Mock Version: 3.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/pymol.spec'], chrootPath='/var/lib/mock/rhel+epel-8-x86_64-1675244409.748214/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f41174c3310>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.121ydqb7:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.121ydqb7:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '908992889de54620b5a82972ef298ad7', '-D', '/var/lib/mock/rhel+epel-8-x86_64-1675244409.748214/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.121ydqb7:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/pymol.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
sh: /usr/bin/python3.6: No such file or directory
warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn <tim.fenn@gmail.com> - 1.5.0.2-3.20120218svn3982
warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn <fenn@stanford.edu> - 1.2-5.20090709svn3827
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/pymol-2.5.0-6.el8.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/pymol.spec'], chrootPath='/var/lib/mock/rhel+epel-8-x86_64-1675244409.748214/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f41174c3310>timeout=0uid=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.121ydqb7:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True)
Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.121ydqb7:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '5d193fe14bf8404ba5a0938717a7b625', '-D', '/var/lib/mock/rhel+epel-8-x86_64-1675244409.748214/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.121ydqb7:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007"', '--setenv=PS1=<mock-chroot> \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/pymol.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn <tim.fenn@gmail.com> - 1.5.0.2-3.20120218svn3982
warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn <fenn@stanford.edu> - 1.2-5.20090709svn3827
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.maTcoK
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf pymol-open-source-2.5.0
+ /usr/bin/gzip -dc /builddir/build/SOURCES/pymol-open-source-2.5.0.tar.gz
+ /usr/bin/tar -xof -
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd pymol-open-source-2.5.0
+ /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-2.5.0-bug186.patch
+ /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch
+ ln -sr modules/web modules/pymol_web
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.hmyR1H
+ umask 022
+ cd /builddir/build/BUILD
+ cd pymol-open-source-2.5.0
+ 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'
++ /usr/bin/getconf _NPROCESSORS_ONLN
+ 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 --use-openmp=yes --jobs 2
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_manager.py -> build/lib.linux-x86_64-3.6/pymol
copying modules/pymol/shortcut_dict.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/save_shortcut.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/mpeg_encode.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/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/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/__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/shortcut_menu_gui.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/shortcut_menu.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms
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/help_shortcut.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/create_shortcut.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/change_confirm.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/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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:1904:9: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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)
            ^~~~~~~~~~~
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);
       ~~~~~^~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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) {
                   ^~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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/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)
                    ^~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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/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);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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) {
             ^~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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,
          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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,
          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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,
          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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,
          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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);
     ^~~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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]) {
             ^~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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,
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
       __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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) {
            ^~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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) {
            ^~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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) {
             ^~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/CarveHelper.cpp -o build/temp.linux-x86_64-3.6/layer0/CarveHelper.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
In file included from layer0/CarveHelper.cpp:8:
layer0/CarveHelper.h: In constructor ‘CarveHelper::CarveHelper(PyMOLGlobals*, float, const float*, std::size_t)’:
layer0/CarveHelper.h:23:9: warning: ‘CarveHelper::m_cutoff’ will be initialized after [-Wreorder]
   float m_cutoff;
         ^~~~~~~~
layer0/CarveHelper.h:22:16: warning:   ‘const float* CarveHelper::m_vertices’ [-Wreorder]
   const float* m_vertices;
                ^~~~~~~~~~
layer0/CarveHelper.cpp:20:1: warning:   when initialized here [-Wreorder]
 CarveHelper::CarveHelper(PyMOLGlobals* G, float cutoff, const float* vertices,
 ^~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/ContourSurf.cpp -o build/temp.linux-x86_64-3.6/layer0/ContourSurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer0/ContourSurf.cpp:11:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {long unsigned int, long unsigned int, long unsigned int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = float; SizeTs = {long unsigned int, long unsigned int, long unsigned int}]’
layer0/ContourSurf.cpp:410:58:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {long unsigned int, long unsigned int, long unsigned int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = float; SizeTs = {long unsigned int, long unsigned int, long unsigned int, int}]’
layer0/ContourSurf.cpp:419:47:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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;
              ~~~~~~~~~~^~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Field.cpp:26:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’
layer0/Field.cpp:343:17:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer0/Isosurf.cpp:25:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int, int}]’:
layer0/Isosurf.cpp:552:24:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer0/Isosurf.cpp:1459:32:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = PointType; SizeTs = {int, int, int, int}]’:
layer0/Field.h:134:33:   required from ‘T* CFieldTyped<T>::ptr(SizeTs ...) [with SizeTs = {int, int, int, int}; T = PointType]’
layer0/Isosurf.cpp:1617:19:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = int; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = int; SizeTs = {int, int, int}]’
layer0/Field.h:144:33:   required from ‘T& CFieldTyped<T>::get(SizeTs ...) [with SizeTs = {int, int, int}; T = int]’
layer0/Isosurf.cpp:1456:15:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = int; SizeTs = {int, int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = int; SizeTs = {int, int, int, int}]’
layer0/Field.h:144:33:   required from ‘T& CFieldTyped<T>::get(SizeTs ...) [with SizeTs = {int, int, int, int}; T = int]’
layer0/Isosurf.cpp:1487:13:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer0/Tetsurf.cpp:24:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int, int}]’:
layer0/Tetsurf.cpp:802:18:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = PointType; SizeTs = {int, int, int, int}]’:
layer0/Tetsurf.cpp:831:27:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = int; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = int; SizeTs = {int, int, int}]’
layer0/Tetsurf.cpp:791:16:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’
layer0/Tetsurf.cpp:822:18:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/MemoryUsage.cpp -o build/temp.linux-x86_64-3.6/layer0/MemoryUsage.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
layer0/MemoryUsage.cpp: In function ‘size_t pymol::memory_usage()’:
layer0/MemoryUsage.cpp:38:21: warning: use of assignment suppression and length modifier together in gnu_scanf format [-Wformat=]
     std::fscanf(fp, "%*zu%zu", &vmRSS);
                     ^~~~~~~~~
layer0/MemoryUsage.cpp:38:16: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result]
     std::fscanf(fp, "%*zu%zu", &vmRSS);
     ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer0/MyPNG.cpp: In function ‘int MyPNGWrite(const char*, const pymol::Image&, float, int, int, float, float, png_outbuf_t*)’:
layer0/MyPNG.cpp:299:20: 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:340:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
           for(b = 0; b < height; b++) {
                      ~~^~~~~~~~
layer0/MyPNG.cpp:341:26: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/ccealignmodule.cpp -o build/temp.linux-x86_64-3.6/layer0/ccealignmodule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
In file included from include/tnt/tnt.h:49,
                 from layer0/ccealignmodule.cpp:39:
include/tnt/tnt_array2d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Array2D<T>&)’:
include/tnt/tnt_array2d_utils.h:62:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
     for (int i=0; i<M; i++)
     ^~~
include/tnt/tnt_array2d_utils.h:68:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  A = B;
  ^
In file included from include/tnt/tnt.h:50,
                 from layer0/ccealignmodule.cpp:39:
include/tnt/tnt_array3d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Array3D<T>&)’:
include/tnt/tnt_array3d_utils.h:47:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
     for (int i=0; i<M; i++)
     ^~~
include/tnt/tnt_array3d_utils.h:52:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  A = B;
  ^
In file included from include/tnt/tnt.h:56,
                 from layer0/ccealignmodule.cpp:39:
include/tnt/tnt_fortran_array2d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Fortran_Array2D<T>&)’:
include/tnt/tnt_fortran_array2d_utils.h:61:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
     for (int i=1; i<=M; i++)
     ^~~
include/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 include/tnt/tnt.h:57,
                 from layer0/ccealignmodule.cpp:39:
include/tnt/tnt_fortran_array3d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Fortran_Array3D<T>&)’:
include/tnt/tnt_fortran_array3d_utils.h:65:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
     for (int i=1; i<=M; i++)
     ^~~
include/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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/marching_cubes.cpp -o build/temp.linux-x86_64-3.6/layer0/marching_cubes.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
layer0/marching_cubes.cpp: In function ‘mc::Mesh mc::march(const mc::Field&, float, bool)’:
layer0/marching_cubes.cpp:517:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare]
   for (int z = 0; z < zDim; ++z) {
                   ~~^~~~~~
layer0/marching_cubes.cpp:550:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare]
   for (int z = 0; z < zEnd; ++z) {
                   ~~^~~~~~
layer0/marching_cubes.cpp:603:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
           if (z == zEnd - 1) {
               ~~^~~~~~~~~~~
layer0/marching_cubes.cpp:608:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
         if (z == zEnd - 1) {
             ~~^~~~~~~~~~~
layer0/marching_cubes.cpp: In function ‘void mc::calculateNormals(mc::Mesh&)’:
layer0/marching_cubes.cpp:681:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i = 0; i < vertexCount; ++i) {
                   ~~^~~~~~~~~~~~~
layer0/marching_cubes.cpp:686:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i = 0; i < triangleCount; ++i) {
                   ~~^~~~~~~~~~~~~~~
layer0/marching_cubes.cpp:720:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i = 0; i < vertexCount; ++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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Ortho.cpp:783:6: warning: ‘void OrthoKeyCmmd(PyMOLGlobals*, unsigned char)’ defined but not used [-Wunused-function]
 void OrthoKeyCmmd(PyMOLGlobals * G, unsigned char k)
      ^~~~~~~~~~~~
In file included from /usr/include/string.h:495,
                 from /usr/include/python3.6m/Python.h:30,
                 from layer0/os_python.h:34,
                 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:332:13:
/usr/include/bits/string_fortified.h:143:33: 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, __glibc_objsize (__dest));
          ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘char* strcat(char*, const char*)’,
    inlined from ‘void OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at layer1/Ortho.cpp:349:13:
/usr/include/bits/string_fortified.h:143:33: 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, __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:86:39: note: in definition of macro ‘DeleteP’
 #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}}
                                       ^~~
layer1/P.cpp: In function ‘int WrapperObjectAssignSubScript(PyObject*, PyObject*, PyObject*)’:
layer1/P.cpp:825:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
       if (strlen(valstr) > ap->maxlen) {
           ~~~~~~~~~~~~~~~^~~~~~~~~~~~
layer1/P.cpp:849:18: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
       if (valint == -1 && PyErr_Occurred())
           ~~~~~~~^~~~~
layer1/P.cpp: At global scope:
layer1/P.cpp:2422:13: warning: ‘void PLockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function]
 static void PLockAPIWhileBlocked(PyMOLGlobals * G)
             ^~~~~~~~~~~~~~~~~~~~
layer1/P.cpp:2411:13: warning: ‘void PUnlockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function]
 static void PUnlockAPIWhileBlocked(PyMOLGlobals * 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/CGO.cpp: In function ‘void CheckAttributesForUsage(const CGO*, AttribDataDesc&, AttribDataDesc&, CGO*, bool&)’:
layer1/CGO.cpp:10842:28: 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<int, int>&, std::map<int, std::map<int, AttribOp*> >&, AttribDataDesc&, AttribDataDesc&, int&, bool)’:
layer1/CGO.cpp:10920:37: 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:11222:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AttribDesc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for (auto idx = 0; idx < attrData.size(); ++idx){
                                ~~~~^~~~~~~~~~~~~~~~~
layer1/CGO.cpp:11234:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<AttribDesc>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for (auto idx = 0; idx < attrData.size(); ++idx){
                                ~~~~^~~~~~~~~~~~~~~~~
layer1/CGO.cpp:11243:33: 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/PConv.cpp: In function ‘int PConvPyListToBitmask(PyObject*, int*, ov_size)’:
layer1/PConv.cpp:83:20: 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++)
                  ~~^~~~
layer1/PConv.cpp: In function ‘PyObject* PConvLabPosVecToPyList(const std::vector<LabPosType>&)’:
layer1/PConv.cpp:1194:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<LabPosType>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (int a = 0; a < vec.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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:86:39: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Ray.cpp: In function ‘void RayRender(CRay*, unsigned int*, double, float, int, unsigned int*)’:
layer1/Ray.cpp:6065:17: 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:6067:17: 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:6148:20: 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:6149:22: 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:6160:16: 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:6171:16: 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:6232:26: 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:6233:28: 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:6243:24: 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:6255:24: 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:6306:24: 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:6326:26: 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:6345:24: 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:6359:24: 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:6373:30: 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:6380:30: 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:6387:25: 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:6387:47: 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:6543:20: 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:6544:15: 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 ‘int RayTraceThread(CRayThreadInfo*)’:
layer1/Ray.cpp:3606:32: 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 );
               ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer1/Ray.cpp: In function ‘void RayRenderVRML2(CRay*, int, int, char**, float, float, float, float, float)’:
layer1/Ray.cpp:1531:19: 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:1540:72:
                   vert2[2] - mid[2], axis[0], axis[1], axis[2], angle, geometry);
                                                                        ~~~~~~~~
layer1/Ray.cpp:1530:18: 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);
                   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Scene.cpp: In function ‘int SceneViewEqual(float*, float*)’:
layer1/Scene.cpp:127:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(i = 0; i < cSceneViewSize; i++) {
              ~~^~~~~~~~~~~~~~~~
layer1/Scene.cpp: In function ‘void SceneFree(PyMOLGlobals*)’:
layer1/Scene.cpp:4071:13: warning: deleting object of polymorphic class type ‘CScene’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   delete G->Scene;
             ^~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/SceneMouse.cpp -o build/temp.linux-x86_64-3.6/layer1/SceneMouse.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Color.cpp: In function ‘ObjectGadgetRamp* ColorGetRamp(PyMOLGlobals*, int)’:
layer1/Color.cpp:180:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ExtRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if (index < I->Ext.size()) {
         ~~~~~~^~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘int ColorExtFromPyList(PyMOLGlobals*, PyObject*, int)’:
layer1/Color.cpp:501:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int a = 0; a < n_ext; ++a) {
                   ~~^~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from /usr/include/glm/detail/setup.hpp:28,
                 from /usr/include/glm/detail/precision.hpp:6,
                 from /usr/include/glm/detail/type_vec.hpp:6,
                 from /usr/include/glm/detail/type_vec2.hpp:6,
                 from /usr/include/glm/vec2.hpp:6,
                 from layer0/GenericBuffer.h:12,
                 from layer0/ShaderMgr.h:24,
                 from layer1/Scene.h:29,
                 from layer3/Executive.h:35,
                 from layer1/Color.cpp:31:
layer1/Color.cpp:515:18: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<ExtRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(a_new <= I->Ext.size());
            ~~~~~~^~~~~~~~~~~~~~~~
layer1/Color.cpp:518:15: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘std::vector<ExtRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if (a_new == I->Ext.size()) {
         ~~~~~~^~~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘int ColorFromPyList(PyMOLGlobals*, PyObject*, int)’:
layer1/Color.cpp:569:44: warning: comparison of integer expressions of different signedness: ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
     if (partial_restore && I->Color.size() > index) {
                            ~~~~~~~~~~~~~~~~^~~~~~~
layer1/Color.cpp:575:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if (index >= I->Color.size()) {
         ~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from /usr/include/glm/detail/setup.hpp:28,
                 from /usr/include/glm/detail/precision.hpp:6,
                 from /usr/include/glm/detail/type_vec.hpp:6,
                 from /usr/include/glm/detail/type_vec2.hpp:6,
                 from /usr/include/glm/vec2.hpp:6,
                 from layer0/GenericBuffer.h:12,
                 from layer0/ShaderMgr.h:24,
                 from layer1/Scene.h:29,
                 from layer3/Executive.h:35,
                 from layer1/Color.cpp:31:
layer1/Color.cpp:576:30: warning: comparison of integer expressions of different signedness: ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
       assert(I->Color.size() == index);
              ~~~~~~~~~~~~~~~~^~~~~~~~
layer1/Color.cpp: In function ‘int ColorGetIndex(PyMOLGlobals*, const char*)’:
layer1/Color.cpp:683:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       if((i < I->Color.size()) && (i >= 0))
           ~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘const char* ColorGetName(PyMOLGlobals*, int)’:
layer1/Color.cpp:764:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if((index >= 0) && (index < I->Color.size())) {
                       ~~~~~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp:776:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ExtRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if (a < I->Ext.size()) {
         ~~^~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘int ColorGetStatus(PyMOLGlobals*, int)’:
layer1/Color.cpp:792:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if((index >= 0) && (index < I->Color.size())) {
                       ~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from /usr/include/glm/detail/setup.hpp:28,
                 from /usr/include/glm/detail/precision.hpp:6,
                 from /usr/include/glm/detail/type_vec.hpp:6,
                 from /usr/include/glm/detail/type_vec2.hpp:6,
                 from /usr/include/glm/vec2.hpp:6,
                 from layer0/GenericBuffer.h:12,
                 from layer0/ShaderMgr.h:24,
                 from layer1/Scene.h:29,
                 from layer3/Executive.h:35,
                 from layer1/Color.cpp:31:
layer1/Color.cpp: In function ‘void ColorReset(PyMOLGlobals*)’:
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1026:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("white", 1.F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1027:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("black", 0.F, 0.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1028:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("blue", 0.F, 0.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1029:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("green", 0.F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1030:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("red", 1.F, 0.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1031:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("cyan", 0.F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1032:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("yellow", 1.F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1033:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("dash", 1.F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1034:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("magenta", 1.F, 0.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1035:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("salmon", 1.F, 0.6F, 0.6F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1036:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lime", 0.5F, 1.F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1037:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("slate", 0.5F, 0.5F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1038:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("hotpink", 1.F, 0.F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1039:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("orange", 1.F, 0.5F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1040:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("chartreuse", 0.5F, 1.F, 0.F); /* AKA puke green */
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1041:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("limegreen", 0.F, 1.F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1042:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("purpleblue", 0.5F, 0.F, 1.F); /* legacy name */
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1043:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("marine", 0.F, 0.5F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1044:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("olive", 0.77F, 0.7F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1045:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("purple", 0.75F, 0.F, 0.75F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1046:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("teal", 0.F, 0.75F, 0.75F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1047:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("ruby", 0.6F, 0.2F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1048:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("forest", 0.2F, 0.6F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1049:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("deepblue", 0.25F, 0.25F, 0.65F); /* was "deep" */
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1050:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("grey", 0.5F, 0.5F, 0.5F); /* english spelling */
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1051:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("gray", 0.5F, 0.5F, 0.5F); /* american spelling */
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1052:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("carbon", 0.2F, 1.F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1053:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("nitrogen", 0.2F, 0.2F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1054:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("oxygen", 1.F, 0.3F, 0.3F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1055:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("hydrogen", 0.9F, 0.9F, 0.9F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1056:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("brightorange", 1.F, 0.7F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1057:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("sulfur", 0.9F, 0.775F, 0.25F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1058:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tv_red", 1.F, 0.2F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1059:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tv_green", 0.2F, 1.F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1060:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tv_blue", 0.3F, 0.3F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1061:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tv_yellow", 1.F, 1.F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1062:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("yelloworange", 1.F, 0.87F, 0.37F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1063:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tv_orange", 1.F, 0.55F, 0.15F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1064:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br0", 0.1F, 0.1F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1065:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br1", 0.2F, 0.1F, 0.9F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1066:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br2", 0.3F, 0.1F, 0.8F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1067:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br3", 0.4F, 0.1F, 0.7F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1068:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br4", 0.5F, 0.1F, 0.6F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1069:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br5", 0.6F, 0.1F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1070:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br6", 0.7F, 0.1F, 0.4F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1071:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br7", 0.8F, 0.1F, 0.3F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1072:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br8", 0.9F, 0.1F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1073:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("br9", 1.F, 0.1F, 0.1F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1074:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("pink", 1.F, 0.65F, 0.85F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1075:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("firebrick", 0.698F, 0.13F, 0.13F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1076:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("chocolate", 0.555F, 0.222F, 0.111F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1077:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("brown", 0.65F, 0.32F, 0.17F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1078:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("wheat", 0.99F, 0.82F, 0.65F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1079:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("violet", 1.F, 0.5F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1088:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name, a / 99.F, a / 99.F, a / 99.F);
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1091:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lightmagenta", 1.F, 0.2F, 0.8F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1105:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name,
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1121:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name,
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1137:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name,
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1155:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name,
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1161:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("density", 0.1F, 0.1F, 0.6F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1168:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name, a / 99.F, a / 99.F, a / 99.F);
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1183:5: note: in expansion of macro ‘reg_named_color’
     reg_named_color(name,
     ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1189:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("paleyellow", 1.F, 1.F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1190:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("aquamarine", 0.5F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1191:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("deepsalmon", 1.F, 0.5F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1192:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("palegreen", 0.65F, 0.9F, 0.65F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1193:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("deepolive", 0.6F, 0.6F, 0.1F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1194:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("deeppurple", 0.6F, 0.1F, 0.6F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1195:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("deepteal", 0.1F, 0.6F, 0.6F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1196:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lightblue", 0.75F, 0.75F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1197:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lightorange", 1.F, 0.8F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1198:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("palecyan", 0.8F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1199:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lightteal", 0.4F, 0.7F, 0.7F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1200:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("splitpea", 0.52F, 0.75F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1201:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("raspberry", 0.7F, 0.3F, 0.4F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1202:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("sand", 0.72F, 0.55F, 0.3F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1203:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("smudge", 0.55F, 0.7F, 0.4F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1204:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("violetpurple", 0.55F, 0.25F, 0.6F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1205:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("dirtyviolet", 0.7F, 0.5F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1208:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("_deepsalmon", 1.F, 0.42F, 0.42F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1210:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lightpink", 1.F, 0.75F, 0.87F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1211:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("greencyan", 0.25F, 1.F, 0.75F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1212:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("limon", 0.75F, 1.F, 0.25F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1213:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("skyblue", 0.2F, 0.5F, 0.8F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1214:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("bluewhite", 0.85F, 0.85F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1215:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("warmpink", 0.85F, 0.2F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1216:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("darksalmon", 0.73F, 0.55F, 0.52F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1217:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("helium", 0.850980392F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1218:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lithium", 0.8F, 0.501960784F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1219:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("beryllium", 0.760784314F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1220:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("boron", 1.F, 0.709803922F, 0.709803922F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1221:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("fluorine", 0.701960784F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1222:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("neon", 0.701960784F, 0.890196078F, 0.960784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1223:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("sodium", 0.670588235F, 0.360784314F, 0.949019608F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1224:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("magnesium", 0.541176471F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1225:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("aluminum", 0.749019608F, 0.650980392F, 0.650980392F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1226:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("silicon", 0.941176471F, 0.784313725F, 0.62745098F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1227:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("phosphorus", 1.F, 0.501960784F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1228:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("chlorine", 0.121568627F, 0.941176471F, 0.121568627F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1229:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("argon", 0.501960784F, 0.819607843F, 0.890196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1230:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("potassium", 0.560784314F, 0.250980392F, 0.831372549F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1231:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("calcium", 0.239215686F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1232:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("scandium", 0.901960784F, 0.901960784F, 0.901960784F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1233:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("titanium", 0.749019608F, 0.760784314F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1234:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("vanadium", 0.650980392F, 0.650980392F, 0.670588235F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1235:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("chromium", 0.541176471F, 0.6F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1236:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("manganese", 0.611764706F, 0.478431373F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1237:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("iron", 0.878431373F, 0.4F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1238:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("cobalt", 0.941176471F, 0.564705882F, 0.62745098F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1239:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("nickel", 0.31372549F, 0.815686275F, 0.31372549F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1240:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("copper", 0.784313725F, 0.501960784F, 0.2F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1241:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("zinc", 0.490196078F, 0.501960784F, 0.690196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1242:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("gallium", 0.760784314F, 0.560784314F, 0.560784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1243:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("germanium", 0.4F, 0.560784314F, 0.560784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1244:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("arsenic", 0.741176471F, 0.501960784F, 0.890196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1245:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("selenium", 1.F, 0.631372549F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1246:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("bromine", 0.650980392F, 0.160784314F, 0.160784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1247:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("krypton", 0.360784314F, 0.721568627F, 0.819607843F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1248:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("rubidium", 0.439215686F, 0.180392157F, 0.690196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1249:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("strontium", 0.F, 1.F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1250:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("yttrium", 0.580392157F, 1.F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1251:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("zirconium", 0.580392157F, 0.878431373F, 0.878431373F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1252:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("niobium", 0.450980392F, 0.760784314F, 0.788235294F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1253:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("molybdenum", 0.329411765F, 0.709803922F, 0.709803922F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1254:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("technetium", 0.231372549F, 0.619607843F, 0.619607843F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1255:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("ruthenium", 0.141176471F, 0.560784314F, 0.560784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1256:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("rhodium", 0.039215686F, 0.490196078F, 0.549019608F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1257:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("palladium", 0.F, 0.411764706F, 0.521568627F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1258:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("silver", 0.752941176F, 0.752941176F, 0.752941176F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1259:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("cadmium", 1.F, 0.850980392F, 0.560784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1260:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("indium", 0.650980392F, 0.458823529F, 0.450980392F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1261:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tin", 0.4F, 0.501960784F, 0.501960784F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1262:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("antimony", 0.619607843F, 0.388235294F, 0.709803922F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1263:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tellurium", 0.831372549F, 0.478431373F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1264:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("iodine", 0.580392157F, 0.F, 0.580392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1265:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("xenon", 0.258823529F, 0.619607843F, 0.690196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1266:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("cesium", 0.341176471F, 0.090196078F, 0.560784314F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1267:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("barium", 0.F, 0.788235294F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1268:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lanthanum", 0.439215686F, 0.831372549F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1269:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("cerium", 1.F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1270:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("praseodymium", 0.850980392F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1271:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("neodymium", 0.780392157F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1272:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("promethium", 0.639215686F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1273:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("samarium", 0.560784314F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1274:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("europium", 0.380392157F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1275:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("gadolinium", 0.270588235F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1276:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("terbium", 0.188235294F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1277:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("dysprosium", 0.121568627F, 1.F, 0.780392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1278:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("holmium", 0.F, 1.F, 0.611764706F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1279:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("erbium", 0.F, 0.901960784F, 0.458823529F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1280:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("thulium", 0.F, 0.831372549F, 0.321568627F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1281:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("ytterbium", 0.F, 0.749019608F, 0.219607843F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1282:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lutetium", 0.F, 0.670588235F, 0.141176471F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1283:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("hafnium", 0.301960784F, 0.760784314F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1284:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tantalum", 0.301960784F, 0.650980392F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1285:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("tungsten", 0.129411765F, 0.580392157F, 0.839215686F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1286:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("rhenium", 0.149019608F, 0.490196078F, 0.670588235F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1287:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("osmium", 0.149019608F, 0.4F, 0.588235294F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1288:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("iridium", 0.090196078F, 0.329411765F, 0.529411765F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1289:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("platinum", 0.815686275F, 0.815686275F, 0.878431373F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1290:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("gold", 1.F, 0.819607843F, 0.137254902F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1291:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("mercury", 0.721568627F, 0.721568627F, 0.815686275F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1292:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("thallium", 0.650980392F, 0.329411765F, 0.301960784F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1293:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lead", 0.341176471F, 0.349019608F, 0.380392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1294:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("bismuth", 0.619607843F, 0.309803922F, 0.709803922F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1295:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("polonium", 0.670588235F, 0.360784314F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1296:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("astatine", 0.458823529F, 0.309803922F, 0.270588235F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1297:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("radon", 0.258823529F, 0.509803922F, 0.588235294F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1298:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("francium", 0.258823529F, 0.F, 0.4F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1299:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("radium", 0.F, 0.490196078F, 0.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1300:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("actinium", 0.439215686F, 0.670588235F, 0.980392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1301:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("thorium", 0.F, 0.729411765F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1302:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("protactinium", 0.F, 0.631372549F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1303:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("uranium", 0.F, 0.560784314F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1304:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("neptunium", 0.F, 0.501960784F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1305:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("plutonium", 0.F, 0.419607843F, 1.F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1306:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("americium", 0.329411765F, 0.360784314F, 0.949019608F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1307:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("curium", 0.470588235F, 0.360784314F, 0.890196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1308:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("berkelium", 0.541176471F, 0.309803922F, 0.890196078F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1309:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("californium", 0.631372549F, 0.211764706F, 0.831372549F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1310:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("einsteinium", 0.701960784F, 0.121568627F, 0.831372549F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1311:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("fermium", 0.701960784F, 0.121568627F, 0.729411765F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1312:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("mendelevium", 0.701960784F, 0.050980392F, 0.650980392F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1313:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("nobelium", 0.741176471F, 0.050980392F, 0.529411765F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1314:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lawrencium", 0.780392157F, 0.F, 0.4F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1315:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("rutherfordium", 0.8F, 0.F, 0.349019608F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1316:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("dubnium", 0.819607843F, 0.F, 0.309803922F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1317:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("seaborgium", 0.850980392F, 0.F, 0.270588235F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1318:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("bohrium", 0.878431373F, 0.F, 0.219607843F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1319:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("hassium", 0.901960784F, 0.F, 0.180392157F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1320:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("meitnerium", 0.921568627F, 0.F, 0.149019608F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1321:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("deuterium", 0.9F, 0.9F, 0.9F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1322:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("lonepair", 0.5F, 0.5F, 0.5F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp:1023:25: warning: comparison of integer expressions of different signedness: ‘std::unordered_map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     assert(I->Idx[name] == Color.size() - 1);                                  \
layer1/Color.cpp:1323:3: note: in expansion of macro ‘reg_named_color’
   reg_named_color("pseudoatom", 0.9F, 0.9F, 0.9F);
   ^~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘void ColorUpdateFromLut(PyMOLGlobals*, int)’:
layer1/Color.cpp:1695:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(i = 0; i < I->Color.size(); i++) {
              ~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp:1699:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if(index < I->Color.size()) {
        ~~~~~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘const float* ColorGet(PyMOLGlobals*, int)’:
layer1/Color.cpp:1808:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if((index >= 0) && (index < I->Color.size())) {
                       ~~~~~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘const float* ColorGetRaw(PyMOLGlobals*, int)’:
layer1/Color.cpp:1835:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if((index >= 0) && (index < I->Color.size())) {
                       ~~~~~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp: In function ‘int ColorGetEncoded(PyMOLGlobals*, int, float*)’:
layer1/Color.cpp:1853:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if((index >= 0) && (index < I->Color.size())) {
                       ~~~~~~^~~~~~~~~~~~~~~~~
layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitiveName(PyMOLGlobals*, const Sequence&, const char*) [with Sequence = std::vector<ExtRec>]’:
layer1/Color.cpp:304:58:   required from here
layer1/Color.cpp:245:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ExtRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int a = 0; a < seq.size(); ++a) {
layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitiveName(PyMOLGlobals*, const Sequence&, const char*) [with Sequence = std::vector<ColorRec>]’:
layer1/Color.cpp:626:56:   required from here
layer1/Color.cpp:245:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitivePrefix(PyMOLGlobals*, const Sequence&, const char*, int&) [with Sequence = std::vector<ColorRec>]’:
layer1/Color.cpp:741:66:   required from here
layer1/Color.cpp:275:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ColorRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int a = 0; a < seq.size(); ++a) {
layer1/Color.cpp: In instantiation of ‘int findByCaseInsensitivePrefix(PyMOLGlobals*, const Sequence&, const char*, int&) [with Sequence = std::vector<ExtRec>]’:
layer1/Color.cpp:743:76:   required from here
layer1/Color.cpp:275:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ExtRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
layer1/SceneMouse.cpp: In function ‘void SceneClickPickBond(PyMOLGlobals*, int, int, int, const NamedPicking&)’:
layer1/SceneMouse.cpp:513:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
     if (atIndex == LastPicked.src.index)
         ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
layer1/SceneMouse.cpp: In function ‘void SceneClickTransformObject(PyMOLGlobals*, pymol::CObject*, const NamedPicking&, int, bool)’:
layer1/SceneMouse.cpp:455:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 237 [-Wformat-truncation=]
           " You clicked %s -> (%s)\n", buffer.c_str(), name 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:6404,
                 from /usr/include/c++/8/string:52,
                 from /usr/include/c++/8/bits/locale_classes.h:40,
                 from /usr/include/c++/8/bits/ios_base.h:41,
                 from /usr/include/c++/8/ios:42,
                 from /usr/include/c++/8/ostream:38,
                 from include/pymol/zstring_view.h:12,
                 from layer1/SceneMouse.h:4,
                 from layer1/SceneMouse.cpp:1:
/usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output 21 or more bytes (assuming 276) into a destination of size 255
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Seq.cpp: In function ‘int SeqFindRowCol(PyMOLGlobals*, int, int, int*, int*, int)’:
layer1/Seq.cpp:61:41: 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:114:28: 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:392:20: 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:731:14: 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:86:39: note: in definition of macro ‘DeleteP’
 #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}}
                                       ^~~
layer1/Seq.cpp: At global scope:
layer1/Seq.cpp:717:13: warning: ‘void SeqPurgeRowVLA(PyMOLGlobals*)’ defined but not used [-Wunused-function]
 static void SeqPurgeRowVLA(PyMOLGlobals * 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Setting.cpp: In function ‘void SettingGenerateSideEffects(PyMOLGlobals*, int, const char*, int, int)’:
layer1/Setting.cpp:2070:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if (SettingGetGlobal_b(G, cSetting_precomputed_lighting))
     ^~
layer1/Setting.cpp:2072:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
       SceneInvalidate(G);
       ^~~~~~~~~~~~~~~
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:86:39: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Extrude.cpp: In function ‘int ExtrudeCGOSurfaceTube(const CExtrude*, CGO*, cCylCap, const float*, bool, int)’:
layer1/Extrude.cpp:875:14: warning: ‘stop’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   int start, stop;
              ^~~~
layer1/Extrude.cpp:875:7: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer1/Wizard.cpp: In member function ‘virtual int CWizard::release(int, int, int, int)’:
layer1/Wizard.cpp:571:18: warning: unused variable ‘wiz’ [-Wunused-variable]
         if (auto wiz = WizardGet(G)) {
                  ^~~
layer1/Wizard.cpp: In member function ‘virtual void CWizard::draw(CGO*)’:
layer1/Wizard.cpp:727:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation]
     else
     ^~~~
layer1/Wizard.cpp:729:7: 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:27:
layer1/Wizard.cpp: In function ‘void WizardFree(PyMOLGlobals*)’:
layer1/Wizard.cpp:845:14: 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:86:39: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/SymOp.cpp -o build/temp.linux-x86_64-3.6/layer1/SymOp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
layer2/AtomInfo.cpp: In function ‘bool AtomResiFromResv(char*, size_t, int, char)’:
layer2/AtomInfo.cpp:817:56: 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:818:43: 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;
          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
layer1/SymOp.cpp: In member function ‘std::__cxx11::string pymol::SymOp::to_string() const’:
layer1/SymOp.cpp:37:26: warning: ‘%d’ directive output may be truncated writing between 1 and 4 bytes into a region of size between 0 and 5 [-Wformat-truncation=]
   std::snprintf(code, 8, "%u_%d%d%d", index + 1, x + 5, y + 5, z + 5);
                          ^~~~~~~~~~~
layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132]
layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132]
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:6404,
                 from /usr/include/c++/8/string:52,
                 from layer1/SymOp.h:9,
                 from layer1/SymOp.cpp:7:
/usr/include/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ output between 6 and 17 bytes into a destination of size 8
   return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/SymOpPConv.cpp -o build/temp.linux-x86_64-3.6/layer1/SymOpPConv.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/SymOpTools.cpp -o build/temp.linux-x86_64-3.6/layer1/SymOpTools.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/CifMoleculeReader.cpp: In member function ‘void seqvec_t::set(int, const char*)’:
layer2/CifMoleculeReader.cpp:108:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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:114:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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:827:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer3/Executive.h:27,
                 from layer2/CoordSet.cpp:54:
layer2/CoordSet.cpp: In member function ‘int CoordSet::atmToIdx(int) const’:
layer2/CoordSet.cpp:134:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   assert(atm < AtmToIdx.size());
          ~~~~^~~~~~~~~~~~~~~~~
layer2/CoordSet.cpp: In member function ‘void CoordSet::updateNonDiscreteAtmToIdx(unsigned int)’:
layer2/CoordSet.cpp:140:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   assert(!Obj || natom == Obj->NAtom);
                  ~~~~~~^~~~~~~~~~~~~
layer2/CoordSet.cpp:145:16: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘unsigned int’ [-Wsign-compare]
     assert(atm < natom);
            ~~~~^~~~~~~
layer2/CoordSet.cpp: In member function ‘int CoordSet::extendIndices(int)’:
layer2/CoordSet.cpp:1572:21: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(NAtIndex <= nAtom);
            ~~~~~~~~~^~~~~~~~
layer2/CoordSet.cpp:1573:18: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
     if (NAtIndex < nAtom) {
         ~~~~~~~~~^~~~~~~
layer2/CoordSet.cpp: In function ‘void CoordSetAtomToPDBStrVLA(PyMOLGlobals*, char**, int*, const AtomInfoType*, const float*, int, const PDBInfoRec*, const double*)’:
layer2/CoordSet.cpp:1014:14: 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);
       ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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<ObjectVolumeState>::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<ObjectVolumeState>::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<ObjectVolumeState>::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(cRep_t, cRepInv_t, int)’:
layer2/ObjectVolume.cpp:341:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectVolumeState>::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<ObjectVolumeState>::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<float>::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<ObjectVolumeState>::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:1131:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectVolumeState>::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:1232:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectVolumeState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int a = 0; a < I->State.size(); a++) {
                  ~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer2/ObjectMap.h:25,
                 from layer2/ObjectVolume.h:20,
                 from layer2/ObjectVolume.cpp:29:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = unsigned char; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = unsigned char; SizeTs = {int, int, int}]’
layer2/ObjectVolume.cpp:534:52:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer2/DistSet.cpp: In function ‘int DistSetGetLabelVertex(DistSet*, int, float*)’:
layer2/DistSet.cpp:43:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::array<float, 3> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if (at >= 0 && at < I->LabCoord.size()) {
                  ~~~^~~~~~~~~~~~~~~~~~~~
layer2/DistSet.cpp: In member function ‘pymol::Result<std::array<float, 3> > DistSet::getLabelOffset(int) const’:
layer2/DistSet.cpp:59:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<LabPosType>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   if (atm < 0 || atm >= this->LabPos.size()) {
                  ~~~~^~~~~~~~~~~~~~~~~~~~~~
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)
               ^~~~~~~~~~~~~~~~~~~~~~~~~~~
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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectVolume.cpp:20:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/HydrogenAdder.cpp: In function ‘int ObjectMoleculeAddSeleHydrogensRefactored(ObjectMolecule*, int, int)’:
layer2/HydrogenAdder.cpp:283:30: 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:301:30: 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:349:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
     for (unsigned idx = 0; idx < cs->NIndex; ++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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/MmtfMoleculeReader.cpp: In function ‘ObjectMolecule* ObjectMoleculeReadMmtfStr(PyMOLGlobals*, ObjectMolecule*, const char*, int, int, int, int, int, int)’:
layer2/MmtfMoleculeReader.cpp:223:47: 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) {
                                             ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/vla.h:10,
                 from layer1/Symmetry.h:26,
                 from layer1/PyMOLObject.h:27,
                 from layer2/ObjectMolecule.h:24,
                 from layer2/MmtfMoleculeReader.cpp:9:
layer2/MmtfMoleculeReader.cpp:276:34: warning: comparison of integer expressions of different signedness: ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
     assert(cset->IdxToAtm.size() == cset->getNIndex());
            ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
layer2/MmtfMoleculeReader.cpp:287:21: 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/RepCartoon.cpp: In function ‘Rep* RepCartoonNew(CoordSet*, int)’:
layer2/RepCartoon.cpp:3731:53: 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)      * nAtIndex);
                                                     ^
layer2/RepCartoon.cpp:44:7: note: ‘class CCInOut’ declared here
 class CCInOut {
       ^~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:436:11: 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:505:5: note: ‘out’ was declared here
   V out;
     ^~~
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:1593:20: 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:1007:65: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:322:3: 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:321:3: 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:320:3: 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];
                                       ^~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/ObjectCGO.cpp: In function ‘PyObject* ObjectCGOAllStatesAsPyList(ObjectCGO*)’:
layer2/ObjectCGO.cpp:53:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectCGOState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(a = 0; a < I->State.size(); a++) {
              ~~^~~~~~~~~~~~~~~~~
layer2/ObjectCGO.cpp: In function ‘int ObjectCGOAllStatesFromPyList(ObjectCGO*, PyObject*, int)’:
layer2/ObjectCGO.cpp:104:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectCGOState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = 0; a < I->State.size(); a++) {
                ~~^~~~~~~~~~~~~~~~~
layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::invalidate(cRep_t, cRepInv_t, int)’:
layer2/ObjectCGO.cpp:205:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectCGOState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if((state >= 0) && (state < I->State.size())) {
                         ~~~~~~^~~~~~~~~~~~~~~~~
layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::render(RenderInfo*)’:
layer2/ObjectCGO.cpp:488:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
         if (!ray)
         ^~
layer2/ObjectCGO.cpp:490:11: 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);
           ^~~~~~~~~~~~~~~~~~~~
In file included from layer2/ObjectCGO.cpp:24:
layer2/ObjectCGO.h: In copy constructor ‘ObjectCGOState::ObjectCGOState(const ObjectCGOState&)’:
layer2/ObjectCGO.h:28:17: warning: ‘ObjectCGOState::G’ will be initialized after [-Wreorder]
   PyMOLGlobals* G;
                 ^
layer2/ObjectCGO.h:27:25: warning:   ‘pymol::cache_ptr<CGO> ObjectCGOState::renderCGO’ [-Wreorder]
   pymol::cache_ptr<CGO> renderCGO;
                         ^~~~~~~~~
layer2/ObjectCGO.cpp:517:1: warning:   when initialized here [-Wreorder]
 ObjectCGOState::ObjectCGOState(const ObjectCGOState& other)
 ^~~~~~~~~~~~~~
In file included from layer2/ObjectCGO.cpp:24:
layer2/ObjectCGO.h:29:58: warning: ‘ObjectCGOState::hasOpaque’ will be initialized after [-Wreorder]
   bool renderWithShaders, hasTransparency, cgo_lighting, hasOpaque;
                                                          ^~~~~~~~~
layer2/ObjectCGO.h:29:44: warning:   ‘bool ObjectCGOState::cgo_lighting’ [-Wreorder]
   bool renderWithShaders, hasTransparency, cgo_lighting, hasOpaque;
                                            ^~~~~~~~~~~~
layer2/ObjectCGO.cpp:517:1: warning:   when initialized here [-Wreorder]
 ObjectCGOState::ObjectCGOState(const ObjectCGOState& other)
 ^~~~~~~~~~~~~~
layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromCGO(PyMOLGlobals*, ObjectCGO*, CGO*, int)’:
layer2/ObjectCGO.cpp:602:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectCGOState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   if(I->State.size() <= state) {
      ~~~~~~~~~~~~~~~~^~~~~~~~
layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGODefine(PyMOLGlobals*, ObjectCGO*, PyObject*, int)’:
layer2/ObjectCGO.cpp:667:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectCGOState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   if(I->State.size() <= state) {
      ~~~~~~~~~~~~~~~~^~~~~~~~
layer2/ObjectCGO.cpp: In function ‘ObjectCGO* ObjectCGOFromFloatArray(PyMOLGlobals*, ObjectCGO*, float*, int, int, int)’:
layer2/ObjectCGO.cpp:725:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectCGOState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   if(I->State.size() <= state) {
      ~~~~~~~~~~~~~~~~^~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/ObjectDist.cpp: In function ‘int ObjectDistMoveWithObject(ObjectDist*, ObjectMolecule*)’:
layer2/ObjectDist.cpp:111:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pymol::copyable_ptr<DistSet> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (int i=0; i<I->DSet.size(); i++) {
                 ~^~~~~~~~~~~~~~~
layer2/ObjectDist.cpp: In function ‘void ObjectDistUpdateExtents(ObjectDist*)’:
layer2/ObjectDist.cpp:136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pymol::copyable_ptr<DistSet> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int a = 0; a < I->DSet.size(); a++) {
                  ~~^~~~~~~~~~~~~~~~
layer2/ObjectDist.cpp: In function ‘PyObject* ObjectDistDSetAsPyList(ObjectDist*)’:
layer2/ObjectDist.cpp:148:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pymol::copyable_ptr<DistSet> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int a = 0; a < I->DSet.size(); a++) {
                  ~~^~~~~~~~~~~~~~~~
layer2/ObjectDist.cpp: In function ‘int ObjectDistDSetFromPyList(ObjectDist*, PyObject*)’:
layer2/ObjectDist.cpp:165:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pymol::copyable_ptr<DistSet> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(int a = 0; a < I->DSet.size(); a++) {
                    ~~^~~~~~~~~~~~~~~~
layer2/ObjectDist.cpp: In member function ‘virtual void ObjectDist::update()’:
layer2/ObjectDist.cpp:241:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pymol::copyable_ptr<DistSet> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(int a = 0; a < I->DSet.size(); a++)
                  ~~^~~~~~~~~~~~~~~~
layer2/ObjectDist.cpp: In function ‘void ObjectDistInvalidateRep(ObjectDist*, cRep_t)’:
layer2/ObjectDist.cpp:257:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<pymol::copyable_ptr<DistSet> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(a = 0; a < I->DSet.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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/RepDot.cpp: In function ‘Rep* RepDotDoNew(CoordSet*, cRepDot_t, int)’:
layer2/RepDot.cpp:463:46: warning: ‘vn’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     I->VN = ReallocForSure(I->VN, float, (vn - I->VN));
                                              ^
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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<ObjectMapState>::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:914:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:931:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:946:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:1189:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (i=0; i<om->State.size();i++){
             ~^~~~~~~~~~~~~~~~~
layer2/ObjectMap.cpp: In function ‘PyObject* ObjectMapAllStatesAsPyList(ObjectMap*)’:
layer2/ObjectMap.cpp:1279:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:1437:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:1509:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(state = 0; state < src->State.size(); state++) {
                      ~~~~~~^~~~~~~~~~~~~~~~~~~
layer2/ObjectMap.cpp:1518:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:1535:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:1548:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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(cRep_t, cRepInv_t, int)’:
layer2/ObjectMap.cpp:1674:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:2297:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
   if(bytes < 256 * sizeof(int)) {
      ~~~~~~^~~~~~~~~~~~~~~~~~~
layer2/ObjectMap.cpp:2307:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:2942:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:3216:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:3437:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:3766:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:4172:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:4694:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:5245:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   if(I->State.size() <= state) {
      ~~~~~~~~~~~~~~~~^~~~~~~~
layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadXPLOR(PyMOLGlobals*, ObjectMap*, const char*, int, int, int)’:
layer2/ObjectMap.cpp:5557:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:5711:24: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::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:5809:24: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
     if(I->State.size() <= state) {
        ~~~~~~~~~~~~~~~~^~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer2/ObjectMap.h:25,
                 from layer2/ObjectMap.cpp:27:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int, int}]’:
layer2/ObjectMap.cpp:198:30:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer2/ObjectMap.cpp:1605:14:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = int; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = int; SizeTs = {int, int, int}]’
layer2/ObjectMap.cpp:5967:57:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
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)
 ^~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer2/RepMesh.cpp:28:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer2/RepMesh.cpp:970:27:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer2/RepMesh.cpp: In function ‘Rep* RepMeshNew(CoordSet*, int)’:
layer2/RepMesh.cpp:1053:13: warning: ‘field’ may be used uninitialized in this function [-Wmaybe-uninitialized]
     DeleteP(field);
             ^~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int)’:
layer2/ObjectMap.cpp:2961:7: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__s), __fmt,
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~           
layer2/ObjectMap.cpp:2970:7: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__s), __fmt,
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~           
layer2/ObjectMap.cpp:2976:7: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__s), __fmt,
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~           
layer2/ObjectMap.cpp:3058:7: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__s), __fmt,
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~           
layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’:
layer2/ObjectMap.cpp:4290:5: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__s), __fmt,
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __va_arg_pack ());
        ~~~~~~~~~~~~~~~~~           
layer2/ObjectMap.cpp:4290:5: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMap.cpp:21:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:502:11: 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:501:9: note: in expansion of macro ‘PRINTFB’
         PRINTFB(I->G, FB_ObjectMesh, FB_Errors)
         ^~~~~~~
layer2/ObjectMesh.cpp:535:15: 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:534:13: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/ObjectMolecule.cpp: In function ‘int ObjectMoleculeFillOpenValences(ObjectMolecule*, int)’:
layer2/ObjectMolecule.cpp:3531:14: warning: comparison of integer expressions of different signedness: ‘const unsigned int’ and ‘signed char’ [-Wsign-compare]
       if((nn >= ai->valence) || (!flag))
           ~~~^~~~~~~~~~~~~~
layer2/ObjectMolecule.cpp: In function ‘pymol::Result<> ObjectMoleculeAddBondByIndices(ObjectMolecule*, unsigned int, unsigned int, int)’:
layer2/ObjectMolecule.cpp:4328:12: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   if (atm1 >= I->NAtom || atm2 >= I->NAtom) {
       ~~~~~^~~~~~~~~~~
layer2/ObjectMolecule.cpp:4328:32: 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:11713:24: 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) {
                      ~~^~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/ObjectMolecule.cpp: In function ‘const char* findflag(PyMOLGlobals*, const char*, const char*, const char*)’:
layer2/ObjectMolecule.cpp:1417:9: 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:31:
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:1416:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_ObjectMolecule, FB_Errors)
       ^~~~~~~
layer2/ObjectMolecule.cpp:1435:9: 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:31:
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:1434:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_ObjectMolecule, FB_Errors)
       ^~~~~~~
layer2/ObjectMolecule.cpp: In function ‘CoordSet* ObjectMoleculeMOLStr2CoordSet(PyMOLGlobals*, const char*, AtomInfoType**, const char**)’:
layer2/ObjectMolecule.cpp:7579:5: 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:31:
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:7578:3: note: in expansion of macro ‘PRINTFB’
   PRINTFB(G, FB_ObjectMolecule, FB_Blather)
   ^~~~~~~
layer2/ObjectMolecule.cpp:7627:16: 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);
         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.cpp: In function ‘CoordSet* ObjectMoleculeXYZStr2CoordSet(PyMOLGlobals*, const char*, AtomInfoType**, const char**)’:
layer2/ObjectMolecule.cpp:2898:16: 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/RepSurface.cpp: In function ‘void RepSurfaceSmoothEdges(RepSurface*)’:
layer2/RepSurface.cpp:4403:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (auto j = 0; j < edges[i].size(); j += 3) {
                      ~~^~~~~~~~~~~~~~~~~
layer2/RepSurface.cpp:4415:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (auto j = 0; j < edges[i].size(); j += 3) {
                      ~~^~~~~~~~~~~~~~~~~
layer2/RepSurface.cpp:4426:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for (auto i = 0; i < unique_edges.size(); i += 2) {
                      ~~^~~~~~~~~~~~~~~~~~~~~
layer2/ObjectMolecule.cpp: In member function ‘virtual void ObjectMolecule::update()’:
layer2/ObjectMolecule.cpp:10605:15: 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:31:
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:10604:13: 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:10731:21: 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:10731:21: note: directive argument in the range [-2147483647, 2147483647]
layer2/ObjectMolecule.cpp:10731:14: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer2/ObjectMolecule2.cpp: In function ‘bool ObjectMoleculeConnect(ObjectMolecule*, int&, pymol::vla<BondType>&, CoordSet*, int, int, bool)’:
layer2/ObjectMolecule2.cpp:3750:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
     for (unsigned i = 0; i < cs->NIndex; ++i) {
                          ~~^~~~~~~~~~~~
layer2/ObjectMolecule2.cpp: In lambda function:
layer2/ObjectMolecule2.cpp:3779:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare]
         if (i <= j && !symop)
             ~~^~~~
layer2/ObjectMolecule2.cpp: In function ‘bool ObjectMoleculeConnect(ObjectMolecule*, int&, pymol::vla<BondType>&, CoordSet*, int, int, bool)’:
layer2/ObjectMolecule2.cpp:3884:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
       for (unsigned i = 0; i < cs->NIndex; ++i) {
                            ~~^~~~~~~~~~~~
layer2/ObjectMolecule2.cpp:3900:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
     for (unsigned a = 0; a < cs->NTmpBond; ++a) {
                          ~~^~~~~~~~~~~~~~
layer2/ObjectMolecule2.cpp:3950:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
     for (unsigned a = 0; a < cs->NTmpLinkBond; ++a) {
                          ~~^~~~~~~~~~~~~~~~~~
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:335:9: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer2/ObjectMolecule2.cpp:24:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:436:11: 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:505:5: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/ObjectMolecule3.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule3.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
layer2/ObjectMolecule3.cpp: In function ‘std::vector<int> ObjectMoleculeGetMolMappingVec(const ObjectMolecule&)’:
layer2/ObjectMolecule3.cpp:42:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   for (size_t b = 0; b < objmol.NBond; ++b) {
                      ~~^~~~~~~~~~~~~~
layer2/ObjectMolecule3.cpp: In function ‘void ObjectMoleculePBCUnwrap(ObjectMolecule&, bool)’:
layer2/ObjectMolecule3.cpp:151:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
       for (unsigned atm = 0; atm != objmol.NAtom; ++atm) {
                              ~~~~^~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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<TableRec>::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<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (a++; a < I->Table.size(); a++) {
             ~~^~~~~~~~~~~~~~~~~
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<ObjectSliceState>::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(cRep_t, cRepInv_t, int)’:
layer2/ObjectSlice.cpp:210:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSliceState>::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<ObjectSliceState>::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<ObjectSliceState>::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<ObjectSliceState>::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<ObjectSliceState>::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<ObjectSliceState>::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<ObjectSliceState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if(state < I->State.size())
        ~~~~~~^~~~~~~~~~~~~~~~~
layer2/ObjectSlice.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSliceState>::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:1244:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSliceState>::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:1285:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectSliceState>::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:1362:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSliceState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer3/Editor.cpp: In function ‘pymol::Result<> EditorSelect(PyMOLGlobals*, const char*, const char*, const char*, const char*, int, int, int)’:
layer3/Editor.cpp:776:7: 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 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);
     ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer2/ObjectSurface.cpp: In function ‘PyObject* ObjectSurfaceAllStatesAsPyList(ObjectSurface*)’:
layer2/ObjectSurface.cpp:83:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSurfaceState>::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:236:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSurfaceState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     if(state < I->State.size()) {
        ~~~~~~^~~~~~~~~~~~~~~~~
layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::invalidate(cRep_t, cRepInv_t, int)’:
layer2/ObjectSurface.cpp:281:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSurfaceState>::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:311:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSurfaceState>::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, cIsosurfaceMode, float, pymol::vla<float>&&, cIsosurfaceSide, int)’:
layer2/ObjectSurface.cpp:1029:22: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectSurfaceState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   if(I->State.size() <= state) {
      ~~~~~~~~~~~~~~~~^~~~~~~~
layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceSetLevel(ObjectSurface*, float, int, int)’:
layer2/ObjectSurface.cpp:1125:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectSurfaceState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(int a = 0; a < I->State.size(); a++) {
                    ~~^~~~~~~~~~~~~~~~~
layer3/Editor.cpp: In function ‘void EditorPrepareDrag(PyMOLGlobals*, pymol::CObject*, int, int, int, int)’:
layer3/Editor.cpp:1933:9: 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:1932:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_Editor, FB_Blather)
       ^~~~~~~
layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’:
layer2/ObjectSurface.cpp:268:9: 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:35:
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:267:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(I->G, FB_ObjectSurface, FB_Actions)
       ^~~~~~~
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:35:
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:986:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:1132:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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:1305:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         if(map_state >= mapObj->State.size())
            ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from /usr/include/glm/detail/func_exponential.inl:8,
                 from /usr/include/glm/detail/func_exponential.hpp:103,
                 from /usr/include/glm/detail/func_geometric.inl:4,
                 from /usr/include/glm/detail/func_geometric.hpp:113,
                 from /usr/include/glm/geometric.hpp:6,
                 from /usr/include/glm/detail/func_matrix.inl:4,
                 from /usr/include/glm/detail/func_matrix.hpp:149,
                 from /usr/include/glm/detail/type_mat2x2.inl:4,
                 from /usr/include/glm/detail/type_mat2x2.hpp:182,
                 from /usr/include/glm/mat2x2.hpp:6,
                 from /usr/include/glm/glm.hpp:71,
                 from layer3/Executive.cpp:114:
layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSmooth(PyMOLGlobals*, const char*, int, int, int, int, int, int, float, bool)’:
layer3/Executive.cpp:6095:17: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
   assert(n_atom == SelectorCountAtoms(G, sele, cStateAll));
          ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp:6155:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const long unsigned int’ [-Wsign-compare]
       for (int c = 0; c < n_atom; ++c) {
                       ~~^~~~~~~~
layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveMapSet(PyMOLGlobals*, const char*, int, const char*, int, int, int, int)’:
layer3/Executive.cpp:6325:34: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
             if(obj->State.size() > max_n_state)
                ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
layer3/Executive.cpp:6436:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::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<SelectorTmp>&, int, bool)’:
layer3/Executive.cpp:11035:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
   for(a = 0; a < pairs; a++) {
              ~~^~~~~~~
layer3/Executive.cpp:11040:10: 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:12401:7: 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:14066:40: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
             for (unsigned idx = 0; idx < cs->NIndex; ++idx) {
                                    ~~~~^~~~~~~~~~~~
layer3/Executive.cpp:14093:40: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
             for (unsigned atm = 0; atm < new_obj->NAtom; ++atm) {
                                    ~~~~^~~~~~~~~~~~~~~~
layer3/Executive.cpp: In member function ‘virtual int CExecutive::click(int, int, int, int)’:
layer3/Executive.cpp:14873:68: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
               if(((panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) ||
                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp:14874:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
                  ((!panel->is_group) && (((xx) - 1) / DIP2PIXEL(8)) > panel->nest_level)) {
                                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp: In member function ‘virtual int CExecutive::release(int, int, int, int)’:
layer3/Executive.cpp:15162:65: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
                (((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) ||
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp:15163:66: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
                 ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_level))) {
                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’:
layer3/Executive.cpp:15304:70: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
                   if(((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1)) ||
                                            ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp:15305:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
                      ((!panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > panel->nest_level)) {
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp:15340:71: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
                   if(!((panel->is_group) && ((xx - 1) / DIP2PIXEL(8)) > (panel->nest_level + 1))) {
                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from layer0/OOMac.h:22,
                 from layer3/Executive.cpp:37:
layer3/Executive.cpp: In function ‘void ExecutiveFree(PyMOLGlobals*)’:
layer3/Executive.cpp:16294:14: 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:86:39: 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:16607:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         if(map_state >= mapObj->State.size())
            ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from layer3/Executive.h:38,
                 from layer3/Executive.cpp:38:
layer0/TrackerList.h: In instantiation of ‘pymol::TrackerAdapter<T>::TrackerAdapterIterator<IsConst>::TrackerAdapterIterator(CTracker*, int) [with bool IsConst = false; T = SpecRec]’:
layer0/TrackerList.h:99:29:   required from ‘pymol::TrackerAdapter<T>::iterator pymol::TrackerAdapter<T>::begin() [with T = SpecRec; pymol::TrackerAdapter<T>::iterator = pymol::TrackerAdapter<SpecRec>::TrackerAdapterIterator<false>]’
layer3/Executive.cpp:202:62:   required from here
layer0/TrackerList.h:80:15: warning: ‘pymol::TrackerAdapter<SpecRec>::TrackerAdapterIterator<false>::m_tracker’ will be initialized after [-Wreorder]
     CTracker* m_tracker;
               ^~~~~~~~~
layer0/TrackerList.h:79:22: warning:   ‘int pymol::TrackerAdapter<SpecRec>::TrackerAdapterIterator<false>::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)
              ^~~~~~~~~~~~~~~~~~~~~~
layer3/Executive.cpp: In function ‘int ExecutiveSetBondSettingFromString(PyMOLGlobals*, int, const char*, const char*, const char*, int, int, int)’:
layer3/Executive.cpp:11424:17: 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:11424:17: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11423:15: 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:11505:8: 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:11505:8: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11504:6: 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:11605:19: 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:11605:19: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11604:17: note: in expansion of macro ‘PRINTF’
                 PRINTF
                 ^~~~~~
layer3/Executive.cpp:11624:7: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11623:5: 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:11684:15: 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:11684:15: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11683:13: note: in expansion of macro ‘PRINTF’
             PRINTF
             ^~~~~~
layer3/Executive.cpp: In function ‘int ExecutiveSetObjSettingFromString(PyMOLGlobals*, int, const char*, pymol::CObject*, int, int, int)’:
layer3/Executive.cpp:12226:19: 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:12226:19: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12225:17: note: in expansion of macro ‘PRINTF’
                 PRINTF
                 ^~~~~~
layer3/Executive.cpp:12218:19: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12217:17: note: in expansion of macro ‘PRINTF’
                 PRINTF
                 ^~~~~~
layer3/Executive.cpp:12197:18: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12197:11: note: in expansion of macro ‘PRINTF’
           PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G);
           ^~~~~~
layer3/Executive.cpp: In function ‘int ExecutiveSetSettingFromString(PyMOLGlobals*, int, const char*, const char*, int, int, int)’:
layer3/Executive.cpp:12097:21: 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:12097:21: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12096:19: note: in expansion of macro ‘PRINTF’
                   PRINTF
                   ^~~~~~
layer3/Executive.cpp:12094:21: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12093:19: note: in expansion of macro ‘PRINTF’
                   PRINTF
                   ^~~~~~
layer3/Executive.cpp:12129:25: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12128:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:12161:25: 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:12161:25: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12160:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:12153:25: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12152:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:12057:18: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12057:11: note: in expansion of macro ‘PRINTF’
           PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G);
           ^~~~~~
layer3/Executive.cpp: In function ‘bool ExecutiveSetSymmetry(PyMOLGlobals*, pymol::zstring_view, int, const CSymmetry&, bool)’:
layer3/Executive.cpp:5951:7: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:5950:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_Executive, FB_Details)
       ^~~~~~~
layer3/Executive.cpp:5942:7: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
layer0/Feedback.h:274:15: note: ‘snprintf’ output between 84 and 339 bytes into a destination of size 255
     (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT,
               ^
layer3/Executive.cpp:5941:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_Executive, FB_Warnings)
       ^~~~~~~
layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSetSetting(PyMOLGlobals*, int, PyObject*, pymol::zstring_view, int, int, int)’:
layer3/Executive.cpp:11932:9: 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(index)
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ~~~~
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11931:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_Setting, FB_Warnings)
       ^~~~~~~
layer3/Executive.cpp:11788:21: 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:11788:21: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11787:19: note: in expansion of macro ‘PRINTF’
                   PRINTF
                   ^~~~~~
layer3/Executive.cpp:11785:21: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11784:19: note: in expansion of macro ‘PRINTF’
                   PRINTF
                   ^~~~~~
layer3/Executive.cpp:11877:27: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11876:25: note: in expansion of macro ‘PRINTF’
                         PRINTF
                         ^~~~~~
layer3/Executive.cpp:11909:25: 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:11909:25: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11908:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:11902:25: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11901:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:11744:18: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:11744:11: note: in expansion of macro ‘PRINTF’
           PRINTF " Setting: %s set to %s.\n", name, value ENDF(G);
           ^~~~~~
layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveUnsetSetting(PyMOLGlobals*, int, pymol::zstring_view, int, int, int)’:
layer3/Executive.cpp:12338:23: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12337:21: note: in expansion of macro ‘PRINTF’
                     PRINTF
                     ^~~~~~
layer3/Executive.cpp:12360:25: 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:12360:25: note: directive argument in the range [1, 2147483647]
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12359:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:12354:25: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:12353:23: note: in expansion of macro ‘PRINTF’
                       PRINTF
                       ^~~~~~
layer3/Executive.cpp:12276:14: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 223 [-Wformat-truncation=]
       PRINTF " Setting: %s restored to default (%s)\n", name, value ENDF(G);
              ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~        ~~~~~
In file included from layer1/Ortho.h:32,
                 from layer3/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
layer0/Feedback.h:282:53: note: ‘snprintf’ output 35 or more bytes (assuming 1058) into a destination of size 255
 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT,
                                                     ^
layer3/Executive.cpp:12276:7: note: in expansion of macro ‘PRINTF’
       PRINTF " Setting: %s restored to default (%s)\n", name, value ENDF(G);
       ^~~~~~
layer3/Executive.cpp: In function ‘void ExecutiveManageObject(PyMOLGlobals*, pymol::CObject*, int, int)’:
layer3/Executive.cpp:14447:9: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:14446:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_Executive, FB_Warnings)
       ^~~~~~~
layer3/Executive.cpp:14442:9: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:14441:7: note: in expansion of macro ‘PRINTFB’
       PRINTFB(G, FB_Executive, FB_Warnings)
       ^~~~~~~
layer3/Executive.cpp:14467:13: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:14466:11: note: in expansion of macro ‘PRINTFB’
           PRINTFB(G, FB_Executive, FB_Actions)
           ^~~~~~~
layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveCopy(PyMOLGlobals*, const char*, const char*, int)’:
layer3/Executive.cpp:9665:5: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:9664:3: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer3/Executive.cpp: In function ‘int ExecutiveGroup(PyMOLGlobals*, pymol::zstring_view, pymol::zstring_view, int, int)’:
layer3/Executive.cpp:2259:19: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:2258:17: note: in expansion of macro ‘PRINTFB’
                 PRINTFB(G, FB_Executive, FB_Actions)
                 ^~~~~~~
layer3/Executive.cpp: In function ‘pymol::Result<std::vector<DiscardedRec> > ExecutiveSetName(PyMOLGlobals*, pymol::zstring_view, pymol::zstring_view, bool)’:
layer3/Executive.cpp:3523:7: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:3522:5: note: in expansion of macro ‘PRINTFB’
     PRINTFB(G, FB_Executive, FB_Warnings)
     ^~~~~~~
layer3/Executive.cpp: In function ‘int ExecutiveProcessPDBFile(PyMOLGlobals*, pymol::CObject*, const char*, const char*, const char*, int, int, int, char*, int, int, int, int)’:
layer3/Executive.cpp:4259:35: 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:4259:35: note: using the range [-2147483648, 2147483647] for directive argument
layer3/Executive.cpp:4259:24: 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:4257:35: 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:4257:35: note: directive argument in the range [1, 2147483647]
layer3/Executive.cpp:4257:24: 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:4246:35: 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:4246:35: note: using the range [-2147483648, 2147483647] for directive argument
layer3/Executive.cpp:4246:24: 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:4237:33: 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:4237:33: note: using the range [-2147483648, 2147483647] for directive argument
layer3/Executive.cpp:4237:22: 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:4235:33: 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:4235:33: note: directive argument in the range [1, 2147483647]
layer3/Executive.cpp:4235:22: 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:4224:33: 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:4224:33: note: using the range [-2147483648, 2147483647] for directive argument
layer3/Executive.cpp:4224:22: 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 function ‘int ExecutiveSetSession(PyMOLGlobals*, PyObject*, int, int)’:
layer3/Executive.cpp:5070:13: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:5069:11: note: in expansion of macro ‘PRINTFB’
           PRINTFB(G, FB_Executive, FB_Errors)
           ^~~~~~~
layer3/Executive.cpp:5095:11: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:5094:9: note: in expansion of macro ‘PRINTFB’
         PRINTFB(G, FB_Executive, FB_Errors)
         ^~~~~~~
layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveRemoveAtoms(PyMOLGlobals*, const char*, int)’:
layer3/Executive.cpp:9007:17: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:9006:15: 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, pymol::zstring_view)’:
layer3/Executive.cpp:9371:19: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:9370:17: note: in expansion of macro ‘PRINTFB’
                 PRINTFB(G, FB_Editor, FB_Actions)
                 ^~~~~~~
layer3/Executive.cpp:9358:19: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:9357:17: note: in expansion of macro ‘PRINTFB’
                 PRINTFB(G, FB_Editor, FB_Actions)
                 ^~~~~~~
layer3/Executive.cpp:9383:19: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:9382:17: 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:4047:7: 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/ExecutiveDef.h:3,
                 from layer3/Executive.h:29,
                 from layer3/Executive.cpp:38:
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:4046:5: note: in expansion of macro ‘PRINTFB’
     PRINTFB(G, FB_Executive, FB_Actions)
     ^~~~~~~
layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’:
layer3/Executive.cpp:15471:42: 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:15471:26: 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");
                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer3/Executive.cpp: In function ‘pymol::Result<std::pair<float, float> > ExecutiveSpectrum(PyMOLGlobals*, pymol::zstring_view, pymol::zstring_view, float, float, int, int, pymol::zstring_view, int, int, int)’:
layer3/Executive.cpp:4764:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 8 equals destination size [-Wstringop-truncation]
                 strncpy(value_s, raw_ptr, sizeof(value_e));
                 ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer3/PlugIOManager.cpp: In function ‘ObjectMap* PlugIOManagerLoadVol(PyMOLGlobals*, ObjectMap*, const char*, int, int, const char*)’:
layer3/PlugIOManager.cpp:416:34: warning: comparison of integer expressions of different signedness: ‘std::vector<ObjectMapState>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
             if(obj->State.size() <= state) {
                ~~~~~~~~~~~~~~~~~~^~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer2/ObjectMap.h:25,
                 from layer3/PlugIOManager.h:23,
                 from layer3/PlugIOManager.cpp:24:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer0/Field.h:114:12:   required from ‘T& CField::get(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’
layer3/PlugIOManager.cpp:541:21:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer3/PlugIOManager.cpp: In function ‘pymol::CObject* PlugIOManagerLoad(PyMOLGlobals*, pymol::CObject**, const char*, int, int, const char*, int)’:
layer3/PlugIOManager.cpp:946:9: 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/c++/8/cstdio:42,
                 from /usr/include/c++/8/ext/string_conversions.h:43,
                 from /usr/include/c++/8/bits/basic_string.h:6404,
                 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/bits/unique_ptr.h:37,
                 from /usr/include/c++/8/memory:80,
                 from layer0/os_python.h:23,
                 from layer3/PlugIOManager.cpp:20:
/usr/include/bits/stdio2.h:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer3/RingFinder.cpp: In member function ‘void AbstractRingFinder::recursion(int, int)’:
layer3/RingFinder.cpp:23:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer3/Seeker.cpp: In function ‘void SeekerRefresh(PyMOLGlobals*, std::vector<CSeqRow>&)’:
layer3/Seeker.cpp:485:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
   for(int b = 0; b < nRow; b++) {
                  ~~^~~~~~
layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’:
layer3/Seeker.cpp:1150:23: 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:1186:23: 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:1248:30: 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:1930:27: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
           if(row->ext_len < stop)
              ~~~~~~~~~~~~~^~~~~~
In file included from layer0/vla.h:7,
                 from layer1/Symmetry.h:26,
                 from layer1/PyMOLObject.h:27,
                 from layer1/Seq.h:21,
                 from layer3/Seeker.cpp:26:
layer3/Seeker.cpp: In function ‘void SeekerFree(PyMOLGlobals*)’:
layer3/Seeker.cpp:1964:14: warning: deleting object of polymorphic class type ‘CSeeker’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor]
   DeleteP(G->Seeker);
              ^~~~~~
layer0/MemoryDebug.h:86:39: note: in definition of macro ‘DeleteP’
 #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}}
                                       ^~~
layer3/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveSetRawAlignment(PyMOLGlobals*, pymol::zstring_view, PyObject*, pymol::zstring_view, int, int)’:
layer3/ExecutivePython.cpp:171:23: 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:180:25: 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:146:5: 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:6404,
                 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:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:436:11: 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:505:5: note: ‘out’ was declared here
   V out;
     ^~~
layer3/Selector.cpp: In member function ‘virtual bool SelectorAtomIterator::next()’:
layer3/Selector.cpp:185:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:1028:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:1082:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   while(a < I->Table.size()) {
         ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:1106:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:1519:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SelectionInfoRec>::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:1653:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:1680:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             while(a1 < I->Table.size()) {
                   ~~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:1874:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:2687:18: 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:2703:16: 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:2715:18: 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:2763:18: 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:2768:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:2772:20: 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:2873:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<SelectionInfoRec>::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:2952:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3446:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3470:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3488:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3503:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3589:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3648:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:3813:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (a = cNDummyAtoms; a < I->Table.size(); a++) {
                          ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetFirstObjectMolecule(PyMOLGlobals*, SelectorID_t)’:
layer3/Selector.cpp:3843:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for (a = cNDummyAtoms; a < I->Table.size(); a++) {
                          ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp: In function ‘ObjectMolecule** SelectorGetObjectMoleculeVLA(PyMOLGlobals*, SelectorID_t)’:
layer3/Selector.cpp:3867:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:4266:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:4570:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:4600:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:4761:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:5121:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(a = 0; a < I->Table.size(); a++) {
              ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:5165:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:5373:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:6062:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   if(ob)
   ^~
layer3/Selector.cpp:6066:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
     SelectorUpdateTable(G, source, -1);
     ^~~~~~~~~~~~~~~~~~~
layer3/Selector.cpp:6077:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:6103:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                         ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:6133:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMolecule*>::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:6159:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:6200:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:6224:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:6660:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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<int, int>&)’:
layer3/Selector.cpp:6755:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(int a = cNDummyAtoms; a < I->Table.size(); a++) {
                                 ~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer2/ObjectMap.h:25,
                 from layer3/Selector.h:27,
                 from layer3/Selector.cpp:39:
layer3/Selector.cpp: In function ‘void SelectorUpdateTableSingleObject(PyMOLGlobals*, ObjectMolecule*, int, bool)’:
layer3/Selector.cpp:6997:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   assert(c == I->Table.size());
          ~~^~~~~~~~~~~~~~~~~~
layer3/Selector.cpp: In function ‘sele_array_t SelectorGetSeleArrayForAtomIndices(CSelector*, ObjectMolecule*, const int*, int, bool)’:
layer3/Selector.cpp:7010:26: warning: comparison of integer expressions of different signedness: ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   assert(I->Table.size() == cNDummyAtoms + obj->NAtom);
          ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
layer3/Selector.cpp: In function ‘int SelectorModulate1(PyMOLGlobals*, EvalElem*, int)’:
layer3/Selector.cpp:7293:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
           for (a = cNDummyAtoms; a < I->Table.size(); a++) {
                                  ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7316:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
                   for(a = 0; ok && a < I->Table.size(); a++) {
                                    ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7379:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = 0; a < I->Table.size(); a++) {
                  ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7393:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
           for(a = 0; a < I->Table.size(); a++) {
                      ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7416:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
                   for(a = 0; ok && a < I->Table.size(); a++) {
                                    ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7457:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:7490:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7501:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++)
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7506:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++)
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7513:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7517:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7521:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7525:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7529:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7538:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7555:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7560:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7565:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7570:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7575:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7580:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7585:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7589:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7593:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7598:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7603:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++)
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7610:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7626:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7632:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = 0; a < I->Table.size(); a++) {
                ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7641:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = 0; a < I->Table.size(); a++) {
                ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7653:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:7673:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:8378:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMolecule*>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
           for(a = cNDummyModels; a < I->Obj.size(); a++)
                                  ~~^~~~~~~~~~~~~~~
layer3/Selector.cpp:8388:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<ObjectMolecule*>::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:8470:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++)
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8474:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                               ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8522:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8533:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8544:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8555:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8570:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8581:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8592:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8603:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8618:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8629:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8640:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:8651:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
             for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                                   ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp: In function ‘int SelectorLogic1(PyMOLGlobals*, EvalElem*, int)’:
layer3/Selector.cpp:9128:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
           for(a = 0; a < I->Table.size(); a++) {
                      ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:9157:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:9416:24: 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:9438:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
                   for(a = 0; a < I->Table.size(); a++) {
                              ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:9468:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for(a = 0; a < I->Table.size(); a++) {
                    ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:9473:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
       for(a = cNDummyAtoms; a < I->Table.size(); a++)
                             ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp: In function ‘pymol::Result<std::unique_ptr<int [], std::default_delete<int []> > > SelectorEvaluate(PyMOLGlobals*, std::vector<std::__cxx11::basic_string<char> >&, int, int)’:
layer3/Selector.cpp:9622:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::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:10213:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:10495:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:10519:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::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:10724:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
     for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                           ~~^~~~~~~~~~~~~~~~~
layer3/Selector.cpp:10801:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<TableRec>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
         for(a = cNDummyAtoms; a < I->Table.size(); a++) {
                               ~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/cassert:44,
                 from layer0/Field.h:24,
                 from layer0/Isosurf.h:24,
                 from layer2/ObjectMap.h:25,
                 from layer3/Selector.h:27,
                 from layer3/Selector.cpp:39:
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int, int}]’:
layer3/Selector.cpp:4800:18:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
     assert(sizeof...(pos) <= n_dim());
            ~~~~~~~~~~~~~~~^~~~~~~~~~
layer0/Field.h: In instantiation of ‘T* CField::ptr(SizeTs ...) [with T = float; SizeTs = {int, int, int}]’:
layer3/Selector.cpp:5309:20:   required from here
layer0/Field.h:100:27: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
layer3/Selector.cpp: In function ‘int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’:
layer3/Selector.cpp:1722:21: 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:6404,
                 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:68:35: 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,
          ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        __glibc_objsize (__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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/SpecRec.cpp -o build/temp.linux-x86_64-3.6/layer3/SpecRec.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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/SpecRecSpecial.cpp -o build/temp.linux-x86_64-3.6/layer3/SpecRecSpecial.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
layer4/Cmd.cpp: In function ‘PyObject* CmdPushUndo(PyObject*, PyObject*)’:
layer4/Cmd.cpp:2216:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
     if(ok)
     ^~
layer4/Cmd.cpp:2218:7: 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* CmdGetMinMax(PyObject*, PyObject*)’:
layer4/Cmd.cpp:4469:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable]
   int ok = false;
       ^~
In file included from layer4/Cmd.cpp:77:
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:380:27:   required from ‘PyObject* APIResult(PyMOLGlobals*, pymol::Result<T>&) [with T = std::array<float, 3>; PyObject = _object]’
layer4/Cmd.cpp:4034:29:   required from here
layer1/PConv.h:259:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
   for (int i = 0; i < N; ++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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
In file included from layer0/OOMac.h:22,
                 from layer4/PopUp.cpp:23:
layer4/PopUp.cpp: In function ‘void PopUpFree(Block*)’:
layer4/PopUp.cpp:401:11: 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:86:39: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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:1546:27: 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:1987:14: 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:86:39: 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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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 -DPYMOL_OPENMP -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -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 -fopenmp
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/CarveHelper.o build/temp.linux-x86_64-3.6/layer0/ContourSurf.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/MemoryUsage.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/ccealignmodule.o build/temp.linux-x86_64-3.6/layer0/marching_cubes.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/SceneMouse.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/SymOp.o build/temp.linux-x86_64-3.6/layer1/SymOpPConv.o build/temp.linux-x86_64-3.6/layer1/SymOpTools.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/ObjectMolecule3.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/layer3/SpecRec.o build/temp.linux-x86_64-3.6/layer3/SpecRecSpecial.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/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 -lnetcdf -lpython3.6m -o build/lib.linux-x86_64-3.6/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so -fopenmp
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.PDDMay
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64
++ dirname /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64
+ cd pymol-open-source-2.5.0
+ 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-2.5.0-6.el8.x86_64 --use-msgpackc=c++11 --use-openmp=yes --pymol-path=/usr/lib64/python3.6/site-packages/pymol
running install
running install_lib
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/champ
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/fast
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/arc.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/bonds.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/brick.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/cc1.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/charge.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/cif.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/cpv.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/dictdb.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/gamess1.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/gms.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/hetatm.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/io.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/lst.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/mae.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/map.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/mass.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/mmd.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/models.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/mol.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/mol2.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/neighbor.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/pdb.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/pkl.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/place.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/protein.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/sdf.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/solvate.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
copying build/lib.linux-x86_64-3.6/chempy/xyz.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms
copying build/lib.linux-x86_64-3.6/pmg_qt/forms/change_confirm.ui -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms
copying build/lib.linux-x86_64-3.6/pmg_qt/forms/create_shortcut.ui -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms
copying build/lib.linux-x86_64-3.6/pmg_qt/forms/help_shortcut.ui -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms
copying build/lib.linux-x86_64-3.6/pmg_qt/forms/shortcut_menu.ui -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt
copying build/lib.linux-x86_64-3.6/pmg_qt/shortcut_menu_gui.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_tk
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_tk
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/__main__.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/_gui.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/api.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/callback.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/cgo.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/checking.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/cmd.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/colorprinting.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/colorramping.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/commanding.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/completing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/computing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/constants.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/controlling.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/creating.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/diagnosing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/editing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/editor.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/experimenting.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/exporting.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/externing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/feedingback.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/fitting.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/gui.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/headering.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/helping.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/importing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/internal.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/invocation.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/keyboard.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/keywords.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/lazyio.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/locking.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/menu.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/monitoring.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/morphing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/movie.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/moving.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/mpeg_encode.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/parser.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/parsing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/povray.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/preset.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/pymolhttpd.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/querying.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/rpc.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/save_shortcut.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/selecting.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/selector.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/seqalign.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/setting.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/shortcut.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/shortcut_dict.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/shortcut_manager.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/util.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/vfont.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/viewing.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/wizarding.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/xray.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying build/lib.linux-x86_64-3.6/pymol/xwin.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol2
copying build/lib.linux-x86_64-3.6/pymol2/__init__.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol2
copying build/lib.linux-x86_64-3.6/pymol2/cmd2.py -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol2
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/commands.py to commands.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/realtime.py to realtime.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/state.py to state.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/util.py to util.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/amber99.py to amber99.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/assign.py to assign.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/fast/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf/io.py to io.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/amber.py to amber.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/keyword.py to keyword.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/realtime.py to realtime.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/state.py to state.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/arc.py to arc.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bond_amber.py to bond_amber.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bond_mmff.py to bond_mmff.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/bonds.py to bonds.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/brick.py to brick.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/cc1.py to cc1.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/charge.py to charge.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/cif.py to cif.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/cpv.py to cpv.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/dictdb.py to dictdb.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/gamess1.py to gamess1.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/gms.py to gms.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/hetatm.py to hetatm.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/io.py to io.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/lst.py to lst.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mae.py to mae.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/map.py to map.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mass.py to mass.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mmd.py to mmd.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/models.py to models.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mol.py to mol.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/mol2.py to mol2.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/neighbor.py to neighbor.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/pdb.py to pdb.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/pkl.py to pkl.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/place.py to place.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/protein.py to protein.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_amber.py to protein_amber.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_amber99.py to protein_amber99.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_mmff.py to protein_mmff.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_residues.py to protein_residues.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/sdf.py to sdf.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/solvate.py to solvate.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/water_amber.py to water_amber.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/water_residues.py to water_residues.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/xyz.py to xyz.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/pml.py to pml.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/pmlparser.py to pmlparser.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/python.py to python.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/TextEditor.py to TextEditor.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/__init__.py to __init__.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/builder.py to builder.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/keymapping.py to keymapping.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/shortcut_menu_gui.py to shortcut_menu_gui.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/volume.py to volume.cpython-36.pyc
byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/__init__.py to __init__.cpython-36.pyc
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byte-compiling /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/movie.py to movie.cpython-36.pyc
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writing byte-compilation script '/tmp/tmph9pb5zs8.py'
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Writing /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol-2.5.0-py3.6.egg-info
copying LICENSE -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol
copying data -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/data
copying test -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/test
copying examples -> /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/examples
creating /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/link_demo.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/particle01.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/particle02.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B03.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B05.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B11.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/test/ref/T01.log
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/link_demo.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/particle01.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/particle02.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B03.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B05.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B11.py
+ rm -f /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/ref/T01.log
+ mkdir -p /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/bin
+ install -p -m 755 pymol /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/bin/
+ desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/applications /builddir/build/SOURCES/pymol.desktop
+ mkdir -p /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/pixmaps
+ install -p -m 644 /builddir/build/SOURCES/pymol.png /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/pixmaps/
+ mkdir -p /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/metainfo
+ install -p -m 644 /builddir/build/SOURCES/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/metainfo/
+ appstream-util validate-relax --nonet /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64//usr/share/metainfo/pymol.appdata.xml
/builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64//usr/share/metainfo/pymol.appdata.xml: OK
+ /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 2.5.0-6.el8 --unique-debug-suffix -2.5.0-6.el8.x86_64 --unique-debug-src-base pymol-2.5.0-6.el8.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pymol-open-source-2.5.0
extracting debug info from /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so
extracting debug info from /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so
/usr/lib/rpm/sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match.
51209 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-2.5.0-6.el8.x86_64/usr/lib/debug/usr/lib64/python3.6 using /usr/libexec/platform-python
Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.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-2.5.0-6.el8.x86_64/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/pymol-2.5.0-6.el8.x86_64/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/pymol-2.5.0-6.el8.x86_64/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/pymol-2.5.0-6.el8.x86_64/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit
Processing files: pymol-2.5.0-6.el8.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.T4JlZ0
+ umask 022
+ cd /builddir/build/BUILD
+ cd pymol-open-source-2.5.0
+ DOCDIR=/builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/doc/pymol
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/doc/pymol
+ cp -pr AUTHORS /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/doc/pymol
+ cp -pr DEVELOPERS /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/doc/pymol
+ cp -pr README.md /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/doc/pymol
+ cp -pr ChangeLog /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/doc/pymol
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.VbDPWH
+ umask 022
+ cd /builddir/build/BUILD
+ cd pymol-open-source-2.5.0
+ LICENSEDIR=/builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/licenses/pymol
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/licenses/pymol
+ cp -pr LICENSE /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64/usr/share/licenses/pymol
+ exit 0
Provides: PyMOL(x86-64) = 0:2.5.0-6.el8 application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 2.5.0-6.el8 pymol(x86-64) = 2.5.0-6.el8 python3.6dist(pymol) = 2.5.0 python3dist(pymol) = 2.5.0
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/sh 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) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(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-2.5.0-6.el8.x86_64
Provides: pymol-debugsource = 2.5.0-6.el8 pymol-debugsource(x86-64) = 2.5.0-6.el8
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: pymol-debuginfo-2.5.0-6.el8.x86_64
Provides: debuginfo(build-id) = 8e12698237dfae2535decb9a228310fd92322792 debuginfo(build-id) = e441234133e8ee64412a7bd8dd74e2b95069305a pymol-debuginfo = 2.5.0-6.el8 pymol-debuginfo(x86-64) = 2.5.0-6.el8
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: pymol-debugsource(x86-64) = 2.5.0-6.el8
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64
Wrote: /builddir/build/RPMS/pymol-2.5.0-6.el8.x86_64.rpm
Wrote: /builddir/build/RPMS/pymol-debugsource-2.5.0-6.el8.x86_64.rpm
Wrote: /builddir/build/RPMS/pymol-debuginfo-2.5.0-6.el8.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.2AbXPQ
+ umask 022
+ cd /builddir/build/BUILD
+ cd pymol-open-source-2.5.0
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/pymol-2.5.0-6.el8.x86_64
+ exit 0
Child return code was: 0