Warning: Permanently added '54.144.199.235' (ECDSA) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 2181625 --chroot epel-8-x86_64 --detached Version: 0.50 Task: {'background': False, 'bootstrap': 'off', 'build_id': 2181625, 'buildroot_pkgs': [], 'chroot': 'epel-8-x86_64', 'enable_net': True, 'fedora_review': False, 'git_hash': 'f9837c8d1d84fdc9ee7bbf28d83329abc2989b93', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/orrisroot/pymol/pymol.git', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'pymol', 'package_version': '2.4.0-4.1.el8.ors', 'project_dirname': 'pymol', 'project_name': 'pymol', 'project_owner': 'orrisroot', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/orrisroot/pymol/epel-8-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}, {'baseurl': 'https://download.copr.fedorainfracloud.org/results/orrisroot/el8-devel/epel-8-x86_64/', 'id': 'copr_orrisroot_el8_devel_epel_8_basearch', 'name': 'Additional repo copr_orrisroot_el8_devel_epel_8_basearch'}], 'sandbox': 'orrisroot/pymol--orrisroot', 'source_json': {}, 'source_type': None, 'submitter': 'orrisroot', 'task_id': '2181625-epel-8-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/orrisroot/pymol/pymol.git /var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol --depth 500 --no-single-branch cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/orrisroot/pymol/pymol.git', '/var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol', '--depth', '500', '--no-single-branch'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol'... Running: git checkout f9837c8d1d84fdc9ee7bbf28d83329abc2989b93 cmd: ['git', 'checkout', 'f9837c8d1d84fdc9ee7bbf28d83329abc2989b93'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol rc: 0 stdout: stderr: Note: switching to 'f9837c8d1d84fdc9ee7bbf28d83329abc2989b93'. 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 f9837c8 automatic import of pymol Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol rc: 0 stdout: /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated 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 pymol-open-source-2.4.0.tar.gz INFO: Calling: curl -H Pragma: -o pymol-open-source-2.4.0.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/orrisroot/pymol/pymol/pymol-open-source-2.4.0.tar.gz/md5/5049bd9388279dbd673b17651cea357f/pymol-open-source-2.4.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 10.0M 100 10.0M 0 0 159M 0 --:--:-- --:--:-- --:--:-- 159M INFO: Reading stdout from command: md5sum pymol-open-source-2.4.0.tar.gz INFO: Downloading pymol.png INFO: Calling: curl -H Pragma: -o pymol.png --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/orrisroot/pymol/pymol/pymol.png/md5/3bbd85dbd40f588f505ad988b6df2933/pymol.png % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 19466 100 19466 0 0 1267k 0 --:--:-- --:--:-- --:--:-- 1267k INFO: Reading stdout from command: md5sum pymol.png Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol/pymol.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1620741551.244243 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 2.10 starting (python version = 3.9.1, NVR = mock-2.10-1.fc33)... 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-05l5186u/pymol/pymol.spec) Config(epel-8-x86_64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/epel-8-x86_64-1620741551.244243/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Mock Version: 2.10 INFO: Mock Version: 2.10 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Copr repository 24 kB/s | 3.6 kB 00:00 Copr repository 289 kB/s | 28 kB 00:00 Additional repo copr_orrisroot_el8_devel_epel_8 50 kB/s | 3.6 kB 00:00 CentOS-8 - Base 18 kB/s | 3.9 kB 00:00 CentOS-8 - AppStream 57 kB/s | 4.3 kB 00:00 CentOS-8 - PowerTools 62 kB/s | 4.3 kB 00:00 CentOS-8 - Extras 21 kB/s | 1.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 3.8 kB/s | 4.7 kB 00:01 Dependencies resolved. ======================================================================================================================= Package Arch Version Repository Size ======================================================================================================================= Installing: bash  x86_64 4.4.19-12.el8 baseos 1.5 M bzip2  x86_64 1.0.6-26.el8 baseos 60 k centos-linux-release  noarch 8.3-1.2011.el8 baseos 22 k coreutils  x86_64 8.30-8.el8 baseos 1.2 M cpio  x86_64 2.12-8.el8 baseos 265 k diffutils  x86_64 3.6-6.el8 baseos 358 k epel-release  noarch 8-10.el8 epel 22 k epel-rpm-macros  noarch 8-19 epel 23 k fedpkg-minimal  noarch 1.2.0-1.el8 epel 19 k findutils  x86_64 1:4.6.0-20.el8 baseos 528 k gawk  x86_64 4.2.1-1.el8 baseos 1.1 M gcc  x86_64 8.3.1-5.1.el8 appstream 23 M gcc-c++  x86_64 8.3.1-5.1.el8 appstream 12 M grep  x86_64 3.1-6.el8 baseos 274 k gzip  x86_64 1.9-9.el8 baseos 167 k info  x86_64 6.5-6.el8 baseos 198 k make  x86_64 1:4.2.1-10.el8 baseos 498 k patch  x86_64 2.7.6-11.el8 baseos 138 k redhat-rpm-config  noarch 123-1.el8 appstream 84 k rpm-build  x86_64 4.14.3-4.el8 appstream 172 k sed  x86_64 4.5-2.el8 baseos 298 k shadow-utils  x86_64 2:4.6-11.el8 baseos 1.2 M tar  x86_64 2:1.30-5.el8 baseos 838 k unzip  x86_64 6.0-43.el8 baseos 195 k util-linux  x86_64 2.32.1-24.el8 baseos 2.5 M which  x86_64 2.21-12.el8 baseos 49 k xz  x86_64 5.2.4-3.el8 baseos 153 k Installing dependencies: acl  x86_64 2.2.53-1.el8 baseos 81 k annobin  x86_64 9.23-1.el8 appstream 104 k audit-libs  x86_64 3.0-0.17.20191104git1c2f876.el8 baseos 116 k basesystem  noarch 11-5.el8 baseos 10 k binutils  x86_64 2.30-79.el8 baseos 5.7 M brotli  x86_64 1.0.6-2.el8 baseos 322 k bzip2-libs  x86_64 1.0.6-26.el8 baseos 48 k ca-certificates  noarch 2020.2.41-80.0.el8_2 baseos 391 k centos-gpg-keys  noarch 1:8-2.el8 baseos 12 k centos-linux-repos  noarch 8-2.el8 baseos 20 k chkconfig  x86_64 1.13-2.el8 baseos 194 k coreutils-common  x86_64 8.30-8.el8 baseos 2.0 M cpp  x86_64 8.3.1-5.1.el8 appstream 10 M cracklib  x86_64 2.9.6-15.el8 baseos 93 k crypto-policies  noarch 20210209-1.gitbfb6bed.el8_3 baseos 62 k cryptsetup-libs  x86_64 2.3.3-2.el8 baseos 470 k curl  x86_64 7.61.1-14.el8_3.1 baseos 353 k cyrus-sasl-lib  x86_64 2.1.27-5.el8 baseos 123 k dbus  x86_64 1:1.12.8-12.el8_3 baseos 41 k dbus-common  noarch 1:1.12.8-12.el8_3 baseos 45 k dbus-daemon  x86_64 1:1.12.8-12.el8_3 baseos 240 k dbus-libs  x86_64 1:1.12.8-12.el8_3 baseos 183 k dbus-tools  x86_64 1:1.12.8-12.el8_3 baseos 85 k device-mapper  x86_64 8:1.02.171-5.el8 baseos 373 k device-mapper-libs  x86_64 8:1.02.171-5.el8 baseos 406 k dracut  x86_64 049-95.git20200804.el8_3.4 baseos 368 k dwz  x86_64 0.12-9.el8 appstream 109 k efi-srpm-macros  noarch 3-2.el8 appstream 22 k elfutils  x86_64 0.180-1.el8 baseos 542 k elfutils-default-yama-scope  noarch 0.180-1.el8 baseos 48 k elfutils-libelf  x86_64 0.180-1.el8 baseos 215 k elfutils-libs  x86_64 0.180-1.el8 baseos 293 k expat  x86_64 2.2.5-4.el8 baseos 111 k file  x86_64 5.33-16.el8_3.1 baseos 77 k file-libs  x86_64 5.33-16.el8_3.1 baseos 543 k filesystem  x86_64 3.8-3.el8 baseos 1.1 M fpc-srpm-macros  noarch 1.3-1.el8 epel 8.2 k gc  x86_64 7.6.4-3.el8 appstream 109 k gdb-headless  x86_64 8.2-12.el8 appstream 3.7 M gdbm  x86_64 1:1.18-1.el8 baseos 130 k gdbm-libs  x86_64 1:1.18-1.el8 baseos 60 k gettext  x86_64 0.19.8.1-17.el8 baseos 1.1 M gettext-libs  x86_64 0.19.8.1-17.el8 baseos 314 k ghc-srpm-macros  noarch 1.4.2-7.el8 appstream 9.3 k glib2  x86_64 2.56.4-8.el8 baseos 2.5 M glibc  x86_64 2.28-127.el8 baseos 3.6 M glibc-all-langpacks  x86_64 2.28-127.el8 baseos 25 M glibc-common  x86_64 2.28-127.el8 baseos 1.3 M glibc-devel  x86_64 2.28-127.el8 baseos 1.0 M glibc-headers  x86_64 2.28-127.el8 baseos 475 k gmp  x86_64 1:6.1.2-10.el8 baseos 322 k gnupg2  x86_64 2.2.20-2.el8 baseos 2.4 M gnutls  x86_64 3.6.14-8.el8_3 baseos 1.0 M go-srpm-macros  noarch 2-16.el8 appstream 14 k grub2-common  noarch 1:2.02-90.el8_3.1 baseos 885 k grub2-tools  x86_64 1:2.02-90.el8_3.1 baseos 2.0 M grub2-tools-minimal  x86_64 1:2.02-90.el8_3.1 baseos 206 k guile  x86_64 5:2.0.14-7.el8 appstream 3.5 M ima-evm-utils  x86_64 1.1-5.el8 baseos 56 k iptables-libs  x86_64 1.8.4-15.el8_3.3 baseos 106 k isl  x86_64 0.16.1-6.el8 appstream 841 k json-c  x86_64 0.13.1-0.2.el8 baseos 40 k kbd-legacy  noarch 2.0.4-10.el8 baseos 481 k kbd-misc  noarch 2.0.4-10.el8 baseos 1.5 M kernel-headers  x86_64 4.18.0-240.22.1.el8_3 baseos 5.6 M keyutils-libs  x86_64 1.5.10-6.el8 baseos 34 k kmod  x86_64 25-16.el8 baseos 126 k kmod-libs  x86_64 25-16.el8 baseos 68 k krb5-libs  x86_64 1.18.2-5.el8 baseos 837 k libacl  x86_64 2.2.53-1.el8 baseos 35 k libarchive  x86_64 3.3.3-1.el8 copr_orrisroot_el8_devel_epel_8_basearch 359 k libassuan  x86_64 2.5.1-3.el8 baseos 83 k libatomic_ops  x86_64 7.6.2-3.el8 appstream 38 k libattr  x86_64 2.4.48-3.el8 baseos 27 k libbabeltrace  x86_64 1.5.4-3.el8 baseos 200 k libblkid  x86_64 2.32.1-24.el8 baseos 216 k libcap  x86_64 2.26-4.el8 baseos 60 k libcap-ng  x86_64 0.7.9-5.el8 baseos 33 k libcom_err  x86_64 1.45.6-1.el8 baseos 49 k libcroco  x86_64 0.6.12-4.el8_2.1 baseos 113 k libcurl  x86_64 7.61.1-14.el8_3.1 baseos 299 k libdb  x86_64 5.3.28-39.el8 baseos 750 k libdb-utils  x86_64 5.3.28-39.el8 baseos 149 k libfdisk  x86_64 2.32.1-24.el8 baseos 249 k libffi  x86_64 3.1-22.el8 baseos 37 k libgcc  x86_64 8.3.1-5.1.el8 baseos 78 k libgcrypt  x86_64 1.8.5-4.el8 baseos 463 k libgomp  x86_64 8.3.1-5.1.el8 baseos 204 k libgpg-error  x86_64 1.31-1.el8 baseos 242 k libidn2  x86_64 2.2.0-1.el8 baseos 94 k libipt  x86_64 1.6.1-8.el8 appstream 50 k libkcapi  x86_64 1.2.0-2.el8 baseos 48 k libkcapi-hmaccalc  x86_64 1.2.0-2.el8 baseos 31 k libksba  x86_64 1.3.5-7.el8 baseos 135 k libmetalink  x86_64 0.1.3-7.el8 baseos 32 k libmount  x86_64 2.32.1-24.el8 baseos 232 k libmpc  x86_64 1.0.2-9.el8 appstream 59 k libnghttp2  x86_64 1.33.0-3.el8_2.1 baseos 77 k libnsl2  x86_64 1.2.0-2.20180605git4a062cf.el8 baseos 58 k libpcap  x86_64 14:1.9.1-4.el8 baseos 166 k libpkgconf  x86_64 1.4.2-1.el8 baseos 35 k libpsl  x86_64 0.20.2-6.el8 baseos 61 k libpwquality  x86_64 1.4.0-9.el8 baseos 103 k libseccomp  x86_64 2.4.3-1.el8 baseos 67 k libsecret  x86_64 0.18.6-1.el8 baseos 163 k libselinux  x86_64 2.9-4.el8_3 baseos 165 k libsemanage  x86_64 2.9-3.el8 baseos 165 k libsepol  x86_64 2.9-1.el8 baseos 340 k libsigsegv  x86_64 2.11-5.el8 baseos 30 k libsmartcols  x86_64 2.32.1-24.el8 baseos 175 k libssh  x86_64 0.9.4-2.el8 baseos 215 k libssh-config  noarch 0.9.4-2.el8 baseos 18 k libstdc++  x86_64 8.3.1-5.1.el8 baseos 451 k libstdc++-devel  x86_64 8.3.1-5.1.el8 appstream 2.0 M libtasn1  x86_64 4.13-3.el8 baseos 76 k libtirpc  x86_64 1.1.4-4.el8 baseos 113 k libtool-ltdl  x86_64 2.4.6-25.el8 baseos 58 k libunistring  x86_64 0.9.9-3.el8 baseos 422 k libusbx  x86_64 1.0.23-4.el8 baseos 74 k libutempter  x86_64 1.1.6-14.el8 baseos 32 k libuuid  x86_64 2.32.1-24.el8 baseos 95 k libverto  x86_64 0.3.0-5.el8 baseos 24 k libxcrypt  x86_64 4.1.1-4.el8 baseos 73 k libxcrypt-devel  x86_64 4.1.1-4.el8 baseos 25 k libxml2  x86_64 2.9.7-8.el8 baseos 696 k libzstd  x86_64 1.4.4-1.el8 baseos 266 k lua-libs  x86_64 5.3.4-11.el8 baseos 118 k lua-srpm-macros  noarch 1-3.el8 epel 8.1 k lz4-libs  x86_64 1.8.3-2.el8 baseos 66 k mpfr  x86_64 3.1.6-1.el8 baseos 221 k ncurses  x86_64 6.1-7.20180224.el8 baseos 387 k ncurses-base  noarch 6.1-7.20180224.el8 baseos 81 k ncurses-libs  x86_64 6.1-7.20180224.el8 baseos 335 k nettle  x86_64 3.4.1-4.el8_3 baseos 301 k npth  x86_64 1.5-4.el8 baseos 26 k ocaml-srpm-macros  noarch 5-4.el8 appstream 9.4 k openblas-srpm-macros  noarch 2-2.el8 appstream 7.9 k openldap  x86_64 2.4.46-15.el8 baseos 351 k openssl  x86_64 1:1.1.1g-15.el8_3 baseos 707 k openssl-libs  x86_64 1:1.1.1g-15.el8_3 baseos 1.5 M os-prober  x86_64 1.74-6.el8 baseos 51 k p11-kit  x86_64 0.23.14-5.el8_0 baseos 272 k p11-kit-trust  x86_64 0.23.14-5.el8_0 baseos 139 k pam  x86_64 1.3.1-11.el8 baseos 738 k pcre  x86_64 8.42-4.el8 baseos 208 k pcre2  x86_64 10.32-2.el8 baseos 246 k perl-srpm-macros  noarch 1-25.el8 appstream 11 k pkgconf  x86_64 1.4.2-1.el8 baseos 38 k pkgconf-m4  noarch 1.4.2-1.el8 baseos 17 k pkgconf-pkg-config  x86_64 1.4.2-1.el8 baseos 15 k platform-python  x86_64 3.6.8-31.el8 baseos 83 k platform-python-setuptools  noarch 39.2.0-6.el8 baseos 632 k popt  x86_64 1.16-14.el8 baseos 61 k procps-ng  x86_64 3.3.15-3.el8_3.1 baseos 328 k publicsuffix-list-dafsa  noarch 20180723-1.el8 baseos 56 k python-rpm-macros  noarch 3-39.el8 appstream 14 k python-srpm-macros  noarch 3-39.el8 appstream 14 k python2-rpm-macros  noarch 3-38.module_el8.3.0+478+7570e00c appstream 13 k python3-libs  x86_64 3.6.8-31.el8 baseos 7.8 M python3-pip-wheel  noarch 9.0.3-18.el8 baseos 1.0 M python3-rpm-macros  noarch 3-39.el8 appstream 13 k python3-setuptools-wheel  noarch 39.2.0-6.el8 baseos 289 k qt5-srpm-macros  noarch 5.12.5-3.el8 appstream 10 k readline  x86_64 7.0-10.el8 baseos 199 k rpm  x86_64 4.14.3-4.el8 baseos 541 k rpm-build-libs  x86_64 4.14.3-4.el8 baseos 154 k rpm-libs  x86_64 4.14.3-4.el8 baseos 338 k rust-srpm-macros  noarch 5-2.el8 appstream 9.2 k setup  noarch 2.12.2-6.el8 baseos 181 k sqlite-libs  x86_64 3.26.0-11.el8 baseos 580 k systemd-libs  x86_64 239-41.el8_3.2 baseos 1.1 M systemd-pam  x86_64 239-41.el8_3.2 baseos 456 k systemd-udev  x86_64 239-41.el8_3.2 baseos 1.3 M trousers-lib  x86_64 0.3.14-4.el8 baseos 169 k tzdata  noarch 2021a-1.el8 baseos 473 k xkeyboard-config  noarch 2.28-1.el8 appstream 782 k xz-libs  x86_64 5.2.4-3.el8 baseos 94 k zip  x86_64 3.0-23.el8 baseos 270 k zlib  x86_64 1.2.11-16.2.el8_3 baseos 102 k zstd  x86_64 1.4.4-1.el8 appstream 393 k Installing weak dependencies: cracklib-dicts  x86_64 2.9.6-15.el8 baseos 4.0 M crypto-policies-scripts  noarch 20210209-1.gitbfb6bed.el8_3 baseos 67 k elfutils-debuginfod-client  x86_64 0.180-1.el8 baseos 64 k gnupg2-smime  x86_64 2.2.20-2.el8 baseos 283 k grubby  x86_64 8.40-41.el8 baseos 49 k hardlink  x86_64 1:1.3-6.el8 baseos 29 k kbd  x86_64 2.0.4-10.el8 baseos 390 k kpartx  x86_64 0.8.4-5.el8 baseos 108 k libxkbcommon  x86_64 0.9.1-1.el8 appstream 116 k memstrack  x86_64 0.1.11-1.el8 baseos 48 k openssl-pkcs11  x86_64 0.4.10-2.el8 baseos 66 k pigz  x86_64 2.4-4.el8 baseos 79 k pinentry  x86_64 1.1.0-2.el8 appstream 100 k platform-python-pip  noarch 9.0.3-18.el8 baseos 1.7 M shared-mime-info  x86_64 1.9-3.el8 baseos 329 k systemd  x86_64 239-41.el8_3.2 baseos 3.5 M trousers  x86_64 0.3.14-4.el8 baseos 153 k Enabling module streams: python27 2.7 Transaction Summary ======================================================================================================================= Install 224 Packages Total size: 177 M Installed size: 886 M Downloading Packages: [SKIPPED] libarchive-3.3.3-1.el8.x86_64.rpm: Already downloaded [SKIPPED] acl-2.2.53-1.el8.x86_64.rpm: Already downloaded [SKIPPED] audit-libs-3.0-0.17.20191104git1c2f876.el8.x86_64.rpm: Already downloaded [SKIPPED] basesystem-11-5.el8.noarch.rpm: Already downloaded [SKIPPED] bash-4.4.19-12.el8.x86_64.rpm: Already downloaded [SKIPPED] binutils-2.30-79.el8.x86_64.rpm: Already downloaded [SKIPPED] brotli-1.0.6-2.el8.x86_64.rpm: Already downloaded [SKIPPED] bzip2-1.0.6-26.el8.x86_64.rpm: Already downloaded [SKIPPED] bzip2-libs-1.0.6-26.el8.x86_64.rpm: Already downloaded [SKIPPED] ca-certificates-2020.2.41-80.0.el8_2.noarch.rpm: Already downloaded [SKIPPED] centos-gpg-keys-8-2.el8.noarch.rpm: Already downloaded [SKIPPED] centos-linux-release-8.3-1.2011.el8.noarch.rpm: Already downloaded 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/var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/cache/dnf/baseos-586be817612a3cb1/packages/acl-2.2.53-1.el8.x86_64.rpm: Header V3 RSA/SHA256 Signature, key ID 8483c65d: NOKEY CentOS-8 - Base 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x8483C65D: Userid : "CentOS (CentOS Official Signing Key) " Fingerprint: 99DB 70FA E1D7 CE22 7FB6 4882 05B5 55B3 8483 C65D From : /usr/share/distribution-gpg-keys/centos/RPM-GPG-KEY-CentOS-Official Key imported successfully warning: /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/cache/dnf/epel-59dc218ad097ee72/packages/epel-release-8-10.el8.noarch.rpm: Header V4 RSA/SHA256 Signature, key ID 2f86d6a1: NOKEY Extra Packages for Enterprise Linux 8 - x86_64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x2F86D6A1: Userid : "Fedora EPEL (8) " Fingerprint: 94E2 79EB 8D8F 25B2 1810 ADF1 21EA 45AB 2F86 D6A1 From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-8 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.8-3.el8.x86_64 1/1 Preparing : 1/1 Installing : libgcc-8.3.1-5.1.el8.x86_64 1/224 Running scriptlet: libgcc-8.3.1-5.1.el8.x86_64 1/224 Installing : python-srpm-macros-3-39.el8.noarch 2/224 Installing : python3-setuptools-wheel-39.2.0-6.el8.noarch 3/224 Installing : python3-pip-wheel-9.0.3-18.el8.noarch 4/224 Installing : python-rpm-macros-3-39.el8.noarch 5/224 Installing : fpc-srpm-macros-1.3-1.el8.noarch 6/224 Installing : xkeyboard-config-2.28-1.el8.noarch 7/224 Installing : rust-srpm-macros-5-2.el8.noarch 8/224 Installing : qt5-srpm-macros-5.12.5-3.el8.noarch 9/224 Installing : python3-rpm-macros-3-39.el8.noarch 10/224 Installing : python2-rpm-macros-3-38.module_el8.3.0+478+7570e 11/224 Installing : perl-srpm-macros-1-25.el8.noarch 12/224 Installing : openblas-srpm-macros-2-2.el8.noarch 13/224 Installing : ocaml-srpm-macros-5-4.el8.noarch 14/224 Installing : go-srpm-macros-2-16.el8.noarch 15/224 Installing : 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207/224 Running scriptlet: pinentry-1.1.0-2.el8.x86_64 207/224 Installing : ima-evm-utils-1.1-5.el8.x86_64 208/224 Installing : libusbx-1.0.23-4.el8.x86_64 209/224 Installing : gnupg2-smime-2.2.20-2.el8.x86_64 210/224 Installing : gnupg2-2.2.20-2.el8.x86_64 211/224 Installing : rpm-build-libs-4.14.3-4.el8.x86_64 212/224 Running scriptlet: rpm-build-libs-4.14.3-4.el8.x86_64 212/224 Installing : guile-5:2.0.14-7.el8.x86_64 213/224 Running scriptlet: guile-5:2.0.14-7.el8.x86_64 213/224 Installing : gdb-headless-8.2-12.el8.x86_64 214/224 Installing : efi-srpm-macros-3-2.el8.noarch 215/224 Installing : redhat-rpm-config-123-1.el8.noarch 216/224 Installing : lua-srpm-macros-1-3.el8.noarch 217/224 Installing : elfutils-0.180-1.el8.x86_64 218/224 Installing : rpm-build-4.14.3-4.el8.x86_64 219/224 Installing : epel-rpm-macros-8-19.noarch 220/224 Installing : gcc-c++-8.3.1-5.1.el8.x86_64 221/224 Installing : fedpkg-minimal-1.2.0-1.el8.noarch 222/224 Installing : make-1:4.2.1-10.el8.x86_64 223/224 Running scriptlet: make-1:4.2.1-10.el8.x86_64 223/224 Installing : epel-release-8-10.el8.noarch 224/224 Running scriptlet: filesystem-3.8-3.el8.x86_64 224/224 Running scriptlet: glibc-all-langpacks-2.28-127.el8.x86_64 224/224 Running scriptlet: crypto-policies-scripts-20210209-1.gitbfb6bed.el 224/224 Running scriptlet: ca-certificates-2020.2.41-80.0.el8_2.noarch 224/224 Running scriptlet: guile-5:2.0.14-7.el8.x86_64 224/224 Running scriptlet: epel-release-8-10.el8.noarch 224/224 Verifying : libarchive-3.3.3-1.el8.x86_64 1/224 Verifying : acl-2.2.53-1.el8.x86_64 2/224 Verifying : audit-libs-3.0-0.17.20191104git1c2f876.el8.x86_6 3/224 Verifying : basesystem-11-5.el8.noarch 4/224 Verifying : bash-4.4.19-12.el8.x86_64 5/224 Verifying : binutils-2.30-79.el8.x86_64 6/224 Verifying : brotli-1.0.6-2.el8.x86_64 7/224 Verifying : bzip2-1.0.6-26.el8.x86_64 8/224 Verifying : bzip2-libs-1.0.6-26.el8.x86_64 9/224 Verifying : ca-certificates-2020.2.41-80.0.el8_2.noarch 10/224 Verifying : centos-gpg-keys-1:8-2.el8.noarch 11/224 Verifying : centos-linux-release-8.3-1.2011.el8.noarch 12/224 Verifying : centos-linux-repos-8-2.el8.noarch 13/224 Verifying : chkconfig-1.13-2.el8.x86_64 14/224 Verifying : coreutils-8.30-8.el8.x86_64 15/224 Verifying : coreutils-common-8.30-8.el8.x86_64 16/224 Verifying : cpio-2.12-8.el8.x86_64 17/224 Verifying : cracklib-2.9.6-15.el8.x86_64 18/224 Verifying : cracklib-dicts-2.9.6-15.el8.x86_64 19/224 Verifying : crypto-policies-20210209-1.gitbfb6bed.el8_3.noar 20/224 Verifying : crypto-policies-scripts-20210209-1.gitbfb6bed.el 21/224 Verifying : cryptsetup-libs-2.3.3-2.el8.x86_64 22/224 Verifying : curl-7.61.1-14.el8_3.1.x86_64 23/224 Verifying : cyrus-sasl-lib-2.1.27-5.el8.x86_64 24/224 Verifying : dbus-1:1.12.8-12.el8_3.x86_64 25/224 Verifying : dbus-common-1:1.12.8-12.el8_3.noarch 26/224 Verifying : dbus-daemon-1:1.12.8-12.el8_3.x86_64 27/224 Verifying : dbus-libs-1:1.12.8-12.el8_3.x86_64 28/224 Verifying : dbus-tools-1:1.12.8-12.el8_3.x86_64 29/224 Verifying : device-mapper-8:1.02.171-5.el8.x86_64 30/224 Verifying : device-mapper-libs-8:1.02.171-5.el8.x86_64 31/224 Verifying : diffutils-3.6-6.el8.x86_64 32/224 Verifying : dracut-049-95.git20200804.el8_3.4.x86_64 33/224 Verifying : elfutils-0.180-1.el8.x86_64 34/224 Verifying : elfutils-debuginfod-client-0.180-1.el8.x86_64 35/224 Verifying : elfutils-default-yama-scope-0.180-1.el8.noarch 36/224 Verifying : elfutils-libelf-0.180-1.el8.x86_64 37/224 Verifying : elfutils-libs-0.180-1.el8.x86_64 38/224 Verifying : expat-2.2.5-4.el8.x86_64 39/224 Verifying : file-5.33-16.el8_3.1.x86_64 40/224 Verifying : file-libs-5.33-16.el8_3.1.x86_64 41/224 Verifying : filesystem-3.8-3.el8.x86_64 42/224 Verifying : findutils-1:4.6.0-20.el8.x86_64 43/224 Verifying : gawk-4.2.1-1.el8.x86_64 44/224 Verifying : gdbm-1:1.18-1.el8.x86_64 45/224 Verifying : gdbm-libs-1:1.18-1.el8.x86_64 46/224 Verifying : gettext-0.19.8.1-17.el8.x86_64 47/224 Verifying : gettext-libs-0.19.8.1-17.el8.x86_64 48/224 Verifying : glib2-2.56.4-8.el8.x86_64 49/224 Verifying : glibc-2.28-127.el8.x86_64 50/224 Verifying : glibc-all-langpacks-2.28-127.el8.x86_64 51/224 Verifying : glibc-common-2.28-127.el8.x86_64 52/224 Verifying : glibc-devel-2.28-127.el8.x86_64 53/224 Verifying : glibc-headers-2.28-127.el8.x86_64 54/224 Verifying : gmp-1:6.1.2-10.el8.x86_64 55/224 Verifying : gnupg2-2.2.20-2.el8.x86_64 56/224 Verifying : gnupg2-smime-2.2.20-2.el8.x86_64 57/224 Verifying : gnutls-3.6.14-8.el8_3.x86_64 58/224 Verifying : grep-3.1-6.el8.x86_64 59/224 Verifying : grub2-common-1:2.02-90.el8_3.1.noarch 60/224 Verifying : grub2-tools-1:2.02-90.el8_3.1.x86_64 61/224 Verifying : grub2-tools-minimal-1:2.02-90.el8_3.1.x86_64 62/224 Verifying : grubby-8.40-41.el8.x86_64 63/224 Verifying : gzip-1.9-9.el8.x86_64 64/224 Verifying : hardlink-1:1.3-6.el8.x86_64 65/224 Verifying : ima-evm-utils-1.1-5.el8.x86_64 66/224 Verifying : info-6.5-6.el8.x86_64 67/224 Verifying : iptables-libs-1.8.4-15.el8_3.3.x86_64 68/224 Verifying : json-c-0.13.1-0.2.el8.x86_64 69/224 Verifying : kbd-2.0.4-10.el8.x86_64 70/224 Verifying : kbd-legacy-2.0.4-10.el8.noarch 71/224 Verifying : kbd-misc-2.0.4-10.el8.noarch 72/224 Verifying : kernel-headers-4.18.0-240.22.1.el8_3.x86_64 73/224 Verifying : keyutils-libs-1.5.10-6.el8.x86_64 74/224 Verifying : kmod-25-16.el8.x86_64 75/224 Verifying : kmod-libs-25-16.el8.x86_64 76/224 Verifying : kpartx-0.8.4-5.el8.x86_64 77/224 Verifying : krb5-libs-1.18.2-5.el8.x86_64 78/224 Verifying : libacl-2.2.53-1.el8.x86_64 79/224 Verifying : libassuan-2.5.1-3.el8.x86_64 80/224 Verifying : libattr-2.4.48-3.el8.x86_64 81/224 Verifying : libbabeltrace-1.5.4-3.el8.x86_64 82/224 Verifying : libblkid-2.32.1-24.el8.x86_64 83/224 Verifying : libcap-2.26-4.el8.x86_64 84/224 Verifying : libcap-ng-0.7.9-5.el8.x86_64 85/224 Verifying : libcom_err-1.45.6-1.el8.x86_64 86/224 Verifying : libcroco-0.6.12-4.el8_2.1.x86_64 87/224 Verifying : libcurl-7.61.1-14.el8_3.1.x86_64 88/224 Verifying : libdb-5.3.28-39.el8.x86_64 89/224 Verifying : libdb-utils-5.3.28-39.el8.x86_64 90/224 Verifying : libfdisk-2.32.1-24.el8.x86_64 91/224 Verifying : libffi-3.1-22.el8.x86_64 92/224 Verifying : libgcc-8.3.1-5.1.el8.x86_64 93/224 Verifying : libgcrypt-1.8.5-4.el8.x86_64 94/224 Verifying : libgomp-8.3.1-5.1.el8.x86_64 95/224 Verifying : libgpg-error-1.31-1.el8.x86_64 96/224 Verifying : libidn2-2.2.0-1.el8.x86_64 97/224 Verifying : libkcapi-1.2.0-2.el8.x86_64 98/224 Verifying : libkcapi-hmaccalc-1.2.0-2.el8.x86_64 99/224 Verifying : libksba-1.3.5-7.el8.x86_64 100/224 Verifying : libmetalink-0.1.3-7.el8.x86_64 101/224 Verifying : libmount-2.32.1-24.el8.x86_64 102/224 Verifying : libnghttp2-1.33.0-3.el8_2.1.x86_64 103/224 Verifying : libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 104/224 Verifying : libpcap-14:1.9.1-4.el8.x86_64 105/224 Verifying : libpkgconf-1.4.2-1.el8.x86_64 106/224 Verifying : libpsl-0.20.2-6.el8.x86_64 107/224 Verifying : libpwquality-1.4.0-9.el8.x86_64 108/224 Verifying : libseccomp-2.4.3-1.el8.x86_64 109/224 Verifying : libsecret-0.18.6-1.el8.x86_64 110/224 Verifying : libselinux-2.9-4.el8_3.x86_64 111/224 Verifying : libsemanage-2.9-3.el8.x86_64 112/224 Verifying : libsepol-2.9-1.el8.x86_64 113/224 Verifying : libsigsegv-2.11-5.el8.x86_64 114/224 Verifying : libsmartcols-2.32.1-24.el8.x86_64 115/224 Verifying : libssh-0.9.4-2.el8.x86_64 116/224 Verifying : libssh-config-0.9.4-2.el8.noarch 117/224 Verifying : libstdc++-8.3.1-5.1.el8.x86_64 118/224 Verifying : libtasn1-4.13-3.el8.x86_64 119/224 Verifying : libtirpc-1.1.4-4.el8.x86_64 120/224 Verifying : libtool-ltdl-2.4.6-25.el8.x86_64 121/224 Verifying : libunistring-0.9.9-3.el8.x86_64 122/224 Verifying : libusbx-1.0.23-4.el8.x86_64 123/224 Verifying : libutempter-1.1.6-14.el8.x86_64 124/224 Verifying : libuuid-2.32.1-24.el8.x86_64 125/224 Verifying : libverto-0.3.0-5.el8.x86_64 126/224 Verifying : libxcrypt-4.1.1-4.el8.x86_64 127/224 Verifying : libxcrypt-devel-4.1.1-4.el8.x86_64 128/224 Verifying : libxml2-2.9.7-8.el8.x86_64 129/224 Verifying : libzstd-1.4.4-1.el8.x86_64 130/224 Verifying : lua-libs-5.3.4-11.el8.x86_64 131/224 Verifying : lz4-libs-1.8.3-2.el8.x86_64 132/224 Verifying : make-1:4.2.1-10.el8.x86_64 133/224 Verifying : memstrack-0.1.11-1.el8.x86_64 134/224 Verifying : mpfr-3.1.6-1.el8.x86_64 135/224 Verifying : ncurses-6.1-7.20180224.el8.x86_64 136/224 Verifying : ncurses-base-6.1-7.20180224.el8.noarch 137/224 Verifying : ncurses-libs-6.1-7.20180224.el8.x86_64 138/224 Verifying : nettle-3.4.1-4.el8_3.x86_64 139/224 Verifying : npth-1.5-4.el8.x86_64 140/224 Verifying : openldap-2.4.46-15.el8.x86_64 141/224 Verifying : openssl-1:1.1.1g-15.el8_3.x86_64 142/224 Verifying : openssl-libs-1:1.1.1g-15.el8_3.x86_64 143/224 Verifying : openssl-pkcs11-0.4.10-2.el8.x86_64 144/224 Verifying : os-prober-1.74-6.el8.x86_64 145/224 Verifying : p11-kit-0.23.14-5.el8_0.x86_64 146/224 Verifying : p11-kit-trust-0.23.14-5.el8_0.x86_64 147/224 Verifying : pam-1.3.1-11.el8.x86_64 148/224 Verifying : patch-2.7.6-11.el8.x86_64 149/224 Verifying : pcre-8.42-4.el8.x86_64 150/224 Verifying : pcre2-10.32-2.el8.x86_64 151/224 Verifying : pigz-2.4-4.el8.x86_64 152/224 Verifying : pkgconf-1.4.2-1.el8.x86_64 153/224 Verifying : pkgconf-m4-1.4.2-1.el8.noarch 154/224 Verifying : pkgconf-pkg-config-1.4.2-1.el8.x86_64 155/224 Verifying : platform-python-3.6.8-31.el8.x86_64 156/224 Verifying : platform-python-pip-9.0.3-18.el8.noarch 157/224 Verifying : platform-python-setuptools-39.2.0-6.el8.noarch 158/224 Verifying : popt-1.16-14.el8.x86_64 159/224 Verifying : procps-ng-3.3.15-3.el8_3.1.x86_64 160/224 Verifying : publicsuffix-list-dafsa-20180723-1.el8.noarch 161/224 Verifying : python3-libs-3.6.8-31.el8.x86_64 162/224 Verifying : python3-pip-wheel-9.0.3-18.el8.noarch 163/224 Verifying : python3-setuptools-wheel-39.2.0-6.el8.noarch 164/224 Verifying : readline-7.0-10.el8.x86_64 165/224 Verifying : rpm-4.14.3-4.el8.x86_64 166/224 Verifying : rpm-build-libs-4.14.3-4.el8.x86_64 167/224 Verifying : rpm-libs-4.14.3-4.el8.x86_64 168/224 Verifying : sed-4.5-2.el8.x86_64 169/224 Verifying : setup-2.12.2-6.el8.noarch 170/224 Verifying : shadow-utils-2:4.6-11.el8.x86_64 171/224 Verifying : shared-mime-info-1.9-3.el8.x86_64 172/224 Verifying : sqlite-libs-3.26.0-11.el8.x86_64 173/224 Verifying : systemd-239-41.el8_3.2.x86_64 174/224 Verifying : systemd-libs-239-41.el8_3.2.x86_64 175/224 Verifying : systemd-pam-239-41.el8_3.2.x86_64 176/224 Verifying : systemd-udev-239-41.el8_3.2.x86_64 177/224 Verifying : tar-2:1.30-5.el8.x86_64 178/224 Verifying : trousers-0.3.14-4.el8.x86_64 179/224 Verifying : trousers-lib-0.3.14-4.el8.x86_64 180/224 Verifying : tzdata-2021a-1.el8.noarch 181/224 Verifying : unzip-6.0-43.el8.x86_64 182/224 Verifying : util-linux-2.32.1-24.el8.x86_64 183/224 Verifying : which-2.21-12.el8.x86_64 184/224 Verifying : xz-5.2.4-3.el8.x86_64 185/224 Verifying : xz-libs-5.2.4-3.el8.x86_64 186/224 Verifying : zip-3.0-23.el8.x86_64 187/224 Verifying : zlib-1.2.11-16.2.el8_3.x86_64 188/224 Verifying : annobin-9.23-1.el8.x86_64 189/224 Verifying : cpp-8.3.1-5.1.el8.x86_64 190/224 Verifying : dwz-0.12-9.el8.x86_64 191/224 Verifying : efi-srpm-macros-3-2.el8.noarch 192/224 Verifying : gc-7.6.4-3.el8.x86_64 193/224 Verifying : gcc-8.3.1-5.1.el8.x86_64 194/224 Verifying : gcc-c++-8.3.1-5.1.el8.x86_64 195/224 Verifying : gdb-headless-8.2-12.el8.x86_64 196/224 Verifying : ghc-srpm-macros-1.4.2-7.el8.noarch 197/224 Verifying : go-srpm-macros-2-16.el8.noarch 198/224 Verifying : guile-5:2.0.14-7.el8.x86_64 199/224 Verifying : isl-0.16.1-6.el8.x86_64 200/224 Verifying : libatomic_ops-7.6.2-3.el8.x86_64 201/224 Verifying : libipt-1.6.1-8.el8.x86_64 202/224 Verifying : libmpc-1.0.2-9.el8.x86_64 203/224 Verifying : libstdc++-devel-8.3.1-5.1.el8.x86_64 204/224 Verifying : libxkbcommon-0.9.1-1.el8.x86_64 205/224 Verifying : ocaml-srpm-macros-5-4.el8.noarch 206/224 Verifying : openblas-srpm-macros-2-2.el8.noarch 207/224 Verifying : perl-srpm-macros-1-25.el8.noarch 208/224 Verifying : pinentry-1.1.0-2.el8.x86_64 209/224 Verifying : python-rpm-macros-3-39.el8.noarch 210/224 Verifying : python-srpm-macros-3-39.el8.noarch 211/224 Verifying : python2-rpm-macros-3-38.module_el8.3.0+478+7570e 212/224 Verifying : python3-rpm-macros-3-39.el8.noarch 213/224 Verifying : qt5-srpm-macros-5.12.5-3.el8.noarch 214/224 Verifying : redhat-rpm-config-123-1.el8.noarch 215/224 Verifying : rpm-build-4.14.3-4.el8.x86_64 216/224 Verifying : rust-srpm-macros-5-2.el8.noarch 217/224 Verifying : xkeyboard-config-2.28-1.el8.noarch 218/224 Verifying : zstd-1.4.4-1.el8.x86_64 219/224 Verifying : epel-release-8-10.el8.noarch 220/224 Verifying : epel-rpm-macros-8-19.noarch 221/224 Verifying : fedpkg-minimal-1.2.0-1.el8.noarch 222/224 Verifying : fpc-srpm-macros-1.3-1.el8.noarch 223/224 Verifying : lua-srpm-macros-1-3.el8.noarch 224/224 Installed: acl-2.2.53-1.el8.x86_64 annobin-9.23-1.el8.x86_64 audit-libs-3.0-0.17.20191104git1c2f876.el8.x86_64 basesystem-11-5.el8.noarch bash-4.4.19-12.el8.x86_64 binutils-2.30-79.el8.x86_64 brotli-1.0.6-2.el8.x86_64 bzip2-1.0.6-26.el8.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 ca-certificates-2020.2.41-80.0.el8_2.noarch centos-gpg-keys-1:8-2.el8.noarch centos-linux-release-8.3-1.2011.el8.noarch centos-linux-repos-8-2.el8.noarch chkconfig-1.13-2.el8.x86_64 coreutils-8.30-8.el8.x86_64 coreutils-common-8.30-8.el8.x86_64 cpio-2.12-8.el8.x86_64 cpp-8.3.1-5.1.el8.x86_64 cracklib-2.9.6-15.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 crypto-policies-20210209-1.gitbfb6bed.el8_3.noarch crypto-policies-scripts-20210209-1.gitbfb6bed.el8_3.noarch cryptsetup-libs-2.3.3-2.el8.x86_64 curl-7.61.1-14.el8_3.1.x86_64 cyrus-sasl-lib-2.1.27-5.el8.x86_64 dbus-1:1.12.8-12.el8_3.x86_64 dbus-common-1:1.12.8-12.el8_3.noarch dbus-daemon-1:1.12.8-12.el8_3.x86_64 dbus-libs-1:1.12.8-12.el8_3.x86_64 dbus-tools-1:1.12.8-12.el8_3.x86_64 device-mapper-8:1.02.171-5.el8.x86_64 device-mapper-libs-8:1.02.171-5.el8.x86_64 diffutils-3.6-6.el8.x86_64 dracut-049-95.git20200804.el8_3.4.x86_64 dwz-0.12-9.el8.x86_64 efi-srpm-macros-3-2.el8.noarch elfutils-0.180-1.el8.x86_64 elfutils-debuginfod-client-0.180-1.el8.x86_64 elfutils-default-yama-scope-0.180-1.el8.noarch elfutils-libelf-0.180-1.el8.x86_64 elfutils-libs-0.180-1.el8.x86_64 epel-release-8-10.el8.noarch epel-rpm-macros-8-19.noarch expat-2.2.5-4.el8.x86_64 fedpkg-minimal-1.2.0-1.el8.noarch file-5.33-16.el8_3.1.x86_64 file-libs-5.33-16.el8_3.1.x86_64 filesystem-3.8-3.el8.x86_64 findutils-1:4.6.0-20.el8.x86_64 fpc-srpm-macros-1.3-1.el8.noarch gawk-4.2.1-1.el8.x86_64 gc-7.6.4-3.el8.x86_64 gcc-8.3.1-5.1.el8.x86_64 gcc-c++-8.3.1-5.1.el8.x86_64 gdb-headless-8.2-12.el8.x86_64 gdbm-1:1.18-1.el8.x86_64 gdbm-libs-1:1.18-1.el8.x86_64 gettext-0.19.8.1-17.el8.x86_64 gettext-libs-0.19.8.1-17.el8.x86_64 ghc-srpm-macros-1.4.2-7.el8.noarch glib2-2.56.4-8.el8.x86_64 glibc-2.28-127.el8.x86_64 glibc-all-langpacks-2.28-127.el8.x86_64 glibc-common-2.28-127.el8.x86_64 glibc-devel-2.28-127.el8.x86_64 glibc-headers-2.28-127.el8.x86_64 gmp-1:6.1.2-10.el8.x86_64 gnupg2-2.2.20-2.el8.x86_64 gnupg2-smime-2.2.20-2.el8.x86_64 gnutls-3.6.14-8.el8_3.x86_64 go-srpm-macros-2-16.el8.noarch grep-3.1-6.el8.x86_64 grub2-common-1:2.02-90.el8_3.1.noarch grub2-tools-1:2.02-90.el8_3.1.x86_64 grub2-tools-minimal-1:2.02-90.el8_3.1.x86_64 grubby-8.40-41.el8.x86_64 guile-5:2.0.14-7.el8.x86_64 gzip-1.9-9.el8.x86_64 hardlink-1:1.3-6.el8.x86_64 ima-evm-utils-1.1-5.el8.x86_64 info-6.5-6.el8.x86_64 iptables-libs-1.8.4-15.el8_3.3.x86_64 isl-0.16.1-6.el8.x86_64 json-c-0.13.1-0.2.el8.x86_64 kbd-2.0.4-10.el8.x86_64 kbd-legacy-2.0.4-10.el8.noarch kbd-misc-2.0.4-10.el8.noarch kernel-headers-4.18.0-240.22.1.el8_3.x86_64 keyutils-libs-1.5.10-6.el8.x86_64 kmod-25-16.el8.x86_64 kmod-libs-25-16.el8.x86_64 kpartx-0.8.4-5.el8.x86_64 krb5-libs-1.18.2-5.el8.x86_64 libacl-2.2.53-1.el8.x86_64 libarchive-3.3.3-1.el8.x86_64 libassuan-2.5.1-3.el8.x86_64 libatomic_ops-7.6.2-3.el8.x86_64 libattr-2.4.48-3.el8.x86_64 libbabeltrace-1.5.4-3.el8.x86_64 libblkid-2.32.1-24.el8.x86_64 libcap-2.26-4.el8.x86_64 libcap-ng-0.7.9-5.el8.x86_64 libcom_err-1.45.6-1.el8.x86_64 libcroco-0.6.12-4.el8_2.1.x86_64 libcurl-7.61.1-14.el8_3.1.x86_64 libdb-5.3.28-39.el8.x86_64 libdb-utils-5.3.28-39.el8.x86_64 libfdisk-2.32.1-24.el8.x86_64 libffi-3.1-22.el8.x86_64 libgcc-8.3.1-5.1.el8.x86_64 libgcrypt-1.8.5-4.el8.x86_64 libgomp-8.3.1-5.1.el8.x86_64 libgpg-error-1.31-1.el8.x86_64 libidn2-2.2.0-1.el8.x86_64 libipt-1.6.1-8.el8.x86_64 libkcapi-1.2.0-2.el8.x86_64 libkcapi-hmaccalc-1.2.0-2.el8.x86_64 libksba-1.3.5-7.el8.x86_64 libmetalink-0.1.3-7.el8.x86_64 libmount-2.32.1-24.el8.x86_64 libmpc-1.0.2-9.el8.x86_64 libnghttp2-1.33.0-3.el8_2.1.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libpcap-14:1.9.1-4.el8.x86_64 libpkgconf-1.4.2-1.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 libpwquality-1.4.0-9.el8.x86_64 libseccomp-2.4.3-1.el8.x86_64 libsecret-0.18.6-1.el8.x86_64 libselinux-2.9-4.el8_3.x86_64 libsemanage-2.9-3.el8.x86_64 libsepol-2.9-1.el8.x86_64 libsigsegv-2.11-5.el8.x86_64 libsmartcols-2.32.1-24.el8.x86_64 libssh-0.9.4-2.el8.x86_64 libssh-config-0.9.4-2.el8.noarch libstdc++-8.3.1-5.1.el8.x86_64 libstdc++-devel-8.3.1-5.1.el8.x86_64 libtasn1-4.13-3.el8.x86_64 libtirpc-1.1.4-4.el8.x86_64 libtool-ltdl-2.4.6-25.el8.x86_64 libunistring-0.9.9-3.el8.x86_64 libusbx-1.0.23-4.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 libuuid-2.32.1-24.el8.x86_64 libverto-0.3.0-5.el8.x86_64 libxcrypt-4.1.1-4.el8.x86_64 libxcrypt-devel-4.1.1-4.el8.x86_64 libxkbcommon-0.9.1-1.el8.x86_64 libxml2-2.9.7-8.el8.x86_64 libzstd-1.4.4-1.el8.x86_64 lua-libs-5.3.4-11.el8.x86_64 lua-srpm-macros-1-3.el8.noarch lz4-libs-1.8.3-2.el8.x86_64 make-1:4.2.1-10.el8.x86_64 memstrack-0.1.11-1.el8.x86_64 mpfr-3.1.6-1.el8.x86_64 ncurses-6.1-7.20180224.el8.x86_64 ncurses-base-6.1-7.20180224.el8.noarch ncurses-libs-6.1-7.20180224.el8.x86_64 nettle-3.4.1-4.el8_3.x86_64 npth-1.5-4.el8.x86_64 ocaml-srpm-macros-5-4.el8.noarch openblas-srpm-macros-2-2.el8.noarch openldap-2.4.46-15.el8.x86_64 openssl-1:1.1.1g-15.el8_3.x86_64 openssl-libs-1:1.1.1g-15.el8_3.x86_64 openssl-pkcs11-0.4.10-2.el8.x86_64 os-prober-1.74-6.el8.x86_64 p11-kit-0.23.14-5.el8_0.x86_64 p11-kit-trust-0.23.14-5.el8_0.x86_64 pam-1.3.1-11.el8.x86_64 patch-2.7.6-11.el8.x86_64 pcre-8.42-4.el8.x86_64 pcre2-10.32-2.el8.x86_64 perl-srpm-macros-1-25.el8.noarch pigz-2.4-4.el8.x86_64 pinentry-1.1.0-2.el8.x86_64 pkgconf-1.4.2-1.el8.x86_64 pkgconf-m4-1.4.2-1.el8.noarch pkgconf-pkg-config-1.4.2-1.el8.x86_64 platform-python-3.6.8-31.el8.x86_64 platform-python-pip-9.0.3-18.el8.noarch platform-python-setuptools-39.2.0-6.el8.noarch popt-1.16-14.el8.x86_64 procps-ng-3.3.15-3.el8_3.1.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch python-rpm-macros-3-39.el8.noarch python-srpm-macros-3-39.el8.noarch python2-rpm-macros-3-38.module_el8.3.0+478+7570e00c.noarch python3-libs-3.6.8-31.el8.x86_64 python3-pip-wheel-9.0.3-18.el8.noarch python3-rpm-macros-3-39.el8.noarch python3-setuptools-wheel-39.2.0-6.el8.noarch qt5-srpm-macros-5.12.5-3.el8.noarch readline-7.0-10.el8.x86_64 redhat-rpm-config-123-1.el8.noarch rpm-4.14.3-4.el8.x86_64 rpm-build-4.14.3-4.el8.x86_64 rpm-build-libs-4.14.3-4.el8.x86_64 rpm-libs-4.14.3-4.el8.x86_64 rust-srpm-macros-5-2.el8.noarch sed-4.5-2.el8.x86_64 setup-2.12.2-6.el8.noarch shadow-utils-2:4.6-11.el8.x86_64 shared-mime-info-1.9-3.el8.x86_64 sqlite-libs-3.26.0-11.el8.x86_64 systemd-239-41.el8_3.2.x86_64 systemd-libs-239-41.el8_3.2.x86_64 systemd-pam-239-41.el8_3.2.x86_64 systemd-udev-239-41.el8_3.2.x86_64 tar-2:1.30-5.el8.x86_64 trousers-0.3.14-4.el8.x86_64 trousers-lib-0.3.14-4.el8.x86_64 tzdata-2021a-1.el8.noarch unzip-6.0-43.el8.x86_64 util-linux-2.32.1-24.el8.x86_64 which-2.21-12.el8.x86_64 xkeyboard-config-2.28-1.el8.noarch xz-5.2.4-3.el8.x86_64 xz-libs-5.2.4-3.el8.x86_64 zip-3.0-23.el8.x86_64 zlib-1.2.11-16.2.el8_3.x86_64 zstd-1.4.4-1.el8.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: kbd-legacy-2.0.4-10.el8.noarch libidn2-2.2.0-1.el8.x86_64 xkeyboard-config-2.28-1.el8.noarch centos-linux-release-8.3-1.2011.el8.noarch libtasn1-4.13-3.el8.x86_64 zip-3.0-23.el8.x86_64 isl-0.16.1-6.el8.x86_64 cracklib-2.9.6-15.el8.x86_64 npth-1.5-4.el8.x86_64 coreutils-8.30-8.el8.x86_64 libblkid-2.32.1-24.el8.x86_64 os-prober-1.74-6.el8.x86_64 libcroco-0.6.12-4.el8_2.1.x86_64 trousers-0.3.14-4.el8.x86_64 cryptsetup-libs-2.3.3-2.el8.x86_64 expat-2.2.5-4.el8.x86_64 zstd-1.4.4-1.el8.x86_64 gcc-8.3.1-5.1.el8.x86_64 shared-mime-info-1.9-3.el8.x86_64 dracut-049-95.git20200804.el8_3.4.x86_64 libgcc-8.3.1-5.1.el8.x86_64 libtirpc-1.1.4-4.el8.x86_64 gzip-1.9-9.el8.x86_64 libmount-2.32.1-24.el8.x86_64 kernel-headers-4.18.0-240.22.1.el8_3.x86_64 libffi-3.1-22.el8.x86_64 libdb-5.3.28-39.el8.x86_64 python2-rpm-macros-3-38.module_el8.3.0+478+7570e00c.noarch basesystem-11-5.el8.noarch grub2-common-2.02-90.el8_3.1.noarch libfdisk-2.32.1-24.el8.x86_64 libcom_err-1.45.6-1.el8.x86_64 pigz-2.4-4.el8.x86_64 keyutils-libs-1.5.10-6.el8.x86_64 dbus-1.12.8-12.el8_3.x86_64 p11-kit-0.23.14-5.el8_0.x86_64 gpg-pubkey-2f86d6a1-5cf7cefb gc-7.6.4-3.el8.x86_64 shadow-utils-4.6-11.el8.x86_64 libattr-2.4.48-3.el8.x86_64 python3-libs-3.6.8-31.el8.x86_64 libzstd-1.4.4-1.el8.x86_64 libtool-ltdl-2.4.6-25.el8.x86_64 crypto-policies-scripts-20210209-1.gitbfb6bed.el8_3.noarch pam-1.3.1-11.el8.x86_64 file-5.33-16.el8_3.1.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch gnutls-3.6.14-8.el8_3.x86_64 tzdata-2021a-1.el8.noarch grub2-tools-minimal-2.02-90.el8_3.1.x86_64 libsmartcols-2.32.1-24.el8.x86_64 lz4-libs-1.8.3-2.el8.x86_64 dbus-common-1.12.8-12.el8_3.noarch dbus-tools-1.12.8-12.el8_3.x86_64 libselinux-2.9-4.el8_3.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 p11-kit-trust-0.23.14-5.el8_0.x86_64 make-4.2.1-10.el8.x86_64 epel-rpm-macros-8-19.noarch sqlite-libs-3.26.0-11.el8.x86_64 coreutils-common-8.30-8.el8.x86_64 pcre2-10.32-2.el8.x86_64 python3-setuptools-wheel-39.2.0-6.el8.noarch glib2-2.56.4-8.el8.x86_64 libsemanage-2.9-3.el8.x86_64 glibc-all-langpacks-2.28-127.el8.x86_64 redhat-rpm-config-123-1.el8.noarch libnghttp2-1.33.0-3.el8_2.1.x86_64 gnupg2-2.2.20-2.el8.x86_64 python-srpm-macros-3-39.el8.noarch chkconfig-1.13-2.el8.x86_64 ca-certificates-2020.2.41-80.0.el8_2.noarch filesystem-3.8-3.el8.x86_64 elfutils-0.180-1.el8.x86_64 centos-linux-repos-8-2.el8.noarch zlib-1.2.11-16.2.el8_3.x86_64 libsepol-2.9-1.el8.x86_64 elfutils-debuginfod-client-0.180-1.el8.x86_64 findutils-4.6.0-20.el8.x86_64 util-linux-2.32.1-24.el8.x86_64 libsecret-0.18.6-1.el8.x86_64 diffutils-3.6-6.el8.x86_64 patch-2.7.6-11.el8.x86_64 cyrus-sasl-lib-2.1.27-5.el8.x86_64 systemd-239-41.el8_3.2.x86_64 ghc-srpm-macros-1.4.2-7.el8.noarch glibc-2.28-127.el8.x86_64 libcap-2.26-4.el8.x86_64 dwz-0.12-9.el8.x86_64 libseccomp-2.4.3-1.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 ima-evm-utils-1.1-5.el8.x86_64 libksba-1.3.5-7.el8.x86_64 libgcrypt-1.8.5-4.el8.x86_64 setup-2.12.2-6.el8.noarch libssh-config-0.9.4-2.el8.noarch libssh-0.9.4-2.el8.x86_64 platform-python-setuptools-39.2.0-6.el8.noarch libpwquality-1.4.0-9.el8.x86_64 annobin-9.23-1.el8.x86_64 go-srpm-macros-2-16.el8.noarch kbd-misc-2.0.4-10.el8.noarch platform-python-3.6.8-31.el8.x86_64 lua-srpm-macros-1-3.el8.noarch glibc-headers-2.28-127.el8.x86_64 gdbm-libs-1.18-1.el8.x86_64 openssl-libs-1.1.1g-15.el8_3.x86_64 krb5-libs-1.18.2-5.el8.x86_64 binutils-2.30-79.el8.x86_64 libbabeltrace-1.5.4-3.el8.x86_64 libcurl-7.61.1-14.el8_3.1.x86_64 libxml2-2.9.7-8.el8.x86_64 elfutils-libelf-0.180-1.el8.x86_64 cpp-8.3.1-5.1.el8.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 dbus-libs-1.12.8-12.el8_3.x86_64 pkgconf-pkg-config-1.4.2-1.el8.x86_64 qt5-srpm-macros-5.12.5-3.el8.noarch audit-libs-3.0-0.17.20191104git1c2f876.el8.x86_64 hardlink-1.3-6.el8.x86_64 libpcap-1.9.1-4.el8.x86_64 libkcapi-hmaccalc-1.2.0-2.el8.x86_64 glibc-devel-2.28-127.el8.x86_64 libxkbcommon-0.9.1-1.el8.x86_64 openldap-2.4.46-15.el8.x86_64 xz-libs-5.2.4-3.el8.x86_64 libmetalink-0.1.3-7.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 brotli-1.0.6-2.el8.x86_64 fpc-srpm-macros-1.3-1.el8.noarch libxcrypt-4.1.1-4.el8.x86_64 libgpg-error-1.31-1.el8.x86_64 gettext-0.19.8.1-17.el8.x86_64 ncurses-6.1-7.20180224.el8.x86_64 kmod-25-16.el8.x86_64 systemd-libs-239-41.el8_3.2.x86_64 bzip2-1.0.6-26.el8.x86_64 rpm-build-libs-4.14.3-4.el8.x86_64 perl-srpm-macros-1-25.el8.noarch lua-libs-5.3.4-11.el8.x86_64 file-libs-5.33-16.el8_3.1.x86_64 iptables-libs-1.8.4-15.el8_3.3.x86_64 openssl-pkcs11-0.4.10-2.el8.x86_64 rpm-4.14.3-4.el8.x86_64 kbd-2.0.4-10.el8.x86_64 rust-srpm-macros-5-2.el8.noarch acl-2.2.53-1.el8.x86_64 libatomic_ops-7.6.2-3.el8.x86_64 efi-srpm-macros-3-2.el8.noarch gettext-libs-0.19.8.1-17.el8.x86_64 libacl-2.2.53-1.el8.x86_64 libxcrypt-devel-4.1.1-4.el8.x86_64 platform-python-pip-9.0.3-18.el8.noarch elfutils-default-yama-scope-0.180-1.el8.noarch crypto-policies-20210209-1.gitbfb6bed.el8_3.noarch libipt-1.6.1-8.el8.x86_64 libcap-ng-0.7.9-5.el8.x86_64 python-rpm-macros-3-39.el8.noarch pkgconf-m4-1.4.2-1.el8.noarch gmp-6.1.2-10.el8.x86_64 libsigsegv-2.11-5.el8.x86_64 device-mapper-libs-1.02.171-5.el8.x86_64 systemd-udev-239-41.el8_3.2.x86_64 gdb-headless-8.2-12.el8.x86_64 libstdc++-devel-8.3.1-5.1.el8.x86_64 xz-5.2.4-3.el8.x86_64 which-2.21-12.el8.x86_64 info-6.5-6.el8.x86_64 cpio-2.12-8.el8.x86_64 sed-4.5-2.el8.x86_64 pkgconf-1.4.2-1.el8.x86_64 systemd-pam-239-41.el8_3.2.x86_64 libassuan-2.5.1-3.el8.x86_64 glibc-common-2.28-127.el8.x86_64 kpartx-0.8.4-5.el8.x86_64 popt-1.16-14.el8.x86_64 device-mapper-1.02.171-5.el8.x86_64 pinentry-1.1.0-2.el8.x86_64 libgomp-8.3.1-5.1.el8.x86_64 gdbm-1.18-1.el8.x86_64 libarchive-3.3.3-1.el8.x86_64 grep-3.1-6.el8.x86_64 libstdc++-8.3.1-5.1.el8.x86_64 python3-rpm-macros-3-39.el8.noarch libmpc-1.0.2-9.el8.x86_64 gawk-4.2.1-1.el8.x86_64 python3-pip-wheel-9.0.3-18.el8.noarch unzip-6.0-43.el8.x86_64 curl-7.61.1-14.el8_3.1.x86_64 gpg-pubkey-8483c65d-5ccc5b19 nettle-3.4.1-4.el8_3.x86_64 libverto-0.3.0-5.el8.x86_64 procps-ng-3.3.15-3.el8_3.1.x86_64 json-c-0.13.1-0.2.el8.x86_64 bash-4.4.19-12.el8.x86_64 elfutils-libs-0.180-1.el8.x86_64 openblas-srpm-macros-2-2.el8.noarch ncurses-base-6.1-7.20180224.el8.noarch grub2-tools-2.02-90.el8_3.1.x86_64 centos-gpg-keys-8-2.el8.noarch memstrack-0.1.11-1.el8.x86_64 ocaml-srpm-macros-5-4.el8.noarch libpkgconf-1.4.2-1.el8.x86_64 libunistring-0.9.9-3.el8.x86_64 readline-7.0-10.el8.x86_64 grubby-8.40-41.el8.x86_64 gnupg2-smime-2.2.20-2.el8.x86_64 pcre-8.42-4.el8.x86_64 libdb-utils-5.3.28-39.el8.x86_64 mpfr-3.1.6-1.el8.x86_64 openssl-1.1.1g-15.el8_3.x86_64 fedpkg-minimal-1.2.0-1.el8.noarch gcc-c++-8.3.1-5.1.el8.x86_64 libkcapi-1.2.0-2.el8.x86_64 trousers-lib-0.3.14-4.el8.x86_64 tar-1.30-5.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 guile-2.0.14-7.el8.x86_64 libusbx-1.0.23-4.el8.x86_64 libuuid-2.32.1-24.el8.x86_64 ncurses-libs-6.1-7.20180224.el8.x86_64 kmod-libs-25-16.el8.x86_64 rpm-libs-4.14.3-4.el8.x86_64 dbus-daemon-1.12.8-12.el8_3.x86_64 rpm-build-4.14.3-4.el8.x86_64 epel-release-8-10.el8.noarch Start: buildsrpm Start: rpmbuild -bs warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn - 1.5.0.2-3.20120218svn3982 warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn - 1.2-5.20090709svn3827 Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/pymol-2.4.0-4.1.el8.ors.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/log/dnf.rpm.log /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/log/dnf.librepo.log /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-05l5186u/pymol/pymol.spec) Config(child) 1 minutes 17 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running (timeout=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/pymol-2.4.0-4.1.el8.ors.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1620741551.244243 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 2.10 starting (python version = 3.9.1, NVR = mock-2.10-1.fc33)... Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/results/pymol-2.4.0-4.1.el8.ors.src.rpm) Config(epel-8-x86_64) Start: clean chroot Finish: clean chroot Start: chroot init INFO: mounting tmpfs at /var/lib/mock/epel-8-x86_64-1620741551.244243/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin Mock Version: 2.10 INFO: Mock Version: 2.10 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Copr repository 58 kB/s | 3.6 kB 00:00 Additional repo copr_orrisroot_el8_devel_epel_8 96 kB/s | 3.6 kB 00:00 CentOS-8 - Base 52 kB/s | 3.9 kB 00:00 CentOS-8 - AppStream 25 kB/s | 4.3 kB 00:00 CentOS-8 - PowerTools 25 kB/s | 4.3 kB 00:00 CentOS-8 - Extras 8.8 kB/s | 1.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 115 kB/s | 4.7 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for pymol-2.4.0-4.1.el8.ors.src.rpm Start: build setup for pymol-2.4.0-4.1.el8.ors.src.rpm warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn - 1.5.0.2-3.20120218svn3982 warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn - 1.2-5.20090709svn3827 Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/pymol-2.4.0-4.1.el8.ors.src.rpm No matches found for the following disable plugin patterns: local, spacewalk Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Invalid configuration value: failovermethod=priority in /var/lib/mock/epel-8-x86_64-1620741551.244243/root/etc/dnf/dnf.conf; Configuration: OptionBinding with id "failovermethod" does not exist Copr repository 98 kB/s | 3.6 kB 00:00 Additional repo copr_orrisroot_el8_devel_epel_8 32 kB/s | 3.6 kB 00:00 CentOS-8 - Base 23 kB/s | 3.9 kB 00:00 CentOS-8 - AppStream 25 kB/s | 4.3 kB 00:00 CentOS-8 - PowerTools 25 kB/s | 4.3 kB 00:00 CentOS-8 - Extras 8.8 kB/s | 1.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 160 kB/s | 4.7 kB 00:00 Package gcc-c++-8.3.1-5.1.el8.x86_64 is already installed. Dependencies resolved. ============================================================================================================================= Package Arch Version Repository Size ============================================================================================================================= Installing: catch-devel  x86_64 2.10.2-1.el8 epel 199 k desktop-file-utils  x86_64 0.23-8.el8 appstream 80 k freeglut-devel  x86_64 3.0.0-8.el8 appstream 121 k freetype-devel  x86_64 2.9.1-4.el8_3.1 baseos 464 k glew-devel  x86_64 2.0.0-6.el8 powertools 194 k glm-devel  noarch 0.9.8.5-2.el8 powertools 206 k libappstream-glib  x86_64 0.7.14-3.el8 baseos 338 k libpng-devel  x86_64 2:1.6.34-5.el8 baseos 327 k libxml2-devel  x86_64 2.9.7-8.el8 appstream 1.0 M mesa-libGL-devel  x86_64 20.1.4-1.el8 appstream 51 k mmtf-cpp-devel  x86_64 1.0.0-5.el8 epel 27 k msgpack-devel  x86_64 3.1.0-3.el8 epel 308 k netcdf-devel  x86_64 4.7.0-2.el8 epel 121 k python3-mmtf  noarch 1.1.2-4.el8 epel 56 k python3-numpy  x86_64 1:1.14.3-9.el8 appstream 3.7 M python3-qt5-devel  x86_64 5.13.1-1.el8 powertools 551 k python3-setuptools  noarch 39.2.0-6.el8 baseos 163 k python3-simplejson  x86_64 3.17.0-2.el8 epel 286 k python36-devel  x86_64 3.6.8-2.module_el8.3.0+562+e162826a appstream 16 k Installing dependencies: alsa-lib  x86_64 1.2.3.2-1.el8 appstream 469 k avahi-libs  x86_64 0.7-19.el8 baseos 62 k bluez-libs  x86_64 5.52-1.el8 baseos 92 k bzip2-devel  x86_64 1.0.6-26.el8 baseos 224 k cairo  x86_64 1.15.12-3.el8 appstream 721 k cmake  x86_64 3.18.2-9.el8 copr_orrisroot_el8_devel_epel_8_basearch 9.8 M cmake-data  noarch 3.18.2-9.el8 copr_orrisroot_el8_devel_epel_8_basearch 1.6 M cmake-filesystem  x86_64 3.18.2-9.el8 copr_orrisroot_el8_devel_epel_8_basearch 44 k cmake-rpm-macros  noarch 3.18.2-9.el8 copr_orrisroot_el8_devel_epel_8_basearch 43 k cups-libs  x86_64 1:2.2.6-38.el8 baseos 433 k dbus-glib  x86_64 0.110-2.el8 baseos 127 k dejavu-fonts-common  noarch 2.35-6.el8 baseos 74 k dejavu-sans-mono-fonts  noarch 2.35-6.el8 baseos 447 k emacs-filesystem  noarch 1:26.1-5.el8 baseos 69 k flac-libs  x86_64 1.3.2-9.el8 appstream 217 k fontconfig  x86_64 2.13.1-3.el8 baseos 275 k fontpackages-filesystem  noarch 1.44-22.el8 baseos 16 k freeglut  x86_64 3.0.0-8.el8 appstream 191 k freetype  x86_64 2.9.1-4.el8_3.1 baseos 394 k fribidi  x86_64 1.0.4-8.el8 appstream 89 k gcc-gfortran  x86_64 8.3.1-5.1.el8 appstream 12 M gdk-pixbuf2  x86_64 2.36.12-5.el8 baseos 467 k gl-manpages  noarch 1.1-15.20161227.el8 appstream 1.2 M glib-networking  x86_64 2.56.1-1.1.el8 baseos 155 k glx-utils  x86_64 8.4.0-5.20181118git1830dcb.el8 appstream 44 k graphite2  x86_64 1.3.10-10.el8 appstream 122 k groff-base  x86_64 1.22.3-18.el8 baseos 1.0 M gsettings-desktop-schemas  x86_64 3.32.0-5.el8 baseos 633 k gsm  x86_64 1.0.17-5.el8 appstream 37 k gstreamer1  x86_64 1.16.1-2.el8 appstream 1.3 M gstreamer1-plugins-bad-free  x86_64 1.16.1-1.el8 appstream 1.8 M gstreamer1-plugins-base  x86_64 1.16.1-1.el8 appstream 2.0 M harfbuzz  x86_64 1.7.5-3.el8 appstream 295 k hdf  x86_64 4.2.14-5.el8 epel 651 k hdf5  x86_64 1.10.5-4.el8 epel 2.1 M hdf5-devel  x86_64 1.10.5-4.el8 epel 1.2 M hwdata  noarch 0.314-8.6.el8 baseos 1.6 M iso-codes  noarch 3.79-2.el8 appstream 3.4 M json-glib  x86_64 1.4.4-1.el8 baseos 144 k lcms2  x86_64 2.9-2.el8 appstream 165 k libGLEW  x86_64 2.0.0-6.el8 powertools 143 k libICE  x86_64 1.0.9-15.el8 appstream 74 k libSM  x86_64 1.2.3-1.el8 appstream 48 k libX11  x86_64 1.6.8-3.el8 appstream 611 k libX11-common  noarch 1.6.8-3.el8 appstream 158 k libX11-devel  x86_64 1.6.8-3.el8 appstream 976 k libX11-xcb  x86_64 1.6.8-3.el8 appstream 14 k libXau  x86_64 1.0.9-3.el8 appstream 37 k libXau-devel  x86_64 1.0.9-3.el8 appstream 21 k libXdamage  x86_64 1.1.4-14.el8 appstream 27 k libXext  x86_64 1.3.4-1.el8 appstream 45 k libXfixes  x86_64 5.0.3-7.el8 appstream 25 k libXft  x86_64 2.3.3-1.el8 appstream 67 k libXi  x86_64 1.7.10-1.el8 appstream 49 k libXrender  x86_64 0.9.10-7.el8 appstream 33 k libXtst  x86_64 1.2.3-7.el8 appstream 22 k libXv  x86_64 1.0.11-7.el8 appstream 20 k libXxf86vm  x86_64 1.1.4-9.el8 appstream 19 k libaec  x86_64 1.0.2-3.el8 powertools 39 k libaec-devel  x86_64 1.0.2-3.el8 powertools 12 k libasyncns  x86_64 0.8-14.el8 appstream 32 k libatomic  x86_64 8.3.1-5.1.el8 baseos 22 k libcurl-devel  x86_64 7.61.1-14.el8_3.1 baseos 832 k libdatrie  x86_64 0.2.9-7.el8 appstream 33 k libdrm  x86_64 2.4.101-1.el8 appstream 165 k libdrm-devel  x86_64 2.4.101-1.el8 appstream 157 k libdvdnav  x86_64 5.0.3-8.el8 appstream 61 k libdvdread  x86_64 5.0.3-9.el8 appstream 75 k libgfortran  x86_64 8.3.1-5.1.el8 baseos 639 k libglvnd  x86_64 1:1.2.0-6.el8 appstream 98 k libglvnd-core-devel  x86_64 1:1.2.0-6.el8 appstream 25 k libglvnd-devel  x86_64 1:1.2.0-6.el8 appstream 184 k libglvnd-egl  x86_64 1:1.2.0-6.el8 appstream 50 k libglvnd-gles  x86_64 1:1.2.0-6.el8 appstream 40 k libglvnd-glx  x86_64 1:1.2.0-6.el8 appstream 136 k libglvnd-opengl  x86_64 1:1.2.0-6.el8 appstream 48 k libgudev  x86_64 232-4.el8 baseos 33 k libicu  x86_64 60.3-2.el8_1 baseos 8.8 M libjpeg-turbo  x86_64 1.5.3-10.el8 appstream 156 k libmodman  x86_64 2.0.1-17.el8 baseos 36 k libogg  x86_64 2:1.3.2-10.el8 appstream 31 k libpciaccess  x86_64 0.14-1.el8 baseos 32 k libpng  x86_64 2:1.6.34-5.el8 baseos 126 k libproxy  x86_64 0.4.15-5.2.el8 baseos 75 k libquadmath  x86_64 8.3.1-5.1.el8 baseos 169 k libquadmath-devel  x86_64 8.3.1-5.1.el8 appstream 22 k librsvg2  x86_64 2.42.7-4.el8 appstream 571 k libsndfile  x86_64 1.0.28-10.el8 appstream 193 k libsoup  x86_64 2.62.3-2.el8 baseos 424 k libsrtp  x86_64 1.5.4-8.el8 appstream 282 k libstemmer  x86_64 0-10.585svn.el8 baseos 73 k libthai  x86_64 0.1.27-2.el8 appstream 203 k libtheora  x86_64 1:1.1.1-21.el8 appstream 184 k libuv  x86_64 1:1.40.0-1.el8 copr_orrisroot_el8_devel_epel_8_basearch 154 k libvisual  x86_64 1:0.4.0-24.el8 appstream 145 k libvorbis  x86_64 1:1.3.6-2.el8 appstream 196 k libwayland-client  x86_64 1.17.0-1.el8 appstream 39 k libwayland-cursor  x86_64 1.17.0-1.el8 appstream 26 k libwayland-egl  x86_64 1.17.0-1.el8 appstream 19 k libwayland-server  x86_64 1.17.0-1.el8 appstream 45 k libwebp  x86_64 1.0.0-1.el8 appstream 273 k libxcb  x86_64 1.13.1-1.el8 appstream 229 k libxcb-devel  x86_64 1.13.1-1.el8 appstream 1.1 M libxshmfence  x86_64 1.3-2.el8 appstream 13 k mesa-libEGL  x86_64 20.1.4-1.el8 appstream 138 k mesa-libGL  x86_64 20.1.4-1.el8 appstream 189 k mesa-libGLU  x86_64 9.0.0-15.el8 appstream 185 k mesa-libGLU-devel  x86_64 9.0.0-15.el8 appstream 15 k mesa-libgbm  x86_64 20.1.4-1.el8 appstream 60 k mesa-libglapi  x86_64 20.1.4-1.el8 appstream 64 k msgpack  x86_64 3.1.0-3.el8 epel 29 k netcdf  x86_64 4.7.0-2.el8 epel 647 k openal-soft  x86_64 1.18.2-7.el8 appstream 394 k openblas  x86_64 0.3.3-5.el8 appstream 4.3 M openblas-threads  x86_64 0.3.3-5.el8 appstream 4.3 M opus  x86_64 1.3-0.4.beta.el8 appstream 204 k orc  x86_64 0.4.28-3.el8 appstream 175 k pango  x86_64 1.42.4-6.el8 appstream 298 k pcre2-utf16  x86_64 10.32-2.el8 baseos 229 k perl-Carp  noarch 1.42-396.el8 baseos 30 k perl-Data-Dumper  x86_64 2.167-399.el8 baseos 58 k perl-Digest  noarch 1.17-395.el8 appstream 27 k perl-Digest-MD5  x86_64 2.55-396.el8 appstream 37 k perl-Encode  x86_64 4:2.97-3.el8 baseos 1.5 M perl-Errno  x86_64 1.28-416.el8 baseos 76 k perl-Exporter  noarch 5.72-396.el8 baseos 34 k perl-File-Path  noarch 2.15-2.el8 baseos 38 k perl-File-Temp  noarch 0.230.600-1.el8 baseos 63 k perl-Getopt-Long  noarch 1:2.50-4.el8 baseos 63 k perl-HTTP-Tiny  noarch 0.074-1.el8 baseos 58 k perl-IO  x86_64 1.38-416.el8 baseos 141 k perl-MIME-Base64  x86_64 3.15-396.el8 baseos 31 k perl-Net-SSLeay  x86_64 1.88-1.module_el8.3.0+410+ff426aa3 appstream 379 k perl-PathTools  x86_64 3.74-1.el8 baseos 90 k perl-Pod-Escapes  noarch 1:1.07-395.el8 baseos 20 k perl-Pod-Perldoc  noarch 3.28-396.el8 baseos 86 k perl-Pod-Simple  noarch 1:3.35-395.el8 baseos 213 k perl-Pod-Usage  noarch 4:1.69-395.el8 baseos 34 k perl-Scalar-List-Utils  x86_64 3:1.49-2.el8 baseos 68 k perl-Socket  x86_64 4:2.027-3.el8 baseos 59 k perl-Storable  x86_64 1:3.11-3.el8 baseos 98 k perl-Term-ANSIColor  noarch 4.06-396.el8 baseos 46 k perl-Term-Cap  noarch 1.17-395.el8 baseos 23 k perl-Text-ParseWords  noarch 3.30-395.el8 baseos 18 k perl-Text-Tabs+Wrap  noarch 2013.0523-395.el8 baseos 24 k perl-Time-Local  noarch 1:1.280-1.el8 baseos 34 k perl-URI  noarch 1.73-3.el8 appstream 116 k perl-Unicode-Normalize  x86_64 1.25-396.el8 baseos 82 k perl-constant  noarch 1.33-396.el8 baseos 25 k perl-interpreter  x86_64 4:5.26.3-416.el8 baseos 6.3 M perl-libnet  noarch 3.11-3.el8 appstream 121 k perl-libs  x86_64 4:5.26.3-416.el8 baseos 1.6 M perl-macros  x86_64 4:5.26.3-416.el8 baseos 72 k perl-parent  noarch 1:0.237-1.el8 baseos 20 k perl-podlators  noarch 4.11-1.el8 baseos 118 k perl-threads  x86_64 1:2.21-2.el8 baseos 61 k perl-threads-shared  x86_64 1.58-2.el8 baseos 48 k pixman  x86_64 0.38.4-1.el8 appstream 257 k platform-python-devel  x86_64 3.6.8-31.el8 appstream 247 k pulseaudio-libs  x86_64 13.99.1-1.el8 appstream 698 k pulseaudio-libs-glib2  x86_64 13.99.1-1.el8 appstream 30 k python-qt5-rpm-macros  noarch 5.13.1-1.el8 appstream 17 k python3-dbus  x86_64 1.2.4-15.el8 baseos 134 k python3-msgpack  x86_64 0.6.2-1.el8 epel 92 k python3-pip  noarch 9.0.3-18.el8 appstream 20 k python3-pyqt5-sip  x86_64 4.19.19-2.el8 appstream 92 k python3-qt5  x86_64 5.13.1-1.el8 appstream 1.1 M python3-qt5-base  x86_64 5.13.1-1.el8 appstream 3.2 M python3-rpm-generators  noarch 5-6.el8 appstream 24 k python3-sip-devel  x86_64 4.19.19-2.el8 powertools 65 k python36  x86_64 3.6.8-2.module_el8.3.0+562+e162826a appstream 19 k python36-rpm-macros  noarch 3.6.8-2.module_el8.3.0+562+e162826a appstream 15 k qt5-qtbase  x86_64 5.12.5-6.el8 appstream 3.4 M qt5-qtbase-common  noarch 5.12.5-6.el8 appstream 40 k qt5-qtbase-devel  x86_64 5.12.5-6.el8 appstream 3.2 M qt5-qtbase-gui  x86_64 5.12.5-6.el8 appstream 5.8 M qt5-qtconnectivity  x86_64 5.12.5-1.el8 appstream 523 k qt5-qtdeclarative  x86_64 5.12.5-1.el8 appstream 3.7 M qt5-qtlocation  x86_64 5.12.5-1.el8 appstream 3.1 M qt5-qtmultimedia  x86_64 5.12.5-1.el8 appstream 869 k qt5-qtsensors  x86_64 5.12.5-1.el8 appstream 221 k qt5-qtserialport  x86_64 5.12.5-1.el8 appstream 71 k qt5-qtsvg  x86_64 5.12.5-1.el8 appstream 184 k qt5-qttools-common  noarch 5.12.5-2.el8 appstream 21 k qt5-qttools-libs-designer  x86_64 5.12.5-2.el8 appstream 2.7 M qt5-qttools-libs-help  x86_64 5.12.5-2.el8 appstream 152 k qt5-qtwebchannel  x86_64 5.12.5-1.el8 appstream 94 k qt5-qtwebsockets  x86_64 5.12.5-2.el8 appstream 97 k qt5-qtx11extras  x86_64 5.12.5-1.el8 appstream 40 k qt5-qtxmlpatterns  x86_64 5.12.5-1.el8 appstream 1.1 M qt5-rpm-macros  noarch 5.12.5-3.el8 appstream 12 k sip  x86_64 4.19.19-2.el8 appstream 190 k soundtouch  x86_64 2.0.0-2.el8 appstream 76 k vim-filesystem  noarch 2:8.0.1763-15.el8 appstream 48 k webrtc-audio-processing  x86_64 0.3-9.el8 appstream 297 k xcb-util  x86_64 0.4.0-10.el8 appstream 22 k xcb-util-image  x86_64 0.4.0-9.el8 appstream 21 k xcb-util-keysyms  x86_64 0.4.0-7.el8 appstream 16 k xcb-util-renderutil  x86_64 0.3.9-10.el8 appstream 19 k xcb-util-wm  x86_64 0.4.1-12.el8 appstream 32 k xml-common  noarch 0.6.3-50.el8 baseos 39 k xorg-x11-proto-devel  noarch 2020.1-3.el8 appstream 280 k xz-devel  x86_64 5.2.4-3.el8 baseos 62 k zlib-devel  x86_64 1.2.11-16.2.el8_3 baseos 58 k Installing weak dependencies: abattis-cantarell-fonts  noarch 0.0.25-4.el8 appstream 155 k perl-IO-Socket-IP  noarch 0.39-5.el8 appstream 47 k perl-IO-Socket-SSL  noarch 2.066-4.module_el8.3.0+410+ff426aa3 appstream 298 k perl-Mozilla-CA  noarch 20160104-7.module_el8.3.0+416+dee7bcef appstream 15 k Enabling module streams: perl 5.26 perl-IO-Socket-SSL 2.066 perl-libwww-perl 6.34 python36 3.6 Transaction Summary ============================================================================================================================= Install 227 Packages Total size: 128 M Total download size: 74 M Installed size: 468 M Downloading Packages: [SKIPPED] cmake-3.18.2-9.el8.x86_64.rpm: Already downloaded [SKIPPED] cmake-data-3.18.2-9.el8.noarch.rpm: Already downloaded [SKIPPED] cmake-filesystem-3.18.2-9.el8.x86_64.rpm: Already downloaded [SKIPPED] cmake-rpm-macros-3.18.2-9.el8.noarch.rpm: Already downloaded [SKIPPED] libuv-1.40.0-1.el8.x86_64.rpm: Already downloaded [SKIPPED] avahi-libs-0.7-19.el8.x86_64.rpm: Already downloaded [SKIPPED] cups-libs-2.2.6-38.el8.x86_64.rpm: Already downloaded [SKIPPED] emacs-filesystem-26.1-5.el8.noarch.rpm: Already downloaded [SKIPPED] fontconfig-2.13.1-3.el8.x86_64.rpm: Already downloaded [SKIPPED] fontpackages-filesystem-1.44-22.el8.noarch.rpm: Already downloaded [SKIPPED] freetype-2.9.1-4.el8_3.1.x86_64.rpm: Already downloaded [SKIPPED] gdk-pixbuf2-2.36.12-5.el8.x86_64.rpm: Already downloaded [SKIPPED] groff-base-1.22.3-18.el8.x86_64.rpm: Already downloaded [SKIPPED] libgfortran-8.3.1-5.1.el8.x86_64.rpm: Already downloaded [SKIPPED] libicu-60.3-2.el8_1.x86_64.rpm: Already downloaded [SKIPPED] libpng-1.6.34-5.el8.x86_64.rpm: Already downloaded [SKIPPED] libquadmath-8.3.1-5.1.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Carp-1.42-396.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Data-Dumper-2.167-399.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Encode-2.97-3.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Errno-1.28-416.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Exporter-5.72-396.el8.noarch.rpm: Already downloaded [SKIPPED] perl-File-Path-2.15-2.el8.noarch.rpm: Already downloaded [SKIPPED] perl-File-Temp-0.230.600-1.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Getopt-Long-2.50-4.el8.noarch.rpm: Already downloaded [SKIPPED] perl-HTTP-Tiny-0.074-1.el8.noarch.rpm: Already downloaded [SKIPPED] perl-IO-1.38-416.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-MIME-Base64-3.15-396.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-PathTools-3.74-1.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Pod-Escapes-1.07-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Perldoc-3.28-396.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Simple-3.35-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Pod-Usage-1.69-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Scalar-List-Utils-1.49-2.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Socket-2.027-3.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Storable-3.11-3.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Term-ANSIColor-4.06-396.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Term-Cap-1.17-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Text-ParseWords-3.30-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Text-Tabs+Wrap-2013.0523-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Time-Local-1.280-1.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Unicode-Normalize-1.25-396.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-constant-1.33-396.el8.noarch.rpm: Already downloaded [SKIPPED] perl-interpreter-5.26.3-416.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-libs-5.26.3-416.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-macros-5.26.3-416.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-parent-0.237-1.el8.noarch.rpm: Already downloaded [SKIPPED] perl-podlators-4.11-1.el8.noarch.rpm: Already downloaded [SKIPPED] perl-threads-2.21-2.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-threads-shared-1.58-2.el8.x86_64.rpm: Already downloaded [SKIPPED] python3-setuptools-39.2.0-6.el8.noarch.rpm: Already downloaded [SKIPPED] zlib-devel-1.2.11-16.2.el8_3.x86_64.rpm: Already downloaded [SKIPPED] cairo-1.15.12-3.el8.x86_64.rpm: Already downloaded [SKIPPED] fribidi-1.0.4-8.el8.x86_64.rpm: Already downloaded [SKIPPED] graphite2-1.3.10-10.el8.x86_64.rpm: Already downloaded [SKIPPED] harfbuzz-1.7.5-3.el8.x86_64.rpm: Already downloaded [SKIPPED] lcms2-2.9-2.el8.x86_64.rpm: Already downloaded [SKIPPED] libICE-1.0.9-15.el8.x86_64.rpm: Already downloaded [SKIPPED] libSM-1.2.3-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libX11-1.6.8-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libX11-common-1.6.8-3.el8.noarch.rpm: Already downloaded [SKIPPED] libXau-1.0.9-3.el8.x86_64.rpm: Already downloaded [SKIPPED] libXdamage-1.1.4-14.el8.x86_64.rpm: Already downloaded [SKIPPED] libXext-1.3.4-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libXfixes-5.0.3-7.el8.x86_64.rpm: Already downloaded [SKIPPED] libXft-2.3.3-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libXi-1.7.10-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libXrender-0.9.10-7.el8.x86_64.rpm: Already downloaded [SKIPPED] libXxf86vm-1.1.4-9.el8.x86_64.rpm: Already downloaded [SKIPPED] libdatrie-0.2.9-7.el8.x86_64.rpm: Already downloaded [SKIPPED] libjpeg-turbo-1.5.3-10.el8.x86_64.rpm: Already downloaded [SKIPPED] librsvg2-2.42.7-4.el8.x86_64.rpm: Already downloaded [SKIPPED] libthai-0.1.27-2.el8.x86_64.rpm: Already downloaded [SKIPPED] libwebp-1.0.0-1.el8.x86_64.rpm: Already downloaded [SKIPPED] libxcb-1.13.1-1.el8.x86_64.rpm: Already downloaded [SKIPPED] openblas-0.3.3-5.el8.x86_64.rpm: Already downloaded [SKIPPED] openblas-threads-0.3.3-5.el8.x86_64.rpm: Already downloaded [SKIPPED] pango-1.42.4-6.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-Digest-1.17-395.el8.noarch.rpm: Already downloaded [SKIPPED] perl-Digest-MD5-2.55-396.el8.x86_64.rpm: Already downloaded [SKIPPED] perl-IO-Socket-IP-0.39-5.el8.noarch.rpm: Already downloaded [SKIPPED] perl-IO-Socket-SSL-2.066-4.module_el8.3.0+410+ff426aa3.noarch.rpm: Already downloaded [SKIPPED] perl-Mozilla-CA-20160104-7.module_el8.3.0+416+dee7bcef.noarch.rpm: Already downloaded [SKIPPED] perl-Net-SSLeay-1.88-1.module_el8.3.0+410+ff426aa3.x86_64.rpm: Already downloaded [SKIPPED] perl-URI-1.73-3.el8.noarch.rpm: Already downloaded [SKIPPED] perl-libnet-3.11-3.el8.noarch.rpm: Already downloaded [SKIPPED] pixman-0.38.4-1.el8.x86_64.rpm: Already downloaded [SKIPPED] platform-python-devel-3.6.8-31.el8.x86_64.rpm: Already downloaded [SKIPPED] python3-numpy-1.14.3-9.el8.x86_64.rpm: Already downloaded [SKIPPED] python3-pip-9.0.3-18.el8.noarch.rpm: Already downloaded [SKIPPED] python3-rpm-generators-5-6.el8.noarch.rpm: Already downloaded [SKIPPED] python36-3.6.8-2.module_el8.3.0+562+e162826a.x86_64.rpm: Already downloaded [SKIPPED] python36-devel-3.6.8-2.module_el8.3.0+562+e162826a.x86_64.rpm: Already downloaded [SKIPPED] python36-rpm-macros-3.6.8-2.module_el8.3.0+562+e162826a.noarch.rpm: Already downloaded [SKIPPED] vim-filesystem-8.0.1763-15.el8.noarch.rpm: Already downloaded (96/227): dbus-glib-0.110-2.el8.x86_64.rpm 16 MB/s | 127 kB 00:00 (97/227): bluez-libs-5.52-1.el8.x86_64.rpm 8.9 MB/s | 92 kB 00:00 (98/227): dejavu-fonts-common-2.35-6.el8.noarch 21 MB/s | 74 kB 00:00 (99/227): bzip2-devel-1.0.6-26.el8.x86_64.rpm 15 MB/s | 224 kB 00:00 (100/227): glib-networking-2.56.1-1.1.el8.x86_6 28 MB/s | 155 kB 00:00 (101/227): freetype-devel-2.9.1-4.el8_3.1.x86_6 43 MB/s | 464 kB 00:00 (102/227): dejavu-sans-mono-fonts-2.35-6.el8.no 27 MB/s | 447 kB 00:00 (103/227): json-glib-1.4.4-1.el8.x86_64.rpm 33 MB/s | 144 kB 00:00 (104/227): gsettings-desktop-schemas-3.32.0-5.e 40 MB/s | 633 kB 00:00 (105/227): libappstream-glib-0.7.14-3.el8.x86_6 28 MB/s | 338 kB 00:00 (106/227): hwdata-0.314-8.6.el8.noarch.rpm 58 MB/s | 1.6 MB 00:00 (107/227): libatomic-8.3.1-5.1.el8.x86_64.rpm 1.3 MB/s | 22 kB 00:00 (108/227): libgudev-232-4.el8.x86_64.rpm 11 MB/s | 33 kB 00:00 (109/227): libmodman-2.0.1-17.el8.x86_64.rpm 11 MB/s | 36 kB 00:00 (110/227): libpciaccess-0.14-1.el8.x86_64.rpm 13 MB/s | 32 kB 00:00 (111/227): libcurl-devel-7.61.1-14.el8_3.1.x86_ 38 MB/s | 832 kB 00:00 (112/227): libproxy-0.4.15-5.2.el8.x86_64.rpm 11 MB/s | 75 kB 00:00 (113/227): libpng-devel-1.6.34-5.el8.x86_64.rpm 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libvisual-1:0.4.0-24.el8.x86_64 134/227 Verifying : libvorbis-1:1.3.6-2.el8.x86_64 135/227 Verifying : libwayland-client-1.17.0-1.el8.x86_64 136/227 Verifying : libwayland-cursor-1.17.0-1.el8.x86_64 137/227 Verifying : libwayland-egl-1.17.0-1.el8.x86_64 138/227 Verifying : libwayland-server-1.17.0-1.el8.x86_64 139/227 Verifying : libwebp-1.0.0-1.el8.x86_64 140/227 Verifying : libxcb-1.13.1-1.el8.x86_64 141/227 Verifying : libxcb-devel-1.13.1-1.el8.x86_64 142/227 Verifying : libxml2-devel-2.9.7-8.el8.x86_64 143/227 Verifying : libxshmfence-1.3-2.el8.x86_64 144/227 Verifying : mesa-libEGL-20.1.4-1.el8.x86_64 145/227 Verifying : mesa-libGL-20.1.4-1.el8.x86_64 146/227 Verifying : mesa-libGL-devel-20.1.4-1.el8.x86_64 147/227 Verifying : mesa-libGLU-9.0.0-15.el8.x86_64 148/227 Verifying : mesa-libGLU-devel-9.0.0-15.el8.x86_64 149/227 Verifying : mesa-libgbm-20.1.4-1.el8.x86_64 150/227 Verifying : mesa-libglapi-20.1.4-1.el8.x86_64 151/227 Verifying : openal-soft-1.18.2-7.el8.x86_64 152/227 Verifying : openblas-0.3.3-5.el8.x86_64 153/227 Verifying : openblas-threads-0.3.3-5.el8.x86_64 154/227 Verifying : opus-1.3-0.4.beta.el8.x86_64 155/227 Verifying : orc-0.4.28-3.el8.x86_64 156/227 Verifying : pango-1.42.4-6.el8.x86_64 157/227 Verifying : perl-Digest-1.17-395.el8.noarch 158/227 Verifying : perl-Digest-MD5-2.55-396.el8.x86_64 159/227 Verifying : perl-IO-Socket-IP-0.39-5.el8.noarch 160/227 Verifying : perl-IO-Socket-SSL-2.066-4.module_el8.3.0+410+ff 161/227 Verifying : perl-Mozilla-CA-20160104-7.module_el8.3.0+416+de 162/227 Verifying : perl-Net-SSLeay-1.88-1.module_el8.3.0+410+ff426a 163/227 Verifying : perl-URI-1.73-3.el8.noarch 164/227 Verifying : perl-libnet-3.11-3.el8.noarch 165/227 Verifying : pixman-0.38.4-1.el8.x86_64 166/227 Verifying : platform-python-devel-3.6.8-31.el8.x86_64 167/227 Verifying : pulseaudio-libs-13.99.1-1.el8.x86_64 168/227 Verifying : pulseaudio-libs-glib2-13.99.1-1.el8.x86_64 169/227 Verifying : python-qt5-rpm-macros-5.13.1-1.el8.noarch 170/227 Verifying : python3-numpy-1:1.14.3-9.el8.x86_64 171/227 Verifying : python3-pip-9.0.3-18.el8.noarch 172/227 Verifying : python3-pyqt5-sip-4.19.19-2.el8.x86_64 173/227 Verifying : python3-qt5-5.13.1-1.el8.x86_64 174/227 Verifying : python3-qt5-base-5.13.1-1.el8.x86_64 175/227 Verifying : python3-rpm-generators-5-6.el8.noarch 176/227 Verifying : python36-3.6.8-2.module_el8.3.0+562+e162826a.x86 177/227 Verifying : python36-devel-3.6.8-2.module_el8.3.0+562+e16282 178/227 Verifying : python36-rpm-macros-3.6.8-2.module_el8.3.0+562+e 179/227 Verifying : qt5-qtbase-5.12.5-6.el8.x86_64 180/227 Verifying : qt5-qtbase-common-5.12.5-6.el8.noarch 181/227 Verifying : qt5-qtbase-devel-5.12.5-6.el8.x86_64 182/227 Verifying : qt5-qtbase-gui-5.12.5-6.el8.x86_64 183/227 Verifying : qt5-qtconnectivity-5.12.5-1.el8.x86_64 184/227 Verifying : qt5-qtdeclarative-5.12.5-1.el8.x86_64 185/227 Verifying : qt5-qtlocation-5.12.5-1.el8.x86_64 186/227 Verifying : qt5-qtmultimedia-5.12.5-1.el8.x86_64 187/227 Verifying : qt5-qtsensors-5.12.5-1.el8.x86_64 188/227 Verifying : qt5-qtserialport-5.12.5-1.el8.x86_64 189/227 Verifying : qt5-qtsvg-5.12.5-1.el8.x86_64 190/227 Verifying : qt5-qttools-common-5.12.5-2.el8.noarch 191/227 Verifying : qt5-qttools-libs-designer-5.12.5-2.el8.x86_64 192/227 Verifying : qt5-qttools-libs-help-5.12.5-2.el8.x86_64 193/227 Verifying : qt5-qtwebchannel-5.12.5-1.el8.x86_64 194/227 Verifying : qt5-qtwebsockets-5.12.5-2.el8.x86_64 195/227 Verifying : qt5-qtx11extras-5.12.5-1.el8.x86_64 196/227 Verifying : qt5-qtxmlpatterns-5.12.5-1.el8.x86_64 197/227 Verifying : qt5-rpm-macros-5.12.5-3.el8.noarch 198/227 Verifying : sip-4.19.19-2.el8.x86_64 199/227 Verifying : soundtouch-2.0.0-2.el8.x86_64 200/227 Verifying : vim-filesystem-2:8.0.1763-15.el8.noarch 201/227 Verifying : webrtc-audio-processing-0.3-9.el8.x86_64 202/227 Verifying : xcb-util-0.4.0-10.el8.x86_64 203/227 Verifying : xcb-util-image-0.4.0-9.el8.x86_64 204/227 Verifying : xcb-util-keysyms-0.4.0-7.el8.x86_64 205/227 Verifying : xcb-util-renderutil-0.3.9-10.el8.x86_64 206/227 Verifying : xcb-util-wm-0.4.1-12.el8.x86_64 207/227 Verifying : xorg-x11-proto-devel-2020.1-3.el8.noarch 208/227 Verifying : glew-devel-2.0.0-6.el8.x86_64 209/227 Verifying : glm-devel-0.9.8.5-2.el8.noarch 210/227 Verifying : libGLEW-2.0.0-6.el8.x86_64 211/227 Verifying : libaec-1.0.2-3.el8.x86_64 212/227 Verifying : libaec-devel-1.0.2-3.el8.x86_64 213/227 Verifying : python3-qt5-devel-5.13.1-1.el8.x86_64 214/227 Verifying : python3-sip-devel-4.19.19-2.el8.x86_64 215/227 Verifying : catch-devel-2.10.2-1.el8.x86_64 216/227 Verifying : hdf-4.2.14-5.el8.x86_64 217/227 Verifying : hdf5-1.10.5-4.el8.x86_64 218/227 Verifying : hdf5-devel-1.10.5-4.el8.x86_64 219/227 Verifying : mmtf-cpp-devel-1.0.0-5.el8.x86_64 220/227 Verifying : msgpack-3.1.0-3.el8.x86_64 221/227 Verifying : msgpack-devel-3.1.0-3.el8.x86_64 222/227 Verifying : netcdf-4.7.0-2.el8.x86_64 223/227 Verifying : netcdf-devel-4.7.0-2.el8.x86_64 224/227 Verifying : python3-mmtf-1.1.2-4.el8.noarch 225/227 Verifying : python3-msgpack-0.6.2-1.el8.x86_64 226/227 Verifying : python3-simplejson-3.17.0-2.el8.x86_64 227/227 Installed: abattis-cantarell-fonts-0.0.25-4.el8.noarch alsa-lib-1.2.3.2-1.el8.x86_64 avahi-libs-0.7-19.el8.x86_64 bluez-libs-5.52-1.el8.x86_64 bzip2-devel-1.0.6-26.el8.x86_64 cairo-1.15.12-3.el8.x86_64 catch-devel-2.10.2-1.el8.x86_64 cmake-3.18.2-9.el8.x86_64 cmake-data-3.18.2-9.el8.noarch cmake-filesystem-3.18.2-9.el8.x86_64 cmake-rpm-macros-3.18.2-9.el8.noarch cups-libs-1:2.2.6-38.el8.x86_64 dbus-glib-0.110-2.el8.x86_64 dejavu-fonts-common-2.35-6.el8.noarch dejavu-sans-mono-fonts-2.35-6.el8.noarch desktop-file-utils-0.23-8.el8.x86_64 emacs-filesystem-1:26.1-5.el8.noarch flac-libs-1.3.2-9.el8.x86_64 fontconfig-2.13.1-3.el8.x86_64 fontpackages-filesystem-1.44-22.el8.noarch freeglut-3.0.0-8.el8.x86_64 freeglut-devel-3.0.0-8.el8.x86_64 freetype-2.9.1-4.el8_3.1.x86_64 freetype-devel-2.9.1-4.el8_3.1.x86_64 fribidi-1.0.4-8.el8.x86_64 gcc-gfortran-8.3.1-5.1.el8.x86_64 gdk-pixbuf2-2.36.12-5.el8.x86_64 gl-manpages-1.1-15.20161227.el8.noarch glew-devel-2.0.0-6.el8.x86_64 glib-networking-2.56.1-1.1.el8.x86_64 glm-devel-0.9.8.5-2.el8.noarch glx-utils-8.4.0-5.20181118git1830dcb.el8.x86_64 graphite2-1.3.10-10.el8.x86_64 groff-base-1.22.3-18.el8.x86_64 gsettings-desktop-schemas-3.32.0-5.el8.x86_64 gsm-1.0.17-5.el8.x86_64 gstreamer1-1.16.1-2.el8.x86_64 gstreamer1-plugins-bad-free-1.16.1-1.el8.x86_64 gstreamer1-plugins-base-1.16.1-1.el8.x86_64 harfbuzz-1.7.5-3.el8.x86_64 hdf-4.2.14-5.el8.x86_64 hdf5-1.10.5-4.el8.x86_64 hdf5-devel-1.10.5-4.el8.x86_64 hwdata-0.314-8.6.el8.noarch iso-codes-3.79-2.el8.noarch json-glib-1.4.4-1.el8.x86_64 lcms2-2.9-2.el8.x86_64 libGLEW-2.0.0-6.el8.x86_64 libICE-1.0.9-15.el8.x86_64 libSM-1.2.3-1.el8.x86_64 libX11-1.6.8-3.el8.x86_64 libX11-common-1.6.8-3.el8.noarch libX11-devel-1.6.8-3.el8.x86_64 libX11-xcb-1.6.8-3.el8.x86_64 libXau-1.0.9-3.el8.x86_64 libXau-devel-1.0.9-3.el8.x86_64 libXdamage-1.1.4-14.el8.x86_64 libXext-1.3.4-1.el8.x86_64 libXfixes-5.0.3-7.el8.x86_64 libXft-2.3.3-1.el8.x86_64 libXi-1.7.10-1.el8.x86_64 libXrender-0.9.10-7.el8.x86_64 libXtst-1.2.3-7.el8.x86_64 libXv-1.0.11-7.el8.x86_64 libXxf86vm-1.1.4-9.el8.x86_64 libaec-1.0.2-3.el8.x86_64 libaec-devel-1.0.2-3.el8.x86_64 libappstream-glib-0.7.14-3.el8.x86_64 libasyncns-0.8-14.el8.x86_64 libatomic-8.3.1-5.1.el8.x86_64 libcurl-devel-7.61.1-14.el8_3.1.x86_64 libdatrie-0.2.9-7.el8.x86_64 libdrm-2.4.101-1.el8.x86_64 libdrm-devel-2.4.101-1.el8.x86_64 libdvdnav-5.0.3-8.el8.x86_64 libdvdread-5.0.3-9.el8.x86_64 libgfortran-8.3.1-5.1.el8.x86_64 libglvnd-1:1.2.0-6.el8.x86_64 libglvnd-core-devel-1:1.2.0-6.el8.x86_64 libglvnd-devel-1:1.2.0-6.el8.x86_64 libglvnd-egl-1:1.2.0-6.el8.x86_64 libglvnd-gles-1:1.2.0-6.el8.x86_64 libglvnd-glx-1:1.2.0-6.el8.x86_64 libglvnd-opengl-1:1.2.0-6.el8.x86_64 libgudev-232-4.el8.x86_64 libicu-60.3-2.el8_1.x86_64 libjpeg-turbo-1.5.3-10.el8.x86_64 libmodman-2.0.1-17.el8.x86_64 libogg-2:1.3.2-10.el8.x86_64 libpciaccess-0.14-1.el8.x86_64 libpng-2:1.6.34-5.el8.x86_64 libpng-devel-2:1.6.34-5.el8.x86_64 libproxy-0.4.15-5.2.el8.x86_64 libquadmath-8.3.1-5.1.el8.x86_64 libquadmath-devel-8.3.1-5.1.el8.x86_64 librsvg2-2.42.7-4.el8.x86_64 libsndfile-1.0.28-10.el8.x86_64 libsoup-2.62.3-2.el8.x86_64 libsrtp-1.5.4-8.el8.x86_64 libstemmer-0-10.585svn.el8.x86_64 libthai-0.1.27-2.el8.x86_64 libtheora-1:1.1.1-21.el8.x86_64 libuv-1:1.40.0-1.el8.x86_64 libvisual-1:0.4.0-24.el8.x86_64 libvorbis-1:1.3.6-2.el8.x86_64 libwayland-client-1.17.0-1.el8.x86_64 libwayland-cursor-1.17.0-1.el8.x86_64 libwayland-egl-1.17.0-1.el8.x86_64 libwayland-server-1.17.0-1.el8.x86_64 libwebp-1.0.0-1.el8.x86_64 libxcb-1.13.1-1.el8.x86_64 libxcb-devel-1.13.1-1.el8.x86_64 libxml2-devel-2.9.7-8.el8.x86_64 libxshmfence-1.3-2.el8.x86_64 mesa-libEGL-20.1.4-1.el8.x86_64 mesa-libGL-20.1.4-1.el8.x86_64 mesa-libGL-devel-20.1.4-1.el8.x86_64 mesa-libGLU-9.0.0-15.el8.x86_64 mesa-libGLU-devel-9.0.0-15.el8.x86_64 mesa-libgbm-20.1.4-1.el8.x86_64 mesa-libglapi-20.1.4-1.el8.x86_64 mmtf-cpp-devel-1.0.0-5.el8.x86_64 msgpack-3.1.0-3.el8.x86_64 msgpack-devel-3.1.0-3.el8.x86_64 netcdf-4.7.0-2.el8.x86_64 netcdf-devel-4.7.0-2.el8.x86_64 openal-soft-1.18.2-7.el8.x86_64 openblas-0.3.3-5.el8.x86_64 openblas-threads-0.3.3-5.el8.x86_64 opus-1.3-0.4.beta.el8.x86_64 orc-0.4.28-3.el8.x86_64 pango-1.42.4-6.el8.x86_64 pcre2-utf16-10.32-2.el8.x86_64 perl-Carp-1.42-396.el8.noarch perl-Data-Dumper-2.167-399.el8.x86_64 perl-Digest-1.17-395.el8.noarch perl-Digest-MD5-2.55-396.el8.x86_64 perl-Encode-4:2.97-3.el8.x86_64 perl-Errno-1.28-416.el8.x86_64 perl-Exporter-5.72-396.el8.noarch perl-File-Path-2.15-2.el8.noarch perl-File-Temp-0.230.600-1.el8.noarch perl-Getopt-Long-1:2.50-4.el8.noarch perl-HTTP-Tiny-0.074-1.el8.noarch perl-IO-1.38-416.el8.x86_64 perl-IO-Socket-IP-0.39-5.el8.noarch perl-IO-Socket-SSL-2.066-4.module_el8.3.0+410+ff426aa3.noarch perl-MIME-Base64-3.15-396.el8.x86_64 perl-Mozilla-CA-20160104-7.module_el8.3.0+416+dee7bcef.noarch perl-Net-SSLeay-1.88-1.module_el8.3.0+410+ff426aa3.x86_64 perl-PathTools-3.74-1.el8.x86_64 perl-Pod-Escapes-1:1.07-395.el8.noarch perl-Pod-Perldoc-3.28-396.el8.noarch perl-Pod-Simple-1:3.35-395.el8.noarch perl-Pod-Usage-4:1.69-395.el8.noarch perl-Scalar-List-Utils-3:1.49-2.el8.x86_64 perl-Socket-4:2.027-3.el8.x86_64 perl-Storable-1:3.11-3.el8.x86_64 perl-Term-ANSIColor-4.06-396.el8.noarch perl-Term-Cap-1.17-395.el8.noarch perl-Text-ParseWords-3.30-395.el8.noarch perl-Text-Tabs+Wrap-2013.0523-395.el8.noarch perl-Time-Local-1:1.280-1.el8.noarch perl-URI-1.73-3.el8.noarch perl-Unicode-Normalize-1.25-396.el8.x86_64 perl-constant-1.33-396.el8.noarch perl-interpreter-4:5.26.3-416.el8.x86_64 perl-libnet-3.11-3.el8.noarch perl-libs-4:5.26.3-416.el8.x86_64 perl-macros-4:5.26.3-416.el8.x86_64 perl-parent-1:0.237-1.el8.noarch perl-podlators-4.11-1.el8.noarch perl-threads-1:2.21-2.el8.x86_64 perl-threads-shared-1.58-2.el8.x86_64 pixman-0.38.4-1.el8.x86_64 platform-python-devel-3.6.8-31.el8.x86_64 pulseaudio-libs-13.99.1-1.el8.x86_64 pulseaudio-libs-glib2-13.99.1-1.el8.x86_64 python-qt5-rpm-macros-5.13.1-1.el8.noarch python3-dbus-1.2.4-15.el8.x86_64 python3-mmtf-1.1.2-4.el8.noarch python3-msgpack-0.6.2-1.el8.x86_64 python3-numpy-1:1.14.3-9.el8.x86_64 python3-pip-9.0.3-18.el8.noarch python3-pyqt5-sip-4.19.19-2.el8.x86_64 python3-qt5-5.13.1-1.el8.x86_64 python3-qt5-base-5.13.1-1.el8.x86_64 python3-qt5-devel-5.13.1-1.el8.x86_64 python3-rpm-generators-5-6.el8.noarch python3-setuptools-39.2.0-6.el8.noarch python3-simplejson-3.17.0-2.el8.x86_64 python3-sip-devel-4.19.19-2.el8.x86_64 python36-3.6.8-2.module_el8.3.0+562+e162826a.x86_64 python36-devel-3.6.8-2.module_el8.3.0+562+e162826a.x86_64 python36-rpm-macros-3.6.8-2.module_el8.3.0+562+e162826a.noarch qt5-qtbase-5.12.5-6.el8.x86_64 qt5-qtbase-common-5.12.5-6.el8.noarch qt5-qtbase-devel-5.12.5-6.el8.x86_64 qt5-qtbase-gui-5.12.5-6.el8.x86_64 qt5-qtconnectivity-5.12.5-1.el8.x86_64 qt5-qtdeclarative-5.12.5-1.el8.x86_64 qt5-qtlocation-5.12.5-1.el8.x86_64 qt5-qtmultimedia-5.12.5-1.el8.x86_64 qt5-qtsensors-5.12.5-1.el8.x86_64 qt5-qtserialport-5.12.5-1.el8.x86_64 qt5-qtsvg-5.12.5-1.el8.x86_64 qt5-qttools-common-5.12.5-2.el8.noarch qt5-qttools-libs-designer-5.12.5-2.el8.x86_64 qt5-qttools-libs-help-5.12.5-2.el8.x86_64 qt5-qtwebchannel-5.12.5-1.el8.x86_64 qt5-qtwebsockets-5.12.5-2.el8.x86_64 qt5-qtx11extras-5.12.5-1.el8.x86_64 qt5-qtxmlpatterns-5.12.5-1.el8.x86_64 qt5-rpm-macros-5.12.5-3.el8.noarch sip-4.19.19-2.el8.x86_64 soundtouch-2.0.0-2.el8.x86_64 vim-filesystem-2:8.0.1763-15.el8.noarch webrtc-audio-processing-0.3-9.el8.x86_64 xcb-util-0.4.0-10.el8.x86_64 xcb-util-image-0.4.0-9.el8.x86_64 xcb-util-keysyms-0.4.0-7.el8.x86_64 xcb-util-renderutil-0.3.9-10.el8.x86_64 xcb-util-wm-0.4.1-12.el8.x86_64 xml-common-0.6.3-50.el8.noarch xorg-x11-proto-devel-2020.1-3.el8.noarch xz-devel-5.2.4-3.el8.x86_64 zlib-devel-1.2.11-16.2.el8_3.x86_64 Complete! Finish: build setup for pymol-2.4.0-4.1.el8.ors.src.rpm Start: rpmbuild pymol-2.4.0-4.1.el8.ors.src.rpm warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn - 1.5.0.2-3.20120218svn3982 warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn - 1.2-5.20090709svn3827 Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.GruKsP + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pymol-open-source-2.4.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/pymol-open-source-2.4.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd pymol-open-source-2.4.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/bin/cat /builddir/build/SOURCES/pymol-setup.py.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-wmclass-main.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-wmclass-pmgapp.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-mmtf.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-python3.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-2.4.0-fix_bug119.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + ln -sr modules/web modules/pymol_web + sed -i 1d modules/pmg_tk/startup/apbs_tools.py + pathfix.py -pn -i /usr/bin/python3.6 test/cyg test/run test/show test/cyg: updating test/run: updating test/show: updating + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.gZHIZA + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + export 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + /usr/bin/python3.6 setup.py build '--executable=/usr/bin/python3.6 -s' --use-msgpackc=c++11 --glut running build running build_py creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-x86_64-3.6/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-x86_64-3.6/pymol2 creating build/lib.linux-x86_64-3.6/pymol copying modules/pymol/xwin.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/seqalign.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/pymolhttpd.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/morphing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/lazyio.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/diagnosing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/colorprinting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/_gui.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/__main__.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/__init__.py -> build/lib.linux-x86_64-3.6/pymol creating build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-3.6/pymol/wizard creating build/lib.linux-x86_64-3.6/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.linux-x86_64-3.6/pymol/stereochemistry creating build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-x86_64-3.6/pymol/plugins creating build/lib.linux-x86_64-3.6/pymol/opengl copying modules/pymol/opengl/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl creating build/lib.linux-x86_64-3.6/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl/glut creating build/lib.linux-x86_64-3.6/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl/glu creating build/lib.linux-x86_64-3.6/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl/gl creating build/lib.linux-x86_64-3.6/pymol/contrib copying modules/pymol/contrib/__init__.py -> build/lib.linux-x86_64-3.6/pymol/contrib creating build/lib.linux-x86_64-3.6/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.linux-x86_64-3.6/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.linux-x86_64-3.6/pymol/Qt creating build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-3.6/pmg_tk creating build/lib.linux-x86_64-3.6/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-x86_64-3.6/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/startup creating build/lib.linux-x86_64-3.6/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins creating build/lib.linux-x86_64-3.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/normal creating build/lib.linux-x86_64-3.6/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/demo creating build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.linux-x86_64-3.6/pmg_qt creating build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax creating build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.linux-x86_64-3.6/pmg_qt/forms creating build/lib.linux-x86_64-3.6/chempy copying modules/chempy/xyz.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/__init__.py -> build/lib.linux-x86_64-3.6/chempy creating build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-3.6/chempy/tinker creating build/lib.linux-x86_64-3.6/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.linux-x86_64-3.6/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.linux-x86_64-3.6/chempy/mmtf creating build/lib.linux-x86_64-3.6/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-3.6/chempy/fragments creating build/lib.linux-x86_64-3.6/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-3.6/chempy/fast creating build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-3.6/chempy/champ creating build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/pmg_qt/forms/save_object.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/askpartial.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms running build_ext building 'pymol._cmd' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/build creating build/temp.linux-x86_64-3.6/build/generated creating build/temp.linux-x86_64-3.6/contrib creating build/temp.linux-x86_64-3.6/contrib/mmtf-c creating build/temp.linux-x86_64-3.6/contrib/uiuc creating build/temp.linux-x86_64-3.6/contrib/uiuc/plugins creating build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin creating build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src creating build/temp.linux-x86_64-3.6/layer0 creating build/temp.linux-x86_64-3.6/layer1 creating build/temp.linux-x86_64-3.6/layer2 creating build/temp.linux-x86_64-3.6/layer3 creating build/temp.linux-x86_64-3.6/layer4 creating build/temp.linux-x86_64-3.6/layer5 creating build/temp.linux-x86_64-3.6/modules creating build/temp.linux-x86_64-3.6/modules/cealign creating build/temp.linux-x86_64-3.6/modules/cealign/src creating build/temp.linux-x86_64-3.6/ov creating build/temp.linux-x86_64-3.6/ov/src g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD build/generated/ShaderText.cpp -o build/temp.linux-x86_64-3.6/build/generated/ShaderText.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/mmtf-c/mmtf_parser.cpp -o build/temp.linux-x86_64-3.6/contrib/mmtf-c/mmtf_parser.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/inthash.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/inthash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/mmtf-c/mmtf_parser.cpp: In function ‘bool MMTF_unpack_from_file(const char*, MMTF_container*)’: contrib/mmtf-c/mmtf_parser.cpp:1075:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, fileLen, 1, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function ‘int {anonymous}::write_structure(void*, int, const molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1902:9: warning: unused variable ‘last_ctnumber’ [-Wunused-variable] int last_ctnumber = -1; ^~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerInitAll’: contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:271:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ok) ok = ok && (molfile_xyzplugin_init() == VMDPLUGIN_SUCCESS); ^~ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:273:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(ok) { ^~ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerFreeAll’: contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:411:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ok) ok = ok && (molfile_xyzplugin_fini() == VMDPLUGIN_SUCCESS); ^~ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:413:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ return ok; ^~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘DEN_read_volumetric_data’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘POT_read_volumetric_data’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘abinit_header’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(skip, 1, 8, fp); ^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘GEO_read_next_timestep’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, "%*s %f %f %f", &x, &y, &z); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] static void whereami(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] static void thisline(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: ‘fpexpftoc’ defined but not used [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: ‘have_keyline’ defined but not used [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:962:12: warning: ‘goto_keyline’ defined but not used [-Wunused-function] static int goto_keyline(FILE *file, ...) { ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: ‘strtoupper’ defined but not used [-Wunused-function] static char *strtoupper(char *s) { ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: ‘iswhiteline’ defined but not used [-Wunused-function] static int iswhiteline(char *s) { ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:846:13: warning: ‘eatwhitelines’ defined but not used [-Wunused-function] static void eatwhitelines(FILE *file) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:13: warning: ‘eatline’ defined but not used [-Wunused-function] static void eatline(FILE * fd, int n) ^~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: ‘symmetry_expand’ defined but not used [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:540:13: warning: ‘angular_momentum_expon’ defined but not used [-Wunused-function] static void angular_momentum_expon(int *ang_mom_expon, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: ‘del_wavefunction’ defined but not used [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: ‘replace_wavefunction’ defined but not used [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:471:27: warning: ‘add_wavefunction’ defined but not used [-Wunused-function] static qm_wavefunction_t* add_wavefunction(qm_timestep_t *ts) { ^~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:437:18: warning: ‘init_qmdata’ defined but not used [-Wunused-function] static qmdata_t* init_qmdata() { ^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_timestep(void*, int, molfile_timestep_t*)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_bonds_aux(void*, int*, int**, int**, float**)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘void* open_bgf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function ‘open_binpos_read’: contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magicchar,sizeof(char),4,fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&igarb,sizeof(int),1,fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function ‘int read_brix_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(brick, sizeof(char), 512, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function ‘void* open_brix_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%3s", keyWord); ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:109:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f %f %f %f %f %f", keyWord, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &prod); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &plus); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &sigma); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_timestep’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘open_car_read’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:29: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] sprintf(atom->resname, "%d", resid); ^~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:28: note: directive argument in the range [-2147483648, 9999999] sprintf(atom->resname, "%d", resid); ^~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:85: /usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 12 bytes into a destination of size 8 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘int read_ccp4_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:495:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(rowdata, sizeof(char), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:525:67: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(rowdata, sizeof(unsigned char), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:556:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(rowdata, sizeof(float), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:588:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(rowdata, sizeof(short), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:623:67: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(rowdata, sizeof(unsigned short), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:655:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(rowdata, sizeof(uchar3), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘void* open_ccp4_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:304:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(symData, 81, fd); ~~~~~^~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:42: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘void* open_ccp4_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:287:42: warning: ‘dataOffset’ may be used uninitialized in this function [-Wmaybe-uninitialized] } else if ((dataOffset > CCP4HDSIZE) && (dataOffset < (1024*1024))) { ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function ‘void* open_cube_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:175:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); // go on to next line ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); // skip second header line ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:326:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:337:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:339:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(cube->fd, "%d", &cube->nsets); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:344:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(cube->fd, "%d", &orb); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); // gobble up rest of line ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: At global scope: contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:107:13: warning: ‘void cube_buildrotmat(cube_t*, float*, float*, float*)’ defined but not used [-Wunused-function] static void cube_buildrotmat(cube_t *cube, float *o, float *a, float *b) ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:42: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘int get_pte_idx_from_string(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘int read_mdf_bonds(void*, int*, int**, int**, float**, int**, int*, char***)’: contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:278:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:297:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:319:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:357:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘int read_mdf_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:223:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:241:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘void* open_mdf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:164:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:176:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:183:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function ‘read_dcdstep’: contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable ‘readlen’ set but not used [-Wunused-but-set-variable] fio_size_t readlen; /* number of bytes actually read */ ^~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: At top level: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:609:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2_timestep(void*, int, molfile_timestep_t*)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:289:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2_bonds_aux(void*, int*, int**, int**, float**)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:199:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:209:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:127:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:138:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘void* open_mol2_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:74:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:81:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_name ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:82:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read the molecule info ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:91:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_type ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read the charge_type ~~~~~^~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_structure’: contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:292:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (NULL == fgets(fbuffer, 1024, data->file)) ^~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:295:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (NULL == fgets(fbuffer, 1024, data->file)) ^~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘read_molden_rundata’: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:596:25: warning: variable ‘hessian_data’ set but not used [-Wunused-but-set-variable] molfile_qm_hessian_t *hessian_data; ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_timestep’: contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:669:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(fbuffer, 1024, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_timestep’: contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:554:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(fbuffer, 1024, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘count_orbitals’: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1165:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, " Ene= %f\n", &orbenergy); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1166:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, " Spin= %s\n", spin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1167:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, " Occup= %f\n", &occu); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); ^~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘open_molden_read’: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:224:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, "%d", &natm); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: At top level: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] static void whereami(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] static void thisline(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: ‘have_keyline’ defined but not used [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: ‘symmetry_expand’ defined but not used [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: ‘del_wavefunction’ defined but not used [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: ‘replace_wavefunction’ defined but not used [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: ‘get_pte_vdw_radius’ defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: ‘get_pte_mass’ defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘get_pte_label’ defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function ‘int read_dsn6_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(brick, sizeof(char), 512, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function ‘void* open_dsn6_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(fileHeader, sizeof(short), 19, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:63: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:91:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:116:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:132:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:149:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:155:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:161:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); //one more read to keep us in sync ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:170:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:217:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:237:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:256:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘read_next_timestep’: contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:103:10: warning: variable ‘numatoms’ set but not used [-Wunused-but-set-variable] int i, numatoms; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘open_namdbin_read’: contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:78:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&filen, sizeof(namdbin_int32), 1, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:70: contrib/uiuc/plugins/molfile_plugin/src/vmddir.h:145:12: warning: ‘int vmd_file_is_executable(const char*)’ defined but not used [-Wunused-function] static int vmd_file_is_executable(const char * filename) { ^~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp: In function ‘int read_parm7_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:78:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:25: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_atoms(const char*, int, molfile_atom_t*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:204:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_atype(const char*, int, molfile_atom_t*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:257:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_resnames(const char*, int, char*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:275:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_respointers(const char*, int, molfile_atom_t*, int, const char*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:289:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " %d", &cur); ~~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘parmstruct* read_parm7_header(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:368:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sdum, 512, file); ~~~~~^~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:371:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", sdum); // "%FLAG" ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:378:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", sdum); // "TITLE" or "CTITLE" ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:385:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", sdum); // "FORMAT (20a4)" ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:399:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(prm->title, sizeof(prm->title), file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:427:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sdum, sizeof(sdum), file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:439:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file,parm7, ~~~~~~^~~~~~~~~~~~ &prm->Natom, &prm->Ntypes, &prm->Nbonh, &prm->Nbona, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Ntheth, &prm->Ntheta, &prm->Nphih, &prm->Nphia, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Jparm, &prm->Nparm); ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:443:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, parm7, ~~~~~~^~~~~~~~~~~~~ &prm->Nnb, &prm->Nres, &prm->Mbona, &prm->Mtheta, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Mphia, &prm->Numbnd, &prm->Numang, &prm->Mptra, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Natyp, &prm->Nphb); ~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:447:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, parm7, &prm->Ifpert, &prm->Nbper, &prm->Ngper, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Ndper, &prm->Mbper, &prm->Mgper, &prm->Mdper, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->IfBox, &prm->Nmxrs, &prm->IfCap); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:451:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file,"%8d",&prm->Numextra); //BB ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int read_parm7_flag(FILE*, const char*, const char*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:79:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ~~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:87:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ~~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:97:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h: In member function ‘int {anonymous}::ReadPARM::readparm(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Charges[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:444:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Masses[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:510:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Rk[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:517:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Req[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:524:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Tk[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:531:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Teq[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:538:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pk[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:545:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pn[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:552:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Phase[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:559:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Solty[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:567:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn1[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:575:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn2[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:756:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB12[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:763:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB6[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:771:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &H[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:853:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT " " DBLFMT " " DBLFMT, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Box[0], &prm->Box[1], &prm->Box[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:867:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " %d " DBLFMT " " DBLFMT " " DBLFMT " " DBLFMT, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Natcap, &prm->Cutcap, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Xcap, &prm->Ycap, &prm->Zcap); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:53: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘int getUniqueResID(char*, int)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable ‘i’ [-Wunused-variable] int i, uid; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable ‘j’ [-Wunused-variable] int i, count, atomdata, pos, idx, xyzcount, j; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable ‘oldChain’ [-Wunused-variable] char oldChain[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readAngleBonds(molfile_atom_t*, pdbxParser*)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable ‘bondTable’ [-Wunused-variable] int bondTable[32]; ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable ‘j’ [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable ‘modelNum’ [-Wunused-variable] char modelNum[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable ‘atom’ [-Wunused-variable] molfile_atom_t * atom; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable ‘test’ [-Wunused-variable] int test = parser->nbonds + bnum; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readRMSDBonds(molfile_atom_t*, pdbxParser*)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable ‘bondTable’ [-Wunused-variable] int bondTable[32]; ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable ‘j’ [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable ‘modelNum’ [-Wunused-variable] char modelNum[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable ‘atom’ [-Wunused-variable] molfile_atom_t * atom; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘void* open_file_write(const char*, const char*, int)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable ‘fd’ [-Wunused-variable] FILE* fd; ^~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: At global scope: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:313:14: warning: ‘float stringToFloat(char*)’ defined but not used [-Wunused-function] static float stringToFloat(char * str) { ^~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:25: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘const char* get_pte_label(int)’ defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘void DDmkdir(const string&, mode_t, int, int)’: contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:15: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] sprintf(sub, "%03x/", i); ^~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:15: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:22: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] sprintf(subsub, "%03x", j); ^~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:22: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘std::__cxx11::string framefile(const string&, size_t, size_t, int, int)’: contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(answer, "%03x/", d1); ^~~~~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:22: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] sprintf(answer, "%03x/%03x/", d1, d2); ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:22: note: directive argument in the range [0, 2147483646] In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘int read_plt_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:143:51: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(datablock, sizeof(float), ndata, fd) != ndata ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘void* open_plt_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(intHeader, sizeof(int), 5, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(floatHeader, sizeof(float), 6, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void put_element_ply(PlyFile*, void*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:459:7: warning: unused variable ‘i’ [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void ascii_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable ‘i’ [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable ‘i’ [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:107:17: warning: variable ‘vert_other’ set but not used [-Wunused-but-set-variable] PlyOtherProp *vert_other=NULL; ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:108:17: warning: variable ‘face_other’ set but not used [-Wunused-but-set-variable] PlyOtherProp *face_other=NULL; ^~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (&len, sizeof(int), 1, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (str, len, 1, fp); ~~~~~~^~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void get_binary_item(FILE*, int, int*, unsigned int*, double*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 1, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 1, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 2, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 2, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 4, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 4, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 4, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 8, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:27: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void ascii_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1497:18: warning: ‘item’ may be used uninitialized in this function [-Wmaybe-uninitialized] item += item_size; ~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1477:19: warning: ‘other_data’ may be used uninitialized in this function [-Wmaybe-uninitialized] store_array = (char **) (elem_data + prop->offset); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1620:18: warning: ‘item’ may be used uninitialized in this function [-Wmaybe-uninitialized] item += item_size; ~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1601:19: warning: ‘other_data’ may be used uninitialized in this function [-Wmaybe-uninitialized] store_array = (char **) (elem_data + prop->offset); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘get_atom_radius’: contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] char *name, *type; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable ‘name’ set but not used [-Wunused-but-set-variable] char *name, *type; ^~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: ‘fortread_4’ defined but not used [-Wunused-function] static int fortread_4(void *dest, int n, int swap, FILE *fd) { ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘fort_get_endian_reclen’ defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘fort_eat_recmark’ defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28, from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘swap8_aligned’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function ‘open_rst_read’: contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:48:11: warning: variable ‘timesteprst’ set but not used [-Wunused-but-set-variable] double timesteprst; ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:67:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(title, 82, fd); ^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:70:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 82, fd); ^~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘int read_edm_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:240:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 13, edm->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘void eatline(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:44:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function ‘int read_spider_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(datablock, total * sizeof(float), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:36: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function ‘void* open_fs4_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:48: contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: ‘void strnwscpy(char*, const char*, int)’ defined but not used [-Wunused-function] static void strnwscpy(char *target, const char *source, const int len) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘int fort_get_endian_reclen(int, int, int, int*, int*)’ defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘int fort_eat_recmark(FILE*, int)’ defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:47: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘have_gamess’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1106:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] char word[3][BUFSIZ]; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_stats’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2264:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] char word[7][BUFSIZ]; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_wavefunction’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:3573:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] char word[6][BUFSIZ]; ^~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); ^~~~~~~~~~~~~~~~~~~~~~~~ At top level: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1002:13: warning: ‘print_input_data’ defined but not used [-Wunused-function] static void print_input_data(qmdata_t *data) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: ‘get_pte_vdw_radius’ defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: ‘get_pte_mass’ defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘get_pte_label’ defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] static void whereami(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] static void thisline(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: ‘fpexpftoc’ defined but not used [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: ‘strtoupper’ defined but not used [-Wunused-function] static char *strtoupper(char *s) { ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: ‘iswhiteline’ defined but not used [-Wunused-function] static int iswhiteline(char *s) { ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:22: warning: variable ‘o’ set but not used [-Wunused-but-set-variable] float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:28: warning: variable ‘s’ set but not used [-Wunused-but-set-variable] float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘int read_uhbd_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:254:66: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(datablock + z*xysize, sizeof(float), xysize, fd) != xysize) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&headersize, sizeof(int), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:224:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘open_vasp5xdatcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_data’: contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:237:60: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:282:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_metadata’: contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘open_vaspchgcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: At top level: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_options’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1398:41: warning: ‘%s’ directive writing up to 8191 bytes into a region of size 8190 [-Wformat-overflow=] sprintf(data->basis_string, "%d-%s%sG%s", ^~ ngauss, (data->gbasis+1), diffuse, ~~~~~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:27, from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: /usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 4 or more bytes (assuming 16386) into a destination of size 8192 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1394:43: warning: ‘%s’ directive writing up to 8191 bytes into a region of size between 8176 and 8186 [-Wformat-overflow=] sprintf(data->basis_string, "STO-%dG%s%s", ^~ ngauss, diffuse, polarization); ~~~~~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:27, from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: /usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16399 bytes into a destination of size 8192 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:239:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:242:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:204:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘open_vaspoutcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:87:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_data’: contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_metadata’: contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘open_vaspparchg_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: At top level: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘write_vaspposcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:360:40: warning: argument to ‘sizeof’ in ‘strncpy’ call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess] strncpy(tmptype, atom->type, sizeof(atom->type)); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘open_vaspposcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:69:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:73:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:283:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:228:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 4; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:233:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:237:32: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:252:44: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 10 - data->version; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘open_vaspxdatcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:89:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:92:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:97:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:111:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:121:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘void line3(FILE*, GRASSP*)’: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line3, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(vertex, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(access, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(normal, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(triangle, 3 * sizeof(int), ntriangles, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(properties, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(striangle, sizeof(short), 3 * ntriangles, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(properties, sizeof(float), 3 * nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘read_vaspxml_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:139:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:144:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘open_vaspxml_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:86:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:92:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp:51: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function ‘void* open_grid_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:60: contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: ‘void strnwscpy(char*, const char*, int)’ defined but not used [-Wunused-function] static void strnwscpy(char *target, const char *source, const int len) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘int fort_get_endian_reclen(int, int, int, int*, int*)’ defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘int fort_eat_recmark(FILE*, int)’ defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:59: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function ‘int mdio_readline(md_file*, char*, int, int)’: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, n, mf->f); ~~~~~^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:48, from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:276:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data_ex(void*, molfile_volumetric_readwrite_t*)’: contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:338:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:371:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:306:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:72: contrib/uiuc/plugins/include/vmdconio.h: At global scope: contrib/uiuc/plugins/include/vmdconio.h:56:12: warning: ‘int vmdcon_printf(int, const char*, ...)’ defined but not used [-Wunused-function] static int vmdcon_printf(int lvl, const char *fmt, ...) { ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_timestep(void*, int, molfile_timestep_t*)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_bonds_aux(void*, int*, int**, int**, float**)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘void* open_xbgf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Matrix.cpp -o build/temp.linux-x86_64-3.6/layer0/Matrix.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void eatline(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:238:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void* open_xsf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:408:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:442:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:444:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:446:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:448:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:450:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:473:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:508:16: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:37: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘int get_pte_idx_from_string(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Block.cpp -o build/temp.linux-x86_64-3.6/layer0/Block.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Crystal.cpp -o build/temp.linux-x86_64-3.6/layer0/Crystal.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/MemoryDebug.cpp -o build/temp.linux-x86_64-3.6/layer0/MemoryDebug.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer0/MemoryDebug.cpp: In function ‘void* VLADeleteRaw(void*, int, unsigned int)’: layer0/MemoryDebug.cpp:223:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(index < -old_size) ~~~~~~^~~~~~~~~~~ layer0/MemoryDebug.cpp:235:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] (index < vla->size) && ((count + index) <= vla->size)) { ~~~~~~^~~~~~~~~~~ layer0/MemoryDebug.cpp: In function ‘void* VLAInsertRaw(void*, int, unsigned int)’: layer0/MemoryDebug.cpp:256:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(index < -old_size) ~~~~~~^~~~~~~~~~~ layer0/MemoryDebug.cpp:263:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(index > old_size) ~~~~~~^~~~~~~~~~ layer0/MemoryDebug.cpp:266:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if((index >= 0) && (count > 0) && (index <= old_size)) { ~~~~~~^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/MyPNG.cpp -o build/temp.linux-x86_64-3.6/layer0/MyPNG.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Deferred.cpp -o build/temp.linux-x86_64-3.6/layer0/Deferred.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Err.cpp -o build/temp.linux-x86_64-3.6/layer0/Err.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer0/MyPNG.cpp: In function ‘int MyPNGWrite(const char*, const pymol::Image&, float, int, int, float, float, void*)’: layer0/MyPNG.cpp:301:20: warning: comparison of integer expressions of different signedness: ‘png_uint_32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] for(k = 0; k < height; k++) ~~^~~~~~~~ layer0/MyPNG.cpp:342:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] for(b = 0; b < height; b++) { ~~^~~~~~~~ layer0/MyPNG.cpp:343:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] for(a = 0; a < width; a++) { ~~^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Parse.cpp -o build/temp.linux-x86_64-3.6/layer0/Parse.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Feedback.cpp -o build/temp.linux-x86_64-3.6/layer0/Feedback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Pixmap.cpp -o build/temp.linux-x86_64-3.6/layer0/Pixmap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/PostProcess.cpp -o build/temp.linux-x86_64-3.6/layer0/PostProcess.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Field.cpp -o build/temp.linux-x86_64-3.6/layer0/Field.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer0/Field.cpp: In function ‘PyObject* FieldAsNumPyArray(CField*, short int)’: layer0/Field.cpp:83:1: warning: label ‘ok_except1’ defined but not used [-Wunused-label] ok_except1: ^~~~~~~~~~ layer0/Field.cpp: In function ‘CField* FieldNewFromPyList(PyMOLGlobals*, PyObject*)’: layer0/Field.cpp:179:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] ok = ok && I->size() == size; ~~~~~~~~~~^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/ShaderMgr.cpp -o build/temp.linux-x86_64-3.6/layer0/ShaderMgr.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/File.cpp -o build/temp.linux-x86_64-3.6/layer0/File.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/GenericBuffer.cpp -o build/temp.linux-x86_64-3.6/layer0/GenericBuffer.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/GraphicsUtil.cpp -o build/temp.linux-x86_64-3.6/layer0/GraphicsUtil.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Isosurf.cpp -o build/temp.linux-x86_64-3.6/layer0/Isosurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Map.cpp -o build/temp.linux-x86_64-3.6/layer0/Map.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Match.cpp -o build/temp.linux-x86_64-3.6/layer0/Match.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/ShaderPrg.cpp -o build/temp.linux-x86_64-3.6/layer0/ShaderPrg.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUT.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUT.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Sphere.cpp -o build/temp.linux-x86_64-3.6/layer0/Sphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUT8x13.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUT8x13.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUT9x15.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUT9x15.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Tetsurf.cpp -o build/temp.linux-x86_64-3.6/layer0/Tetsurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUTHel10.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel10.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUTHel12.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel12.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUTHel18.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel18.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontType.cpp -o build/temp.linux-x86_64-3.6/layer1/FontType.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/FontType.cpp:529:13: warning: ‘void FontTypeFree(CFont*)’ defined but not used [-Wunused-function] static void FontTypeFree(CFont * font) ^~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Movie.cpp -o build/temp.linux-x86_64-3.6/layer1/Movie.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Texture.cpp -o build/temp.linux-x86_64-3.6/layer0/Texture.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Tracker.cpp -o build/temp.linux-x86_64-3.6/layer0/Tracker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Triangle.cpp -o build/temp.linux-x86_64-3.6/layer0/Triangle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Ortho.cpp -o build/temp.linux-x86_64-3.6/layer1/Ortho.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Ortho.cpp:784:6: warning: ‘void OrthoKeyCmmd(PyMOLGlobals*, unsigned char)’ defined but not used [-Wunused-function] void OrthoKeyCmmd(PyMOLGlobals * G, unsigned char k) ^~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Util.cpp -o build/temp.linux-x86_64-3.6/layer0/Util.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from /usr/include/string.h:495, from /usr/include/python3.6m/Python.h:30, from layer0/os_python.h:32, from layer1/Ortho.cpp:24: In function ‘char* strcat(char*, const char*)’, inlined from ‘void OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at layer1/Ortho.cpp:333:13: /usr/include/bits/string_fortified.h:128:33: warning: ‘char* __builtin_strcat(char*, const char*)’ accessing 81 or more bytes at offsets [80, 261200] and [0, 9223372036854775807] may overlap 1 byte at offset [80, 9223372036854775807] [-Wrestrict] return __builtin___strcat_chk (__dest, __src, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strcat(char*, const char*)’, inlined from ‘void OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at layer1/Ortho.cpp:350:13: /usr/include/bits/string_fortified.h:128:33: warning: ‘char* __builtin_strcat(char*, const char*)’ accessing 81 or more bytes at offsets [80, 261200] and [0, 9223372036854775807] may overlap 1 byte at offset [80, 9223372036854775807] [-Wrestrict] return __builtin___strcat_chk (__dest, __src, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Util2.cpp -o build/temp.linux-x86_64-3.6/layer0/Util2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/P.cpp -o build/temp.linux-x86_64-3.6/layer1/P.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Vector.cpp -o build/temp.linux-x86_64-3.6/layer0/Vector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/P.cpp: In function ‘int WrapperObjectAssignSubScript(PyObject*, PyObject*, PyObject*)’: layer1/P.cpp:822:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (strlen(valstr) > ap->maxlen){ ~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Word.cpp -o build/temp.linux-x86_64-3.6/layer0/Word.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/P.cpp: At global scope: layer1/P.cpp:2764:13: warning: ‘void PLockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function] static void PLockAPIWhileBlocked(PyMOLGlobals * G) ^~~~~~~~~~~~~~~~~~~~ layer1/P.cpp:2753:13: warning: ‘void PUnlockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function] static void PUnlockAPIWhileBlocked(PyMOLGlobals * G) ^~~~~~~~~~~~~~~~~~~~~~ layer1/P.cpp: In function ‘int PLabelAtomAlt(PyMOLGlobals*, AtomInfoType*, const char*, const char*, int)’: layer1/P.cpp:322:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(label, origexpr, OrthoLineLength); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/PConv.cpp -o build/temp.linux-x86_64-3.6/layer1/PConv.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/os_gl.cpp -o build/temp.linux-x86_64-3.6/layer0/os_gl.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Basis.cpp -o build/temp.linux-x86_64-3.6/layer1/Basis.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/PConv.cpp: In function ‘int PConvPyListToBitmask(PyObject*, int*, ov_size)’: layer1/PConv.cpp:89:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] for(int i = 0; i < ll; i++) ~~^~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Picking.cpp -o build/temp.linux-x86_64-3.6/layer1/Picking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Pop.cpp -o build/temp.linux-x86_64-3.6/layer1/Pop.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer1/Pop.cpp:22: layer1/Pop.cpp: In function ‘void PopFree(PyMOLGlobals*)’: layer1/Pop.cpp:54:14: warning: deleting object of polymorphic class type ‘CPop’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Pop); ^~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/PyMOLObject.cpp -o build/temp.linux-x86_64-3.6/layer1/PyMOLObject.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/ButMode.cpp -o build/temp.linux-x86_64-3.6/layer1/ButMode.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer1/ButMode.cpp:22: layer1/ButMode.cpp: In function ‘void ButModeFree(PyMOLGlobals*)’: layer1/ButMode.cpp:144:14: warning: deleting object of polymorphic class type ‘CButMode’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->ButMode); ^~~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/CGO.cpp -o build/temp.linux-x86_64-3.6/layer1/CGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Ray.cpp -o build/temp.linux-x86_64-3.6/layer1/Ray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/CGO.cpp: In function ‘void CheckAttributesForUsage(const CGO*, AttribDataDesc&, AttribDataDesc&, CGO*, bool&)’: layer1/CGO.cpp:10716:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto idx = 0; idx < attrIdx; ++idx){ ~~~~^~~~~~~~~ layer1/CGO.cpp: In function ‘void PopulateOpsIntoStructuresForConversion(std::map&, std::map >&, AttribDataDesc&, AttribDataDesc&, int&, bool)’: layer1/CGO.cpp:10794:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (attrOp->incr_vertices != vertsperpickinfo){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ layer1/CGO.cpp: In function ‘CGO* CGOConvertToShader(const CGO*, AttribDataDesc&, AttribDataDesc&, int, GenericBuffer<34962>::buffer_layout, bool, int*, int, int)’: layer1/CGO.cpp:11096:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto idx = 0; idx < attrData.size(); ++idx){ ~~~~^~~~~~~~~~~~~~~~~ layer1/CGO.cpp:11108:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto idx = 0; idx < attrData.size(); ++idx){ ~~~~^~~~~~~~~~~~~~~~~ layer1/CGO.cpp:11117:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for (int nxt = 0; nxt < attribOp->incr_vertices; ++nxt){ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Ray.cpp: In function ‘void RayRender(CRay*, unsigned int*, double, float, int, unsigned int*)’: layer1/Ray.cpp:6064:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x_stop > width) ~~~~~~~^~~~~~~ layer1/Ray.cpp:6066:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y_stop > height) ~~~~~~~^~~~~~~~ layer1/Ray.cpp:6147:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++) ~~^~~~~~~~ layer1/Ray.cpp:6148:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp:6159:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x < (width - 1)) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6170:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y < (height - 1)) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6233:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++) ~~^~~~~~~~ layer1/Ray.cpp:6234:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp:6244:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x < (width - 1)) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6256:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y < (height - 1)) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6307:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++){ ~~^~~~~~~~ layer1/Ray.cpp:6327:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp:6346:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x < (width - 1)) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6360:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y < (height - 1)) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6374:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x && (y < (height - 1))) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6381:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y && (x < (width - 1))) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6388:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if((y < (height - 1)) && (x < (width - 1))) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6388:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if((y < (height - 1)) && (x < (width - 1))) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6544:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++) { ~~^~~~~~~~ layer1/Ray.cpp:6545:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp: In function ‘void RayRenderVRML2(CRay*, int, int, char**, float, float, float, float, float)’: layer1/Ray.cpp:1534:19: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 0 and 914 [-Wformat-overflow=] "Transform {\n" ^~~~~~~~~~~~~~~ " translation %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " rotation %8.6f %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " children [\n" ~~~~~~~~~~~~~~~ "%s" ~~~~ " ]\n" ~~~~~~ "}\n", ~~~~~ layer1/Ray.cpp:1543:72: vert2[2] - mid[2], axis[0], axis[1], axis[2], angle, geometry); ~~~~~~~~ layer1/Ray.cpp:1533:18: note: ‘sprintf’ output between 116 and 3302 bytes into a destination of size 1024 sprintf(buffer, ~~~~~~~^~~~~~~~ "Transform {\n" ~~~~~~~~~~~~~~~ " translation %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " rotation %8.6f %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " children [\n" ~~~~~~~~~~~~~~~ "%s" ~~~~ " ]\n" ~~~~~~ "}\n", ~~~~~~ vert2[0] - mid[0], ~~~~~~~~~~~~~~~~~~ vert2[1] - mid[1], ~~~~~~~~~~~~~~~~~~ vert2[2] - mid[2], axis[0], axis[1], axis[2], angle, geometry); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Ray.cpp: In function ‘int RayTraceThread(CRayThreadInfo*)’: layer1/Ray.cpp:3612:32: warning: ‘hl’ may be used uninitialized in this function [-Wmaybe-uninitialized] compute_background_for_pixel(bkrd_uc, isOutsideInY, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bg_image_mode, bg_image_tilesize, bg_rgb, bg_image_linear, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (unsigned char*) T->bkrd_data, T->bgWidth, T->bgHeight, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x, wr, hl, hpixelx, orig_opaque_back ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Rep.cpp -o build/temp.linux-x86_64-3.6/layer1/Rep.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.6/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Scene.cpp: In function ‘int SceneClick(Block*, int, int, int, int, double)’: layer1/Scene.cpp:4109:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] if(atIndex == I->LastPicked.src.index) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp: In function ‘void SceneFree(PyMOLGlobals*)’: layer1/Scene.cpp:5967:13: warning: deleting object of polymorphic class type ‘CScene’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete G->Scene; ^~~~~ layer1/Scene.cpp: In function ‘int SceneClick(Block*, int, int, int, int, double)’: layer1/Scene.cpp:4227:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 14 and 1037 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4227:15: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4097:20: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s -> (%s)", buffer, cEditorSele1 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 23 and 1046 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4097:13: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s -> (%s)", buffer, cEditorSele1 ENDF(G); ^~~~~~ layer1/Scene.cpp:4113:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s -> (%s)", buffer, cEditorSele2 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 23 and 1046 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4113:15: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s -> (%s)", buffer, cEditorSele2 ENDF(G); ^~~~~~ layer1/Scene.cpp:4121:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1014 [-Wformat-overflow=] sprintf(buffer, "cmd.edit(\"%s\",\"%s\")", buf1, buf2); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4121:22: note: ‘sprintf’ output between 16 and 2062 bytes into a destination of size 1024 sprintf(buffer, "cmd.edit(\"%s\",\"%s\")", buf1, buf2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:3984:24: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s -> (%s)\n", buffer, cEditorSele1 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 24 and 1047 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:3984:17: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s -> (%s)\n", buffer, cEditorSele1 ENDF(G); ^~~~~~ layer1/Scene.cpp:3990:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1014 [-Wformat-overflow=] sprintf(buf2, "cmd.edit(\"%s\",pkresi=1)", buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ layer1/Scene.cpp:3990:24: note: ‘sprintf’ output between 22 and 1045 bytes into a destination of size 1024 sprintf(buf2, "cmd.edit(\"%s\",pkresi=1)", buffer); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4018:24: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] PRINTF " You unpicked %s.", buffer ENDF(G); ^~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 16 and 1039 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4018:17: note: in expansion of macro ‘PRINTF’ PRINTF " You unpicked %s.", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4031:50: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTFB(G, FB_Scene, FB_Results) " You clicked %s -> (%s)\n", buffer, ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 21 and 1299 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4031:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Scene, FB_Results) " You clicked %s -> (%s)\n", buffer, ^~~~~~~ layer1/Scene.cpp:4285:20: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 14 and 1037 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4285:13: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4319:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] sprintf(buffer, "cmd.drag(\"byobject (%s)\")", buf1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4319:22: note: ‘sprintf’ output between 24 and 1047 bytes into a destination of size 1024 sprintf(buffer, "cmd.drag(\"byobject (%s)\")", buf1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4310:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1007 [-Wformat-overflow=] sprintf(buffer, "cmd.drag(\"bymol (%s)\")", buf1); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4310:22: note: ‘sprintf’ output between 21 and 1044 bytes into a destination of size 1024 sprintf(buffer, "cmd.drag(\"bymol (%s)\")", buf1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4369:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1012 [-Wformat-overflow=] sprintf(buffer, "cmd.center(\"%s\",state=%d)", buf1, I->LastPicked.context.state + 1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4369:31: note: directive argument in the range [-2147483647, 2147483647] layer1/Scene.cpp:4369:22: note: ‘sprintf’ output between 23 and 1056 bytes into a destination of size 1024 sprintf(buffer, "cmd.center(\"%s\",state=%d)", buf1, I->LastPicked.context.state + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4341:33: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1012 [-Wformat-overflow=] sprintf(buffer, "cmd.origin(\"%s\")", buf1); ^~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4341:24: note: ‘sprintf’ output between 15 and 1038 bytes into a destination of size 1024 sprintf(buffer, "cmd.origin(\"%s\")", buf1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4347:24: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 14 and 1037 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4347:17: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4434:29: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 1023 [-Wformat-overflow=] sprintf(buf2, "%s(%s)", sel_mode_kw, buffer); ^~~~~~~~ layer1/Scene.cpp:4434:22: note: ‘sprintf’ output 3 or more bytes (assuming 1026) into a destination of size 1024 sprintf(buf2, "%s(%s)", sel_mode_kw, buffer); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4441:35: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 753 and 1008 [-Wformat-overflow=] sprintf(buffer, "cmd.select('%s',\"%s(%s)\")", selName, sel_mode_kw, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~ layer1/Scene.cpp:4441:26: note: ‘sprintf’ output 20 or more bytes (assuming 1298) into a destination of size 1024 sprintf(buffer, "cmd.select('%s',\"%s(%s)\")", selName, sel_mode_kw, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~~ layer1/Scene.cpp:4416:29: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 760 and 1015 [-Wformat-overflow=] sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~ layer1/Scene.cpp:4416:22: note: ‘sprintf’ output 35 or more bytes (assuming 2591) into a destination of size 1024 sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName); ~~~~~~~~ layer1/Scene.cpp:4425:33: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 760 and 1015 [-Wformat-overflow=] sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~ layer1/Scene.cpp:4425:26: note: ‘sprintf’ output 35 or more bytes (assuming 2591) into a destination of size 1024 sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName); ~~~~~~~~ layer1/Scene.cpp:4428:35: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 753 and 1008 [-Wformat-overflow=] sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf2); ~~~~ layer1/Scene.cpp:4428:26: note: ‘sprintf’ output 29 or more bytes (assuming 1307) into a destination of size 1024 sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf2); ~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4393:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1022 [-Wformat-overflow=] sprintf(buf2, "(%s(%s))", sel_mode_kw, buffer); ^~~~~~~~~~ ~~~~~~ layer1/Scene.cpp:4393:20: note: ‘sprintf’ output 5 or more bytes (assuming 1028) into a destination of size 1024 sprintf(buf2, "(%s(%s))", sel_mode_kw, buffer); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4404:33: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 753 and 1008 [-Wformat-overflow=] sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf1); ~~~~ layer1/Scene.cpp:4404:24: note: ‘sprintf’ output 29 or more bytes (assuming 1307) into a destination of size 1024 sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf1); ~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/ScenePicking.cpp -o build/temp.linux-x86_64-3.6/layer1/ScenePicking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/ScenePicking.cpp: In function ‘void SceneRenderPicking(PyMOLGlobals*, int, int*, int, Picking*, int, int, Multipick*, SceneUnitContext*, GLenum)’: layer1/ScenePicking.cpp:249:7: warning: ‘previous.Picking::src.Pickable::index’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (pik->src.index != previous.src.index || ^~ layer1/ScenePicking.cpp:238:11: note: ‘previous.Picking::src.Pickable::index’ was declared here Picking previous; ^~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/COLLADA.cpp -o build/temp.linux-x86_64-3.6/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/SceneRay.cpp -o build/temp.linux-x86_64-3.6/layer1/SceneRay.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Character.cpp -o build/temp.linux-x86_64-3.6/layer1/Character.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/SceneRender.cpp -o build/temp.linux-x86_64-3.6/layer1/SceneRender.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/SceneRender.cpp:561:6: warning: ‘void AppendCopyWithChangedShader(PyMOLGlobals*, CGO*, CGO*, int, int)’ defined but not used [-Wunused-function] void AppendCopyWithChangedShader(PyMOLGlobals * G, CGO *destCGO, CGO *srcCGO, int frommode, int tomode){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Color.cpp -o build/temp.linux-x86_64-3.6/layer1/Color.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/ScrollBar.cpp -o build/temp.linux-x86_64-3.6/layer1/ScrollBar.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Seq.cpp -o build/temp.linux-x86_64-3.6/layer1/Seq.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Seq.cpp: In function ‘int SeqFindRowCol(PyMOLGlobals*, int, int, int*, int*, int)’: layer1/Seq.cpp:90:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if((char_num >= 0) && (char_num < row->ext_len) && (row->char2col)) { ~~~~~~~~~^~~~~~~~~~~~~~ layer1/Seq.cpp: In member function ‘virtual void CSeq::reshape(int, int)’: layer1/Seq.cpp:144:28: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->Row[a].ext_len > I->Size) ~~~~~~~~~~~~~~~~~~^~~~~~~~~ layer1/Seq.cpp: In member function ‘virtual void CSeq::draw(CGO*)’: layer1/Seq.cpp:427:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(max_len < row->ext_len) ~~~~~~~~^~~~~~~~~~~~~~ In file included from layer0/vla.h:7, from layer1/Symmetry.h:26, from layer1/PyMOLObject.h:27, from layer1/Seq.h:21, from layer1/Seq.cpp:22: layer1/Seq.cpp: In function ‘void SeqFree(PyMOLGlobals*)’: layer1/Seq.cpp:781:14: warning: deleting object of polymorphic class type ‘CSeq’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Seq); ^~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Control.cpp -o build/temp.linux-x86_64-3.6/layer1/Control.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Setting.cpp -o build/temp.linux-x86_64-3.6/layer1/Setting.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer0/vla.h:7, from layer1/Symmetry.h:26, from layer1/PyMOLObject.h:27, from layer1/Scene.h:22, from layer1/Control.cpp:25: layer1/Control.cpp: In function ‘void ControlFree(PyMOLGlobals*)’: layer1/Control.cpp:410:14: warning: deleting object of polymorphic class type ‘CControl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Control); ^~~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ layer1/Setting.cpp: In function ‘void SettingGenerateSideEffects(PyMOLGlobals*, int, const char*, int, int)’: layer1/Setting.cpp:2036:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (SettingGetGlobal_b(G, cSetting_precomputed_lighting)) ^~ layer1/Setting.cpp:2038:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ SceneInvalidate(G); ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Extrude.cpp -o build/temp.linux-x86_64-3.6/layer1/Extrude.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Extrude.cpp: In function ‘int ExtrudeCGOSurfaceTube(CExtrude*, CGO*, int, const float*, bool, int)’: layer1/Extrude.cpp:743:14: warning: ‘stop’ may be used uninitialized in this function [-Wmaybe-uninitialized] int start, stop; ^~~~ layer1/Extrude.cpp:743:7: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized] int start, stop; ^~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Font.cpp -o build/temp.linux-x86_64-3.6/layer1/Font.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/View.cpp -o build/temp.linux-x86_64-3.6/layer1/View.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Wizard.cpp -o build/temp.linux-x86_64-3.6/layer1/Wizard.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Wizard.cpp: In member function ‘virtual void CWizard::draw(CGO*)’: layer1/Wizard.cpp:880:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ layer1/Wizard.cpp:882:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ drawTopEdge(); ^~~~~~~~~~~ In file included from layer1/Wizard.cpp:25: layer1/Wizard.cpp: In function ‘void WizardFree(PyMOLGlobals*)’: layer1/Wizard.cpp:1034:14: warning: deleting object of polymorphic class type ‘CWizard’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Wizard); ^~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/AssemblyHelpers.cpp -o build/temp.linux-x86_64-3.6/layer2/AssemblyHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/AtomInfo.cpp -o build/temp.linux-x86_64-3.6/layer2/AtomInfo.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/AtomInfo.cpp: In function ‘bool AtomResiFromResv(char*, size_t, int, char)’: layer2/AtomInfo.cpp:821:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] return snprintf(resi, size, "%d%c", resv, inscode) < size; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ layer2/AtomInfo.cpp:822:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] return snprintf(resi, size, "%d", resv) < size; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/AtomInfoHistory.cpp -o build/temp.linux-x86_64-3.6/layer2/AtomInfoHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/BondTypeHistory.cpp -o build/temp.linux-x86_64-3.6/layer2/BondTypeHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Shaker.cpp -o build/temp.linux-x86_64-3.6/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/CifFile.cpp -o build/temp.linux-x86_64-3.6/layer2/CifFile.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Symmetry.cpp -o build/temp.linux-x86_64-3.6/layer1/Symmetry.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Text.cpp -o build/temp.linux-x86_64-3.6/layer1/Text.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/CifMoleculeReader.cpp -o build/temp.linux-x86_64-3.6/layer2/CifMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/CifMoleculeReader.cpp: In member function ‘void seqvec_t::set(int, const char*)’: layer2/CifMoleculeReader.cpp:99:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if (i > size()) ~~^~~~~~~~ layer2/CifMoleculeReader.cpp: In member function ‘const char* seqvec_t::get(int) const’: layer2/CifMoleculeReader.cpp:105:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if (i < 1 || i > size()) ~~^~~~~~~~ layer2/CifMoleculeReader.cpp: In function ‘CoordSet** read_pdbx_struct_assembly(PyMOLGlobals*, const pymol::cif_data*, const AtomInfoType*, const CoordSet*, const char*)’: layer2/CifMoleculeReader.cpp:765:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while (j < c_src_len * c_it->size()) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/CoordSet.cpp -o build/temp.linux-x86_64-3.6/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/CoordSet.cpp: In member function ‘void CoordSet::invalidateRep(int, int)’: layer2/CoordSet.cpp:1157:28: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (I->Spheroid.size() != ~~~~~~~~~~~~~~~~~~~^~ I->NAtIndex * GetSpheroidSphereRec(G)->nDot) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/CoordSet.cpp: In function ‘void CoordSetAtomToPDBStrVLA(PyMOLGlobals*, char**, int*, const AtomInfoType*, const float*, int, const PDBInfoRec*, const double*)’: layer2/CoordSet.cpp:987:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 6 bytes from a string of the same length [-Wstringop-truncation] strncpy(anisoline, "ANISOU", 6); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ layer2/CoordSet.cpp: In member function ‘void CoordSet::update(int)’: layer2/CoordSet.cpp:1240:39: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 223 [-Wformat-truncation=] PRINTFB(G, FB_CoordSet, FB_Blather) " CoordSetUpdate-Entered: object %s state %d cset %p\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/DistSet.cpp -o build/temp.linux-x86_64-3.6/layer2/DistSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/GadgetSet.cpp -o build/temp.linux-x86_64-3.6/layer2/GadgetSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/TypeFace.cpp -o build/temp.linux-x86_64-3.6/layer1/TypeFace.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectSlice.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectSlice.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/HydrogenAdder.cpp -o build/temp.linux-x86_64-3.6/layer2/HydrogenAdder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectSlice.cpp: In function ‘PyObject* ObjectSliceAllStatesAsPyList(ObjectSlice*)’: layer2/ObjectSlice.cpp:78:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::invalidate(int, int, int)’: layer2/ObjectSlice.cpp:210:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < State.size(); a++) { ~~^~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: layer2/ObjectSlice.cpp:633:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘void ObjectSliceDrag(ObjectSlice*, int, int, float*, float*, float*)’: layer2/ObjectSlice.cpp:679:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘int ObjectSliceGetVertex(ObjectSlice*, int, int, float*)’: layer2/ObjectSlice.cpp:750:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::render(RenderInfo*)’: layer2/ObjectSlice.cpp:925:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp:967:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(cur_state >= I->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp:981:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp:1229:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(cur_state >= I->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘ObjectSliceState* ObjectSliceStateGetActive(ObjectSlice*, int)’: layer2/ObjectSlice.cpp:1247:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘ObjectSlice* ObjectSliceFromMap(PyMOLGlobals*, ObjectSlice*, ObjectMap*, int, int)’: layer2/ObjectSlice.cpp:1288:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectSlice.cpp: In function ‘void ObjectSliceRecomputeExtent(ObjectSlice*)’: layer2/ObjectSlice.cpp:1365:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/HydrogenAdder.cpp: In function ‘int ObjectMoleculeAddSeleHydrogensRefactored(ObjectMolecule*, int, int)’: layer2/HydrogenAdder.cpp:286:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] for (unsigned atm = 0; atm < n_atom_old; atm++) { ~~~~^~~~~~~~~~~~ layer2/HydrogenAdder.cpp:306:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] for (unsigned atm = 0; atm < n_atom_old; ++atm) { ~~~~^~~~~~~~~~~~ layer2/HydrogenAdder.cpp:360:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] for (unsigned idx = 0; idx < cs->NIndex; ++idx) { ~~~~^~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: layer2/ObjectSlice.cpp:639:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 225 [-Wformat-truncation=] "ObjectSliceUpdate-Error: map '%s' has been deleted.\n", oss->MapName ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSlice.cpp:34: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 51 and 306 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSlice.cpp:638:9: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSlice, FB_Errors) ^~~~~~~ layer2/ObjectSlice.cpp:650:13: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 231 [-Wformat-truncation=] " ObjectSlice: updating \"%s\".\n", I->Name ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSlice.cpp:34: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 28 and 283 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSlice.cpp:649:11: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSlice, FB_Blather) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/MmodTyping.cpp -o build/temp.linux-x86_64-3.6/layer2/MmodTyping.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/MmtfMoleculeReader.cpp -o build/temp.linux-x86_64-3.6/layer2/MmtfMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectSurface.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/MmtfMoleculeReader.cpp: In function ‘ObjectMolecule* ObjectMoleculeReadMmtfStr(PyMOLGlobals*, ObjectMolecule*, const char*, int, int, int, int, int, int)’: layer2/MmtfMoleculeReader.cpp:230:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for (int l = 0, offset = atomIndex; l < group->bondAtomListCount / 2; ++l) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/MmtfMoleculeReader.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for (int l = 0; l < container->bondAtomListCount / 2; ++l) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘PyObject* ObjectSurfaceAllStatesAsPyList(ObjectSurface*)’: layer2/ObjectSurface.cpp:81:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: layer2/ObjectSurface.cpp:232:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::invalidate(int, int, int)’: layer2/ObjectSurface.cpp:277:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceInvalidateMapName(ObjectSurface*, const char*, const char*)’: layer2/ObjectSurface.cpp:307:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘ObjectSurface* ObjectSurfaceFromBox(PyMOLGlobals*, ObjectSurface*, ObjectMap*, int, int, float*, float*, float, int, float, float*, int, int)’: layer2/ObjectSurface.cpp:1043:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectSurface.cpp: In function ‘pymol::Result ObjectSurfaceGetLevel(ObjectSurface*, int)’: layer2/ObjectSurface.cpp:1117:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state >= I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceSetLevel(ObjectSurface*, float, int, int)’: layer2/ObjectSurface.cpp:1136:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state >= I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp:1139:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/Mol2Typing.cpp -o build/temp.linux-x86_64-3.6/layer2/Mol2Typing.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: layer2/ObjectSurface.cpp:264:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] " ObjectSurfaceDump: %s written to %s\n", I->Name, fname ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSurface.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output 34 or more bytes (assuming 289) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSurface.cpp:263:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSurface, FB_Actions) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/MolV3000.cpp -o build/temp.linux-x86_64-3.6/layer2/MolV3000.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::update()’: layer2/ObjectSurface.cpp:493:15: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] " ObjectSurface: updating \"%s\".\n", I->Name ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSurface.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 30 and 285 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSurface.cpp:492:13: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSurface, FB_Details) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectAlignment.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectAlignment.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectVolume.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectVolume.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectVolume.cpp: In function ‘PyObject* ObjectVolumeAllStatesAsPyList(ObjectVolume*)’: layer2/ObjectVolume.cpp:127:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeAllStatesFromPyList(ObjectVolume*, PyObject*)’: layer2/ObjectVolume.cpp:248:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeInvalidateMapName(ObjectVolume*, const char*, const char*)’: layer2/ObjectVolume.cpp:313:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::invalidate(int, int, int)’: layer2/ObjectVolume.cpp:341:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::update()’: layer2/ObjectVolume.cpp:402:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp:440:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (i = 0; i < vs->Ramp.size(); i += 5) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::render(RenderInfo*)’: layer2/ObjectVolume.cpp:759:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); ++a) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In function ‘ObjectVolume* ObjectVolumeFromXtalSym(PyMOLGlobals*, ObjectVolume*, ObjectMap*, CSymmetry*, int, int, float*, float*, float, int, float, float*, int)’: layer2/ObjectVolume.cpp:1130:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectVolume.cpp: In function ‘void ObjectVolumeRecomputeExtent(ObjectVolume*)’: layer2/ObjectVolume.cpp:1231:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: At global scope: layer2/ObjectVolume.cpp:657:15: warning: ‘size_t createPreintegrationTexture(PyMOLGlobals*, const float*, int)’ defined but not used [-Wunused-function] static size_t createPreintegrationTexture(PyMOLGlobals * G, const float *Table, const int count) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer0/Map.h:24, from layer1/Basis.h:20, from layer1/Ray.h:24, from layer1/PyMOLObject.h:24, from layer2/ObjectAlignment.h:22, from layer2/ObjectAlignment.cpp:27: layer0/Vector.h: In member function ‘virtual void ObjectAlignment::update()’: layer0/Vector.h:362:3: warning: ‘*((void*)& gvert +8)’ may be used uninitialized in this function [-Wmaybe-uninitialized] dst[2] = src[2]; ^~~ layer2/ObjectAlignment.cpp:926:39: note: ‘*((void*)& gvert +8)’ was declared here float mean[3], vert[3], gvert[3]; ^~~~~ In file included from layer0/Map.h:24, from layer1/Basis.h:20, from layer1/Ray.h:24, from layer1/PyMOLObject.h:24, from layer2/ObjectAlignment.h:22, from layer2/ObjectAlignment.cpp:27: layer0/Vector.h:361:3: warning: ‘*((void*)& gvert +4)’ may be used uninitialized in this function [-Wmaybe-uninitialized] dst[1] = src[1]; ^~~ layer2/ObjectAlignment.cpp:926:39: note: ‘*((void*)& gvert +4)’ was declared here float mean[3], vert[3], gvert[3]; ^~~~~ In file included from layer0/Map.h:24, from layer1/Basis.h:20, from layer1/Ray.h:24, from layer1/PyMOLObject.h:24, from layer2/ObjectAlignment.h:22, from layer2/ObjectAlignment.cpp:27: layer0/Vector.h:360:3: warning: ‘gvert’ may be used uninitialized in this function [-Wmaybe-uninitialized] dst[0] = src[0]; ^~~ layer2/ObjectAlignment.cpp:926:39: note: ‘gvert’ was declared here float mean[3], vert[3], gvert[3]; ^~~~~ layer2/ObjectVolume.cpp: In function ‘ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)’: layer2/ObjectVolume.cpp:74:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] "ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectVolume.cpp:20: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 46 and 301 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectCGO.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectCGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::render(RenderInfo*)’: layer2/ObjectCGO.cpp:502:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (!ray) ^~ layer2/ObjectCGO.cpp:504:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ ObjectCGORenderState(G, pass, ray, I, info, sobj, color, ramp, use_shader, cgo_lighting); ^~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepAngle.cpp -o build/temp.linux-x86_64-3.6/layer2/RepAngle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectCallback.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectCallback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepCartoon.cpp -o build/temp.linux-x86_64-3.6/layer2/RepCartoon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectDist.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectDist.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepCartoon.cpp: In function ‘Rep* RepCartoonNew(CoordSet*, int)’: layer2/RepCartoon.cpp:3715:57: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class CCInOut’; use assignment or value-initialization instead [-Wclass-memaccess] memset(car, 0, sizeof(*car) * cs->NAtIndex); ^ layer2/RepCartoon.cpp:39:7: note: ‘class CCInOut’ declared here class CCInOut { ^~~~~~~ layer2/ObjectDist.cpp:40:13: warning: ‘void ObjectDistFree(ObjectDist*)’ declared ‘static’ but never defined [-Wunused-function] static void ObjectDistFree(ObjectDist * I); ^~~~~~~~~~~~~~ In file included from layer2/CoordSet.h:24, from layer2/RepCartoon.h:21, from layer2/RepCartoon.cpp:27: layer1/Setting.h: In function ‘V AtomSettingGetWD(PyMOLGlobals*, T*, int, V) [with V = bool; T = const AtomInfoType]’: layer1/Setting.h:421:11: warning: ‘out’ is used uninitialized in this function [-Wuninitialized] int i = *out; ^~~~ In file included from layer2/ObjectMolecule.h:25, from layer2/CoordSet.h:25, from layer2/RepCartoon.h:21, from layer2/RepCartoon.cpp:27: layer2/AtomInfo.h:500:5: note: ‘out’ was declared here V out; ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectGadget.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectGadget.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepCartoon.cpp: In function ‘int GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals*, ObjectMolecule*, CoordSet*, CGO*, CExtrude*, int, int*, float*, float*, float*, const CCInOut*, int*, float*, int, int, float, float)’: layer2/RepCartoon.cpp:1596:20: warning: ‘atom_index2’ may be used uninitialized in this function [-Wmaybe-uninitialized] int atom_index1, atom_index2, *s, ^~~~~~~~~~~ layer2/RepCartoon.cpp: In function ‘void do_ring(PyMOLGlobals*, nuc_acid_data*, int, int*, ObjectMolecule*, CoordSet*, float, CGO*, int, float, int, int, int, float, float, int*, float*, float)’: layer2/RepCartoon.cpp:1010:65: warning: ‘i’ may be used uninitialized in this function [-Wmaybe-uninitialized] float ladder_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], cSetting_cartoon_transparency, 1.0f - alpha); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectGadgetRamp.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectGadgetRamp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepCylBond.cpp -o build/temp.linux-x86_64-3.6/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectGroup.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectGroup.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMap.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDihedral.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDihedral.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘int ObjectMapValidXtal(ObjectMap*, int)’: layer2/ObjectMap.cpp:133:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if((state >= 0) && (state < I->State.size())) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapTrim(ObjectMap*, int, float*, float*, int)’: layer2/ObjectMap.cpp:912:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapDouble(ObjectMap*, int)’: layer2/ObjectMap.cpp:929:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapHalve(ObjectMap*, int, int)’: layer2/ObjectMap.cpp:944:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘void ObjectMapRegeneratePoints(ObjectMap*)’: layer2/ObjectMap.cpp:1187:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (i=0; iState.size();i++){ ~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘PyObject* ObjectMapAllStatesAsPyList(ObjectMap*)’: layer2/ObjectMap.cpp:1277:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapAllStatesFromPyList(ObjectMap*, PyObject*)’: layer2/ObjectMap.cpp:1435:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapNewCopy(PyMOLGlobals*, const ObjectMap*, ObjectMap**, int, int)’: layer2/ObjectMap.cpp:1507:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(state = 0; state < src->State.size(); state++) { ~~~~~~^~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:1516:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(source_state < src->State.size()) { ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMapState* ObjectMapStatePrime(ObjectMap*, int)’: layer2/ObjectMap.cpp:1533:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘void ObjectMapUpdateExtents(ObjectMap*)’: layer2/ObjectMap.cpp:1546:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In member function ‘virtual void ObjectMap::invalidate(int, int, int)’: layer2/ObjectMap.cpp:1672:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapCCP4StrToMap(ObjectMap*, char*, int, int, int, int)’: layer2/ObjectMap.cpp:2300:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] if(bytes < 256 * sizeof(int)) { ~~~~~~^~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:2310:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:2958:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapXPLORStrToMap(ObjectMap*, char*, int, int)’: layer2/ObjectMap.cpp:3232:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapFLDStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:3445:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapBRIXStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:3774:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:4179:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadCCP4(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int, int)’: layer2/ObjectMap.cpp:4695:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapDXStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:4885:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadDXFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5173:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapACNTStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:5207:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadACNTFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5403:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadFLDFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5439:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadBRIXFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5475:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadGRDFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5512:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadXPLOR(PyMOLGlobals*, ObjectMap*, const char*, int, int, int)’: layer2/ObjectMap.cpp:5561:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyBrick(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: layer2/ObjectMap.cpp:5715:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyMap(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: layer2/ObjectMap.cpp:5813:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27, from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from layer0/os_numpy.h:8, from layer2/ObjectMap.cpp:22: /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope: /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] _import_array(void) ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDistDash.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDistDash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘void ObjectMapDump(const ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5982:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 239 [-Wformat-truncation=] " ObjectMapDump: %s written to %s\n", om->Name, fname ENDFB(om->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output 30 or more bytes (assuming 285) into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDistLabel.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDistLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int)’: layer2/ObjectMap.cpp:2977:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:2986:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:2992:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:3074:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDot.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDot.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:4297:5: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] " ObjectMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 14 and 1037 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:4297:5: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] " ObjectMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 14 and 1037 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMesh.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepEllipsoid.cpp -o build/temp.linux-x86_64-3.6/layer2/RepEllipsoid.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepLabel.cpp -o build/temp.linux-x86_64-3.6/layer2/RepLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMesh.cpp: In function ‘void ObjectMeshDump(ObjectMesh*, const char*, int, int)’: layer2/ObjectMesh.cpp:329:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] " ObjectMeshDump: %s written to %s\n", I->Name, fname ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectMesh.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output 31 or more bytes (assuming 286) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMesh.cpp:328:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectMesh, FB_Actions) ^~~~~~~ layer2/ObjectMesh.cpp: In member function ‘virtual void ObjectMesh::update()’: layer2/ObjectMesh.cpp:507:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 226 [-Wformat-truncation=] "ObjectMeshUpdate-Error: map '%s' has been deleted.\n", ms->MapName ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectMesh.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 50 and 305 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMesh.cpp:506:9: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectMesh, FB_Errors) ^~~~~~~ layer2/ObjectMesh.cpp:540:15: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 232 [-Wformat-truncation=] " ObjectMesh: updating \"%s\".\n", I->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectMesh.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 27 and 282 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMesh.cpp:539:13: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMesh, FB_Details) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMolecule.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepMesh.cpp -o build/temp.linux-x86_64-3.6/layer2/RepMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule.cpp: In function ‘pymol::Result<> ObjectMoleculeAddBondByIndices(ObjectMolecule*, unsigned int, unsigned int, int)’: layer2/ObjectMolecule.cpp:4416:12: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if (atm1 >= I->NAtom || atm2 >= I->NAtom) { ~~~~~^~~~~~~~~~~ layer2/ObjectMolecule.cpp:4416:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if (atm1 >= I->NAtom || atm2 >= I->NAtom) { ~~~~~^~~~~~~~~~~ layer2/ObjectMolecule.cpp: In member function ‘bool ObjectMolecule::atomHasAnyCoordinates(size_t) const’: layer2/ObjectMolecule.cpp:12085:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] for (size_t i = 0; i < NCSet; ++i) { ~~^~~~~~~ layer2/RepMesh.cpp: In function ‘Rep* RepMeshNew(CoordSet*, int)’: layer2/RepMesh.cpp:1062:13: warning: ‘field’ may be used uninitialized in this function [-Wmaybe-uninitialized] DeleteP(field); ^~~~~ layer2/ObjectMolecule.cpp: In function ‘const char* findflag(PyMOLGlobals*, const char*, const char*, const char*)’: layer2/ObjectMolecule.cpp:1451:9: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 194 [-Wformat-truncation=] " ObjectMolecule-Error: Unrecognized file format (can't find \"%s\").\n", pat ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 66 and 1089 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:1450:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Errors) ^~~~~~~ layer2/ObjectMolecule.cpp:1469:9: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 194 [-Wformat-truncation=] " ObjectMolecule-Error: Unrecognized file format (can't find \"%s\").\n", pat ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 66 and 1089 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:1468:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Errors) ^~~~~~~ layer2/ObjectMolecule.cpp: In function ‘CoordSet* ObjectMoleculeXYZStr2CoordSet(PyMOLGlobals*, const char*, AtomInfoType**, const char**)’: layer2/ObjectMolecule.cpp:2972:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4 bytes from a string of length 1023 [-Wstringop-truncation] strncpy(ai->elem, cc, cElemNameLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.cpp: In function ‘CoordSet* ObjectMoleculeMOLStr2CoordSet(PyMOLGlobals*, const char*, AtomInfoType**, const char**)’: layer2/ObjectMolecule.cpp:7785:5: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 224 [-Wformat-truncation=] " ObjMolMOLStr2CoordSet: title '%s'\n", nameTmp ENDFB(G) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 34 and 289 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:7784:3: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Blather) ^~~~~~~ layer2/ObjectMolecule.cpp:7833:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4 bytes from a string of length 1023 [-Wstringop-truncation] strncpy(atInfo[a].elem, cc, cElemNameLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepNonbonded.cpp -o build/temp.linux-x86_64-3.6/layer2/RepNonbonded.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepNonbondedSphere.cpp -o build/temp.linux-x86_64-3.6/layer2/RepNonbondedSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule.cpp: In member function ‘virtual void ObjectMolecule::update()’: layer2/ObjectMolecule.cpp:10827:15: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] " ObjectMolecule-DEBUG: updating representations for state %d of \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 68 and 333 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:10826:13: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Blather) ^~~~~~~ layer2/ObjectMolecule.cpp: In function ‘int ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, const float*, int, int)’: layer2/ObjectMolecule.cpp:10955:21: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer, v[0], v[1], v[2], state + 1, mode, 0); ~~~~~~ layer2/ObjectMolecule.cpp:10955:21: note: directive argument in the range [-2147483647, 2147483647] layer2/ObjectMolecule.cpp:10955:14: note: ‘sprintf’ output between 78 and 2036 bytes into a destination of size 1024 sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer, v[0], v[1], v[2], state + 1, mode, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepRibbon.cpp -o build/temp.linux-x86_64-3.6/layer2/RepRibbon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSphere.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepSphere.cpp: In function ‘int RepGetSphereMode(PyMOLGlobals*, RepSphere*, bool)’: layer2/RepSphere.cpp:141:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (sphere_mode == 4) // sphere_mode 4 no longer exists, use default ^~ layer2/RepSphere.cpp:143:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ switch (sphere_mode) { ^~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepSphere.cpp: In function ‘Rep* RepSphereNew(CoordSet*, int)’: layer2/RepSphere.cpp:611:42: warning: ‘transp’ may be used uninitialized in this function [-Wmaybe-uninitialized] RepSphereAddAtomVisInfoToStoredVC(I, obj, cs, state, a1, ati1, a, sphere_scale, sphere_color, transp, &variable_alpha, sphere_add); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/RepSphere.cpp:656:12: warning: ‘sphere_color’ may be used uninitialized in this function [-Wmaybe-uninitialized] *(lc++) = sphere_color; ~~~~~~~~^~~~~~~~~~~~~~ layer2/RepSphere.cpp:611:42: warning: ‘sphere_scale’ may be used uninitialized in this function [-Wmaybe-uninitialized] RepSphereAddAtomVisInfoToStoredVC(I, obj, cs, state, a1, ati1, a, sphere_scale, sphere_color, transp, &variable_alpha, sphere_add); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSphereGenerate.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSphereGenerate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule2.cpp:3268:13: warning: ‘void AtomColumnFromPyList(ObjectMolecule&, PyObject*, std::function)’ defined but not used [-Wunused-function] static void AtomColumnFromPyList(ObjectMolecule& mol, PyObject* list, ^~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule2.cpp:3221:18: warning: ‘PyObject* AtomColumnAsPyList(const ObjectMolecule&, std::function<_object*(const AtomInfoType&)>)’ defined but not used [-Wunused-function] static PyObject* AtomColumnAsPyList(const ObjectMolecule& mol, ^~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSphereImmediate.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSphereImmediate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule2.cpp: In function ‘int ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, const char*, const char*, const char*, const char*, const char*, const char*, float, int, float, float, const char*, const float*, int, int, int, int)’: layer2/ObjectMolecule2.cpp:313:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] " ObjMol: created %s/%s/%s/%s`%d%c/%s\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMolecule2.cpp:20: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output 26 or more bytes (assuming 281) into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSurface.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Editor.cpp -o build/temp.linux-x86_64-3.6/layer3/Editor.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepSurface.cpp: In function ‘int RepSurfaceCGOGenerate(RepSurface*, RenderInfo*)’: layer2/RepSurface.cpp:669:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ok && pick_surface) ^~ layer2/RepSurface.cpp:671:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ok && I->VAO){ ^~ layer2/RepSurface.cpp: In function ‘void RepSurfaceSmoothEdges(RepSurface*)’: layer2/RepSurface.cpp:4417:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto j = 0; j < edges[i].size(); j += 3) { ~~^~~~~~~~~~~~~~~~~ layer2/RepSurface.cpp:4429:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto j = 0; j < edges[i].size(); j += 3) { ~~^~~~~~~~~~~~~~~~~ layer2/RepSurface.cpp:4440:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto i = 0; i < unique_edges.size(); i += 2) { ~~^~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp: In function ‘pymol::Result<> EditorSelect(PyMOLGlobals*, const char*, const char*, const char*, const char*, int, int, int)’: layer3/Editor.cpp:777:7: warning: variable ‘result’ set but not used [-Wunused-but-set-variable] int result = false; ^~~~~~ layer3/Editor.cpp: In function ‘int EditorLogState(PyMOLGlobals*, int)’: layer3/Editor.cpp:585:23: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1015 [-Wformat-overflow=] sprintf(buffer, "cmd.edit(%s,%s,%s,%s,pkresi=%d,pkbond=%d)", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1, buf2, buf3, buf4, pkresi ? 1 : 0, pkbond ? 1 : 0); ~~~~ layer3/Editor.cpp:585:23: note: directive argument in the range [0, 1] layer3/Editor.cpp:585:23: note: directive argument in the range [0, 1] layer3/Editor.cpp:585:14: note: ‘sprintf’ output between 32 and 4124 bytes into a destination of size 1024 sprintf(buffer, "cmd.edit(%s,%s,%s,%s,pkresi=%d,pkbond=%d)", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1, buf2, buf3, buf4, pkresi ? 1 : 0, pkbond ? 1 : 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp: In function ‘void EditorPrepareDrag(PyMOLGlobals*, CObject*, int, int, int, int)’: layer3/Editor.cpp:1944:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] " Editor: grabbing (%s).", name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer1/ButMode.h:20, from layer3/Editor.cpp:28: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 22 and 277 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Editor.cpp:1943:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Blather) ^~~~~~~ layer3/Editor.cpp: In function ‘void EditorDefineExtraPks(PyMOLGlobals*)’: layer3/Editor.cpp:335:21: warning: ‘%s’ directive writing up to 255 bytes into a region of size 249 [-Wformat-overflow=] sprintf(buffer, "(byres %s)", name); ^~~~~~~~~~~~ ~~~~ layer3/Editor.cpp:335:12: note: ‘sprintf’ output between 9 and 264 bytes into a destination of size 256 sprintf(buffer, "(byres %s)", name); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp:337:21: warning: ‘%s’ directive writing up to 255 bytes into a region of size 247 [-Wformat-overflow=] sprintf(buffer, "(bychain %s)", name); ^~~~~~~~~~~~~~ ~~~~ layer3/Editor.cpp:337:12: note: ‘sprintf’ output between 11 and 266 bytes into a destination of size 256 sprintf(buffer, "(bychain %s)", name); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp:339:21: warning: ‘%s’ directive writing up to 255 bytes into a region of size 246 [-Wformat-overflow=] sprintf(buffer, "(byobject %s)", name); ^~~~~~~~~~~~~~~ ~~~~ layer3/Editor.cpp:339:12: note: ‘sprintf’ output between 12 and 267 bytes into a destination of size 256 sprintf(buffer, "(byobject %s)", name); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Executive.cpp -o build/temp.linux-x86_64-3.6/layer3/Executive.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepWireBond.cpp -o build/temp.linux-x86_64-3.6/layer2/RepWireBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveIsosurfaceEtc(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int, int, int)’: layer3/Executive.cpp:1046:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveIsomeshEtc(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int, int, float)’: layer3/Executive.cpp:1191:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveVolume(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int)’: layer3/Executive.cpp:1364:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveLoad(PyMOLGlobals*, const ExecutiveLoadArgs&)’: layer3/Executive.cpp:3914:15: warning: unused variable ‘object_props’ [-Wunused-variable] const char* object_props = args.object_props.c_str(); ^~~~~~~~~~~~ layer3/Executive.cpp:3915:15: warning: unused variable ‘atom_props’ [-Wunused-variable] const char* atom_props = args.atom_props.c_str(); ^~~~~~~~~~ layer3/Executive.cpp:3924:8: warning: unused variable ‘mimic’ [-Wunused-variable] auto mimic = args.mimic; ^~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveMapSet(PyMOLGlobals*, const char*, int, const char*, int, int, int, int)’: layer3/Executive.cpp:6368:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(obj->State.size() > max_n_state) ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ layer3/Executive.cpp:6479:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(src_state < obj->State.size()) { ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘float ExecutiveRMSPairs(PyMOLGlobals*, const std::vector&, int, bool)’: layer3/Executive.cpp:11201:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for(a = 0; a < pairs; a++) { ~~^~~~~~~ layer3/Executive.cpp:11206:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] if(a < (pairs - 1)) ~~^~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveColor(PyMOLGlobals*, const char*, const char*, int, int)’: layer3/Executive.cpp:12555:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] int ok = false; ^~ layer3/Executive.cpp: In function ‘void ExecutiveSymExp(PyMOLGlobals*, const char*, const char*, const char*, float, int, int)’: layer3/Executive.cpp:14097:28: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(a = 0; a < nsymmat; a++) { ~~^~~~~~~~~ In file included from layer0/OOMac.h:22, from layer3/Executive.cpp:30: layer3/Executive.cpp: In function ‘void ExecutiveFree(PyMOLGlobals*)’: layer3/Executive.cpp:16361:14: warning: deleting object of polymorphic class type ‘CExecutive’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Executive); ^~~~~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSliceNew(PyMOLGlobals*, const char*, const char*, int, int)’: layer3/Executive.cpp:16674:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from layer3/Executive.h:37, from layer3/Executive.cpp:31: layer0/TrackerList.h: In instantiation of ‘pymol::TrackerAdapter::TrackerAdapterIterator::TrackerAdapterIterator(CTracker*, int) [with bool IsConst = false; T = SpecRec]’: layer0/TrackerList.h:99:29: required from ‘pymol::TrackerAdapter::iterator pymol::TrackerAdapter::begin() [with T = SpecRec; pymol::TrackerAdapter::iterator = pymol::TrackerAdapter::TrackerAdapterIterator]’ layer3/Executive.cpp:263:62: required from here layer0/TrackerList.h:80:15: warning: ‘pymol::TrackerAdapter::TrackerAdapterIterator::m_tracker’ will be initialized after [-Wreorder] CTracker* m_tracker; ^~~~~~~~~ layer0/TrackerList.h:79:22: warning: ‘int pymol::TrackerAdapter::TrackerAdapterIterator::m_iter_id’ [-Wreorder] int m_iter_id = -1; ^ layer0/TrackerList.h:35:14: warning: when initialized here [-Wreorder] explicit TrackerAdapterIterator(CTracker* tracker, int list_id) ^~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/Sculpt.cpp -o build/temp.linux-x86_64-3.6/layer2/Sculpt.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘int ExecutiveSetBondSettingFromString(PyMOLGlobals*, int, const char*, const char*, const char*, int, int, int)’: layer3/Executive.cpp:11590:17: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11590:17: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 560 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11589:15: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘PyObject* ExecutiveGetBondSetting(PyMOLGlobals*, int, char*, const char*, int, int, int)’: layer3/Executive.cpp:11672:8: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Getting: %s for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11672:8: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 38 and 556 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11671:6: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetBondSetting(PyMOLGlobals*, int, PyObject*, const char*, const char*, int, int, int)’: layer3/Executive.cpp:11775:19: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11775:19: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 560 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11774:17: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:11794:7: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 236 [-Wformat-truncation=] " Setting-Warning: '%s' is not a bond-level setting\n", name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 50 and 304 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11793:5: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Setting, FB_Warnings) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveUnsetBondSetting(PyMOLGlobals*, int, const char*, const char*, int, int, int)’: layer3/Executive.cpp:11851:15: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s unset for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, rec->obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11851:15: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 44 and 562 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11850:13: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetSetting(PyMOLGlobals*, int, PyObject*, const char*, int, int, int)’: layer3/Executive.cpp:12089:9: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 236 [-Wformat-truncation=] " Setting-Warning: '%s' is a %s-level setting\n", name, SettingLevelGetName(G, index) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output 42 or more bytes (assuming 296) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12088:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Setting, FB_Warnings) ^~~~~~~ layer3/Executive.cpp:11945:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects, state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value, nObj, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:11945:21: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1339 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11944:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:11942:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects.\n", name, value, nObj ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1321 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11941:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12034:27: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d atoms in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, op.i4, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 561 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12033:25: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12066:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value, rec->obj->Name, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12066:25: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12065:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12059:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12058:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:11901:18: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] PRINTF " Setting: %s set to %s.\n", name, value ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11901:11: note: in expansion of macro ‘PRINTF’ PRINTF " Setting: %s set to %s.\n", name, value ENDF(G); ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetSettingFromString(PyMOLGlobals*, int, const char*, const char*, int, int, int)’: layer3/Executive.cpp:12251:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects, state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, nObj, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12251:21: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1339 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12250:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12248:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects.\n", name, value2, nObj ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1321 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12247:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12283:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d atoms in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, op.i4, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 561 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12282:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12315:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, rec->obj->Name, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12315:25: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12314:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12307:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12306:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12211:18: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12211:11: note: in expansion of macro ‘PRINTF’ PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetObjSettingFromString(PyMOLGlobals*, int, const char*, CObject*, int, int, int)’: layer3/Executive.cpp:12380:19: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, obj->Name, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12380:19: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12379:17: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12372:19: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12371:17: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12351:18: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12351:11: note: in expansion of macro ‘PRINTF’ PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveUnsetSetting(PyMOLGlobals*, int, const char*, int, int, int)’: layer3/Executive.cpp:12490:23: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 215 [-Wformat-truncation=] " Setting: %s unset for %d atoms in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output 44 or more bytes (assuming 299) into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12489:21: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12515:25: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 227 [-Wformat-truncation=] " Setting: %s unset in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:12515:25: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output 41 or more bytes (assuming 305) into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12514:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12509:25: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 227 [-Wformat-truncation=] " Setting: %s unset in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output 32 or more bytes (assuming 287) into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12508:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘bool ExecutiveSetSymmetry(PyMOLGlobals*, pymol::zstring_view, int, const CSymmetry&, bool)’: layer3/Executive.cpp:6023:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 202 [-Wformat-truncation=] " %s-Details: Updated symmetry for '%s'\n", __func__, obj->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 56 and 311 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:6022:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Details) ^~~~~~~ layer3/Executive.cpp:6014:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 199 [-Wformat-truncation=] " %s-Warning: Cannot set symmetry for '%s' (type %s)\n", __func__, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 76 and 331 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:6013:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/SculptCache.cpp -o build/temp.linux-x86_64-3.6/layer2/SculptCache.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/SideChainHelper.cpp -o build/temp.linux-x86_64-3.6/layer2/SideChainHelper.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer1/PyMOLObject.h:26, from layer2/ObjectMolecule.h:24, from layer2/SideChainHelper.h:9, from layer2/SideChainHelper.cpp:10: layer1/Setting.h: In function ‘V AtomSettingGetWD(PyMOLGlobals*, T*, int, V) [with V = bool; T = const AtomInfoType]’: layer1/Setting.h:421:11: warning: ‘out’ is used uninitialized in this function [-Wuninitialized] int i = *out; ^~~~ In file included from layer2/ObjectMolecule.h:25, from layer2/SideChainHelper.h:9, from layer2/SideChainHelper.cpp:10: layer2/AtomInfo.h:500:5: note: ‘out’ was declared here V out; ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/VFont.cpp -o build/temp.linux-x86_64-3.6/layer2/VFont.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘void ExecutiveManageObject(PyMOLGlobals*, CObject*, int, int)’: layer3/Executive.cpp:14515:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] " Executive-Warning: name \"%s\" collides with a selection language keyword.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 73 and 328 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14514:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ layer3/Executive.cpp:14510:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] " Executive: object name \"%s\" is illegal -- renamed to 'all_'.\n", obj->Name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 61 and 316 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14509:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ layer3/Executive.cpp:14535:13: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] " Executive: object \"%s\" created.\n", obj->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 32 and 287 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14534:11: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveGroup(PyMOLGlobals*, const char*, const char*, int, int)’: layer3/Executive.cpp:2366:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] " Executive: adding '%s' to group '%s'.\n", rec->name, rec->group_name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 36 and 546 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:2365:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetSession(PyMOLGlobals*, PyObject*, int, int)’: layer3/Executive.cpp:5145:13: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 213 [-Wformat-truncation=] " Executive: skipping unrecognized object \"%s\" of type %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 56 and 321 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:5144:11: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Errors) ^~~~~~~ layer3/Executive.cpp:5170:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 210 [-Wformat-truncation=] "ExectiveSetNamedEntries-Error: after object \"%s\".\n", rec->name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 49 and 304 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:5169:9: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Errors) ^~~~~~~ layer3/Executive.cpp: In function ‘void ExecutiveSelectRect(PyMOLGlobals*, BlockRect*, int)’: layer3/Executive.cpp:7355:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7355:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7341:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7341:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7331:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7331:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7323:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7323:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7314:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 751 and 1008 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"(%s)\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7314:20: note: ‘sprintf’ output between 30 and 1310 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"(%s)\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveCopy(PyMOLGlobals*, const char*, const char*, int)’: layer3/Executive.cpp:9799:5: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] " Executive: object %s created.\n", oDst->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 30 and 285 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9798:3: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/AtomIterators.cpp -o build/temp.linux-x86_64-3.6/layer3/AtomIterators.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘void ExecutiveSymExp(PyMOLGlobals*, const char*, const char*, const char*, float, int, int)’: layer3/Executive.cpp:14181:21: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 238 [-Wformat-truncation=] "new_name before: %s\n", new_name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 19 and 1042 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14180:19: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Blather) ^~~~~~~ layer3/Executive.cpp:14184:21: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 236 [-Wformat-truncation=] "Making new object: %s from name=%s, a=%d, x=%d, y=%d, z=%d\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ new_name, name, (int)a, x, y, z ENDFB(G); ~~~~~~~~ layer3/Executive.cpp:14184:21: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:14184:21: note: directive argument in the range [-1, 2] layer3/Executive.cpp:14184:21: note: directive argument in the range [-1, 2] layer3/Executive.cpp:14184:21: note: directive argument in the range [-1, 2] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output 52 or more bytes (assuming 1078) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14183:19: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Blather) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveProcessPDBFile(PyMOLGlobals*, CObject*, const char*, const char*, const char*, int, int, int, char*, int, int, int, int)’: layer3/Executive.cpp:4344:35: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4344:35: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4344:24: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4342:35: warning: ‘%04d’ directive writing between 4 and 10 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, model_number); ^~~~~~~~~ layer3/Executive.cpp:4342:35: note: directive argument in the range [1, 2147483647] layer3/Executive.cpp:4342:24: note: ‘sprintf’ output between 6 and 267 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, model_number); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4331:35: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4331:35: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4331:24: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4322:33: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4322:33: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4322:22: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4320:33: warning: ‘%04d’ directive writing between 4 and 10 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, model_number); ^~~~~~~~~ layer3/Executive.cpp:4320:33: note: directive argument in the range [1, 2147483647] layer3/Executive.cpp:4320:22: note: ‘sprintf’ output between 6 and 267 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, model_number); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4309:33: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4309:33: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4309:22: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’: layer3/Executive.cpp:15534:42: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order_input, (location == -2) ? "upper" : "current"); ~~~~~~~~~~~ layer3/Executive.cpp:15534:26: note: ‘sprintf’ output between 32 and 1057 bytes into a destination of size 1024 sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order_input, (location == -2) ? "upper" : "current"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSetName(PyMOLGlobals*, const char*, const char*)’: layer3/Executive.cpp:3623:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 222 [-Wformat-truncation=] " Warning: Invalid characters in '%s' have been replaced or stripped\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name ENDFB(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 67 and 322 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:3622:5: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ layer3/AtomIterators.cpp: In member function ‘virtual bool SeleAtomIterator::next()’: layer3/AtomIterators.cpp:61:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while ((++a) < I->Table.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer3/AtomIterators.cpp: In member function ‘virtual bool SeleCoordIterator::next()’: layer3/AtomIterators.cpp:129:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (a++; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/CifDataValueFormatter.cpp -o build/temp.linux-x86_64-3.6/layer3/CifDataValueFormatter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveRemoveAtoms(PyMOLGlobals*, const char*, int)’: layer3/Executive.cpp:9162:17: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 207 and 217 [-Wformat-truncation=] " Remove: eliminated %d atoms in model \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 42 and 307 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9161:15: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveBond(PyMOLGlobals*, const char*, const char*, int, int, int)’: layer3/Executive.cpp:9508:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 200 and 210 [-Wformat-truncation=] " Valence: %d bond valences adjusted in model \"%s\".\n", cnt, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 49 and 314 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9507:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp:9495:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 214 and 224 [-Wformat-truncation=] " Bond: %d bonds added to model \"%s\".\n", cnt, rec->obj->Name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 35 and 300 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9494:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp:9520:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 208 and 218 [-Wformat-truncation=] " Unbond: %d bonds removed from model \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 41 and 306 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9519:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveLoad(PyMOLGlobals*, const ExecutiveLoadArgs&)’: layer3/Executive.cpp:4132:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 255 [-Wformat-truncation=] "%s", buf ENDFB(G); ^~~~ ~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 1 and 1024 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:4131:5: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result > ExecutiveSpectrum(PyMOLGlobals*, const char*, const char*, float, float, int, int, const char*, int, int, int)’: layer3/Executive.cpp:4839:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 8 equals destination size [-Wstringop-truncation] strncpy(value_s, raw_ptr, sizeof(value_e)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/ExecutivePython.cpp -o build/temp.linux-x86_64-3.6/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveSetRawAlignment(PyMOLGlobals*, pymol::zstring_view, PyObject*, pymol::zstring_view, int, int)’: layer3/ExecutivePython.cpp:175:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] for(size_t c = 0; c < n_cols; ++c) { ~~^~~~~~~~ layer3/ExecutivePython.cpp:184:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] for(size_t i = 0; i < n_idx; ++i) { ~~^~~~~~~ layer3/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveLoadObject(PyMOLGlobals*, const char*, PyObject*, int, int, int, int, int, int)’: layer3/ExecutivePython.cpp:150:5: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 255 [-Wformat-truncation=] "%s", buf ENDFB(G); ^~~~ ~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from layer3/Executive.h:20, from layer3/ExecutivePython.h:3, from layer3/ExecutivePython.cpp:1: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin_snprintf’ output between 1 and 1024 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/MaeExportHelpers.cpp -o build/temp.linux-x86_64-3.6/layer3/MaeExportHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer2/AtomInfo.h:23, from layer3/MaeExportHelpers.h:11, from layer3/MaeExportHelpers.cpp:11: layer1/Setting.h: In function ‘int MaeExportGetAtomStyle(PyMOLGlobals*, const SeleCoordIterator&)’: layer1/Setting.h:421:11: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized] int i = *out; ^~~~ In file included from layer3/MaeExportHelpers.h:11, from layer3/MaeExportHelpers.cpp:11: layer2/AtomInfo.h:500:5: note: ‘out’ was declared here V out; ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/MoleculeExporter.cpp -o build/temp.linux-x86_64-3.6/layer3/MoleculeExporter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/MovieScene.cpp -o build/temp.linux-x86_64-3.6/layer3/MovieScene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/PlugIOManager.cpp -o build/temp.linux-x86_64-3.6/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/PlugIOManager.cpp: In function ‘ObjectMap* PlugIOManagerLoadVol(PyMOLGlobals*, ObjectMap*, const char*, int, int, const char*)’: layer3/PlugIOManager.cpp:403:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(obj->State.size() <= state) { ~~~~~~~~~~~~~~~~~~^~~~~~~~ layer3/PlugIOManager.cpp: In function ‘CObject* PlugIOManagerLoad(PyMOLGlobals*, CObject**, const char*, int, int, const char*, int)’: layer3/PlugIOManager.cpp:939:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 200 [-Wformat-truncation=] " PlugIOManagerLoad: can't load trajectory into object '%s'\n", obj->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer3/PlugIOManager.cpp:20: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 58 and 313 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/RingFinder.cpp -o build/temp.linux-x86_64-3.6/layer3/RingFinder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/RingFinder.cpp: In member function ‘void AbstractRingFinder::recursion(int, int)’: layer3/RingFinder.cpp:24:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if (depth < m_indices.size() - 1) { ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Seeker.cpp -o build/temp.linux-x86_64-3.6/layer3/Seeker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: layer3/Seeker.cpp:1207:23: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(row->len < min_pad) { ~~~~~~~~~^~~~~~~~~ layer3/Seeker.cpp:1243:23: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(row->len < min_pad) { ~~~~~~~~~^~~~~~~~~ layer3/Seeker.cpp: In lambda function: layer3/Seeker.cpp:1305:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for(int i = 0; i < str_size; i++){ ~~^~~~~~~~~~ layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: layer3/Seeker.cpp:1989:27: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(row->ext_len < stop) ~~~~~~~~~~~~~^~~~~~ layer3/Seeker.cpp: In function ‘void SeekerSelectionToggle(PyMOLGlobals*, CSeqRow*, int, int, int, int)’: layer3/Seeker.cpp:232:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer3/Seeker.cpp:20: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 28 and 1308 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Seeker.cpp: In function ‘void SeekerSelectionToggleRange(PyMOLGlobals*, CSeqRow*, int, int, int, int, int)’: layer3/Seeker.cpp:148:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer3/Seeker.cpp:20: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 28 and 1308 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Selector.cpp -o build/temp.linux-x86_64-3.6/layer3/Selector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Selector.cpp: In member function ‘virtual bool SelectorAtomIterator::next()’: layer3/Selector.cpp:212:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if ((++a) >= selector->Table.size()) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘bool SelectorIsSelectionDiscrete(PyMOLGlobals*, SelectorID_t, bool)’: layer3/Selector.cpp:1055:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorClassifyAtoms(PyMOLGlobals*, int, int, ObjectMolecule*)’: layer3/Selector.cpp:1184:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(a < I->Table.size()) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:1208:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(a1 < I->Table.size()) { ~~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘const char* SelectorGetNameFromIndex(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:1625:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 1; a < I->Info.size(); a++) { ~~^~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: layer3/Selector.cpp:1760:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:1788:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(a1 < I->Table.size()) { ~~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:1982:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘PyObject* SelectorColorectionGet(PyMOLGlobals*, const char*)’: layer3/Selector.cpp:2795:18: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(b = 0; b < n_used; b++) { ~~^~~~~~~~ layer3/Selector.cpp:2811:16: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(a = 0; a < n_used; a++) { ~~^~~~~~~~ layer3/Selector.cpp:2823:18: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(b = 0; b < n_used; b++) { ~~^~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorColorectionApply(PyMOLGlobals*, PyObject*, const char*)’: layer3/Selector.cpp:2871:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] for(b = 0; b < n_used; b++) { /* update selection indices */ ~~^~~~~~~~ layer3/Selector.cpp:2876:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:2880:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] for(b = 0; b < n_used; b++) { ~~^~~~~~~~ layer3/Selector.cpp: In function ‘PyObject* SelectorSecretsAsPyList(PyMOLGlobals*)’: layer3/Selector.cpp:2981:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->Info.size(); a++) { ~~^~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘PyObject* SelectorAsPyList(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3060:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCountStates(PyMOLGlobals*, int)’: layer3/Selector.cpp:3554:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCheckIntersection(PyMOLGlobals*, int, int)’: layer3/Selector.cpp:3578:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCountAtoms(PyMOLGlobals*, int, int)’: layer3/Selector.cpp:3596:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘void SelectorSetDeleteFlagOnSelectionInObject(PyMOLGlobals*, int, ObjectMolecule*, signed char)’: layer3/Selector.cpp:3611:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int* SelectorGetIndexVLAImpl(PyMOLGlobals*, CSelector*, SelectorID_t)’: layer3/Selector.cpp:3697:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘void SelectorLogSele(PyMOLGlobals*, const char*)’: layer3/Selector.cpp:3757:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetSingleObjectMolecule(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3922:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetFirstObjectMolecule(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3952:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘ObjectMolecule** SelectorGetObjectMoleculeVLA(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3976:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSubdivide(PyMOLGlobals*, const char*, SelectorID_t, SelectorID_t, SelectorID_t, SelectorID_t, const char*, const char*, int*)’: layer3/Selector.cpp:4434:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorGetSeleNCSet(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:4800:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorGetArrayNCSet(PyMOLGlobals*, const sele_array_t&, int)’: layer3/Selector.cpp:4830:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = start; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorMapMaskVDW(PyMOLGlobals*, int, ObjectMapState*, float, int)’: layer3/Selector.cpp:4991:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorMapGaussian(PyMOLGlobals*, int, ObjectMapState*, float, int, int, int, int, float)’: layer3/Selector.cpp:5348:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:5392:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorMapCoulomb(PyMOLGlobals*, int, ObjectMapState*, float, int, int, int, float)’: layer3/Selector.cpp:5600:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCreateObjectMolecule(PyMOLGlobals*, SelectorID_t, const char*, int, int, int, int, int, int, int)’: layer3/Selector.cpp:6288:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ob) ^~ layer3/Selector.cpp:6292:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ SelectorUpdateTable(G, source, -1); ^~~~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6303:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In lambda function: layer3/Selector.cpp:6329:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6359:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyModels; a < I->Obj.size(); a++) { /* find bonds wholly contained in the selection */ ~~^~~~~~~~~~~~~~~ layer3/Selector.cpp:6385:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6452:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) /* any selected atoms in this state? */ ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorEmbedSelection(PyMOLGlobals*, const int*, pymol::zstring_view, ObjectMolecule*, int, int)’: layer3/Selector.cpp:6892:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = start; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘sele_array_t SelectorSelectFromTagDict(PyMOLGlobals*, const std::unordered_map&)’: layer3/Selector.cpp:6987:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorModulate1(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:7548:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7570:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; ok && a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7613:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; ok && a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7642:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7679:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; ok && a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7720:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSelect0(PyMOLGlobals*, EvalElem*)’: layer3/Selector.cpp:7753:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7765:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7770:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7777:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7781:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7785:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7789:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7793:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7802:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7819:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7824:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7829:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7834:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7839:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7844:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7849:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7853:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7857:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7862:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7867:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7874:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7890:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7896:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7905:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7917:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7938:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘pymol::Result<> SelectorSelect1(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:8643:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyModels; a < I->Obj.size(); a++) ~~^~~~~~~~~~~~~~~ layer3/Selector.cpp:8653:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] else if(model > I->Obj.size()) ~~~~~~^~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSelect2(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:8735:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8739:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8787:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8798:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8809:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8820:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8835:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8846:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8857:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8868:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8883:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8894:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8905:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8916:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSelect3(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:8948:1: warning: label ‘ok_except1’ defined but not used [-Wunused-label] ok_except1: ^~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorLogic1(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:9415:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:9446:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorOperator22(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:9707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] for(a = 0; a < table_size; a++) { ~~^~~~~~~~~~~~ layer3/Selector.cpp:9729:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:9759:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:9764:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘pymol::Result > SelectorEvaluate(PyMOLGlobals*, std::vector >&, int, int)’: layer3/Selector.cpp:9913:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(ok && c < word.size()) { ~~^~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘DistSet* SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, float, float*)’: layer3/Selector.cpp:10503:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘DistSet* SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, float*, int*)’: layer3/Selector.cpp:10786:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:10799:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:10827:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘DistSet* SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, int, int, float*, int*)’: layer3/Selector.cpp:11032:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:11084:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:11130:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: At global scope: layer3/Selector.cpp:173:13: warning: ‘void SelectorCleanImpl(PyMOLGlobals*, CSelector*)’ declared ‘static’ but never defined [-Wunused-function] static void SelectorCleanImpl(PyMOLGlobals * G, CSelector *I); ^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: layer3/Selector.cpp:1830:21: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /usr/include/c++/8/tuple:39, from /usr/include/c++/8/functional:54, from layer3/Selector.cpp:19: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output 59 or more bytes (assuming 314) into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/SelectorTmp.cpp -o build/temp.linux-x86_64-3.6/layer3/SelectorTmp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.6/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer4/Cmd.cpp: In function ‘PyObject* CmdPushUndo(PyObject*, PyObject*)’: layer4/Cmd.cpp:2339:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ok) ^~ layer4/Cmd.cpp:2341:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(s0[0]) ^~ layer4/Cmd.cpp: In function ‘PyObject* Cmd_New(PyObject*, PyObject*)’: layer4/Cmd.cpp:3599:11: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] int ok = true; ^~ layer4/Cmd.cpp: In function ‘PyObject* CmdGetMinMax(PyObject*, PyObject*)’: layer4/Cmd.cpp:4648:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] int ok = false; ^~ In file included from layer4/Cmd.cpp:74: layer1/PConv.h: In instantiation of ‘PyObject* PConvToPyObject(const std::array<_Tp, _Nm>&) [with T = float; long unsigned int N = 3; PyObject = _object]’: layer4/Cmd.cpp:377:27: required from ‘PyObject* APIResult(PyMOLGlobals*, pymol::Result&) [with T = std::array; PyObject = _object; PyMOLGlobals = _PyMOLGlobals]’ layer4/Cmd.cpp:4212:29: required from here layer1/PConv.h:248:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for (int i = 0; i < N; ++i) { ~~^~~ layer4/Cmd.cpp: In function ‘PyObject* CmdLoadTraj(PyObject*, PyObject*)’: layer4/Cmd.cpp:5883:9: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 255 [-Wformat-truncation=] "%s", buf ENDFB(G); ^~~~ ~~~ In file included from layer1/Ortho.h:32, from layer1/ButMode.h:20, from layer4/Cmd.cpp:56: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 1 and 1024 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer4/Cmd.cpp:5882:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer4/Menu.cpp -o build/temp.linux-x86_64-3.6/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer4/PopUp.cpp -o build/temp.linux-x86_64-3.6/layer4/PopUp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer0/OOMac.h:22, from layer4/PopUp.cpp:23: layer4/PopUp.cpp: In function ‘void PopUpFree(Block*)’: layer4/PopUp.cpp:390:11: warning: deleting object of polymorphic class type ‘CPopUp’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(I); ^ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer5/PyMOL.cpp -o build/temp.linux-x86_64-3.6/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer5/PyMOL.cpp: In function ‘PyMOLreturn_status Loader(CPyMOL*, const char*, const char*, int, const char*, const char*, int, int, int, int, int, int)’: layer5/PyMOL.cpp:1541:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare] if((stop - start) >= sizeof(WordType)) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from layer5/PyMOL.cpp:23: layer5/PyMOL.cpp: In function ‘void PyMOL_Stop(CPyMOL*)’: layer5/PyMOL.cpp:2061:14: warning: deleting object of polymorphic class type ‘CMovie’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Movie); ^~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ layer5/PyMOL.cpp: In function ‘char* PyMOL_GetClickString(CPyMOL*, int)’: layer5/PyMOL.cpp:2717:19: warning: ‘%s’ directive writing up to 255 bytes into a region of size between 137 and 914 [-Wformat-overflow=] "type=object:molecule\nobject=%s\nindex=%d\nrank=%d\nid=%d\nsegi=%s\nchain=%s\nresn=%s\nresi=%d%s\nname=%s\nalt=%s\nclick=%s\nmod_keys=%s\nx=%d\ny=%d\n%s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer5/PyMOL.cpp:2727:70: ai->alt, butstr, modstr, I->ClickedX, I->ClickedY, posstr); ~~~~~~ layer5/PyMOL.cpp:2716:18: note: ‘sprintf’ output 112 or more bytes (assuming 1144) into a destination of size 1025 sprintf(result, ~~~~~~~^~~~~~~~ "type=object:molecule\nobject=%s\nindex=%d\nrank=%d\nid=%d\nsegi=%s\nchain=%s\nresn=%s\nresi=%d%s\nname=%s\nalt=%s\nclick=%s\nmod_keys=%s\nx=%d\ny=%d\n%s", ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I->ClickedObject, ~~~~~~~~~~~~~~~~~ I->ClickedIndex + 1, ~~~~~~~~~~~~~~~~~~~~ ai->rank, ~~~~~~~~~ ai->id, ~~~~~~~ LexStr(I->G, ai->segi), ~~~~~~~~~~~~~~~~~~~~~~~ LexStr(I->G, ai->chain), ~~~~~~~~~~~~~~~~~~~~~~~~ LexStr(I->G, ai->resn), ~~~~~~~~~~~~~~~~~~~~~~~ ai->resv, inscode_str, ~~~~~~~~~~~~~~~~~~~~~~ LexStr(I->G, ai->name), ~~~~~~~~~~~~~~~~~~~~~~~ ai->alt, butstr, modstr, I->ClickedX, I->ClickedY, posstr); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer5/TestPyMOL.cpp -o build/temp.linux-x86_64-3.6/layer5/TestPyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer5/main.cpp -o build/temp.linux-x86_64-3.6/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer5/main.cpp: In function ‘int MainCreateWindow(const char*)’: layer5/main.cpp:882:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] hint->res_name = "pymol"; ^~~~~~~ layer5/main.cpp:883:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] hint->res_class = "Pymol"; ^~~~~~~ layer5/main.cpp: In function ‘void launch(CPyMOLOptions*, int)’: layer5/main.cpp:1330:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] char *myArgv[8] = {"pymol"}; ^ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-x86_64-3.6/modules/cealign/src/ccealignmodule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from modules/cealign/src/tnt/tnt.h:49, from modules/cealign/src/ccealignmodule.cpp:38: modules/cealign/src/tnt/tnt_array2d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Array2D&)’: modules/cealign/src/tnt/tnt_array2d_utils.h:62:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=0; i>(std::istream&, TNT::Array3D&)’: modules/cealign/src/tnt/tnt_array3d_utils.h:47:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=0; i>(std::istream&, TNT::Fortran_Array2D&)’: modules/cealign/src/tnt/tnt_fortran_array2d_utils.h:61:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=1; i<=M; i++) ^~~ modules/cealign/src/tnt/tnt_fortran_array2d_utils.h:67:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ A = B; ^ In file included from modules/cealign/src/tnt/tnt.h:57, from modules/cealign/src/ccealignmodule.cpp:38: modules/cealign/src/tnt/tnt_fortran_array3d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Fortran_Array3D&)’: modules/cealign/src/tnt/tnt_fortran_array3d_utils.h:65:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=1; i<=M; i++) ^~~ modules/cealign/src/tnt/tnt_fortran_array3d_utils.h:70:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ A = B; ^ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVContext.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 ov/src/OVContext.cpp: In function ‘void OVContext_Del(OVContext*)’: ov/src/OVContext.cpp:21:13: warning: variable ‘heap’ set but not used [-Wunused-but-set-variable] OVHeap *heap = I->heap; ^~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVHeap.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVHeap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVHeapArray.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVHeapArray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVLexicon.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVLexicon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVOneToAny.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVOneToAny.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVOneToOne.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVOneToOne.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVRandom.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVRandom.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/ov_utility.cpp -o build/temp.linux-x86_64-3.6/ov/src/ov_utility.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.6/build/generated/ShaderText.o build/temp.linux-x86_64-3.6/contrib/mmtf-c/mmtf_parser.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/hash.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/inthash.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o build/temp.linux-x86_64-3.6/layer0/Block.o build/temp.linux-x86_64-3.6/layer0/Crystal.o build/temp.linux-x86_64-3.6/layer0/Deferred.o build/temp.linux-x86_64-3.6/layer0/Err.o build/temp.linux-x86_64-3.6/layer0/Feedback.o build/temp.linux-x86_64-3.6/layer0/Field.o build/temp.linux-x86_64-3.6/layer0/File.o build/temp.linux-x86_64-3.6/layer0/GenericBuffer.o build/temp.linux-x86_64-3.6/layer0/GraphicsUtil.o build/temp.linux-x86_64-3.6/layer0/Isosurf.o build/temp.linux-x86_64-3.6/layer0/Map.o build/temp.linux-x86_64-3.6/layer0/Match.o build/temp.linux-x86_64-3.6/layer0/Matrix.o build/temp.linux-x86_64-3.6/layer0/MemoryDebug.o build/temp.linux-x86_64-3.6/layer0/MyPNG.o build/temp.linux-x86_64-3.6/layer0/Parse.o build/temp.linux-x86_64-3.6/layer0/Pixmap.o build/temp.linux-x86_64-3.6/layer0/PostProcess.o build/temp.linux-x86_64-3.6/layer0/ShaderMgr.o build/temp.linux-x86_64-3.6/layer0/ShaderPrg.o build/temp.linux-x86_64-3.6/layer0/Sphere.o build/temp.linux-x86_64-3.6/layer0/Tetsurf.o build/temp.linux-x86_64-3.6/layer0/Texture.o build/temp.linux-x86_64-3.6/layer0/Tracker.o build/temp.linux-x86_64-3.6/layer0/Triangle.o build/temp.linux-x86_64-3.6/layer0/Util.o build/temp.linux-x86_64-3.6/layer0/Util2.o build/temp.linux-x86_64-3.6/layer0/Vector.o build/temp.linux-x86_64-3.6/layer0/Word.o build/temp.linux-x86_64-3.6/layer0/os_gl.o build/temp.linux-x86_64-3.6/layer1/Basis.o build/temp.linux-x86_64-3.6/layer1/ButMode.o build/temp.linux-x86_64-3.6/layer1/CGO.o build/temp.linux-x86_64-3.6/layer1/COLLADA.o build/temp.linux-x86_64-3.6/layer1/Character.o build/temp.linux-x86_64-3.6/layer1/Color.o build/temp.linux-x86_64-3.6/layer1/Control.o build/temp.linux-x86_64-3.6/layer1/Extrude.o build/temp.linux-x86_64-3.6/layer1/Font.o build/temp.linux-x86_64-3.6/layer1/FontGLUT.o build/temp.linux-x86_64-3.6/layer1/FontGLUT8x13.o build/temp.linux-x86_64-3.6/layer1/FontGLUT9x15.o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel10.o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel12.o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel18.o build/temp.linux-x86_64-3.6/layer1/FontType.o build/temp.linux-x86_64-3.6/layer1/Movie.o build/temp.linux-x86_64-3.6/layer1/Ortho.o build/temp.linux-x86_64-3.6/layer1/P.o build/temp.linux-x86_64-3.6/layer1/PConv.o build/temp.linux-x86_64-3.6/layer1/Picking.o build/temp.linux-x86_64-3.6/layer1/Pop.o build/temp.linux-x86_64-3.6/layer1/PyMOLObject.o build/temp.linux-x86_64-3.6/layer1/Ray.o build/temp.linux-x86_64-3.6/layer1/Rep.o build/temp.linux-x86_64-3.6/layer1/Scene.o build/temp.linux-x86_64-3.6/layer1/ScenePicking.o build/temp.linux-x86_64-3.6/layer1/SceneRay.o build/temp.linux-x86_64-3.6/layer1/SceneRender.o build/temp.linux-x86_64-3.6/layer1/ScrollBar.o build/temp.linux-x86_64-3.6/layer1/Seq.o build/temp.linux-x86_64-3.6/layer1/Setting.o build/temp.linux-x86_64-3.6/layer1/Shaker.o build/temp.linux-x86_64-3.6/layer1/Symmetry.o build/temp.linux-x86_64-3.6/layer1/Text.o build/temp.linux-x86_64-3.6/layer1/TypeFace.o build/temp.linux-x86_64-3.6/layer1/View.o build/temp.linux-x86_64-3.6/layer1/Wizard.o build/temp.linux-x86_64-3.6/layer2/AssemblyHelpers.o build/temp.linux-x86_64-3.6/layer2/AtomInfo.o build/temp.linux-x86_64-3.6/layer2/AtomInfoHistory.o build/temp.linux-x86_64-3.6/layer2/BondTypeHistory.o build/temp.linux-x86_64-3.6/layer2/CifFile.o build/temp.linux-x86_64-3.6/layer2/CifMoleculeReader.o build/temp.linux-x86_64-3.6/layer2/CoordSet.o build/temp.linux-x86_64-3.6/layer2/DistSet.o build/temp.linux-x86_64-3.6/layer2/GadgetSet.o build/temp.linux-x86_64-3.6/layer2/HydrogenAdder.o build/temp.linux-x86_64-3.6/layer2/MmodTyping.o build/temp.linux-x86_64-3.6/layer2/MmtfMoleculeReader.o build/temp.linux-x86_64-3.6/layer2/Mol2Typing.o build/temp.linux-x86_64-3.6/layer2/MolV3000.o build/temp.linux-x86_64-3.6/layer2/ObjectAlignment.o build/temp.linux-x86_64-3.6/layer2/ObjectCGO.o build/temp.linux-x86_64-3.6/layer2/ObjectCallback.o build/temp.linux-x86_64-3.6/layer2/ObjectDist.o build/temp.linux-x86_64-3.6/layer2/ObjectGadget.o build/temp.linux-x86_64-3.6/layer2/ObjectGadgetRamp.o build/temp.linux-x86_64-3.6/layer2/ObjectGroup.o build/temp.linux-x86_64-3.6/layer2/ObjectMap.o build/temp.linux-x86_64-3.6/layer2/ObjectMesh.o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule.o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule2.o build/temp.linux-x86_64-3.6/layer2/ObjectSlice.o build/temp.linux-x86_64-3.6/layer2/ObjectSurface.o build/temp.linux-x86_64-3.6/layer2/ObjectVolume.o build/temp.linux-x86_64-3.6/layer2/RepAngle.o build/temp.linux-x86_64-3.6/layer2/RepCartoon.o build/temp.linux-x86_64-3.6/layer2/RepCylBond.o build/temp.linux-x86_64-3.6/layer2/RepDihedral.o build/temp.linux-x86_64-3.6/layer2/RepDistDash.o build/temp.linux-x86_64-3.6/layer2/RepDistLabel.o build/temp.linux-x86_64-3.6/layer2/RepDot.o build/temp.linux-x86_64-3.6/layer2/RepEllipsoid.o build/temp.linux-x86_64-3.6/layer2/RepLabel.o build/temp.linux-x86_64-3.6/layer2/RepMesh.o build/temp.linux-x86_64-3.6/layer2/RepNonbonded.o build/temp.linux-x86_64-3.6/layer2/RepNonbondedSphere.o build/temp.linux-x86_64-3.6/layer2/RepRibbon.o build/temp.linux-x86_64-3.6/layer2/RepSphere.o build/temp.linux-x86_64-3.6/layer2/RepSphereGenerate.o build/temp.linux-x86_64-3.6/layer2/RepSphereImmediate.o build/temp.linux-x86_64-3.6/layer2/RepSurface.o build/temp.linux-x86_64-3.6/layer2/RepWireBond.o build/temp.linux-x86_64-3.6/layer2/Sculpt.o build/temp.linux-x86_64-3.6/layer2/SculptCache.o build/temp.linux-x86_64-3.6/layer2/SideChainHelper.o build/temp.linux-x86_64-3.6/layer2/VFont.o build/temp.linux-x86_64-3.6/layer3/AtomIterators.o build/temp.linux-x86_64-3.6/layer3/CifDataValueFormatter.o build/temp.linux-x86_64-3.6/layer3/Editor.o build/temp.linux-x86_64-3.6/layer3/Executive.o build/temp.linux-x86_64-3.6/layer3/ExecutivePython.o build/temp.linux-x86_64-3.6/layer3/MaeExportHelpers.o build/temp.linux-x86_64-3.6/layer3/MoleculeExporter.o build/temp.linux-x86_64-3.6/layer3/MovieScene.o build/temp.linux-x86_64-3.6/layer3/PlugIOManager.o build/temp.linux-x86_64-3.6/layer3/RingFinder.o build/temp.linux-x86_64-3.6/layer3/Seeker.o build/temp.linux-x86_64-3.6/layer3/Selector.o build/temp.linux-x86_64-3.6/layer3/SelectorTmp.o build/temp.linux-x86_64-3.6/layer4/Cmd.o build/temp.linux-x86_64-3.6/layer4/Menu.o build/temp.linux-x86_64-3.6/layer4/PopUp.o build/temp.linux-x86_64-3.6/layer5/PyMOL.o build/temp.linux-x86_64-3.6/layer5/TestPyMOL.o build/temp.linux-x86_64-3.6/layer5/main.o build/temp.linux-x86_64-3.6/modules/cealign/src/ccealignmodule.o build/temp.linux-x86_64-3.6/ov/src/OVContext.o build/temp.linux-x86_64-3.6/ov/src/OVHeap.o build/temp.linux-x86_64-3.6/ov/src/OVHeapArray.o build/temp.linux-x86_64-3.6/ov/src/OVLexicon.o build/temp.linux-x86_64-3.6/ov/src/OVOneToAny.o build/temp.linux-x86_64-3.6/ov/src/OVOneToOne.o build/temp.linux-x86_64-3.6/ov/src/OVRandom.o build/temp.linux-x86_64-3.6/ov/src/ov_utility.o -L/usr/lib64 -L/usr/lib -L/usr/lib64 -lpng -lfreetype -lxml2 -lGL -lGLEW -lglut -lnetcdf -lpython3.6m -o build/lib.linux-x86_64-3.6/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so building 'chempy.champ._champ' extension creating build/temp.linux-x86_64-3.6/contrib/champ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/champ.c -o build/temp.linux-x86_64-3.6/contrib/champ/champ.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/chiral.c -o build/temp.linux-x86_64-3.6/contrib/champ/chiral.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/err2.c -o build/temp.linux-x86_64-3.6/contrib/champ/err2.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/feedback2.c -o build/temp.linux-x86_64-3.6/contrib/champ/feedback2.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/list.c -o build/temp.linux-x86_64-3.6/contrib/champ/list.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/os_memory.c -o build/temp.linux-x86_64-3.6/contrib/champ/os_memory.o contrib/champ/os_memory.c: In function ‘OSMemoryZero’: contrib/champ/os_memory.c:55:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] while(count&&(((int)p)&mask)) { ^ contrib/champ/os_memory.c: In function ‘OSMemoryHashAdd’: contrib/champ/os_memory.c:137:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] hash=(int)rec; ^ contrib/champ/os_memory.c: In function ‘OSMemoryHashRemove’: contrib/champ/os_memory.c:150:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] hash=(int)rec; ^ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/sort.c -o build/temp.linux-x86_64-3.6/contrib/champ/sort.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/strblock.c -o build/temp.linux-x86_64-3.6/contrib/champ/strblock.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/vla.c -o build/temp.linux-x86_64-3.6/contrib/champ/vla.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/champ_module.c -o build/temp.linux-x86_64-3.6/contrib/champ/champ_module.o gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.6/contrib/champ/champ.o build/temp.linux-x86_64-3.6/contrib/champ/champ_module.o build/temp.linux-x86_64-3.6/contrib/champ/chiral.o build/temp.linux-x86_64-3.6/contrib/champ/err2.o build/temp.linux-x86_64-3.6/contrib/champ/feedback2.o build/temp.linux-x86_64-3.6/contrib/champ/list.o build/temp.linux-x86_64-3.6/contrib/champ/os_memory.o build/temp.linux-x86_64-3.6/contrib/champ/sort.o build/temp.linux-x86_64-3.6/contrib/champ/strblock.o build/temp.linux-x86_64-3.6/contrib/champ/vla.o -L/usr/lib64 -lpython3.6m -o build/lib.linux-x86_64-3.6/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so + sleep 1 + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.WlAhnr + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 ++ dirname /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 + cd pymol-open-source-2.4.0 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + /usr/bin/python3.6 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 --use-msgpackc=c++11 --glut --pymol-path=/usr/lib64/python3.6/site-packages/pymol running install running install_lib creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6 creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/commands.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/realtime.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/state.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/util.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/amber99.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/assign.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/formal_charges.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fast copying build/lib.linux-x86_64-3.6/chempy/fast/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fast creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments copying build/lib.linux-x86_64-3.6/chempy/fragments/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf copying build/lib.linux-x86_64-3.6/chempy/mmtf/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf copying build/lib.linux-x86_64-3.6/chempy/mmtf/io.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/keyword.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/realtime.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/state.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/arc.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/bond_amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/bond_mmff.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/bonds.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/brick.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/cc1.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/charge.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/cif.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/cpv.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/dictdb.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/gamess1.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/gms.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/hetatm.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/io.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/lst.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mae.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/map.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mass.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mmd.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/models.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mol.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mol2.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/neighbor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/pdb.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/pkl.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/place.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_amber99.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_mmff.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_residues.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/sdf.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/solvate.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/water_amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/water_residues.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/xyz.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/askpartial.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/colors.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/fetch.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_aln.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_mae.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_map.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_mtz.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_traj.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/movieexport.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/pluginitem.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/pluginmanager.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/png.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/props.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/render.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/save_molecule.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/save_object.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/pml.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/pmlparser.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/python.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/TextEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/advanced_settings_gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/builder.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/file_dialogs.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/keymapping.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/mimic_pmg_tk.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/mimic_tk.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/properties_dialog.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/pymol_gl_widget.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/pymol_qt_gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/volume.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo copying build/lib.linux-x86_64-3.6/pmg_tk/skins/demo/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/normal/ModalWindow.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/normal/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/normal/builder.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup copying build/lib.linux-x86_64-3.6/pmg_tk/startup/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup copying build/lib.linux-x86_64-3.6/pmg_tk/startup/apbs_tools.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup copying build/lib.linux-x86_64-3.6/pmg_tk/ColorEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/Demo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/PyMOLMapLoad.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/SetEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/Setting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/TextEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/volume.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/PMGApp.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt copying build/lib.linux-x86_64-3.6/pymol/Qt/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt copying build/lib.linux-x86_64-3.6/pymol/Qt/utils.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/contrib copying build/lib.linux-x86_64-3.6/pymol/contrib/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/contrib creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-3.6/pymol/opengl/gl/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/gl creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glu copying build/lib.linux-x86_64-3.6/pymol/opengl/glu/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glu creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glut copying build/lib.linux-x86_64-3.6/pymol/opengl/glut/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glut copying build/lib.linux-x86_64-3.6/pymol/opengl/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/installation.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/legacysupport.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/managergui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/managergui_qt.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/repository.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry copying build/lib.linux-x86_64-3.6/pymol/stereochemistry/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/annotation.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/appearance.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/benchmark.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/box.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/charge.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/cleanup.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/command.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/demo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/density.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/distance.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/dragging.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/fedora.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/filter.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/label.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/measurement.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/message.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/mutagenesis.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/nucmutagenesis.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/openvr.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/pair_fit.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/pseudoatom.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/renaming.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/sculpting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/security.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/stereodemo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/toggle.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/__main__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/_gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/api.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/callback.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/cgo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/checking.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/cmd.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/colorprinting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/colorramping.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/commanding.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/completing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/computing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/constants.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/constants_palette.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/controlling.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/creating.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/diagnosing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/editing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/editor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/experimenting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/exporting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/externing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/feedingback.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/fitting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/headering.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/helping.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/importing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/internal.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/invocation.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/keyboard.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/keywords.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/lazyio.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/locking.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/menu.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/monitoring.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/morphing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/movie.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/moving.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/parser.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/parsing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/povray.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/preset.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/pymolhttpd.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/querying.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/rpc.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/selecting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/selector.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/seqalign.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/setting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/shortcut.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/util.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/vfont.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/viewing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/wizarding.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/xray.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/xwin.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2 copying build/lib.linux-x86_64-3.6/pymol2/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2 copying build/lib.linux-x86_64-3.6/pymol2/cmd2.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2 byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/commands.py to commands.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/realtime.py to realtime.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/state.py to state.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/util.py to util.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/amber99.py to amber99.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/assign.py to assign.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/formal_charges.py to formal_charges.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fast/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf/io.py to io.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/amber.py to amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/keyword.py to keyword.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/realtime.py to realtime.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/state.py to state.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/arc.py to arc.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bond_amber.py to bond_amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bond_mmff.py to bond_mmff.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bonds.py to bonds.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/brick.py to brick.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/cc1.py to cc1.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/charge.py to charge.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/cif.py to cif.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/cpv.py to cpv.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/dictdb.py to dictdb.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/gamess1.py to gamess1.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/gms.py to gms.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/hetatm.py to hetatm.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/io.py to io.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/lst.py to lst.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mae.py to mae.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/map.py to map.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mass.py to mass.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmd.py to mmd.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/models.py to models.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mol.py to mol.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mol2.py to mol2.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/neighbor.py to neighbor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/pdb.py to pdb.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/pkl.py to pkl.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/place.py to place.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein.py to protein.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_amber.py to protein_amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_amber99.py to protein_amber99.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_mmff.py to protein_mmff.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_residues.py to protein_residues.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/sdf.py to sdf.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/solvate.py to solvate.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/water_amber.py to water_amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/water_residues.py to water_residues.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/xyz.py to xyz.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/pml.py to pml.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/pmlparser.py to pmlparser.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/python.py to python.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/TextEditor.py to TextEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/advanced_settings_gui.py to advanced_settings_gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/builder.py to builder.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/file_dialogs.py to file_dialogs.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/keymapping.py to keymapping.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/mimic_pmg_tk.py to mimic_pmg_tk.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/mimic_tk.py to mimic_tk.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/properties_dialog.py to properties_dialog.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/pymol_gl_widget.py to pymol_gl_widget.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/pymol_qt_gui.py to pymol_qt_gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/volume.py to volume.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal/ModalWindow.py to ModalWindow.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal/builder.py to builder.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup/apbs_tools.py to apbs_tools.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/ColorEditor.py to ColorEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/Demo.py to Demo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/PyMOLMapLoad.py to PyMOLMapLoad.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/SetEditor.py to SetEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/Setting.py to Setting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/TextEditor.py to TextEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/volume.py to volume.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/PMGApp.py to PMGApp.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt/utils.py to utils.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/contrib/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/gl/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glu/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glut/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/installation.py to installation.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/legacysupport.py to legacysupport.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/managergui.py to managergui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/managergui_qt.py to managergui_qt.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/repository.py to repository.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/annotation.py to annotation.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/appearance.py to appearance.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/benchmark.py to benchmark.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/box.py to box.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/charge.py to charge.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/cleanup.py to cleanup.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/command.py to command.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/demo.py to demo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/density.py to density.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/distance.py to distance.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/dragging.py to dragging.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/fedora.py to fedora.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/filter.py to filter.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/label.py to label.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/measurement.py to measurement.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/message.py to message.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/mutagenesis.py to mutagenesis.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/nucmutagenesis.py to nucmutagenesis.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/openvr.py to openvr.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/pair_fit.py to pair_fit.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/pseudoatom.py to pseudoatom.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/renaming.py to renaming.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/sculpting.py to sculpting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/security.py to security.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/stereodemo.py to stereodemo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/toggle.py to toggle.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/__main__.py to __main__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/_gui.py to _gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/api.py to api.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/callback.py to callback.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/cgo.py to cgo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/checking.py to checking.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/cmd.py to cmd.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/colorprinting.py to colorprinting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/colorramping.py to colorramping.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/commanding.py to commanding.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/completing.py to completing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/computing.py to computing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/constants.py to constants.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/constants_palette.py to constants_palette.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/controlling.py to controlling.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/creating.py to creating.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/diagnosing.py to diagnosing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/editing.py to editing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/editor.py to editor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/experimenting.py to experimenting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/exporting.py to exporting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/externing.py to externing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/feedingback.py to feedingback.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/fitting.py to fitting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/gui.py to gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/headering.py to headering.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/helping.py to helping.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/importing.py to importing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/internal.py to internal.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/invocation.py to invocation.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/keyboard.py to keyboard.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/keywords.py to keywords.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/lazyio.py to lazyio.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/locking.py to locking.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/menu.py to menu.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/monitoring.py to monitoring.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/morphing.py to morphing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/movie.py to movie.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/moving.py to moving.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/parser.py to parser.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/parsing.py to parsing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/povray.py to povray.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/preset.py to preset.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymolhttpd.py to pymolhttpd.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/querying.py to querying.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/rpc.py to rpc.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/selecting.py to selecting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/selector.py to selector.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/seqalign.py to seqalign.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/setting.py to setting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/shortcut.py to shortcut.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/util.py to util.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/vfont.py to vfont.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/viewing.py to viewing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizarding.py to wizarding.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/xray.py to xray.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/xwin.py to xwin.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2/cmd2.py to cmd2.cpython-36.pyc writing byte-compilation script '/tmp/tmp8v33nx_6.py' /usr/bin/python3.6 /tmp/tmp8v33nx_6.py removing /tmp/tmp8v33nx_6.py running install_egg_info Writing /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol-2.4.0-py3.6.egg-info copying LICENSE -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying data -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/data copying test -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test copying examples -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/bin + echo '#!/bin/sh' + echo 'export PYMOL_PATH=/usr/lib64/python3.6/site-packages/pymol' + echo 'exec /usr/bin/python3.6 /usr/lib64/python3.6/site-packages/pymol/__init__.py "$@"' + cp -a data examples test /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/ + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/link_demo.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/particle01.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/particle02.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B03.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B05.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B11.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/ref/T01.log + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/link_demo.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/particle01.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/particle02.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B03.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B05.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B11.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/ref/T01.log + mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/bin + install -p -m 755 pymol /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/bin/ + desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/applications /builddir/build/SOURCES/pymol.desktop + mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/pixmaps + install -p -m 644 /builddir/build/SOURCES/pymol.png /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/pixmaps/ + mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/metainfo + install -p -m 644 /builddir/build/SOURCES/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/metainfo/ + appstream-util validate-relax --nonet /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64//usr/share/metainfo/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64//usr/share/metainfo/pymol.appdata.xml: GLib-GIO-Message: 14:06:15.078: Using the 'memory' GSettings backend. Your settings will not be saved or shared with other applications. OK + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 2.4.0-4.1.el8.ors --unique-debug-suffix -2.4.0-4.1.el8.ors.x86_64 --unique-debug-src-base pymol-2.4.0-4.1.el8.ors.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pymol-open-source-2.4.0 extracting debug info from /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so /usr/lib/rpm/sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. 51223 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile '' 1 Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib/debug/usr/lib64/python3.6 using /usr/libexec/platform-python Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6 using /usr/libexec/platform-python + /usr/lib/rpm/brp-python-hardlink + PYTHON3=/usr/bin/python3.6 + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit Processing files: pymol-2.4.0-4.1.el8.ors.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.F9LyI4 + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + DOCDIR=/builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr AUTHORS /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr DEVELOPERS /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr README.md /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr ChangeLog /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.xlsS5H + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/licenses/pymol + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/licenses/pymol + cp -pr LICENSE /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/licenses/pymol + exit 0 Provides: PyMOL(x86-64) = 0:2.4.0-4.1.el8.ors application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 2.4.0-4.1.el8.ors pymol(x86-64) = 2.4.0-4.1.el8.ors python3.6dist(pymol) = 2.4.0 python3dist(pymol) = 2.4.0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/csh /bin/sh /usr/bin/python3.6 libGL.so.1()(64bit) libGLEW.so.2.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libglut.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libnetcdf.so.15()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpython3.6m.so.1.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.3)(64bit) python(abi) = 3.6 rtld(GNU_HASH) Processing files: pymol-debugsource-2.4.0-4.1.el8.ors.x86_64 Provides: pymol-debugsource = 2.4.0-4.1.el8.ors pymol-debugsource(x86-64) = 2.4.0-4.1.el8.ors Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: pymol-debuginfo-2.4.0-4.1.el8.ors.x86_64 Provides: debuginfo(build-id) = 10490c069cc3d2ed2b634bb0482291c280b65ac6 debuginfo(build-id) = 6f4c8b18c2f4d709ad3a82130e6ac834c599c448 pymol-debuginfo = 2.4.0-4.1.el8.ors pymol-debuginfo(x86-64) = 2.4.0-4.1.el8.ors Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: pymol-debugsource(x86-64) = 2.4.0-4.1.el8.ors Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 Wrote: /builddir/build/RPMS/pymol-2.4.0-4.1.el8.ors.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debugsource-2.4.0-4.1.el8.ors.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debuginfo-2.4.0-4.1.el8.ors.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.THI2V7 + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 + exit 0 Finish: rpmbuild pymol-2.4.0-4.1.el8.ors.src.rpm Finish: build phase for pymol-2.4.0-4.1.el8.ors.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/log/dnf.rpm.log /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/log/dnf.librepo.log /var/lib/mock/epel-8-x86_64-1620741551.244243/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/pymol-2.4.0-4.1.el8.ors.src.rpm) Config(child) 7 minutes 10 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run