.dir/crystal09format.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcrystal09format_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/crystal09format.dir/crystal09format.cpp.o -MF CMakeFiles/crystal09format.dir/crystal09format.cpp.o.d -o CMakeFiles/crystal09format.dir/crystal09format.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/crystal09format.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/crystal09format.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/crystal09format.cpp:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 36%] Building CXX object src/formats/CMakeFiles/dmolformat.dir/dmolformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Ddmolformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/dmolformat.dir/dmolformat.cpp.o -MF CMakeFiles/dmolformat.dir/dmolformat.cpp.o.d -o CMakeFiles/dmolformat.dir/dmolformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/dmolformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/dmolformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 37%] Linking CXX shared module ../../lib64/crystal09format.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/crystal09format.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/crystal09format.so CMakeFiles/crystal09format.dir/crystal09format.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 37%] Built target crystal09format make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/fchkformat.dir/build.make src/formats/CMakeFiles/fchkformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 37%] Linking CXX shared module ../../lib64/dmolformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/dmolformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/dmolformat.so CMakeFiles/dmolformat.dir/dmolformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/fchkformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/fchkformat.dir/build.make src/formats/CMakeFiles/fchkformat.dir/build make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 37%] Built target dmolformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/fhiaimsformat.dir/build.make src/formats/CMakeFiles/fhiaimsformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/fhiaimsformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/fhiaimsformat.dir/build.make src/formats/CMakeFiles/fhiaimsformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Building CXX object src/formats/CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfhiaimsformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o -MF CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o.d -o CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fhiaimsformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fhiaimsformat.cpp:15: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Linking CXX shared module ../../lib64/fhiaimsformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/fhiaimsformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/fhiaimsformat.so CMakeFiles/fhiaimsformat.dir/fhiaimsformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Built target fhiaimsformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gamessformat.dir/build.make src/formats/CMakeFiles/gamessformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/gamessformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gamessformat.dir/build.make src/formats/CMakeFiles/gamessformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Building CXX object src/formats/CMakeFiles/fchkformat.dir/fchkformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dfchkformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/fchkformat.dir/fchkformat.cpp.o -MF CMakeFiles/fchkformat.dir/fchkformat.cpp.o.d -o CMakeFiles/fchkformat.dir/fchkformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:24: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/functional:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:16: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp: In member function ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:596:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 596 | if (alphaorb_found && (numAOrb > alphaorb.size())) | ~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:609:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 609 | if (betaorb_found && (numBOrb > betaorb.size())) | ~~~~~~~~^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:668:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less_equal; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 668 | bind2nd(less_equal(), 0)) || | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:671:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 671 | bind2nd(greater(), MxBond)) || | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:674:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = less; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 674 | bind2nd(less(), 0)) || | ~~~~~~~^~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:677:43: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = greater; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 677 | bind2nd(greater(), Natoms))) | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:700:40: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 700 | if (numAOrb > 0 && alphaorb.size() == numAOrb) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/fchkformat.cpp:704:41: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 704 | if (numBOrb > 0 && betaorb.size() == numBOrb) { // open shell calculation | ~~~~~~~~~~~~~~~^~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Linking CXX shared module ../../lib64/fchkformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/fchkformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/fchkformat.so CMakeFiles/fchkformat.dir/fchkformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Built target fchkformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gaussformat.dir/build.make src/formats/CMakeFiles/gaussformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/gaussformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gaussformat.dir/build.make src/formats/CMakeFiles/gaussformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 38%] Building CXX object src/formats/CMakeFiles/gamessformat.dir/gamessformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgamessformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gamessformat.dir/gamessformat.cpp.o -MF CMakeFiles/gamessformat.dir/gamessformat.cpp.o.d -o CMakeFiles/gamessformat.dir/gamessformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:587:38: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 587 | for (unsigned int i=0; i < modeCount; ++i) { | ~~^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:233:9: warning: variable ‘ndummyatoms’ set but not used [-Wunused-but-set-variable] 233 | int ndummyatoms = 0; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:519:11: warning: ‘lowFreqModesBegin’ may be used uninitialized [-Wmaybe-uninitialized] 519 | if (numFreq < lowFreqModesBegin) // imaginary frequency | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:244:9: note: ‘lowFreqModesBegin’ was declared here 244 | int lowFreqModesBegin; // the number of the first low frequency mode | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:521:11: warning: ‘lowFreqModesEnd’ may be used uninitialized [-Wmaybe-uninitialized] 521 | if (numFreq > lowFreqModesEnd) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessformat.cpp:245:9: note: ‘lowFreqModesEnd’ was declared here 245 | int lowFreqModesEnd; // the number of the last low frequency mode | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Linking CXX shared module ../../lib64/gamessformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamessformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/gamessformat.so CMakeFiles/gamessformat.dir/gamessformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 39%] Building CXX object src/formats/CMakeFiles/gaussformat.dir/gaussformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgaussformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gaussformat.dir/gaussformat.cpp.o -MF CMakeFiles/gaussformat.dir/gaussformat.cpp.o.d -o CMakeFiles/gaussformat.dir/gaussformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/data.h:27, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp: In function ‘void OpenBabel::add_unique_pairdata_to_mol(OBMol*, std::string, std::string, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp:285:19: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 285 | if (vs.size() >= start) | ~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp:288:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 288 | for(i=start+1; (i)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gaussformat.cpp:339:17: warning: unused variable ‘pg’ [-Wunused-variable] 339 | const char *pg = obPG.IdentifyPointGroup(); | ^~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Built target gamessformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gausscubeformat.dir/build.make src/formats/CMakeFiles/gausscubeformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/gausscubeformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gausscubeformat.dir/build.make src/formats/CMakeFiles/gausscubeformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Building CXX object src/formats/CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgausscubeformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o -MF CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o.d -o CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:29: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:48, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:30: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/base.h:228:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 228 | virtual const std::string &GetValue() const | ^~~~~~~~ In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:36: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 76 | double GetValue (vector3 pos) const; | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp: In member function ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:432:25: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 432 | while (vgd.size() < nCubes) | ~~~~~~~~~~~^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:479:26: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 479 | while (values.size() < n*nCubes) | ~~~~~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausscubeformat.cpp:114:17: warning: unused variable ‘title’ [-Wunused-variable] 114 | const char* title = pConv->GetTitle(); | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Linking CXX shared module ../../lib64/gaussformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/gaussformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/gaussformat.so CMakeFiles/gaussformat.dir/gaussformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Built target gaussformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gausszmatformat.dir/build.make src/formats/CMakeFiles/gausszmatformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/gausszmatformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gausszmatformat.dir/build.make src/formats/CMakeFiles/gausszmatformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Linking CXX shared module ../../lib64/gausscubeformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/gausscubeformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/gausscubeformat.so CMakeFiles/gausscubeformat.dir/gausscubeformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Built target gausscubeformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gulpformat.dir/build.make src/formats/CMakeFiles/gulpformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/gulpformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gulpformat.dir/build.make src/formats/CMakeFiles/gulpformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Building CXX object src/formats/CMakeFiles/gulpformat.dir/gulpformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgulpformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gulpformat.dir/gulpformat.cpp.o -MF CMakeFiles/gulpformat.dir/gulpformat.cpp.o.d -o CMakeFiles/gulpformat.dir/gulpformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp: In member function ‘OpenBabel::GULPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp:359:14: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 359 | double en_kcal_per_mole = enthalpy_eV * EV_TO_KCAL_PER_MOL; | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp:96:12: note: ‘enthalpy_eV’ was declared here 96 | double enthalpy_eV, pv_eV; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp:360:14: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 360 | double pv_kcal_per_mole = pv_eV * EV_TO_KCAL_PER_MOL; | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gulpformat.cpp:96:25: note: ‘pv_eV’ was declared here 96 | double enthalpy_eV, pv_eV; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 40%] Building CXX object src/formats/CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgausszmatformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o -MF CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o.d -o CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausszmatformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gausszmatformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Linking CXX shared module ../../lib64/gulpformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/gulpformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/gulpformat.so CMakeFiles/gulpformat.dir/gulpformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Built target gulpformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/hinformat.dir/build.make src/formats/CMakeFiles/hinformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/hinformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/hinformat.dir/build.make src/formats/CMakeFiles/hinformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Linking CXX shared module ../../lib64/gausszmatformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/gausszmatformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/gausszmatformat.so CMakeFiles/gausszmatformat.dir/gausszmatformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Built target gausszmatformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/jaguarformat.dir/build.make src/formats/CMakeFiles/jaguarformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/jaguarformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/jaguarformat.dir/build.make src/formats/CMakeFiles/jaguarformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Building CXX object src/formats/CMakeFiles/hinformat.dir/hinformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dhinformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/hinformat.dir/hinformat.cpp.o -MF CMakeFiles/hinformat.dir/hinformat.cpp.o.d -o CMakeFiles/hinformat.dir/hinformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/hinformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/hinformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Linking CXX shared module ../../lib64/hinformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/hinformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/hinformat.so CMakeFiles/hinformat.dir/hinformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Built target hinformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/molproformat.dir/build.make src/formats/CMakeFiles/molproformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/molproformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/molproformat.dir/build.make src/formats/CMakeFiles/molproformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Building CXX object src/formats/CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Djaguarformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o -MF CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o.d -o CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/jaguarformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/jaguarformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Linking CXX shared module ../../lib64/jaguarformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/jaguarformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/jaguarformat.so CMakeFiles/jaguarformat.dir/jaguarformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Built target jaguarformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/mopacformat.dir/build.make src/formats/CMakeFiles/mopacformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/mopacformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/mopacformat.dir/build.make src/formats/CMakeFiles/mopacformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 41%] Building CXX object src/formats/CMakeFiles/molproformat.dir/molproformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmolproformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/molproformat.dir/molproformat.cpp.o -MF CMakeFiles/molproformat.dir/molproformat.cpp.o.d -o CMakeFiles/molproformat.dir/molproformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/molproformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/molproformat.cpp:20: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Linking CXX shared module ../../lib64/molproformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/molproformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/molproformat.so CMakeFiles/molproformat.dir/molproformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Built target molproformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/nwchemformat.dir/build.make src/formats/CMakeFiles/nwchemformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/nwchemformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/nwchemformat.dir/build.make src/formats/CMakeFiles/nwchemformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Building CXX object src/formats/CMakeFiles/mopacformat.dir/mopacformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dmopacformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/mopacformat.dir/mopacformat.cpp.o -MF CMakeFiles/mopacformat.dir/mopacformat.cpp.o.d -o CMakeFiles/mopacformat.dir/mopacformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACCARTFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp:650:19: warning: variable ‘isotopeMass’ set but not used [-Wunused-but-set-variable] 650 | double x,y,z, isotopeMass; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp: In member function ‘OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp:81:12: warning: ‘x’ may be used uninitialized [-Wmaybe-uninitialized] 81 | double x,y,z; | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/mopacformat.cpp:81:14: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 81 | double x,y,z; | ^ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Linking CXX shared module ../../lib64/mopacformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/mopacformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/mopacformat.so CMakeFiles/mopacformat.dir/mopacformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Built target mopacformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/pwscfformat.dir/build.make src/formats/CMakeFiles/pwscfformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/pwscfformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/pwscfformat.dir/build.make src/formats/CMakeFiles/pwscfformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Building CXX object src/formats/CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dnwchemformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o -MF CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o.d -o CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:228:72: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 228 | if ((i>=natoms) || (molecule->GetAtom(i+1)->GetAtomicNum() != atoi(vs[2].c_str()))) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMultipoleMoment(std::istream*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:306:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 306 | else if (vs[0][0] == '1') | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:423:56: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 423 | if (molecule->GetAtom(i++)->GetAtomicNum() != charge) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:571:25: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 571 | if (energies.size() != molecule->NumConformers()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:932:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 932 | if (atoi(buffer) != natoms) | ~~~~~~~~~~~~~^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: At global scope: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:111:20: warning: ‘OpenBabel::BETA_ORBITAL_PATTERN’ defined but not used [-Wunused-variable] 111 | static const char* BETA_ORBITAL_PATTERN = "Beta"; | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::basic_istream >*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:957:21: warning: ‘nbeads’ may be used uninitialized [-Wmaybe-uninitialized] 957 | if (bead_number != nbeads) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:900:18: note: ‘nbeads’ was declared here 900 | unsigned int nbeads; | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp: In member function ‘OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::basic_istream >*, OpenBabel::OBMol*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:772:5: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 772 | if (energy == 0) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/nwchemformat.cpp:750:12: note: ‘energy’ was declared here 750 | double energy; | ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Building CXX object src/formats/CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpwscfformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o -MF CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o.d -o CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54: In function ‘snprintf’, inlined from ‘OpenBabel::PWscfFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp:282:15: /usr/include/bits/stdio2.h:54:35: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp: In member function ‘OpenBabel::PWscfFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp:98:12: note: ‘enthalpy’ was declared here 98 | double enthalpy, pv; | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp:281:14: warning: ‘pv’ may be used uninitialized [-Wmaybe-uninitialized] 281 | double pv_eV = pv / EV_TO_KCAL_PER_MOL; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pwscfformat.cpp:98:22: note: ‘pv’ was declared here 98 | double enthalpy, pv; | ^~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 43%] Linking CXX shared module ../../lib64/pwscfformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pwscfformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/pwscfformat.so CMakeFiles/pwscfformat.dir/pwscfformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 43%] Built target pwscfformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/qchemformat.dir/build.make src/formats/CMakeFiles/qchemformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/qchemformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/qchemformat.dir/build.make src/formats/CMakeFiles/qchemformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 42%] Linking CXX shared module ../../lib64/nwchemformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/nwchemformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/nwchemformat.so CMakeFiles/nwchemformat.dir/nwchemformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 43%] Built target nwchemformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/siestaformat.dir/build.make src/formats/CMakeFiles/siestaformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/siestaformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/siestaformat.dir/build.make src/formats/CMakeFiles/siestaformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 43%] Building CXX object src/formats/CMakeFiles/qchemformat.dir/qchemformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dqchemformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/qchemformat.dir/qchemformat.cpp.o -MF CMakeFiles/qchemformat.dir/qchemformat.cpp.o.d -o CMakeFiles/qchemformat.dir/qchemformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/qchemformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/qchemformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/qchemformat.cpp:16: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/qchemformat.cpp: In member function ‘virtual bool OpenBabel::QChemOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/qchemformat.cpp:194:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 194 | if (nbAtomRead != mol.NumAtoms()) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Building CXX object src/formats/CMakeFiles/siestaformat.dir/siestaformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsiestaformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/siestaformat.dir/siestaformat.cpp.o -MF CMakeFiles/siestaformat.dir/siestaformat.cpp.o.d -o CMakeFiles/siestaformat.dir/siestaformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/siestaformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/siestaformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/siestaformat.cpp: In member function ‘virtual bool OpenBabel::SIESTAFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/siestaformat.cpp:92:10: warning: variable ‘coordsAreAngstrom’ set but not used [-Wunused-but-set-variable] 92 | bool coordsAreAngstrom = false; | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/siestaformat.cpp:98:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 98 | size_t size; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/siestaformat.cpp:102:30: warning: unused variable ‘numSpecies’ [-Wunused-variable] 102 | int atomicNum, numAtoms, numSpecies; | ^~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Linking CXX shared module ../../lib64/qchemformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/qchemformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/qchemformat.so CMakeFiles/qchemformat.dir/qchemformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Built target qchemformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/turbomoleformat.dir/build.make src/formats/CMakeFiles/turbomoleformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/turbomoleformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/turbomoleformat.dir/build.make src/formats/CMakeFiles/turbomoleformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Linking CXX shared module ../../lib64/siestaformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/siestaformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/siestaformat.so CMakeFiles/siestaformat.dir/siestaformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Built target siestaformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/vaspformat.dir/build.make src/formats/CMakeFiles/vaspformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/vaspformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/vaspformat.dir/build.make src/formats/CMakeFiles/vaspformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Building CXX object src/formats/CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dturbomoleformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o -MF CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o.d -o CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/turbomoleformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/turbomoleformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Linking CXX shared module ../../lib64/turbomoleformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/turbomoleformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/turbomoleformat.so CMakeFiles/turbomoleformat.dir/turbomoleformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Built target turbomoleformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/xsfformat.dir/build.make src/formats/CMakeFiles/xsfformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/xsfformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/xsfformat.dir/build.make src/formats/CMakeFiles/xsfformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Building CXX object src/formats/CMakeFiles/xsfformat.dir/xsfformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxsfformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xsfformat.dir/xsfformat.cpp.o -MF CMakeFiles/xsfformat.dir/xsfformat.cpp.o.d -o CMakeFiles/xsfformat.dir/xsfformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/xsfformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/xsfformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Linking CXX shared module ../../lib64/xsfformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/xsfformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/xsfformat.so CMakeFiles/xsfformat.dir/xsfformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Built target xsfformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/zindoformat.dir/build.make src/formats/CMakeFiles/zindoformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/zindoformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/zindoformat.dir/build.make src/formats/CMakeFiles/zindoformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Building CXX object src/formats/CMakeFiles/zindoformat.dir/zindoformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dzindoformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/zindoformat.dir/zindoformat.cpp.o -MF CMakeFiles/zindoformat.dir/zindoformat.cpp.o.d -o CMakeFiles/zindoformat.dir/zindoformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/zindoformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/zindoformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 44%] Building CXX object src/formats/CMakeFiles/vaspformat.dir/vaspformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dvaspformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/vaspformat.dir/vaspformat.cpp.o -MF CMakeFiles/vaspformat.dir/vaspformat.cpp.o.d -o CMakeFiles/vaspformat.dir/vaspformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:451:17: warning: unused variable ‘freqnum’ [-Wunused-variable] 451 | int freqnum = atoi(vs[0].c_str()); | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:535:35: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = not_equal_to; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 535 | std::bind2nd(std::not_equal_to(), 0.0)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:589:36: warning: ‘std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = divides; _Tp = double]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 589 | std::bind2nd(std::divides(), max / 100.0)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:668:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 668 | for(int i = 0; i < atoms_sorted.size(); i++) | ~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp: In member function ‘OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:410:21: warning: ‘fermi’ may be used uninitialized [-Wmaybe-uninitialized] 410 | dos->SetData(fermi, energies, densities, integration); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:392:14: note: ‘fermi’ was declared here 392 | double fermi; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:556:14: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 556 | double en_kcal_per_mole = enthalpy_eV * EV_TO_KCAL_PER_MOL; | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:171:12: note: ‘enthalpy_eV’ was declared here 171 | double enthalpy_eV, pv_eV; | ^~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:557:14: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 557 | double pv_kcal_per_mole = pv_eV * EV_TO_KCAL_PER_MOL; | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/vaspformat.cpp:171:25: note: ‘pv_eV’ was declared here 171 | double enthalpy_eV, pv_eV; | ^~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Linking CXX shared module ../../lib64/zindoformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/zindoformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/zindoformat.so CMakeFiles/zindoformat.dir/zindoformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Built target zindoformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gamessukformat.dir/build.make src/formats/CMakeFiles/gamessukformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/gamessukformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/gamessukformat.dir/build.make src/formats/CMakeFiles/gamessukformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Linking CXX shared module ../../lib64/vaspformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/vaspformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/vaspformat.so CMakeFiles/vaspformat.dir/vaspformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Built target vaspformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/orcaformat.dir/build.make src/formats/CMakeFiles/orcaformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/orcaformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/orcaformat.dir/build.make src/formats/CMakeFiles/orcaformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Building CXX object src/formats/CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dgamessukformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o -MF CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o.d -o CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp:14: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadInitialCartesian(OpenBabel::OBMol&, std::istream&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp:787:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 787 | bool ok=false; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz1(OpenBabel::OBMol&, std::istream&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp:853:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 853 | bool ok=false; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz2(OpenBabel::OBMol&, std::istream&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp:900:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 900 | bool ok=false; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSUKOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/gamessukformat.cpp:1215:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 1215 | bool ok; | ^~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Building CXX object src/formats/CMakeFiles/orcaformat.dir/orcaformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dorcaformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/orcaformat.dir/orcaformat.cpp.o -MF CMakeFiles/orcaformat.dir/orcaformat.cpp.o.d -o CMakeFiles/orcaformat.dir/orcaformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:348:33: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 348 | while(vs.size() == nColumn+1) { | ~~~~~~~~~~^~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:363:48: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 363 | for (unsigned int i = 0; i < nColumn; i++) { | ~~^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:375:44: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 375 | for (unsigned int i = 0; i < nColumn; i++) { | ~~^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:131:12: warning: unused variable ‘energy’ [-Wunused-variable] 131 | double energy=0; | ^~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:138:9: warning: variable ‘nModeAll’ set but not used [-Wunused-but-set-variable] 138 | int nModeAll = 0; | ^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:220:36: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 220 | atom->SetVector(x,y,z); //set atom coordinates | ~~~~~~~~~~~~~~~^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:162:13: note: ‘atom’ was declared here 162 | OBAtom *atom; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:217:37: warning: ‘confCoords’ may be used uninitialized [-Wmaybe-uninitialized] 217 | confCoords[i*3+2] = z; | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/orcaformat.cpp:149:13: note: ‘confCoords’ was declared here 149 | double* confCoords; | ^~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Linking CXX shared module ../../lib64/gamessukformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/gamessukformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/gamessukformat.so CMakeFiles/gamessukformat.dir/gamessukformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Built target gamessukformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/APIInterface.dir/build.make src/formats/CMakeFiles/APIInterface.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/APIInterface.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/APIInterface.dir/build.make src/formats/CMakeFiles/APIInterface.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Building CXX object src/formats/CMakeFiles/APIInterface.dir/APIInterface.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DAPIInterface_EXPORTS -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/APIInterface.dir/APIInterface.cpp.o -MF CMakeFiles/APIInterface.dir/APIInterface.cpp.o.d -o CMakeFiles/APIInterface.dir/APIInterface.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/APIInterface.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/APIInterface.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Linking CXX shared module ../../lib64/APIInterface.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/APIInterface.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/APIInterface.so CMakeFiles/APIInterface.dir/APIInterface.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Built target APIInterface make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/CSRformat.dir/build.make src/formats/CMakeFiles/CSRformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/CSRformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/CSRformat.dir/build.make src/formats/CMakeFiles/CSRformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Linking CXX shared module ../../lib64/orcaformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/orcaformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/orcaformat.so CMakeFiles/orcaformat.dir/orcaformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Built target orcaformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/PQSformat.dir/build.make src/formats/CMakeFiles/PQSformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Building CXX object src/formats/CMakeFiles/CSRformat.dir/CSRformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DCSRformat_EXPORTS -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/CSRformat.dir/CSRformat.cpp.o -MF CMakeFiles/CSRformat.dir/CSRformat.cpp.o.d -o CMakeFiles/CSRformat.dir/CSRformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/CSRformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/CSRformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/CSRformat.cpp: In member function ‘OpenBabel::CSRFormat::PadString(char*, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/CSRformat.cpp:192:12: warning: ‘__strncpy_chk’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation] 192 | strncpy(output, input, strlen(input)); | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/CSRformat.cpp:192:12: note: length computed here 192 | strncpy(output, input, strlen(input)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/PQSformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/PQSformat.dir/build.make src/formats/CMakeFiles/PQSformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Linking CXX shared module ../../lib64/CSRformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/CSRformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/CSRformat.so CMakeFiles/CSRformat.dir/CSRformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Built target CSRformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/MCDLformat.dir/build.make src/formats/CMakeFiles/MCDLformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/MCDLformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/MCDLformat.dir/build.make src/formats/CMakeFiles/MCDLformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 45%] Building CXX object src/formats/CMakeFiles/PQSformat.dir/PQSformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DPQSformat_EXPORTS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/PQSformat.dir/PQSformat.cpp.o -MF CMakeFiles/PQSformat.dir/PQSformat.cpp.o.d -o CMakeFiles/PQSformat.dir/PQSformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/PQSformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/PQSformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/PQSformat.cpp: In member function ‘OpenBabel::PQSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/PQSformat.cpp:263:49: warning: ‘pFormat’ may be used uninitialized [-Wmaybe-uninitialized] 263 | return pFormat->ReadMolecule(&mol,&coordconv); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/PQSformat.cpp:254:31: note: ‘pFormat’ was declared here 254 | OBFormat* pFormat; | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 47%] Linking CXX shared module ../../lib64/PQSformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/PQSformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/PQSformat.so CMakeFiles/PQSformat.dir/PQSformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 47%] Built target PQSformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/alchemyformat.dir/build.make src/formats/CMakeFiles/alchemyformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/alchemyformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/alchemyformat.dir/build.make src/formats/CMakeFiles/alchemyformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 47%] Building CXX object src/formats/CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dalchemyformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o -MF CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o.d -o CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/alchemyformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/alchemyformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 48%] Linking CXX shared module ../../lib64/alchemyformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/alchemyformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/alchemyformat.so CMakeFiles/alchemyformat.dir/alchemyformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 48%] Built target alchemyformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/acrformat.dir/build.make src/formats/CMakeFiles/acrformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/acrformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/acrformat.dir/build.make src/formats/CMakeFiles/acrformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 46%] Building CXX object src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DMCDLformat_EXPORTS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o -MF CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o.d -o CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:21: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:283:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 283 | if (jflag) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:287:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 287 | nt = 1; | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::setMCDL(std::string, OpenBabel::OBMol*, std::string&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:1267:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 1267 | if (nPrev == acount) { | ~~~~~~^~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::indexOf(std::string, std::string, int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:1385:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 1385 | if (result == string::npos) result=-1; | ~~~~~~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:1386:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1386 | if (result >= instring.length()) result=-1; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::lastIndexOf(std::string, std::string)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:1399:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 1399 | if (n == string::npos) | ~~^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp: In member function ‘OpenBabel::MCDLFormat::solve(int, int (*) [4], int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:242:28: warning: ‘jump’ may be used uninitialized [-Wmaybe-uninitialized] 242 | int numdups, dupfrag, jump; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:390:24: warning: ‘numdups’ may be used uninitialized [-Wmaybe-uninitialized] 390 | for (j=0; j dupfrag) | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/MCDLformat.cpp:242:19: note: ‘dupfrag’ was declared here 242 | int numdups, dupfrag, jump; | ^~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Building CXX object src/formats/CMakeFiles/acrformat.dir/acrformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dacrformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/acrformat.dir/acrformat.cpp.o -MF CMakeFiles/acrformat.dir/acrformat.cpp.o.d -o CMakeFiles/acrformat.dir/acrformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp:26: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp:23: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp: In member function ‘OpenBabel::ACRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp:166:12: warning: ‘atoms’ may be used uninitialized [-Wmaybe-uninitialized] 166 | } else if ( pmol->NumAtoms() != atoms ) { | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp:95:18: note: ‘atoms’ was declared here 95 | unsigned int atoms, bonds, tmp; | ^~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp:162:5: warning: ‘bonds’ may be used uninitialized [-Wmaybe-uninitialized] 162 | if ( pmol->NumBonds() != bonds ) { | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/acrformat.cpp:95:25: note: ‘bonds’ was declared here 95 | unsigned int atoms, bonds, tmp; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Linking CXX shared module ../../lib64/acrformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/acrformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/acrformat.so CMakeFiles/acrformat.dir/acrformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Built target acrformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/amberformat.dir/build.make src/formats/CMakeFiles/amberformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/amberformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/amberformat.dir/build.make src/formats/CMakeFiles/amberformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Building CXX object src/formats/CMakeFiles/amberformat.dir/amberformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Damberformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/amberformat.dir/amberformat.cpp.o -MF CMakeFiles/amberformat.dir/amberformat.cpp.o.d -o CMakeFiles/amberformat.dir/amberformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/amberformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/amberformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Linking CXX shared module ../../lib64/amberformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/amberformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/amberformat.so CMakeFiles/amberformat.dir/amberformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Built target amberformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/balstformat.dir/build.make src/formats/CMakeFiles/balstformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/balstformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/balstformat.dir/build.make src/formats/CMakeFiles/balstformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Building CXX object src/formats/CMakeFiles/balstformat.dir/balstformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dbalstformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/balstformat.dir/balstformat.cpp.o -MF CMakeFiles/balstformat.dir/balstformat.cpp.o.d -o CMakeFiles/balstformat.dir/balstformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/balstformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/balstformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Linking CXX shared module ../../lib64/balstformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/balstformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/balstformat.so CMakeFiles/balstformat.dir/balstformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Built target balstformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/bgfformat.dir/build.make src/formats/CMakeFiles/bgfformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/bgfformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/bgfformat.dir/build.make src/formats/CMakeFiles/bgfformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 49%] Linking CXX shared module ../../lib64/MCDLformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/MCDLformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/MCDLformat.so CMakeFiles/MCDLformat.dir/MCDLformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Built target MCDLformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/boxformat.dir/build.make src/formats/CMakeFiles/boxformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/boxformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/boxformat.dir/build.make src/formats/CMakeFiles/boxformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Building CXX object src/formats/CMakeFiles/bgfformat.dir/bgfformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dbgfformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/bgfformat.dir/bgfformat.cpp.o -MF CMakeFiles/bgfformat.dir/bgfformat.cpp.o.d -o CMakeFiles/bgfformat.dir/bgfformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/bgfformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/bgfformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Building CXX object src/formats/CMakeFiles/boxformat.dir/boxformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dboxformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/boxformat.dir/boxformat.cpp.o -MF CMakeFiles/boxformat.dir/boxformat.cpp.o.d -o CMakeFiles/boxformat.dir/boxformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/boxformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/boxformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Linking CXX shared module ../../lib64/bgfformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/bgfformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/bgfformat.so CMakeFiles/bgfformat.dir/bgfformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Built target bgfformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cacaoformat.dir/build.make src/formats/CMakeFiles/cacaoformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/cacaoformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cacaoformat.dir/build.make src/formats/CMakeFiles/cacaoformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Linking CXX shared module ../../lib64/boxformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/boxformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/boxformat.so CMakeFiles/boxformat.dir/boxformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Built target boxformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cacheformat.dir/build.make src/formats/CMakeFiles/cacheformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/cacheformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cacheformat.dir/build.make src/formats/CMakeFiles/cacheformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/cacheformat.dir/cacheformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcacheformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cacheformat.dir/cacheformat.cpp.o -MF CMakeFiles/cacheformat.dir/cacheformat.cpp.o.d -o CMakeFiles/cacheformat.dir/cacheformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cacheformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cacheformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/cacheformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/cacheformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/cacheformat.so CMakeFiles/cacheformat.dir/cacheformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target cacheformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/carformat.dir/build.make src/formats/CMakeFiles/carformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/carformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/carformat.dir/build.make src/formats/CMakeFiles/carformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 50%] Building CXX object src/formats/CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcacaoformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o -MF CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o.d -o CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cacaoformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cacaoformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/cacaoformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/cacaoformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/cacaoformat.so CMakeFiles/cacaoformat.dir/cacaoformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target cacaoformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cccformat.dir/build.make src/formats/CMakeFiles/cccformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/cccformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cccformat.dir/build.make src/formats/CMakeFiles/cccformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/carformat.dir/carformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcarformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/carformat.dir/carformat.cpp.o -MF CMakeFiles/carformat.dir/carformat.cpp.o.d -o CMakeFiles/carformat.dir/carformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/carformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/carformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/cccformat.dir/cccformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcccformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cccformat.dir/cccformat.cpp.o -MF CMakeFiles/cccformat.dir/cccformat.cpp.o.d -o CMakeFiles/cccformat.dir/cccformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cccformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cccformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/carformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/carformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/carformat.so CMakeFiles/carformat.dir/carformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target carformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chem3dformat.dir/build.make src/formats/CMakeFiles/chem3dformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/chem3dformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chem3dformat.dir/build.make src/formats/CMakeFiles/chem3dformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/cccformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/cccformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/cccformat.so CMakeFiles/cccformat.dir/cccformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target cccformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chemdrawct.dir/build.make src/formats/CMakeFiles/chemdrawct.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/chemdrawct.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chemdrawct.dir/build.make src/formats/CMakeFiles/chemdrawct.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchem3dformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o -MF CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o.d -o CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chem3dformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chem3dformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/math/matrix3x3.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chem3dformat.cpp:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemdrawct_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o -MF CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o.d -o CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chemdrawct.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chemdrawct.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/chem3dformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/chem3dformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/chem3dformat.so CMakeFiles/chem3dformat.dir/chem3dformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target chem3dformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chemtoolformat.dir/build.make src/formats/CMakeFiles/chemtoolformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/chemtoolformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chemtoolformat.dir/build.make src/formats/CMakeFiles/chemtoolformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/chemdrawct.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdrawct.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/chemdrawct.so CMakeFiles/chemdrawct.dir/chemdrawct.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target chemdrawct make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cifformat.dir/build.make src/formats/CMakeFiles/cifformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/cifformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cifformat.dir/build.make src/formats/CMakeFiles/cifformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dchemtoolformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o -MF CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o.d -o CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chemtoolformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/chemtoolformat.cpp:19: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Linking CXX shared module ../../lib64/chemtoolformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemtoolformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/chemtoolformat.so CMakeFiles/chemtoolformat.dir/chemtoolformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Built target chemtoolformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cofformat.dir/build.make src/formats/CMakeFiles/cofformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/cofformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/cofformat.dir/build.make src/formats/CMakeFiles/cofformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 51%] Building CXX object src/formats/CMakeFiles/cofformat.dir/cofformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dcofformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/cofformat.dir/cofformat.cpp.o -MF CMakeFiles/cofformat.dir/cofformat.cpp.o.d -o CMakeFiles/cofformat.dir/cofformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp: In member function ‘virtual bool OpenBabel::COFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp:133:22: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 133 | if(vs.size() < offset+9) | ~~~~~~~~~~^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp:180:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 180 | for(int j=0 ; j< natoms ; j++) | ~^~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp: In member function ‘virtual bool OpenBabel::COFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/cofformat.cpp:368:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 368 | for( int j=0; j >&, unsigned int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbqtformat.cpp:345:15: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbqtformat.cpp: In function ‘OpenBabel::OutputAtom(OpenBabel::OBAtom*, std::basic_ostream >&, unsigned int)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbqtformat.cpp:363:60: warning: ‘__snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 363 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); | ^ In function ‘snprintf’, inlined from ‘OpenBabel::OutputAtom(OpenBabel::OBAtom*, std::basic_ostream >&, unsigned int)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbqtformat.cpp:363:19: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbqtformat.cpp: In member function ‘OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pdbqtformat.cpp:923:22: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation] 923 | strncpy(type_name, OBElements::GetSymbol(rotBondTable[rotBondId][bondAtomNum]->GetAtomicNum()), sizeof(type_name)); | ^ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Building CXX object src/formats/CMakeFiles/pqrformat.dir/pqrformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dpqrformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/pqrformat.dir/pqrformat.cpp.o -MF CMakeFiles/pqrformat.dir/pqrformat.cpp.o.d -o CMakeFiles/pqrformat.dir/pqrformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:16: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomCharge(char*, OBMol&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:207:13: warning: unused variable ‘atom’ [-Wunused-variable] 207 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomRadius(char*, OBMol&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:222:13: warning: unused variable ‘atom’ [-Wunused-variable] 222 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp: In member function ‘OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:511:58: warning: ‘__snprintf_chk’ output may be truncated before the last format character [-Wformat-truncation=] 511 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); | ^ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54: In function ‘snprintf’, inlined from ‘OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:511:21: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 11 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp: In member function ‘OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:528:66: warning: ‘%-3s’ directive output may be truncated writing between 3 and 15 bytes into a region of size 9 [-Wformat-truncation=] 528 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); | ^~~~ ~~~ In function ‘snprintf’, inlined from ‘OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/pqrformat.cpp:528:29: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 17 bytes into a destination of size 10 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Linking CXX shared module ../../lib64/pdbqtformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdbqtformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/pdbqtformat.so CMakeFiles/pdbqtformat.dir/pdbqtformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Built target pdbqtformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/shelxformat.dir/build.make src/formats/CMakeFiles/shelxformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/shelxformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/shelxformat.dir/build.make src/formats/CMakeFiles/shelxformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Linking CXX shared module ../../lib64/pqrformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/pqrformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/pqrformat.so CMakeFiles/pqrformat.dir/pqrformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Built target pqrformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/smileyformat.dir/build.make src/formats/CMakeFiles/smileyformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/smileyformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/smileyformat.dir/build.make src/formats/CMakeFiles/smileyformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Building CXX object src/formats/CMakeFiles/shelxformat.dir/shelxformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dshelxformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/shelxformat.dir/shelxformat.cpp.o -MF CMakeFiles/shelxformat.dir/shelxformat.cpp.o.d -o CMakeFiles/shelxformat.dir/shelxformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/shelxformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/shelxformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/math/matrix3x3.h:24, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/shelxformat.cpp:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Linking CXX shared module ../../lib64/shelxformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/shelxformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/shelxformat.so CMakeFiles/shelxformat.dir/shelxformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Built target shelxformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/stlformat.dir/build.make src/formats/CMakeFiles/stlformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/stlformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/stlformat.dir/build.make src/formats/CMakeFiles/stlformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Building CXX object src/formats/CMakeFiles/stlformat.dir/stlformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dstlformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/stlformat.dir/stlformat.cpp.o -MF CMakeFiles/stlformat.dir/stlformat.cpp.o.d -o CMakeFiles/stlformat.dir/stlformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/stlformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/stlformat.cpp:32: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/mol.h:44, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/stlformat.cpp:28: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/stlformat.cpp: In function ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/stlformat.cpp:157:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 157 | for( int i=0 ; i < points.size()-2; i++ ) { | ~~^~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Linking CXX shared module ../../lib64/stlformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/stlformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/stlformat.so CMakeFiles/stlformat.dir/stlformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Built target stlformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/thermoformat.dir/build.make src/formats/CMakeFiles/thermoformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/thermoformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/thermoformat.dir/build.make src/formats/CMakeFiles/thermoformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Building CXX object src/formats/CMakeFiles/smileyformat.dir/smileyformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dsmileyformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/smileyformat.dir/smileyformat.cpp.o -MF CMakeFiles/smileyformat.dir/smileyformat.cpp.o.d -o CMakeFiles/smileyformat.dir/smileyformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:15: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::setChiral(int, Smiley::Chirality, const std::vector&)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘NotChiral’ not handled in switch [-Wswitch] 158 | switch (chirality) { | ^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TH1’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TH2’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘AL1’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘AL2’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘SP1’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘SP2’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘SP3’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB1’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB2’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB3’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB4’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB5’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB6’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB7’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB8’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB9’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB10’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB11’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB12’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB13’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB14’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB15’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB16’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB17’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB18’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB19’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘TB20’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH1’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH2’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH3’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH4’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH5’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH6’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH7’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH8’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH9’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH10’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH11’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH12’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH13’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH14’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH15’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH16’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH17’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH18’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH19’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH20’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH21’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH22’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH23’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH24’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH25’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH26’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH27’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH28’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH29’ not handled in switch [-Wswitch] /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:158:14: warning: enumeration value ‘OH30’ not handled in switch [-Wswitch] In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:26: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h: In instantiation of ‘void Smiley::Parser::processStereochemistry() [with Callback = OpenBabel::OpenBabelCallback]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:2707:9: required from ‘void Smiley::Parser::parse(const std::string&) [with Callback = OpenBabel::OpenBabelCallback; std::string = std::__cxx11::basic_string]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:370:19: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:2642:43: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2642 | if (m_chiralInfo[i].nbrs.size() != expectedValence && m_exceptions & InvalidChiralValence) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h: In instantiation of ‘Smiley::Parser::RingBondInfo::RingBondInfo(int, int, bool, bool, bool, std::size_t) [with Callback = OpenBabel::OpenBabelCallback; std::size_t = long unsigned int]’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:2409:41: required from ‘void Smiley::Parser::processRingBond(int, std::size_t) [with Callback = OpenBabel::OpenBabelCallback; std::size_t = long unsigned int]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:2429:11: required from ‘void Smiley::Parser::parseRingBond() [with Callback = OpenBabel::OpenBabelCallback]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:2507:13: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:2698:9: required from ‘void Smiley::Parser::parse(const std::string&) [with Callback = OpenBabel::OpenBabelCallback; std::string = std::__cxx11::basic_string]’ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smileyformat.cpp:370:19: required from here /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:986:14: warning: ‘Smiley::Parser::RingBondInfo::isExplicit’ will be initialized after [-Wreorder] 986 | bool isExplicit; | ^~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:981:21: warning: ‘std::size_t Smiley::Parser::RingBondInfo::pos’ [-Wreorder] 981 | std::size_t pos; | ^~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/smiley.h:974:9: warning: when initialized here [-Wreorder] 974 | RingBondInfo(int number_, int order_, bool isUp_, bool isDown_, | ^~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 62%] Building CXX object src/formats/CMakeFiles/thermoformat.dir/thermoformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dthermoformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/thermoformat.dir/thermoformat.cpp.o -MF CMakeFiles/thermoformat.dir/thermoformat.cpp.o.d -o CMakeFiles/thermoformat.dir/thermoformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/thermoformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/thermoformat.cpp:23: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/thermoformat.cpp:21: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 63%] Linking CXX shared module ../../lib64/thermoformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/thermoformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/thermoformat.so CMakeFiles/thermoformat.dir/thermoformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 63%] Built target thermoformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/tinkerformat.dir/build.make src/formats/CMakeFiles/tinkerformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/tinkerformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/tinkerformat.dir/build.make src/formats/CMakeFiles/tinkerformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 63%] Linking CXX shared module ../../lib64/smileyformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/smileyformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/smileyformat.so CMakeFiles/smileyformat.dir/smileyformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 63%] Built target smileyformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/unichemformat.dir/build.make src/formats/CMakeFiles/unichemformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/unichemformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/unichemformat.dir/build.make src/formats/CMakeFiles/unichemformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 63%] Building CXX object src/formats/CMakeFiles/unichemformat.dir/unichemformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dunichemformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/unichemformat.dir/unichemformat.cpp.o -MF CMakeFiles/unichemformat.dir/unichemformat.cpp.o.d -o CMakeFiles/unichemformat.dir/unichemformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/unichemformat.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/unichemformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 63%] Building CXX object src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dtinkerformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o -MF CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o.d -o CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/tinkerformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/tinkerformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/tinkerformat.cpp: In function ‘int OpenBabel::SetMM3Type(OBAtom*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/tinkerformat.cpp:415:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 415 | if (b->GetHyb() == 2) // S=C | ^~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/tinkerformat.cpp:416:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 416 | countNeighborC++; break; | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 64%] Linking CXX shared module ../../lib64/unichemformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/unichemformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/unichemformat.so CMakeFiles/unichemformat.dir/unichemformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 64%] Built target unichemformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/viewmolformat.dir/build.make src/formats/CMakeFiles/viewmolformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/viewmolformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/viewmolformat.dir/build.make src/formats/CMakeFiles/viewmolformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 64%] Linking CXX shared module ../../lib64/tinkerformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/tinkerformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/tinkerformat.so CMakeFiles/tinkerformat.dir/tinkerformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 64%] Built target tinkerformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/wlnformat.dir/build.make src/formats/CMakeFiles/wlnformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/wlnformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/wlnformat.dir/build.make src/formats/CMakeFiles/wlnformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 64%] Building CXX object src/formats/CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dviewmolformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o -MF CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o.d -o CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/viewmolformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/viewmolformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Building CXX object src/formats/CMakeFiles/wlnformat.dir/wlnformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dwlnformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/wlnformat.dir/wlnformat.cpp.o -MF CMakeFiles/wlnformat.dir/wlnformat.cpp.o.d -o CMakeFiles/wlnformat.dir/wlnformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/wlnformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/wlnformat.cpp:18: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/wlnformat.cpp: In member function ‘virtual bool OpenBabel::WLNFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/wlnformat.cpp:138:17: warning: unused variable ‘title’ [-Wunused-variable] 138 | const char* title = pConv->GetTitle(); | ^~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Linking CXX shared module ../../lib64/viewmolformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/viewmolformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/viewmolformat.so CMakeFiles/viewmolformat.dir/viewmolformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Built target viewmolformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/xedformat.dir/build.make src/formats/CMakeFiles/xedformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/xedformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/xedformat.dir/build.make src/formats/CMakeFiles/xedformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Building CXX object src/formats/CMakeFiles/xedformat.dir/xedformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxedformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xedformat.dir/xedformat.cpp.o -MF CMakeFiles/xedformat.dir/xedformat.cpp.o.d -o CMakeFiles/xedformat.dir/xedformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/xedformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/xedformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Linking CXX shared module ../../lib64/xedformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/xedformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/xedformat.so CMakeFiles/xedformat.dir/xedformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Built target xedformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/xyzformat.dir/build.make src/formats/CMakeFiles/xyzformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/xyzformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/xyzformat.dir/build.make src/formats/CMakeFiles/xyzformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 65%] Building CXX object src/formats/CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dwlnformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o -MF CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o.d -o CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/wln-nextmove.cpp make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Building CXX object src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dxyzformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/xyzformat.dir/xyzformat.cpp.o -MF CMakeFiles/xyzformat.dir/xyzformat.cpp.o.d -o CMakeFiles/xyzformat.dir/xyzformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/xyzformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/xyzformat.cpp:17: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Linking CXX shared module ../../lib64/xyzformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/xyzformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/xyzformat.so CMakeFiles/xyzformat.dir/xyzformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Built target xyzformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/yasaraformat.dir/build.make src/formats/CMakeFiles/yasaraformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/yasaraformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/yasaraformat.dir/build.make src/formats/CMakeFiles/yasaraformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Linking CXX shared module ../../lib64/wlnformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/wlnformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/wlnformat.so CMakeFiles/wlnformat.dir/wlnformat.cpp.o "CMakeFiles/wlnformat.dir/wln-nextmove.cpp.o" -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Built target wlnformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/rxnformat.dir/build.make src/formats/CMakeFiles/rxnformat.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/rxnformat.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/rxnformat.dir/build.make src/formats/CMakeFiles/rxnformat.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Building CXX object src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Dyasaraformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -MF CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o.d -o CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obmolecformat.h:36, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:34: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp: In function ‘OpenBabel::mobatom* OpenBabel::mob_next(mobatom*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:45:33: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing] 45 | #define mem_inc(POINTER,INC) (*((char**)&(POINTER))+=(INC)) | ~^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:227:3: note: in expansion of macro ‘mem_inc’ 227 | { mem_inc(atom,mob_atomsize(atom)); | ^~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp: In member function ‘virtual bool OpenBabel::YOBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:374:21: warning: variable ‘reslen’ set but not used [-Wunused-but-set-variable] 374 | int /*samenames,*/reslen,charged; | ^~~~~~ In file included from /usr/include/string.h:548, from /usr/include/c++/13/cstring:42, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:29: In function ‘memcpy’, inlined from ‘OpenBabel::YOBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:440:82: /usr/include/bits/string_fortified.h:29:33: warning: ‘memcpy’ accessing 4 bytes at offsets 0 and 1 overlaps 3 bytes at offset 1 [-Wrestrict] 29 | return __builtin___memcpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 30 | __glibc_objsize0 (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp: In function ‘OpenBabel::mob_getid(OpenBabel::atomid*, OpenBabel::mobatom*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:245:26: warning: array subscript 4 is above array bounds of ‘int32[4]’ [-Warray-bounds=] 245 | { inscodealtloc=int32le(atom->link[idpos++]); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:192:9: note: while referencing ‘link’ 192 | int32 link[4]; }; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:253:60: warning: array subscript 4 is above array bounds of ‘int32[4]’ [-Warray-bounds=] 253 | if (flags&MOB_SEGMENTFLAG) id->segment=atom->link[idpos++]; | ~~~~~~~~~~~~~~~~~~^ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:192:9: note: while referencing ‘link’ 192 | int32 link[4]; }; | ^~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp: In member function ‘OpenBabel::YOBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:572:36: warning: ‘__snprintf_chk’ output truncated before the last format character [-Wformat-truncation=] 572 | snprintf(&buffer[12], 4, "%4d",res->GetNum()); } | ^ In file included from /usr/include/stdio.h:980, from /usr/include/c++/13/cstdio:42, from /usr/include/c++/13/ext/string_conversions.h:45, from /usr/include/c++/13/bits/basic_string.h:4109, from /usr/include/c++/13/string:54: In function ‘snprintf’, inlined from ‘OpenBabel::YOBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/yasaraformat.cpp:572:15: /usr/include/bits/stdio2.h:54:35: note: ‘__snprintf_chk’ output between 5 and 12 bytes into a destination of size 4 54 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 55 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 56 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Linking CXX shared module ../../lib64/yasaraformat.so cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/cmake -E cmake_link_script CMakeFiles/yasaraformat.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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -Wl,--enable-new-dtags -Wl,--enable-new-dtags -Wl,--fatal-warnings -Wl,--no-undefined -lc -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -shared -o ../../lib64/yasaraformat.so CMakeFiles/yasaraformat.dir/yasaraformat.cpp.o -lm -ldl -lz -lcairo -linchi -lm ../../lib64/libopenbabel.so.7.0.0 -lm -ldl -lz make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' make[1]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Built target yasaraformat make[1]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chemdrawcdx.dir/build.make src/formats/CMakeFiles/chemdrawcdx.dir/depend make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/openbabel-openbabel-3-1-1 /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats/CMakeFiles/chemdrawcdx.dir/DependInfo.cmake "--color=" make[2]: Leaving directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' /usr/bin/make -f src/formats/CMakeFiles/chemdrawcdx.dir/build.make src/formats/CMakeFiles/chemdrawcdx.dir/build make[2]: Entering directory '/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu' [ 66%] Building CXX object src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o cd /builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/src/formats && /usr/bin/g++ -DBUILD_LINK_AS_DLL -DHAVE_EIGEN -DHAVE_EIGEN3 -DHAVE_LIBZ -DHAVE_RADPIJSON -DHAVE_SHARED_POINTER -DHAVE_WXWIDGETS -DUSING_DYNAMIC_LIBS -DWXUSINGDLL -D_FILE_OFFSET_BITS=64 -D__WXGTK__ -Drxnformat_EXPORTS -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/x86_64-redhat-linux-gnu/include -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/data -I/builddir/build/BUILD/openbabel-openbabel-3-1-1/include -I/usr/include/eigen3 -I/usr/include/cairo -I/usr/include/inchi -I/usr/include/libxml2 -isystem /usr/lib64/wx/include/gtk3-unicode-3.2 -isystem /usr/include/wx-3.2 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -pthread -DNDEBUG -O3 -DNDEBUG -std=gnu++11 -fPIC -MD -MT src/formats/CMakeFiles/rxnformat.dir/rxnformat.cpp.o -MF CMakeFiles/rxnformat.dir/rxnformat.cpp.o.d -o CMakeFiles/rxnformat.dir/rxnformat.cpp.o -c /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/rxnformat.cpp In file included from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/format.h:22, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/obconversion.h:37, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/rxnformat.cpp:26: /builddir/build/BUILD/openbabel-openbabel-3-1-1/include/openbabel/plugin.h:41:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 41 | struct OBERROR CharPtrLess : public std::binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/rxnformat.cpp:18: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/rxnformat.cpp: In member function ‘virtual bool OpenBabel::RXNFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: /builddir/build/BUILD/openbabel-openbabel-3-1-1/src/formats/rxnformat.cpp:196:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 196 | for (int i=0; i