Mock Version: 2.10 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/pymol.spec'], chrootPath='/var/lib/mock/epel-8-x86_64-1620741551.244243/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.gh7rhtvp:/etc/resolv.conf', '--bind=/dev/btrfs-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=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.gh7rhtvp:/etc/resolv.conf', '--bind=/dev/btrfs-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', '85e5bb0a717942e082fd7f7d6acac066', '-D', '/var/lib/mock/epel-8-x86_64-1620741551.244243/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.gh7rhtvp:/etc/resolv.conf', '--bind=/dev/btrfs-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;\\007"', '--setenv=PS1= \\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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn - 1.5.0.2-3.20120218svn3982 warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn - 1.2-5.20090709svn3827 Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/pymol-2.4.0-4.1.el8.ors.src.rpm 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/epel-8-x86_64-1620741551.244243/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.gh7rhtvp:/etc/resolv.conf', '--bind=/dev/btrfs-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=FalseprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.gh7rhtvp:/etc/resolv.conf', '--bind=/dev/btrfs-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', '3e70f3baeb364cd8aa3e16a029071f2c', '-D', '/var/lib/mock/epel-8-x86_64-1620741551.244243/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.gh7rhtvp:/etc/resolv.conf', '--bind=/dev/btrfs-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;\\007"', '--setenv=PS1= \\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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False warning: bogus date in %changelog: Sat Jul 08 2012 Tim Fenn - 1.5.0.2-3.20120218svn3982 warning: bogus date in %changelog: Thu Jul 07 2009 Tim Fenn - 1.2-5.20090709svn3827 Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.GruKsP + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pymol-open-source-2.4.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/pymol-open-source-2.4.0.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd pymol-open-source-2.4.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/bin/cat /builddir/build/SOURCES/pymol-setup.py.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-wmclass-main.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-wmclass-pmgapp.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-mmtf.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-python3.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + /usr/bin/cat /builddir/build/SOURCES/pymol-2.4.0-fix_bug119.patch + /usr/bin/patch -p1 -s --fuzz=0 --no-backup-if-mismatch + ln -sr modules/web modules/pymol_web + sed -i 1d modules/pmg_tk/startup/apbs_tools.py + pathfix.py -pn -i /usr/bin/python3.6 test/cyg test/run test/show test/cyg: updating test/run: updating test/show: updating + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.gZHIZA + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + export 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + /usr/bin/python3.6 setup.py build '--executable=/usr/bin/python3.6 -s' --use-msgpackc=c++11 --glut running build running build_py creating build/lib.linux-x86_64-3.6 creating build/lib.linux-x86_64-3.6/pymol2 copying modules/pymol2/cmd2.py -> build/lib.linux-x86_64-3.6/pymol2 copying modules/pymol2/__init__.py -> build/lib.linux-x86_64-3.6/pymol2 creating build/lib.linux-x86_64-3.6/pymol copying modules/pymol/xwin.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/xray.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/wizarding.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/viewing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/vfont.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/util.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/shortcut.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/setting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/seqalign.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/selector.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/selecting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/rpc.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/querying.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/pymolhttpd.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/preset.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/povray.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/parsing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/parser.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/moving.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/movie.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/morphing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/monitoring.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/menu.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/locking.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/lazyio.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/keywords.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/keyboard.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/invocation.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/internal.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/importing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/helping.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/headering.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/gui.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/fitting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/feedingback.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/externing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/exporting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/experimenting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/editor.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/editing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/diagnosing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/creating.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/controlling.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/constants_palette.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/constants.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/computing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/completing.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/commanding.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/colorramping.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/colorprinting.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/cmd.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/checking.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/cgo.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/callback.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/api.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/_gui.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/__main__.py -> build/lib.linux-x86_64-3.6/pymol copying modules/pymol/__init__.py -> build/lib.linux-x86_64-3.6/pymol creating build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/toggle.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/security.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/sculpting.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/renaming.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/openvr.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/message.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/measurement.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/label.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/filter.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/fedora.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/dragging.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/distance.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/density.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/demo.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/command.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/cleanup.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/charge.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/box.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/benchmark.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/appearance.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/annotation.py -> build/lib.linux-x86_64-3.6/pymol/wizard copying modules/pymol/wizard/__init__.py -> build/lib.linux-x86_64-3.6/pymol/wizard creating build/lib.linux-x86_64-3.6/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> build/lib.linux-x86_64-3.6/pymol/stereochemistry creating build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/repository.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/managergui.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/installation.py -> build/lib.linux-x86_64-3.6/pymol/plugins copying modules/pymol/plugins/__init__.py -> build/lib.linux-x86_64-3.6/pymol/plugins creating build/lib.linux-x86_64-3.6/pymol/opengl copying modules/pymol/opengl/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl creating build/lib.linux-x86_64-3.6/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl/glut creating build/lib.linux-x86_64-3.6/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl/glu creating build/lib.linux-x86_64-3.6/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> build/lib.linux-x86_64-3.6/pymol/opengl/gl creating build/lib.linux-x86_64-3.6/pymol/contrib copying modules/pymol/contrib/__init__.py -> build/lib.linux-x86_64-3.6/pymol/contrib creating build/lib.linux-x86_64-3.6/pymol/Qt copying modules/pymol/Qt/utils.py -> build/lib.linux-x86_64-3.6/pymol/Qt copying modules/pymol/Qt/__init__.py -> build/lib.linux-x86_64-3.6/pymol/Qt creating build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/PMGApp.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/volume.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/TextEditor.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/Setting.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/SetEditor.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/Demo.py -> build/lib.linux-x86_64-3.6/pmg_tk copying modules/pmg_tk/ColorEditor.py -> build/lib.linux-x86_64-3.6/pmg_tk creating build/lib.linux-x86_64-3.6/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> build/lib.linux-x86_64-3.6/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/startup creating build/lib.linux-x86_64-3.6/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins creating build/lib.linux-x86_64-3.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/normal creating build/lib.linux-x86_64-3.6/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> build/lib.linux-x86_64-3.6/pmg_tk/skins/demo creating build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/volume.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/properties_dialog.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/mimic_tk.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/keymapping.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/file_dialogs.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/builder.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/__init__.py -> build/lib.linux-x86_64-3.6/pmg_qt copying modules/pmg_qt/TextEditor.py -> build/lib.linux-x86_64-3.6/pmg_qt creating build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> build/lib.linux-x86_64-3.6/pmg_qt/syntax creating build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> build/lib.linux-x86_64-3.6/pmg_qt/forms creating build/lib.linux-x86_64-3.6/chempy copying modules/chempy/xyz.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/water_residues.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/water_amber.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/solvate.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/sdf.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_residues.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_mmff.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_amber99.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein_amber.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/protein.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/place.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/pkl.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/pdb.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/neighbor.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mol2.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mol.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/models.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mmd.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mass.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/map.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/mae.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/lst.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/io.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/hetatm.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/gms.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/gamess1.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/dictdb.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/cpv.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/cif.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/charge.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/cc1.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/brick.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/bonds.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/bond_mmff.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/bond_amber.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/arc.py -> build/lib.linux-x86_64-3.6/chempy copying modules/chempy/__init__.py -> build/lib.linux-x86_64-3.6/chempy creating build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/state.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/realtime.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/keyword.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/amber.py -> build/lib.linux-x86_64-3.6/chempy/tinker copying modules/chempy/tinker/__init__.py -> build/lib.linux-x86_64-3.6/chempy/tinker creating build/lib.linux-x86_64-3.6/chempy/mmtf copying modules/chempy/mmtf/io.py -> build/lib.linux-x86_64-3.6/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> build/lib.linux-x86_64-3.6/chempy/mmtf creating build/lib.linux-x86_64-3.6/chempy/fragments copying modules/chempy/fragments/__init__.py -> build/lib.linux-x86_64-3.6/chempy/fragments creating build/lib.linux-x86_64-3.6/chempy/fast copying modules/chempy/fast/__init__.py -> build/lib.linux-x86_64-3.6/chempy/fast creating build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/formal_charges.py -> build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/assign.py -> build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/amber99.py -> build/lib.linux-x86_64-3.6/chempy/champ copying modules/chempy/champ/__init__.py -> build/lib.linux-x86_64-3.6/chempy/champ creating build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/util.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/state.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/realtime.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/commands.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/chempy/bmin/__init__.py -> build/lib.linux-x86_64-3.6/chempy/bmin copying modules/pmg_qt/forms/save_object.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/props.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms copying modules/pmg_qt/forms/askpartial.ui -> build/lib.linux-x86_64-3.6/pmg_qt/forms running build_ext building 'pymol._cmd' extension creating build/temp.linux-x86_64-3.6 creating build/temp.linux-x86_64-3.6/build creating build/temp.linux-x86_64-3.6/build/generated creating build/temp.linux-x86_64-3.6/contrib creating build/temp.linux-x86_64-3.6/contrib/mmtf-c creating build/temp.linux-x86_64-3.6/contrib/uiuc creating build/temp.linux-x86_64-3.6/contrib/uiuc/plugins creating build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin creating build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src creating build/temp.linux-x86_64-3.6/layer0 creating build/temp.linux-x86_64-3.6/layer1 creating build/temp.linux-x86_64-3.6/layer2 creating build/temp.linux-x86_64-3.6/layer3 creating build/temp.linux-x86_64-3.6/layer4 creating build/temp.linux-x86_64-3.6/layer5 creating build/temp.linux-x86_64-3.6/modules creating build/temp.linux-x86_64-3.6/modules/cealign creating build/temp.linux-x86_64-3.6/modules/cealign/src creating build/temp.linux-x86_64-3.6/ov creating build/temp.linux-x86_64-3.6/ov/src g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD build/generated/ShaderText.cpp -o build/temp.linux-x86_64-3.6/build/generated/ShaderText.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/mmtf-c/mmtf_parser.cpp -o build/temp.linux-x86_64-3.6/contrib/mmtf-c/mmtf_parser.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/inthash.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/inthash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/mmtf-c/mmtf_parser.cpp: In function ‘bool MMTF_unpack_from_file(const char*, MMTF_container*)’: contrib/mmtf-c/mmtf_parser.cpp:1075:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(buffer, fileLen, 1, file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function ‘int {anonymous}::write_structure(void*, int, const molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1902:9: warning: unused variable ‘last_ctnumber’ [-Wunused-variable] int last_ctnumber = -1; ^~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerInitAll’: contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:271:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ok) ok = ok && (molfile_xyzplugin_init() == VMDPLUGIN_SUCCESS); ^~ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:273:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(ok) { ^~ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function ‘PlugIOManagerFreeAll’: contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:411:1: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ok) ok = ok && (molfile_xyzplugin_fini() == VMDPLUGIN_SUCCESS); ^~ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:413:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ return ok; ^~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘DEN_read_volumetric_data’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘POT_read_volumetric_data’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘abinit_header’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(skip, 1, 8, fp); ^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function ‘GEO_read_next_timestep’: contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, "%*s %f %f %f", &x, &y, &z); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] static void whereami(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] static void thisline(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: ‘fpexpftoc’ defined but not used [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: ‘have_keyline’ defined but not used [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:962:12: warning: ‘goto_keyline’ defined but not used [-Wunused-function] static int goto_keyline(FILE *file, ...) { ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: ‘strtoupper’ defined but not used [-Wunused-function] static char *strtoupper(char *s) { ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: ‘iswhiteline’ defined but not used [-Wunused-function] static int iswhiteline(char *s) { ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:846:13: warning: ‘eatwhitelines’ defined but not used [-Wunused-function] static void eatwhitelines(FILE *file) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:13: warning: ‘eatline’ defined but not used [-Wunused-function] static void eatline(FILE * fd, int n) ^~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: ‘symmetry_expand’ defined but not used [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:540:13: warning: ‘angular_momentum_expon’ defined but not used [-Wunused-function] static void angular_momentum_expon(int *ang_mom_expon, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: ‘del_wavefunction’ defined but not used [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: ‘replace_wavefunction’ defined but not used [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:471:27: warning: ‘add_wavefunction’ defined but not used [-Wunused-function] static qm_wavefunction_t* add_wavefunction(qm_timestep_t *ts) { ^~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:437:18: warning: ‘init_qmdata’ defined but not used [-Wunused-function] static qmdata_t* init_qmdata() { ^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_timestep(void*, int, molfile_timestep_t*)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_bonds_aux(void*, int*, int**, int**, float**)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘int read_bgf_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function ‘void* open_bgf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function ‘open_binpos_read’: contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(magicchar,sizeof(char),4,fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&igarb,sizeof(int),1,fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function ‘int read_brix_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(brick, sizeof(char), 512, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function ‘void* open_brix_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%3s", keyWord); ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:109:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f %f %f %f %f %f", keyWord, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &prod); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &plus); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, " %s %f", keyWord, &sigma); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_timestep’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘open_car_read’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function ‘read_car_structure’: contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:29: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] sprintf(atom->resname, "%d", resid); ^~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:28: note: directive argument in the range [-2147483648, 9999999] sprintf(atom->resname, "%d", resid); ^~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:85: /usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 2 and 12 bytes into a destination of size 8 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘int read_ccp4_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:495:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(rowdata, sizeof(char), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:525:67: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(rowdata, sizeof(unsigned char), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:556:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(rowdata, sizeof(float), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:588:58: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(rowdata, sizeof(short), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:623:67: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(rowdata, sizeof(unsigned short), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:655:60: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(rowdata, sizeof(uchar3), extent[0], fd) != extent[0] ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘void* open_ccp4_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:304:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(symData, 81, fd); ~~~~~^~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:42: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function ‘void* open_ccp4_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:287:42: warning: ‘dataOffset’ may be used uninitialized in this function [-Wmaybe-uninitialized] } else if ((dataOffset > CCP4HDSIZE) && (dataOffset < (1024*1024))) { ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function ‘void* open_cube_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:175:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); // go on to next line ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); // skip second header line ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:326:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:337:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:339:11: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(cube->fd, "%d", &cube->nsets); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:344:13: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(cube->fd, "%d", &orb); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1023, cube->fd); // gobble up rest of line ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: At global scope: contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:107:13: warning: ‘void cube_buildrotmat(cube_t*, float*, float*, float*)’ defined but not used [-Wunused-function] static void cube_buildrotmat(cube_t *cube, float *o, float *a, float *b) ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:42: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘int get_pte_idx_from_string(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘int read_mdf_bonds(void*, int*, int**, int**, float**, int**, int*, char***)’: contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:278:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:297:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:319:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:357:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘int read_mdf_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:223:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:241:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mdf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function ‘void* open_mdf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:164:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:176:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:183:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function ‘read_dcdstep’: contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable ‘readlen’ set but not used [-Wunused-but-set-variable] fio_size_t readlen; /* number of bytes actually read */ ^~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: At top level: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:609:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: ‘fio_readv’ defined but not used [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2_timestep(void*, int, molfile_timestep_t*)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:289:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2_bonds_aux(void*, int*, int**, int**, float**)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:199:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:209:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘int read_mol2(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:127:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:138:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, mol2->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function ‘void* open_mol2_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:74:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:81:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_name ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:82:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read the molecule info ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:91:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_type ~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); // Read the charge_type ~~~~~^~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_structure’: contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:292:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (NULL == fgets(fbuffer, 1024, data->file)) ^~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:295:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (NULL == fgets(fbuffer, 1024, data->file)) ^~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘read_molden_rundata’: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:596:25: warning: variable ‘hessian_data’ set but not used [-Wunused-but-set-variable] molfile_qm_hessian_t *hessian_data; ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_config_timestep’: contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:669:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(fbuffer, 1024, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function ‘read_dlpoly_timestep’: contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:554:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(fbuffer, 1024, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘count_orbitals’: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1165:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, " Ene= %f\n", &orbenergy); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1166:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, " Spin= %s\n", spin); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1167:3: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, " Occup= %f\n", &occu); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); ^~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function ‘open_molden_read’: contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:224:11: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] fscanf(data->file, "%d", &natm); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: At top level: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] static void whereami(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] static void thisline(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: ‘have_keyline’ defined but not used [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: ‘symmetry_expand’ defined but not used [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: ‘del_wavefunction’ defined but not used [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: ‘replace_wavefunction’ defined but not used [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: ‘get_pte_vdw_radius’ defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: ‘get_pte_mass’ defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘get_pte_label’ defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function ‘int read_dsn6_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:14: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(brick, sizeof(char), 512, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function ‘void* open_dsn6_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(fileHeader, sizeof(short), 19, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:63: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:91:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:116:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:132:9: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:149:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:155:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:161:11: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); //one more read to keep us in sync ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:170:27: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:217:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:237:23: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:256:15: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘read_next_timestep’: contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:103:10: warning: variable ‘numatoms’ set but not used [-Wunused-but-set-variable] int i, numatoms; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function ‘open_namdbin_read’: contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:78:3: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result] fread(&filen, sizeof(namdbin_int32), 1, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:70: contrib/uiuc/plugins/molfile_plugin/src/vmddir.h:145:12: warning: ‘int vmd_file_is_executable(const char*)’ defined but not used [-Wunused-function] static int vmd_file_is_executable(const char * filename) { ^~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp: In function ‘int read_parm7_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:78:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:25: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_atoms(const char*, int, molfile_atom_t*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:204:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_atype(const char*, int, molfile_atom_t*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:257:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_resnames(const char*, int, char*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:275:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, 85, file); ~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int parse_parm7_respointers(const char*, int, molfile_atom_t*, int, const char*, FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:289:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " %d", &cur); ~~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘parmstruct* read_parm7_header(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:368:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sdum, 512, file); ~~~~~^~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:371:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", sdum); // "%FLAG" ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:378:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", sdum); // "TITLE" or "CTITLE" ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:385:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", sdum); // "FORMAT (20a4)" ~~~~~~^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:399:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(prm->title, sizeof(prm->title), file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:427:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(sdum, sizeof(sdum), file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:439:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file,parm7, ~~~~~~^~~~~~~~~~~~ &prm->Natom, &prm->Ntypes, &prm->Nbonh, &prm->Nbona, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Ntheth, &prm->Ntheta, &prm->Nphih, &prm->Nphia, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Jparm, &prm->Nparm); ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:443:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, parm7, ~~~~~~^~~~~~~~~~~~~ &prm->Nnb, &prm->Nres, &prm->Mbona, &prm->Mtheta, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Mphia, &prm->Numbnd, &prm->Numang, &prm->Mptra, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Natyp, &prm->Nphb); ~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:447:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, parm7, &prm->Ifpert, &prm->Nbper, &prm->Ngper, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Ndper, &prm->Mbper, &prm->Mgper, &prm->Mdper, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->IfBox, &prm->Nmxrs, &prm->IfCap); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:451:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file,"%8d",&prm->Numextra); //BB ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h: In function ‘int read_parm7_flag(FILE*, const char*, const char*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:79:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ~~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:87:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ~~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:97:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, "%s\n", buf); ~~~~~~^~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h: In member function ‘int {anonymous}::ReadPARM::readparm(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Charges[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:444:10: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Masses[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:510:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Rk[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:517:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Req[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:524:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Tk[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:531:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Teq[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:538:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pk[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:545:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pn[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:552:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Phase[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:559:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Solty[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:567:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn1[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:575:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn2[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:756:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB12[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:763:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB6[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:771:17: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT, &H[i]); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:853:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " " DBLFMT " " DBLFMT " " DBLFMT, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Box[0], &prm->Box[1], &prm->Box[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:867:9: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(file, " %d " DBLFMT " " DBLFMT " " DBLFMT " " DBLFMT, ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Natcap, &prm->Cutcap, ~~~~~~~~~~~~~~~~~~~~~~~~~~~ &prm->Xcap, &prm->Ycap, &prm->Zcap); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp:53: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘int getUniqueResID(char*, int)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable ‘i’ [-Wunused-variable] int i, uid; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable ‘j’ [-Wunused-variable] int i, count, atomdata, pos, idx, xyzcount, j; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable ‘oldChain’ [-Wunused-variable] char oldChain[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readAngleBonds(molfile_atom_t*, pdbxParser*)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable ‘bondTable’ [-Wunused-variable] int bondTable[32]; ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable ‘j’ [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable ‘modelNum’ [-Wunused-variable] char modelNum[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable ‘atom’ [-Wunused-variable] molfile_atom_t * atom; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable ‘test’ [-Wunused-variable] int test = parser->nbonds + bnum; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘bool readRMSDBonds(molfile_atom_t*, pdbxParser*)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable ‘bondTable’ [-Wunused-variable] int bondTable[32]; ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable ‘j’ [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable ‘modelNum’ [-Wunused-variable] char modelNum[8]; ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable ‘atom’ [-Wunused-variable] molfile_atom_t * atom; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function ‘void* open_file_write(const char*, const char*, int)’: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable ‘fd’ [-Wunused-variable] FILE* fd; ^~ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: At global scope: contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:313:14: warning: ‘float stringToFloat(char*)’ defined but not used [-Wunused-function] static float stringToFloat(char * str) { ^~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:25: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘int get_pte_idx(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘const char* get_pte_label(int)’ defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘void DDmkdir(const string&, mode_t, int, int)’: contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:15: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] sprintf(sub, "%03x/", i); ^~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:15: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:22: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] sprintf(subsub, "%03x", j); ^~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:22: note: directive argument in the range [0, 2147483647] In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 4 and 9 bytes into a destination of size 6 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function ‘std::__cxx11::string framefile(const string&, size_t, size_t, int, int)’: contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:22: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=] sprintf(answer, "%03x/", d1); ^~~~~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 5 and 10 bytes into a destination of size 9 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:22: warning: ‘%03x’ directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] sprintf(answer, "%03x/%03x/", d1, d2); ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:22: note: directive argument in the range [0, 2147483646] In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 19 bytes into a destination of size 9 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘int read_plt_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:143:51: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if ( fread(datablock, sizeof(float), ndata, fd) != ndata ) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function ‘void* open_plt_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(intHeader, sizeof(int), 5, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(floatHeader, sizeof(float), 6, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:42: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void put_element_ply(PlyFile*, void*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:459:7: warning: unused variable ‘i’ [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void ascii_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable ‘i’ [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable ‘i’ [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:107:17: warning: variable ‘vert_other’ set but not used [-Wunused-but-set-variable] PlyOtherProp *vert_other=NULL; ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:108:17: warning: variable ‘face_other’ set but not used [-Wunused-but-set-variable] PlyOtherProp *face_other=NULL; ^~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (&len, sizeof(int), 1, fp); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (str, len, 1, fp); ~~~~~~^~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void get_binary_item(FILE*, int, int*, unsigned int*, double*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 1, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 1, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 2, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 2, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 4, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 4, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 4, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:13: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread (ptr, 8, 1, fp); ~~~~~~^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:27: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:110:13: warning: ‘void swap4_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void ascii_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1497:18: warning: ‘item’ may be used uninitialized in this function [-Wmaybe-uninitialized] item += item_size; ~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1477:19: warning: ‘other_data’ may be used uninitialized in this function [-Wmaybe-uninitialized] store_array = (char **) (elem_data + prop->offset); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function ‘void binary_get_element(PlyFile*, char*)’: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1620:18: warning: ‘item’ may be used uninitialized in this function [-Wmaybe-uninitialized] item += item_size; ~~~~~^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1601:19: warning: ‘other_data’ may be used uninitialized in this function [-Wmaybe-uninitialized] store_array = (char **) (elem_data + prop->offset); ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function ‘get_atom_radius’: contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable ‘type’ set but not used [-Wunused-but-set-variable] char *name, *type; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable ‘name’ set but not used [-Wunused-but-set-variable] char *name, *type; ^~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: ‘fortread_4’ defined but not used [-Wunused-function] static int fortread_4(void *dest, int n, int swap, FILE *fd) { ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘fort_get_endian_reclen’ defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘fort_eat_recmark’ defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28, from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘swap8_aligned’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘swap8_unaligned’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘swap4_unaligned’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function ‘open_rst_read’: contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:48:11: warning: variable ‘timesteprst’ set but not used [-Wunused-but-set-variable] double timesteprst; ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:67:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(title, 82, fd); ^~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:70:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 82, fd); ^~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘int read_edm_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:240:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 13, edm->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp: In function ‘void eatline(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:44:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ~~~~~^~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function ‘int read_spider_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(datablock, total * sizeof(float), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:36: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function ‘void* open_fs4_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:48: contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: ‘void strnwscpy(char*, const char*, int)’ defined but not used [-Wunused-function] static void strnwscpy(char *target, const char *source, const int len) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘int fort_get_endian_reclen(int, int, int, int*, int*)’ defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘int fort_eat_recmark(FILE*, int)’ defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:47: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:12: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘have_gamess’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1106:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] char word[3][BUFSIZ]; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_stats’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2264:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] char word[7][BUFSIZ]; ^~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_wavefunction’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:3573:8: warning: variable ‘word’ set but not used [-Wunused-but-set-variable] char word[6][BUFSIZ]; ^~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function ‘eatline’: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); ^~~~~~~~~~~~~~~~~~~~~~~~ At top level: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1002:13: warning: ‘print_input_data’ defined but not used [-Wunused-function] static void print_input_data(qmdata_t *data) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: ‘get_pte_idx’ defined but not used [-Wunused-function] static int get_pte_idx(const char *label) ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: ‘get_pte_vdw_radius’ defined but not used [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: ‘get_pte_mass’ defined but not used [-Wunused-function] static float get_pte_mass(const int idx) ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: ‘get_pte_label’ defined but not used [-Wunused-function] static const char *get_pte_label(const int idx) ^~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: ‘whereami’ defined but not used [-Wunused-function] static void whereami(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: ‘thisline’ defined but not used [-Wunused-function] static void thisline(FILE *file) { ^~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: ‘fpexpftoc’ defined but not used [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: ‘strtoupper’ defined but not used [-Wunused-function] static char *strtoupper(char *s) { ^~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: ‘iswhiteline’ defined but not used [-Wunused-function] static int iswhiteline(char *s) { ^~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: ‘print_matrix4’ defined but not used [-Wunused-function] static void print_matrix4(const float mat[16]) { ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:22: warning: variable ‘o’ set but not used [-Wunused-but-set-variable] float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:90:28: warning: variable ‘s’ set but not used [-Wunused-but-set-variable] float orig[3], ra, o[3], s[3]; //xdelta[3], ydelta[3], zdelta[3]; ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘int read_uhbd_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:254:66: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (fread(datablock + z*xysize, sizeof(float), xysize, fd) != xysize) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function ‘void* open_uhbd_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&headersize, sizeof(int), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:47: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:224:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘read_vasp5xdatcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function ‘open_vasp5xdatcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_data’: contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:237:60: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:282:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘read_vaspchgcar_metadata’: contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function ‘open_vaspchgcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: At top level: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function ‘get_basis_options’: contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1398:41: warning: ‘%s’ directive writing up to 8191 bytes into a region of size 8190 [-Wformat-overflow=] sprintf(data->basis_string, "%d-%s%sG%s", ^~ ngauss, (data->gbasis+1), diffuse, ~~~~~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:27, from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: /usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output 4 or more bytes (assuming 16386) into a destination of size 8192 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1394:43: warning: ‘%s’ directive writing up to 8191 bytes into a region of size between 8176 and 8186 [-Wformat-overflow=] sprintf(data->basis_string, "STO-%dG%s%s", ^~ ngauss, diffuse, polarization); ~~~~~~~ In file included from /usr/include/stdio.h:873, from contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:27, from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: /usr/include/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 7 and 16399 bytes into a destination of size 8192 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:239:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:242:2: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘read_vaspoutcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:204:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function ‘open_vaspoutcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:87:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_data’: contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘read_vaspparchg_metadata’: contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function ‘open_vaspparchg_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: At top level: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: ‘vasp_timestep_unitcell’ defined but not used [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘write_vaspposcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:360:40: warning: argument to ‘sizeof’ in ‘strncpy’ call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess] strncpy(tmptype, atom->type, sizeof(atom->type)); ^ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘read_vaspposcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function ‘open_vaspposcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:69:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:73:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_timestep’: contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:283:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘read_vaspxdatcar_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:228:27: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 4; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:233:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:237:32: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:252:44: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] for (i = 0; i < 10 - data->version; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function ‘open_vaspxdatcar_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:89:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:92:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:97:5: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:111:3: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:121:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘void line3(FILE*, GRASSP*)’: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line3, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function ‘int read_rawgraphics(void*, int*, const molfile_graphics_t**)’: contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(line, 1, 80, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(vertex, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(access, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(normal, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:3: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(triangle, 3 * sizeof(int), ntriangles, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(properties, 3 * sizeof(float), nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(striangle, sizeof(short), 3 * ntriangles, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:20: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] #define TRASH fread(trash, 4, 1, infile) ~~~~~^~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:5: note: in expansion of macro ‘TRASH’ TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:10: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(properties, sizeof(float), 3 * nvert, infile); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:40: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘read_vaspxml_structure’: contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:139:7: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:144:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function ‘open_vaspxml_read’: contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:86:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:92:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47: At top level: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp:51: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function ‘void* open_grid_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:8: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:60: contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:133:13: warning: ‘void strnwscpy(char*, const char*, int)’ defined but not used [-Wunused-function] static void strnwscpy(char *target, const char *source, const int len) { ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: ‘int fort_get_endian_reclen(int, int, int, int*, int*)’ defined but not used [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: ‘int fort_eat_recmark(FILE*, int)’ defined but not used [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:59: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: ‘void swap8_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function ‘int mdio_readline(md_file*, char*, int, int)’: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:7: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(buf, n, mf->f); ~~~~~^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:48, from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: ‘void swap2_aligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: ‘void swap8_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: ‘void swap4_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: ‘void swap2_unaligned(void*, long int)’ defined but not used [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:276:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data_ex(void*, molfile_volumetric_readwrite_t*)’: contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:338:45: warning: variable ‘total’ set but not used [-Wunused-but-set-variable] int x, y, z, xsize, ysize, zsize, xysize, total; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:371:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function ‘int read_vtk_data(void*, int, float*, float*)’: contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:306:15: warning: ignoring return value of ‘int fscanf(FILE*, const char*, ...)’, declared with attribute warn_unused_result [-Wunused-result] fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:72: contrib/uiuc/plugins/include/vmdconio.h: At global scope: contrib/uiuc/plugins/include/vmdconio.h:56:12: warning: ‘int vmdcon_printf(int, const char*, ...)’ defined but not used [-Wunused-function] static int vmdcon_printf(int lvl, const char *fmt, ...) { ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_timestep(void*, int, molfile_timestep_t*)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_bonds_aux(void*, int*, int**, int**, float**)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘int read_xbgf_structure(void*, int*, molfile_atom_t*)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, bgf->file); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function ‘void* open_xbgf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(line, LINESIZE, fd); ~~~~~^~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Matrix.cpp -o build/temp.linux-x86_64-3.6/layer0/Matrix.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void eatline(FILE*)’: contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:238:8: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ~~~~~^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function ‘void* open_xsf_read(const char*, const char*, int*)’: contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:408:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:442:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:444:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:446:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:448:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:450:20: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:473:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:508:16: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result] fgets(readbuf, 256, xsf->fd); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:37: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At global scope: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘int get_pte_idx_from_string(const char*)’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c -o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: ‘get_pte_idx_from_string’ defined but not used [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Block.cpp -o build/temp.linux-x86_64-3.6/layer0/Block.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Crystal.cpp -o build/temp.linux-x86_64-3.6/layer0/Crystal.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/MemoryDebug.cpp -o build/temp.linux-x86_64-3.6/layer0/MemoryDebug.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer0/MemoryDebug.cpp: In function ‘void* VLADeleteRaw(void*, int, unsigned int)’: layer0/MemoryDebug.cpp:223:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(index < -old_size) ~~~~~~^~~~~~~~~~~ layer0/MemoryDebug.cpp:235:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] (index < vla->size) && ((count + index) <= vla->size)) { ~~~~~~^~~~~~~~~~~ layer0/MemoryDebug.cpp: In function ‘void* VLAInsertRaw(void*, int, unsigned int)’: layer0/MemoryDebug.cpp:256:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(index < -old_size) ~~~~~~^~~~~~~~~~~ layer0/MemoryDebug.cpp:263:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(index > old_size) ~~~~~~^~~~~~~~~~ layer0/MemoryDebug.cpp:266:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if((index >= 0) && (count > 0) && (index <= old_size)) { ~~~~~~^~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/MyPNG.cpp -o build/temp.linux-x86_64-3.6/layer0/MyPNG.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Deferred.cpp -o build/temp.linux-x86_64-3.6/layer0/Deferred.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Err.cpp -o build/temp.linux-x86_64-3.6/layer0/Err.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer0/MyPNG.cpp: In function ‘int MyPNGWrite(const char*, const pymol::Image&, float, int, int, float, float, void*)’: layer0/MyPNG.cpp:301:20: warning: comparison of integer expressions of different signedness: ‘png_uint_32’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] for(k = 0; k < height; k++) ~~^~~~~~~~ layer0/MyPNG.cpp:342:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] for(b = 0; b < height; b++) { ~~^~~~~~~~ layer0/MyPNG.cpp:343:26: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] for(a = 0; a < width; a++) { ~~^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Parse.cpp -o build/temp.linux-x86_64-3.6/layer0/Parse.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Feedback.cpp -o build/temp.linux-x86_64-3.6/layer0/Feedback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Pixmap.cpp -o build/temp.linux-x86_64-3.6/layer0/Pixmap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/PostProcess.cpp -o build/temp.linux-x86_64-3.6/layer0/PostProcess.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Field.cpp -o build/temp.linux-x86_64-3.6/layer0/Field.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer0/Field.cpp: In function ‘PyObject* FieldAsNumPyArray(CField*, short int)’: layer0/Field.cpp:83:1: warning: label ‘ok_except1’ defined but not used [-Wunused-label] ok_except1: ^~~~~~~~~~ layer0/Field.cpp: In function ‘CField* FieldNewFromPyList(PyMOLGlobals*, PyObject*)’: layer0/Field.cpp:179:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] ok = ok && I->size() == size; ~~~~~~~~~~^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/ShaderMgr.cpp -o build/temp.linux-x86_64-3.6/layer0/ShaderMgr.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/File.cpp -o build/temp.linux-x86_64-3.6/layer0/File.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/GenericBuffer.cpp -o build/temp.linux-x86_64-3.6/layer0/GenericBuffer.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/GraphicsUtil.cpp -o build/temp.linux-x86_64-3.6/layer0/GraphicsUtil.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Isosurf.cpp -o build/temp.linux-x86_64-3.6/layer0/Isosurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Map.cpp -o build/temp.linux-x86_64-3.6/layer0/Map.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Match.cpp -o build/temp.linux-x86_64-3.6/layer0/Match.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/ShaderPrg.cpp -o build/temp.linux-x86_64-3.6/layer0/ShaderPrg.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUT.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUT.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Sphere.cpp -o build/temp.linux-x86_64-3.6/layer0/Sphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUT8x13.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUT8x13.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUT9x15.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUT9x15.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Tetsurf.cpp -o build/temp.linux-x86_64-3.6/layer0/Tetsurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUTHel10.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel10.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUTHel12.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel12.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontGLUTHel18.cpp -o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel18.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/FontType.cpp -o build/temp.linux-x86_64-3.6/layer1/FontType.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/FontType.cpp:529:13: warning: ‘void FontTypeFree(CFont*)’ defined but not used [-Wunused-function] static void FontTypeFree(CFont * font) ^~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Movie.cpp -o build/temp.linux-x86_64-3.6/layer1/Movie.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Texture.cpp -o build/temp.linux-x86_64-3.6/layer0/Texture.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Tracker.cpp -o build/temp.linux-x86_64-3.6/layer0/Tracker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Triangle.cpp -o build/temp.linux-x86_64-3.6/layer0/Triangle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Ortho.cpp -o build/temp.linux-x86_64-3.6/layer1/Ortho.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Ortho.cpp:784:6: warning: ‘void OrthoKeyCmmd(PyMOLGlobals*, unsigned char)’ defined but not used [-Wunused-function] void OrthoKeyCmmd(PyMOLGlobals * G, unsigned char k) ^~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Util.cpp -o build/temp.linux-x86_64-3.6/layer0/Util.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from /usr/include/string.h:495, from /usr/include/python3.6m/Python.h:30, from layer0/os_python.h:32, from layer1/Ortho.cpp:24: In function ‘char* strcat(char*, const char*)’, inlined from ‘void OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at layer1/Ortho.cpp:333:13: /usr/include/bits/string_fortified.h:128:33: warning: ‘char* __builtin_strcat(char*, const char*)’ accessing 81 or more bytes at offsets [80, 261200] and [0, 9223372036854775807] may overlap 1 byte at offset [80, 9223372036854775807] [-Wrestrict] return __builtin___strcat_chk (__dest, __src, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strcat(char*, const char*)’, inlined from ‘void OrthoSpecial(PyMOLGlobals*, int, int, int, int)’ at layer1/Ortho.cpp:350:13: /usr/include/bits/string_fortified.h:128:33: warning: ‘char* __builtin_strcat(char*, const char*)’ accessing 81 or more bytes at offsets [80, 261200] and [0, 9223372036854775807] may overlap 1 byte at offset [80, 9223372036854775807] [-Wrestrict] return __builtin___strcat_chk (__dest, __src, __bos (__dest)); ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Util2.cpp -o build/temp.linux-x86_64-3.6/layer0/Util2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/P.cpp -o build/temp.linux-x86_64-3.6/layer1/P.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Vector.cpp -o build/temp.linux-x86_64-3.6/layer0/Vector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/P.cpp: In function ‘int WrapperObjectAssignSubScript(PyObject*, PyObject*, PyObject*)’: layer1/P.cpp:822:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (strlen(valstr) > ap->maxlen){ ~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/Word.cpp -o build/temp.linux-x86_64-3.6/layer0/Word.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/P.cpp: At global scope: layer1/P.cpp:2764:13: warning: ‘void PLockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function] static void PLockAPIWhileBlocked(PyMOLGlobals * G) ^~~~~~~~~~~~~~~~~~~~ layer1/P.cpp:2753:13: warning: ‘void PUnlockAPIWhileBlocked(PyMOLGlobals*)’ defined but not used [-Wunused-function] static void PUnlockAPIWhileBlocked(PyMOLGlobals * G) ^~~~~~~~~~~~~~~~~~~~~~ layer1/P.cpp: In function ‘int PLabelAtomAlt(PyMOLGlobals*, AtomInfoType*, const char*, const char*, int)’: layer1/P.cpp:322:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(label, origexpr, OrthoLineLength); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/PConv.cpp -o build/temp.linux-x86_64-3.6/layer1/PConv.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer0/os_gl.cpp -o build/temp.linux-x86_64-3.6/layer0/os_gl.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Basis.cpp -o build/temp.linux-x86_64-3.6/layer1/Basis.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/PConv.cpp: In function ‘int PConvPyListToBitmask(PyObject*, int*, ov_size)’: layer1/PConv.cpp:89:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] for(int i = 0; i < ll; i++) ~~^~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Picking.cpp -o build/temp.linux-x86_64-3.6/layer1/Picking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Pop.cpp -o build/temp.linux-x86_64-3.6/layer1/Pop.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer1/Pop.cpp:22: layer1/Pop.cpp: In function ‘void PopFree(PyMOLGlobals*)’: layer1/Pop.cpp:54:14: warning: deleting object of polymorphic class type ‘CPop’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Pop); ^~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/PyMOLObject.cpp -o build/temp.linux-x86_64-3.6/layer1/PyMOLObject.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/ButMode.cpp -o build/temp.linux-x86_64-3.6/layer1/ButMode.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer1/ButMode.cpp:22: layer1/ButMode.cpp: In function ‘void ButModeFree(PyMOLGlobals*)’: layer1/ButMode.cpp:144:14: warning: deleting object of polymorphic class type ‘CButMode’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->ButMode); ^~~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/CGO.cpp -o build/temp.linux-x86_64-3.6/layer1/CGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Ray.cpp -o build/temp.linux-x86_64-3.6/layer1/Ray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/CGO.cpp: In function ‘void CheckAttributesForUsage(const CGO*, AttribDataDesc&, AttribDataDesc&, CGO*, bool&)’: layer1/CGO.cpp:10716:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto idx = 0; idx < attrIdx; ++idx){ ~~~~^~~~~~~~~ layer1/CGO.cpp: In function ‘void PopulateOpsIntoStructuresForConversion(std::map&, std::map >&, AttribDataDesc&, AttribDataDesc&, int&, bool)’: layer1/CGO.cpp:10794:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (attrOp->incr_vertices != vertsperpickinfo){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ layer1/CGO.cpp: In function ‘CGO* CGOConvertToShader(const CGO*, AttribDataDesc&, AttribDataDesc&, int, GenericBuffer<34962>::buffer_layout, bool, int*, int, int)’: layer1/CGO.cpp:11096:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto idx = 0; idx < attrData.size(); ++idx){ ~~~~^~~~~~~~~~~~~~~~~ layer1/CGO.cpp:11108:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto idx = 0; idx < attrData.size(); ++idx){ ~~~~^~~~~~~~~~~~~~~~~ layer1/CGO.cpp:11117:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for (int nxt = 0; nxt < attribOp->incr_vertices; ++nxt){ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Ray.cpp: In function ‘void RayRender(CRay*, unsigned int*, double, float, int, unsigned int*)’: layer1/Ray.cpp:6064:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x_stop > width) ~~~~~~~^~~~~~~ layer1/Ray.cpp:6066:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y_stop > height) ~~~~~~~^~~~~~~~ layer1/Ray.cpp:6147:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++) ~~^~~~~~~~ layer1/Ray.cpp:6148:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp:6159:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x < (width - 1)) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6170:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y < (height - 1)) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6233:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++) ~~^~~~~~~~ layer1/Ray.cpp:6234:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp:6244:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x < (width - 1)) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6256:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y < (height - 1)) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6307:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++){ ~~^~~~~~~~ layer1/Ray.cpp:6327:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp:6346:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x < (width - 1)) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6360:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y < (height - 1)) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6374:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(x && (y < (height - 1))) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6381:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if(y && (x < (width - 1))) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6388:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if((y < (height - 1)) && (x < (width - 1))) { ~~^~~~~~~~~~~~~~ layer1/Ray.cpp:6388:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] if((y < (height - 1)) && (x < (width - 1))) { ~~^~~~~~~~~~~~~ layer1/Ray.cpp:6544:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(y = 0; y < height; y++) { ~~^~~~~~~~ layer1/Ray.cpp:6545:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for(x = 0; x < width; x++) { ~~^~~~~~~ layer1/Ray.cpp: In function ‘void RayRenderVRML2(CRay*, int, int, char**, float, float, float, float, float)’: layer1/Ray.cpp:1534:19: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 0 and 914 [-Wformat-overflow=] "Transform {\n" ^~~~~~~~~~~~~~~ " translation %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " rotation %8.6f %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " children [\n" ~~~~~~~~~~~~~~~ "%s" ~~~~ " ]\n" ~~~~~~ "}\n", ~~~~~ layer1/Ray.cpp:1543:72: vert2[2] - mid[2], axis[0], axis[1], axis[2], angle, geometry); ~~~~~~~~ layer1/Ray.cpp:1533:18: note: ‘sprintf’ output between 116 and 3302 bytes into a destination of size 1024 sprintf(buffer, ~~~~~~~^~~~~~~~ "Transform {\n" ~~~~~~~~~~~~~~~ " translation %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " rotation %8.6f %8.6f %8.6f %8.6f\n" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ " children [\n" ~~~~~~~~~~~~~~~ "%s" ~~~~ " ]\n" ~~~~~~ "}\n", ~~~~~~ vert2[0] - mid[0], ~~~~~~~~~~~~~~~~~~ vert2[1] - mid[1], ~~~~~~~~~~~~~~~~~~ vert2[2] - mid[2], axis[0], axis[1], axis[2], angle, geometry); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Ray.cpp: In function ‘int RayTraceThread(CRayThreadInfo*)’: layer1/Ray.cpp:3612:32: warning: ‘hl’ may be used uninitialized in this function [-Wmaybe-uninitialized] compute_background_for_pixel(bkrd_uc, isOutsideInY, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bg_image_mode, bg_image_tilesize, bg_rgb, bg_image_linear, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (unsigned char*) T->bkrd_data, T->bgWidth, T->bgHeight, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x, wr, hl, hpixelx, orig_opaque_back ); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Rep.cpp -o build/temp.linux-x86_64-3.6/layer1/Rep.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Scene.cpp -o build/temp.linux-x86_64-3.6/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Scene.cpp: In function ‘int SceneClick(Block*, int, int, int, int, double)’: layer1/Scene.cpp:4109:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] if(atIndex == I->LastPicked.src.index) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp: In function ‘void SceneFree(PyMOLGlobals*)’: layer1/Scene.cpp:5967:13: warning: deleting object of polymorphic class type ‘CScene’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete G->Scene; ^~~~~ layer1/Scene.cpp: In function ‘int SceneClick(Block*, int, int, int, int, double)’: layer1/Scene.cpp:4227:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 14 and 1037 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4227:15: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4097:20: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s -> (%s)", buffer, cEditorSele1 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 23 and 1046 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4097:13: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s -> (%s)", buffer, cEditorSele1 ENDF(G); ^~~~~~ layer1/Scene.cpp:4113:22: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s -> (%s)", buffer, cEditorSele2 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 23 and 1046 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4113:15: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s -> (%s)", buffer, cEditorSele2 ENDF(G); ^~~~~~ layer1/Scene.cpp:4121:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1014 [-Wformat-overflow=] sprintf(buffer, "cmd.edit(\"%s\",\"%s\")", buf1, buf2); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4121:22: note: ‘sprintf’ output between 16 and 2062 bytes into a destination of size 1024 sprintf(buffer, "cmd.edit(\"%s\",\"%s\")", buf1, buf2); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:3984:24: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s -> (%s)\n", buffer, cEditorSele1 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 24 and 1047 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:3984:17: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s -> (%s)\n", buffer, cEditorSele1 ENDF(G); ^~~~~~ layer1/Scene.cpp:3990:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1014 [-Wformat-overflow=] sprintf(buf2, "cmd.edit(\"%s\",pkresi=1)", buffer); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ layer1/Scene.cpp:3990:24: note: ‘sprintf’ output between 22 and 1045 bytes into a destination of size 1024 sprintf(buf2, "cmd.edit(\"%s\",pkresi=1)", buffer); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4018:24: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] PRINTF " You unpicked %s.", buffer ENDF(G); ^~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 16 and 1039 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4018:17: note: in expansion of macro ‘PRINTF’ PRINTF " You unpicked %s.", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4031:50: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTFB(G, FB_Scene, FB_Results) " You clicked %s -> (%s)\n", buffer, ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 21 and 1299 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4031:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Scene, FB_Results) " You clicked %s -> (%s)\n", buffer, ^~~~~~~ layer1/Scene.cpp:4285:20: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 14 and 1037 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4285:13: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4319:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] sprintf(buffer, "cmd.drag(\"byobject (%s)\")", buf1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4319:22: note: ‘sprintf’ output between 24 and 1047 bytes into a destination of size 1024 sprintf(buffer, "cmd.drag(\"byobject (%s)\")", buf1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4310:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1007 [-Wformat-overflow=] sprintf(buffer, "cmd.drag(\"bymol (%s)\")", buf1); ^~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4310:22: note: ‘sprintf’ output between 21 and 1044 bytes into a destination of size 1024 sprintf(buffer, "cmd.drag(\"bymol (%s)\")", buf1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4369:31: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1012 [-Wformat-overflow=] sprintf(buffer, "cmd.center(\"%s\",state=%d)", buf1, I->LastPicked.context.state + 1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4369:31: note: directive argument in the range [-2147483647, 2147483647] layer1/Scene.cpp:4369:22: note: ‘sprintf’ output between 23 and 1056 bytes into a destination of size 1024 sprintf(buffer, "cmd.center(\"%s\",state=%d)", buf1, I->LastPicked.context.state + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4341:33: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1012 [-Wformat-overflow=] sprintf(buffer, "cmd.origin(\"%s\")", buf1); ^~~~~~~~~~~~~~~~~~~~ ~~~~ layer1/Scene.cpp:4341:24: note: ‘sprintf’ output between 15 and 1038 bytes into a destination of size 1024 sprintf(buffer, "cmd.origin(\"%s\")", buf1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4347:24: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~~~~~~~~~~~~ ~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer1/Scene.cpp:33: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 14 and 1037 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer1/Scene.cpp:4347:17: note: in expansion of macro ‘PRINTF’ PRINTF " You clicked %s", buffer ENDF(G); ^~~~~~ layer1/Scene.cpp:4434:29: warning: ‘)’ directive writing 1 byte into a region of size between 0 and 1023 [-Wformat-overflow=] sprintf(buf2, "%s(%s)", sel_mode_kw, buffer); ^~~~~~~~ layer1/Scene.cpp:4434:22: note: ‘sprintf’ output 3 or more bytes (assuming 1026) into a destination of size 1024 sprintf(buf2, "%s(%s)", sel_mode_kw, buffer); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4441:35: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 753 and 1008 [-Wformat-overflow=] sprintf(buffer, "cmd.select('%s',\"%s(%s)\")", selName, sel_mode_kw, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~ layer1/Scene.cpp:4441:26: note: ‘sprintf’ output 20 or more bytes (assuming 1298) into a destination of size 1024 sprintf(buffer, "cmd.select('%s',\"%s(%s)\")", selName, sel_mode_kw, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~~ layer1/Scene.cpp:4416:29: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 760 and 1015 [-Wformat-overflow=] sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~ layer1/Scene.cpp:4416:22: note: ‘sprintf’ output 35 or more bytes (assuming 2591) into a destination of size 1024 sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName); ~~~~~~~~ layer1/Scene.cpp:4425:33: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 760 and 1015 [-Wformat-overflow=] sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~ layer1/Scene.cpp:4425:26: note: ‘sprintf’ output 35 or more bytes (assuming 2591) into a destination of size 1024 sprintf(buf2, "(((%s) or %s(%s)) and not ((%s(%s)) and %s(%s)))", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName, sel_mode_kw, buffer, sel_mode_kw, buffer, sel_mode_kw, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ selName); ~~~~~~~~ layer1/Scene.cpp:4428:35: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 753 and 1008 [-Wformat-overflow=] sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf2); ~~~~ layer1/Scene.cpp:4428:26: note: ‘sprintf’ output 29 or more bytes (assuming 1307) into a destination of size 1024 sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf2); ~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4393:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1022 [-Wformat-overflow=] sprintf(buf2, "(%s(%s))", sel_mode_kw, buffer); ^~~~~~~~~~ ~~~~~~ layer1/Scene.cpp:4393:20: note: ‘sprintf’ output 5 or more bytes (assuming 1028) into a destination of size 1024 sprintf(buf2, "(%s(%s))", sel_mode_kw, buffer); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer1/Scene.cpp:4404:33: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 753 and 1008 [-Wformat-overflow=] sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf1); ~~~~ layer1/Scene.cpp:4404:24: note: ‘sprintf’ output 29 or more bytes (assuming 1307) into a destination of size 1024 sprintf(buffer, "cmd.select('%s',\"%s(%s)\",enable=1)", selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sel_mode_kw, buf1); ~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/ScenePicking.cpp -o build/temp.linux-x86_64-3.6/layer1/ScenePicking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/ScenePicking.cpp: In function ‘void SceneRenderPicking(PyMOLGlobals*, int, int*, int, Picking*, int, int, Multipick*, SceneUnitContext*, GLenum)’: layer1/ScenePicking.cpp:249:7: warning: ‘previous.Picking::src.Pickable::index’ may be used uninitialized in this function [-Wmaybe-uninitialized] if (pik->src.index != previous.src.index || ^~ layer1/ScenePicking.cpp:238:11: note: ‘previous.Picking::src.Pickable::index’ was declared here Picking previous; ^~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/COLLADA.cpp -o build/temp.linux-x86_64-3.6/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/SceneRay.cpp -o build/temp.linux-x86_64-3.6/layer1/SceneRay.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Character.cpp -o build/temp.linux-x86_64-3.6/layer1/Character.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/SceneRender.cpp -o build/temp.linux-x86_64-3.6/layer1/SceneRender.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/SceneRender.cpp:561:6: warning: ‘void AppendCopyWithChangedShader(PyMOLGlobals*, CGO*, CGO*, int, int)’ defined but not used [-Wunused-function] void AppendCopyWithChangedShader(PyMOLGlobals * G, CGO *destCGO, CGO *srcCGO, int frommode, int tomode){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Color.cpp -o build/temp.linux-x86_64-3.6/layer1/Color.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/ScrollBar.cpp -o build/temp.linux-x86_64-3.6/layer1/ScrollBar.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Seq.cpp -o build/temp.linux-x86_64-3.6/layer1/Seq.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Seq.cpp: In function ‘int SeqFindRowCol(PyMOLGlobals*, int, int, int*, int*, int)’: layer1/Seq.cpp:90:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if((char_num >= 0) && (char_num < row->ext_len) && (row->char2col)) { ~~~~~~~~~^~~~~~~~~~~~~~ layer1/Seq.cpp: In member function ‘virtual void CSeq::reshape(int, int)’: layer1/Seq.cpp:144:28: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->Row[a].ext_len > I->Size) ~~~~~~~~~~~~~~~~~~^~~~~~~~~ layer1/Seq.cpp: In member function ‘virtual void CSeq::draw(CGO*)’: layer1/Seq.cpp:427:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] if(max_len < row->ext_len) ~~~~~~~~^~~~~~~~~~~~~~ In file included from layer0/vla.h:7, from layer1/Symmetry.h:26, from layer1/PyMOLObject.h:27, from layer1/Seq.h:21, from layer1/Seq.cpp:22: layer1/Seq.cpp: In function ‘void SeqFree(PyMOLGlobals*)’: layer1/Seq.cpp:781:14: warning: deleting object of polymorphic class type ‘CSeq’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Seq); ^~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Control.cpp -o build/temp.linux-x86_64-3.6/layer1/Control.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Setting.cpp -o build/temp.linux-x86_64-3.6/layer1/Setting.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer0/vla.h:7, from layer1/Symmetry.h:26, from layer1/PyMOLObject.h:27, from layer1/Scene.h:22, from layer1/Control.cpp:25: layer1/Control.cpp: In function ‘void ControlFree(PyMOLGlobals*)’: layer1/Control.cpp:410:14: warning: deleting object of polymorphic class type ‘CControl’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Control); ^~~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ layer1/Setting.cpp: In function ‘void SettingGenerateSideEffects(PyMOLGlobals*, int, const char*, int, int)’: layer1/Setting.cpp:2036:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (SettingGetGlobal_b(G, cSetting_precomputed_lighting)) ^~ layer1/Setting.cpp:2038:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ SceneInvalidate(G); ^~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Extrude.cpp -o build/temp.linux-x86_64-3.6/layer1/Extrude.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Extrude.cpp: In function ‘int ExtrudeCGOSurfaceTube(CExtrude*, CGO*, int, const float*, bool, int)’: layer1/Extrude.cpp:743:14: warning: ‘stop’ may be used uninitialized in this function [-Wmaybe-uninitialized] int start, stop; ^~~~ layer1/Extrude.cpp:743:7: warning: ‘start’ may be used uninitialized in this function [-Wmaybe-uninitialized] int start, stop; ^~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Font.cpp -o build/temp.linux-x86_64-3.6/layer1/Font.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/View.cpp -o build/temp.linux-x86_64-3.6/layer1/View.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Wizard.cpp -o build/temp.linux-x86_64-3.6/layer1/Wizard.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer1/Wizard.cpp: In member function ‘virtual void CWizard::draw(CGO*)’: layer1/Wizard.cpp:880:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] else ^~~~ layer1/Wizard.cpp:882:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ drawTopEdge(); ^~~~~~~~~~~ In file included from layer1/Wizard.cpp:25: layer1/Wizard.cpp: In function ‘void WizardFree(PyMOLGlobals*)’: layer1/Wizard.cpp:1034:14: warning: deleting object of polymorphic class type ‘CWizard’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Wizard); ^~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/AssemblyHelpers.cpp -o build/temp.linux-x86_64-3.6/layer2/AssemblyHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/AtomInfo.cpp -o build/temp.linux-x86_64-3.6/layer2/AtomInfo.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/AtomInfo.cpp: In function ‘bool AtomResiFromResv(char*, size_t, int, char)’: layer2/AtomInfo.cpp:821:56: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] return snprintf(resi, size, "%d%c", resv, inscode) < size; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ layer2/AtomInfo.cpp:822:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] return snprintf(resi, size, "%d", resv) < size; ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/AtomInfoHistory.cpp -o build/temp.linux-x86_64-3.6/layer2/AtomInfoHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/BondTypeHistory.cpp -o build/temp.linux-x86_64-3.6/layer2/BondTypeHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Shaker.cpp -o build/temp.linux-x86_64-3.6/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/CifFile.cpp -o build/temp.linux-x86_64-3.6/layer2/CifFile.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Symmetry.cpp -o build/temp.linux-x86_64-3.6/layer1/Symmetry.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/Text.cpp -o build/temp.linux-x86_64-3.6/layer1/Text.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/CifMoleculeReader.cpp -o build/temp.linux-x86_64-3.6/layer2/CifMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/CifMoleculeReader.cpp: In member function ‘void seqvec_t::set(int, const char*)’: layer2/CifMoleculeReader.cpp:99:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if (i > size()) ~~^~~~~~~~ layer2/CifMoleculeReader.cpp: In member function ‘const char* seqvec_t::get(int) const’: layer2/CifMoleculeReader.cpp:105:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if (i < 1 || i > size()) ~~^~~~~~~~ layer2/CifMoleculeReader.cpp: In function ‘CoordSet** read_pdbx_struct_assembly(PyMOLGlobals*, const pymol::cif_data*, const AtomInfoType*, const CoordSet*, const char*)’: layer2/CifMoleculeReader.cpp:765:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while (j < c_src_len * c_it->size()) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/CoordSet.cpp -o build/temp.linux-x86_64-3.6/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/CoordSet.cpp: In member function ‘void CoordSet::invalidateRep(int, int)’: layer2/CoordSet.cpp:1157:28: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if (I->Spheroid.size() != ~~~~~~~~~~~~~~~~~~~^~ I->NAtIndex * GetSpheroidSphereRec(G)->nDot) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/CoordSet.cpp: In function ‘void CoordSetAtomToPDBStrVLA(PyMOLGlobals*, char**, int*, const AtomInfoType*, const float*, int, const PDBInfoRec*, const double*)’: layer2/CoordSet.cpp:987:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output truncated before terminating nul copying 6 bytes from a string of the same length [-Wstringop-truncation] strncpy(anisoline, "ANISOU", 6); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ layer2/CoordSet.cpp: In member function ‘void CoordSet::update(int)’: layer2/CoordSet.cpp:1240:39: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 223 [-Wformat-truncation=] PRINTFB(G, FB_CoordSet, FB_Blather) " CoordSetUpdate-Entered: object %s state %d cset %p\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/DistSet.cpp -o build/temp.linux-x86_64-3.6/layer2/DistSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/GadgetSet.cpp -o build/temp.linux-x86_64-3.6/layer2/GadgetSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer1/TypeFace.cpp -o build/temp.linux-x86_64-3.6/layer1/TypeFace.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectSlice.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectSlice.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/HydrogenAdder.cpp -o build/temp.linux-x86_64-3.6/layer2/HydrogenAdder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectSlice.cpp: In function ‘PyObject* ObjectSliceAllStatesAsPyList(ObjectSlice*)’: layer2/ObjectSlice.cpp:78:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::invalidate(int, int, int)’: layer2/ObjectSlice.cpp:210:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < State.size(); a++) { ~~^~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: layer2/ObjectSlice.cpp:633:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘void ObjectSliceDrag(ObjectSlice*, int, int, float*, float*, float*)’: layer2/ObjectSlice.cpp:679:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘int ObjectSliceGetVertex(ObjectSlice*, int, int, float*)’: layer2/ObjectSlice.cpp:750:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::render(RenderInfo*)’: layer2/ObjectSlice.cpp:925:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp:967:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(cur_state >= I->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp:981:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp:1229:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(cur_state >= I->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘ObjectSliceState* ObjectSliceStateGetActive(ObjectSlice*, int)’: layer2/ObjectSlice.cpp:1247:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSlice.cpp: In function ‘ObjectSlice* ObjectSliceFromMap(PyMOLGlobals*, ObjectSlice*, ObjectMap*, int, int)’: layer2/ObjectSlice.cpp:1288:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectSlice.cpp: In function ‘void ObjectSliceRecomputeExtent(ObjectSlice*)’: layer2/ObjectSlice.cpp:1365:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/HydrogenAdder.cpp: In function ‘int ObjectMoleculeAddSeleHydrogensRefactored(ObjectMolecule*, int, int)’: layer2/HydrogenAdder.cpp:286:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] for (unsigned atm = 0; atm < n_atom_old; atm++) { ~~~~^~~~~~~~~~~~ layer2/HydrogenAdder.cpp:306:30: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘const int’ [-Wsign-compare] for (unsigned atm = 0; atm < n_atom_old; ++atm) { ~~~~^~~~~~~~~~~~ layer2/HydrogenAdder.cpp:360:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] for (unsigned idx = 0; idx < cs->NIndex; ++idx) { ~~~~^~~~~~~~~~~~ layer2/ObjectSlice.cpp: In member function ‘virtual void ObjectSlice::update()’: layer2/ObjectSlice.cpp:639:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 225 [-Wformat-truncation=] "ObjectSliceUpdate-Error: map '%s' has been deleted.\n", oss->MapName ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSlice.cpp:34: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 51 and 306 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSlice.cpp:638:9: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSlice, FB_Errors) ^~~~~~~ layer2/ObjectSlice.cpp:650:13: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 231 [-Wformat-truncation=] " ObjectSlice: updating \"%s\".\n", I->Name ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSlice.cpp:34: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 28 and 283 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSlice.cpp:649:11: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSlice, FB_Blather) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/MmodTyping.cpp -o build/temp.linux-x86_64-3.6/layer2/MmodTyping.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/MmtfMoleculeReader.cpp -o build/temp.linux-x86_64-3.6/layer2/MmtfMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectSurface.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/MmtfMoleculeReader.cpp: In function ‘ObjectMolecule* ObjectMoleculeReadMmtfStr(PyMOLGlobals*, ObjectMolecule*, const char*, int, int, int, int, int, int)’: layer2/MmtfMoleculeReader.cpp:230:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for (int l = 0, offset = atomIndex; l < group->bondAtomListCount / 2; ++l) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/MmtfMoleculeReader.cpp:296:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] for (int l = 0; l < container->bondAtomListCount / 2; ++l) { ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘PyObject* ObjectSurfaceAllStatesAsPyList(ObjectSurface*)’: layer2/ObjectSurface.cpp:81:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: layer2/ObjectSurface.cpp:232:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::invalidate(int, int, int)’: layer2/ObjectSurface.cpp:277:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceInvalidateMapName(ObjectSurface*, const char*, const char*)’: layer2/ObjectSurface.cpp:307:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘ObjectSurface* ObjectSurfaceFromBox(PyMOLGlobals*, ObjectSurface*, ObjectMap*, int, int, float*, float*, float, int, float, float*, int, int)’: layer2/ObjectSurface.cpp:1043:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectSurface.cpp: In function ‘pymol::Result ObjectSurfaceGetLevel(ObjectSurface*, int)’: layer2/ObjectSurface.cpp:1117:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state >= I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp: In function ‘int ObjectSurfaceSetLevel(ObjectSurface*, float, int, int)’: layer2/ObjectSurface.cpp:1136:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state >= I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~~ layer2/ObjectSurface.cpp:1139:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/Mol2Typing.cpp -o build/temp.linux-x86_64-3.6/layer2/Mol2Typing.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectSurface.cpp: In function ‘void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)’: layer2/ObjectSurface.cpp:264:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] " ObjectSurfaceDump: %s written to %s\n", I->Name, fname ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSurface.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output 34 or more bytes (assuming 289) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSurface.cpp:263:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSurface, FB_Actions) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/MolV3000.cpp -o build/temp.linux-x86_64-3.6/layer2/MolV3000.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectSurface.cpp: In member function ‘virtual void ObjectSurface::update()’: layer2/ObjectSurface.cpp:493:15: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] " ObjectSurface: updating \"%s\".\n", I->Name ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectSurface.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 30 and 285 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectSurface.cpp:492:13: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectSurface, FB_Details) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectAlignment.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectAlignment.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectVolume.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectVolume.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectVolume.cpp: In function ‘PyObject* ObjectVolumeAllStatesAsPyList(ObjectVolume*)’: layer2/ObjectVolume.cpp:127:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeAllStatesFromPyList(ObjectVolume*, PyObject*)’: layer2/ObjectVolume.cpp:248:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In function ‘int ObjectVolumeInvalidateMapName(ObjectVolume*, const char*, const char*)’: layer2/ObjectVolume.cpp:313:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::invalidate(int, int, int)’: layer2/ObjectVolume.cpp:341:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::update()’: layer2/ObjectVolume.cpp:402:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp:440:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (i = 0; i < vs->Ramp.size(); i += 5) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In member function ‘virtual void ObjectVolume::render(RenderInfo*)’: layer2/ObjectVolume.cpp:759:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); ++a) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: In function ‘ObjectVolume* ObjectVolumeFromXtalSym(PyMOLGlobals*, ObjectVolume*, ObjectMap*, CSymmetry*, int, int, float*, float*, float, int, float, float*, int)’: layer2/ObjectVolume.cpp:1130:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectVolume.cpp: In function ‘void ObjectVolumeRecomputeExtent(ObjectVolume*)’: layer2/ObjectVolume.cpp:1231:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectVolume.cpp: At global scope: layer2/ObjectVolume.cpp:657:15: warning: ‘size_t createPreintegrationTexture(PyMOLGlobals*, const float*, int)’ defined but not used [-Wunused-function] static size_t createPreintegrationTexture(PyMOLGlobals * G, const float *Table, const int count) ^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer0/Map.h:24, from layer1/Basis.h:20, from layer1/Ray.h:24, from layer1/PyMOLObject.h:24, from layer2/ObjectAlignment.h:22, from layer2/ObjectAlignment.cpp:27: layer0/Vector.h: In member function ‘virtual void ObjectAlignment::update()’: layer0/Vector.h:362:3: warning: ‘*((void*)& gvert +8)’ may be used uninitialized in this function [-Wmaybe-uninitialized] dst[2] = src[2]; ^~~ layer2/ObjectAlignment.cpp:926:39: note: ‘*((void*)& gvert +8)’ was declared here float mean[3], vert[3], gvert[3]; ^~~~~ In file included from layer0/Map.h:24, from layer1/Basis.h:20, from layer1/Ray.h:24, from layer1/PyMOLObject.h:24, from layer2/ObjectAlignment.h:22, from layer2/ObjectAlignment.cpp:27: layer0/Vector.h:361:3: warning: ‘*((void*)& gvert +4)’ may be used uninitialized in this function [-Wmaybe-uninitialized] dst[1] = src[1]; ^~~ layer2/ObjectAlignment.cpp:926:39: note: ‘*((void*)& gvert +4)’ was declared here float mean[3], vert[3], gvert[3]; ^~~~~ In file included from layer0/Map.h:24, from layer1/Basis.h:20, from layer1/Ray.h:24, from layer1/PyMOLObject.h:24, from layer2/ObjectAlignment.h:22, from layer2/ObjectAlignment.cpp:27: layer0/Vector.h:360:3: warning: ‘gvert’ may be used uninitialized in this function [-Wmaybe-uninitialized] dst[0] = src[0]; ^~~ layer2/ObjectAlignment.cpp:926:39: note: ‘gvert’ was declared here float mean[3], vert[3], gvert[3]; ^~~~~ layer2/ObjectVolume.cpp: In function ‘ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)’: layer2/ObjectVolume.cpp:74:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] "ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectVolume.cpp:20: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 46 and 301 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectCGO.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectCGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectCGO.cpp: In member function ‘virtual void ObjectCGO::render(RenderInfo*)’: layer2/ObjectCGO.cpp:502:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (!ray) ^~ layer2/ObjectCGO.cpp:504:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ ObjectCGORenderState(G, pass, ray, I, info, sobj, color, ramp, use_shader, cgo_lighting); ^~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepAngle.cpp -o build/temp.linux-x86_64-3.6/layer2/RepAngle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectCallback.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectCallback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepCartoon.cpp -o build/temp.linux-x86_64-3.6/layer2/RepCartoon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectDist.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectDist.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepCartoon.cpp: In function ‘Rep* RepCartoonNew(CoordSet*, int)’: layer2/RepCartoon.cpp:3715:57: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class CCInOut’; use assignment or value-initialization instead [-Wclass-memaccess] memset(car, 0, sizeof(*car) * cs->NAtIndex); ^ layer2/RepCartoon.cpp:39:7: note: ‘class CCInOut’ declared here class CCInOut { ^~~~~~~ layer2/ObjectDist.cpp:40:13: warning: ‘void ObjectDistFree(ObjectDist*)’ declared ‘static’ but never defined [-Wunused-function] static void ObjectDistFree(ObjectDist * I); ^~~~~~~~~~~~~~ In file included from layer2/CoordSet.h:24, from layer2/RepCartoon.h:21, from layer2/RepCartoon.cpp:27: layer1/Setting.h: In function ‘V AtomSettingGetWD(PyMOLGlobals*, T*, int, V) [with V = bool; T = const AtomInfoType]’: layer1/Setting.h:421:11: warning: ‘out’ is used uninitialized in this function [-Wuninitialized] int i = *out; ^~~~ In file included from layer2/ObjectMolecule.h:25, from layer2/CoordSet.h:25, from layer2/RepCartoon.h:21, from layer2/RepCartoon.cpp:27: layer2/AtomInfo.h:500:5: note: ‘out’ was declared here V out; ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectGadget.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectGadget.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepCartoon.cpp: In function ‘int GenerateRepCartoonProcessCylindricalHelices(PyMOLGlobals*, ObjectMolecule*, CoordSet*, CGO*, CExtrude*, int, int*, float*, float*, float*, const CCInOut*, int*, float*, int, int, float, float)’: layer2/RepCartoon.cpp:1596:20: warning: ‘atom_index2’ may be used uninitialized in this function [-Wmaybe-uninitialized] int atom_index1, atom_index2, *s, ^~~~~~~~~~~ layer2/RepCartoon.cpp: In function ‘void do_ring(PyMOLGlobals*, nuc_acid_data*, int, int*, ObjectMolecule*, CoordSet*, float, CGO*, int, float, int, int, int, float, float, int*, float*, float)’: layer2/RepCartoon.cpp:1010:65: warning: ‘i’ may be used uninitialized in this function [-Wmaybe-uninitialized] float ladder_alpha = 1.0f - AtomSettingGetWD(G, ai_i[i], cSetting_cartoon_transparency, 1.0f - alpha); ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectGadgetRamp.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectGadgetRamp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepCylBond.cpp -o build/temp.linux-x86_64-3.6/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectGroup.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectGroup.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMap.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDihedral.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDihedral.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘int ObjectMapValidXtal(ObjectMap*, int)’: layer2/ObjectMap.cpp:133:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if((state >= 0) && (state < I->State.size())) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapTrim(ObjectMap*, int, float*, float*, int)’: layer2/ObjectMap.cpp:912:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapDouble(ObjectMap*, int)’: layer2/ObjectMap.cpp:929:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘pymol::Result<> ObjectMapHalve(ObjectMap*, int, int)’: layer2/ObjectMap.cpp:944:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if((state >= 0) && (state < I->State.size()) && (I->State[state].Active)) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘void ObjectMapRegeneratePoints(ObjectMap*)’: layer2/ObjectMap.cpp:1187:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (i=0; iState.size();i++){ ~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘PyObject* ObjectMapAllStatesAsPyList(ObjectMap*)’: layer2/ObjectMap.cpp:1277:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapAllStatesFromPyList(ObjectMap*, PyObject*)’: layer2/ObjectMap.cpp:1435:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapNewCopy(PyMOLGlobals*, const ObjectMap*, ObjectMap**, int, int)’: layer2/ObjectMap.cpp:1507:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(state = 0; state < src->State.size(); state++) { ~~~~~~^~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:1516:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(source_state < src->State.size()) { ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMapState* ObjectMapStatePrime(ObjectMap*, int)’: layer2/ObjectMap.cpp:1533:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘void ObjectMapUpdateExtents(ObjectMap*)’: layer2/ObjectMap.cpp:1546:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In member function ‘virtual void ObjectMap::invalidate(int, int, int)’: layer2/ObjectMap.cpp:1672:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->State.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapCCP4StrToMap(ObjectMap*, char*, int, int, int, int)’: layer2/ObjectMap.cpp:2300:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] if(bytes < 256 * sizeof(int)) { ~~~~~~^~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:2310:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapPHIStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:2958:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapXPLORStrToMap(ObjectMap*, char*, int, int)’: layer2/ObjectMap.cpp:3232:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapFLDStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:3445:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapBRIXStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:3774:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:4179:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadCCP4(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int, int)’: layer2/ObjectMap.cpp:4695:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapDXStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:4885:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadDXFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5173:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘int ObjectMapACNTStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:5207:22: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadACNTFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5403:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadFLDFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5439:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadBRIXFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5475:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadGRDFile(PyMOLGlobals*, ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5512:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadXPLOR(PyMOLGlobals*, ObjectMap*, const char*, int, int, int)’: layer2/ObjectMap.cpp:5561:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(state < I->State.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyBrick(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: layer2/ObjectMap.cpp:5715:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadChemPyMap(PyMOLGlobals*, ObjectMap*, PyObject*, int, int, int)’: layer2/ObjectMap.cpp:5813:24: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(I->State.size() <= state) { ~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:27, from /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4, from layer0/os_numpy.h:8, from layer2/ObjectMap.cpp:22: /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h: At global scope: /usr/lib64/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function] _import_array(void) ^~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDistDash.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDistDash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘void ObjectMapDump(const ObjectMap*, const char*, int, int)’: layer2/ObjectMap.cpp:5982:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 239 [-Wformat-truncation=] " ObjectMapDump: %s written to %s\n", om->Name, fname ENDFB(om->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output 30 or more bytes (assuming 285) into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDistLabel.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDistLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘ObjectMap* ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int)’: layer2/ObjectMap.cpp:2977:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:2986:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:2992:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:3074:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] " PHIStrToMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 16 and 1039 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepDot.cpp -o build/temp.linux-x86_64-3.6/layer2/RepDot.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMap.cpp: In function ‘int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)’: layer2/ObjectMap.cpp:4297:5: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] " ObjectMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 14 and 1037 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp:4297:5: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] " ObjectMap: %s\n", cc ENDFB(I->G); ^~~~~~~~~~~~~~~~~~ ~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMap.cpp:21: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 14 and 1037 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMesh.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepEllipsoid.cpp -o build/temp.linux-x86_64-3.6/layer2/RepEllipsoid.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepLabel.cpp -o build/temp.linux-x86_64-3.6/layer2/RepLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMesh.cpp: In function ‘void ObjectMeshDump(ObjectMesh*, const char*, int, int)’: layer2/ObjectMesh.cpp:329:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] " ObjectMeshDump: %s written to %s\n", I->Name, fname ENDFB(I->G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectMesh.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output 31 or more bytes (assuming 286) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMesh.cpp:328:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectMesh, FB_Actions) ^~~~~~~ layer2/ObjectMesh.cpp: In member function ‘virtual void ObjectMesh::update()’: layer2/ObjectMesh.cpp:507:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 226 [-Wformat-truncation=] "ObjectMeshUpdate-Error: map '%s' has been deleted.\n", ms->MapName ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectMesh.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 50 and 305 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMesh.cpp:506:9: note: in expansion of macro ‘PRINTFB’ PRINTFB(I->G, FB_ObjectMesh, FB_Errors) ^~~~~~~ layer2/ObjectMesh.cpp:540:15: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 232 [-Wformat-truncation=] " ObjectMesh: updating \"%s\".\n", I->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer1/Scene.h:23, from layer2/ObjectMesh.cpp:33: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 27 and 282 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMesh.cpp:539:13: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMesh, FB_Details) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMolecule.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepMesh.cpp -o build/temp.linux-x86_64-3.6/layer2/RepMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule.cpp: In function ‘pymol::Result<> ObjectMoleculeAddBondByIndices(ObjectMolecule*, unsigned int, unsigned int, int)’: layer2/ObjectMolecule.cpp:4416:12: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if (atm1 >= I->NAtom || atm2 >= I->NAtom) { ~~~~~^~~~~~~~~~~ layer2/ObjectMolecule.cpp:4416:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] if (atm1 >= I->NAtom || atm2 >= I->NAtom) { ~~~~~^~~~~~~~~~~ layer2/ObjectMolecule.cpp: In member function ‘bool ObjectMolecule::atomHasAnyCoordinates(size_t) const’: layer2/ObjectMolecule.cpp:12085:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] for (size_t i = 0; i < NCSet; ++i) { ~~^~~~~~~ layer2/RepMesh.cpp: In function ‘Rep* RepMeshNew(CoordSet*, int)’: layer2/RepMesh.cpp:1062:13: warning: ‘field’ may be used uninitialized in this function [-Wmaybe-uninitialized] DeleteP(field); ^~~~~ layer2/ObjectMolecule.cpp: In function ‘const char* findflag(PyMOLGlobals*, const char*, const char*, const char*)’: layer2/ObjectMolecule.cpp:1451:9: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 194 [-Wformat-truncation=] " ObjectMolecule-Error: Unrecognized file format (can't find \"%s\").\n", pat ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 66 and 1089 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:1450:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Errors) ^~~~~~~ layer2/ObjectMolecule.cpp:1469:9: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 194 [-Wformat-truncation=] " ObjectMolecule-Error: Unrecognized file format (can't find \"%s\").\n", pat ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 66 and 1089 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:1468:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Errors) ^~~~~~~ layer2/ObjectMolecule.cpp: In function ‘CoordSet* ObjectMoleculeXYZStr2CoordSet(PyMOLGlobals*, const char*, AtomInfoType**, const char**)’: layer2/ObjectMolecule.cpp:2972:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4 bytes from a string of length 1023 [-Wstringop-truncation] strncpy(ai->elem, cc, cElemNameLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.cpp: In function ‘CoordSet* ObjectMoleculeMOLStr2CoordSet(PyMOLGlobals*, const char*, AtomInfoType**, const char**)’: layer2/ObjectMolecule.cpp:7785:5: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 224 [-Wformat-truncation=] " ObjMolMOLStr2CoordSet: title '%s'\n", nameTmp ENDFB(G) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 34 and 289 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:7784:3: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Blather) ^~~~~~~ layer2/ObjectMolecule.cpp:7833:16: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 4 bytes from a string of length 1023 [-Wstringop-truncation] strncpy(atInfo[a].elem, cc, cElemNameLen); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepNonbonded.cpp -o build/temp.linux-x86_64-3.6/layer2/RepNonbonded.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepNonbondedSphere.cpp -o build/temp.linux-x86_64-3.6/layer2/RepNonbondedSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule.cpp: In member function ‘virtual void ObjectMolecule::update()’: layer2/ObjectMolecule.cpp:10827:15: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] " ObjectMolecule-DEBUG: updating representations for state %d of \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer2/ObjectMolecule.cpp:35: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 68 and 333 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer2/ObjectMolecule.cpp:10826:13: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_ObjectMolecule, FB_Blather) ^~~~~~~ layer2/ObjectMolecule.cpp: In function ‘int ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, const float*, int, int)’: layer2/ObjectMolecule.cpp:10955:21: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer, v[0], v[1], v[2], state + 1, mode, 0); ~~~~~~ layer2/ObjectMolecule.cpp:10955:21: note: directive argument in the range [-2147483647, 2147483647] layer2/ObjectMolecule.cpp:10955:14: note: ‘sprintf’ output between 78 and 2036 bytes into a destination of size 1024 sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer, v[0], v[1], v[2], state + 1, mode, 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepRibbon.cpp -o build/temp.linux-x86_64-3.6/layer2/RepRibbon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSphere.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepSphere.cpp: In function ‘int RepGetSphereMode(PyMOLGlobals*, RepSphere*, bool)’: layer2/RepSphere.cpp:141:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (sphere_mode == 4) // sphere_mode 4 no longer exists, use default ^~ layer2/RepSphere.cpp:143:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ switch (sphere_mode) { ^~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepSphere.cpp: In function ‘Rep* RepSphereNew(CoordSet*, int)’: layer2/RepSphere.cpp:611:42: warning: ‘transp’ may be used uninitialized in this function [-Wmaybe-uninitialized] RepSphereAddAtomVisInfoToStoredVC(I, obj, cs, state, a1, ati1, a, sphere_scale, sphere_color, transp, &variable_alpha, sphere_add); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/RepSphere.cpp:656:12: warning: ‘sphere_color’ may be used uninitialized in this function [-Wmaybe-uninitialized] *(lc++) = sphere_color; ~~~~~~~~^~~~~~~~~~~~~~ layer2/RepSphere.cpp:611:42: warning: ‘sphere_scale’ may be used uninitialized in this function [-Wmaybe-uninitialized] RepSphereAddAtomVisInfoToStoredVC(I, obj, cs, state, a1, ati1, a, sphere_scale, sphere_color, transp, &variable_alpha, sphere_add); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSphereGenerate.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSphereGenerate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule2.cpp:3268:13: warning: ‘void AtomColumnFromPyList(ObjectMolecule&, PyObject*, std::function)’ defined but not used [-Wunused-function] static void AtomColumnFromPyList(ObjectMolecule& mol, PyObject* list, ^~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule2.cpp:3221:18: warning: ‘PyObject* AtomColumnAsPyList(const ObjectMolecule&, std::function<_object*(const AtomInfoType&)>)’ defined but not used [-Wunused-function] static PyObject* AtomColumnAsPyList(const ObjectMolecule& mol, ^~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSphereImmediate.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSphereImmediate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/ObjectMolecule2.cpp: In function ‘int ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, const char*, const char*, const char*, const char*, const char*, const char*, float, int, float, float, const char*, const float*, int, int, int, int)’: layer2/ObjectMolecule2.cpp:313:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] " ObjMol: created %s/%s/%s/%s`%d%c/%s\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer2/ObjectMolecule2.cpp:20: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output 26 or more bytes (assuming 281) into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepSurface.cpp -o build/temp.linux-x86_64-3.6/layer2/RepSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Editor.cpp -o build/temp.linux-x86_64-3.6/layer3/Editor.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer2/RepSurface.cpp: In function ‘int RepSurfaceCGOGenerate(RepSurface*, RenderInfo*)’: layer2/RepSurface.cpp:669:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (ok && pick_surface) ^~ layer2/RepSurface.cpp:671:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if (ok && I->VAO){ ^~ layer2/RepSurface.cpp: In function ‘void RepSurfaceSmoothEdges(RepSurface*)’: layer2/RepSurface.cpp:4417:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto j = 0; j < edges[i].size(); j += 3) { ~~^~~~~~~~~~~~~~~~~ layer2/RepSurface.cpp:4429:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto j = 0; j < edges[i].size(); j += 3) { ~~^~~~~~~~~~~~~~~~~ layer2/RepSurface.cpp:4440:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (auto i = 0; i < unique_edges.size(); i += 2) { ~~^~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp: In function ‘pymol::Result<> EditorSelect(PyMOLGlobals*, const char*, const char*, const char*, const char*, int, int, int)’: layer3/Editor.cpp:777:7: warning: variable ‘result’ set but not used [-Wunused-but-set-variable] int result = false; ^~~~~~ layer3/Editor.cpp: In function ‘int EditorLogState(PyMOLGlobals*, int)’: layer3/Editor.cpp:585:23: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1015 [-Wformat-overflow=] sprintf(buffer, "cmd.edit(%s,%s,%s,%s,pkresi=%d,pkbond=%d)", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1, buf2, buf3, buf4, pkresi ? 1 : 0, pkbond ? 1 : 0); ~~~~ layer3/Editor.cpp:585:23: note: directive argument in the range [0, 1] layer3/Editor.cpp:585:23: note: directive argument in the range [0, 1] layer3/Editor.cpp:585:14: note: ‘sprintf’ output between 32 and 4124 bytes into a destination of size 1024 sprintf(buffer, "cmd.edit(%s,%s,%s,%s,pkresi=%d,pkbond=%d)", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1, buf2, buf3, buf4, pkresi ? 1 : 0, pkbond ? 1 : 0); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp: In function ‘void EditorPrepareDrag(PyMOLGlobals*, CObject*, int, int, int, int)’: layer3/Editor.cpp:1944:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] " Editor: grabbing (%s).", name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer1/ButMode.h:20, from layer3/Editor.cpp:28: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 22 and 277 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Editor.cpp:1943:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Blather) ^~~~~~~ layer3/Editor.cpp: In function ‘void EditorDefineExtraPks(PyMOLGlobals*)’: layer3/Editor.cpp:335:21: warning: ‘%s’ directive writing up to 255 bytes into a region of size 249 [-Wformat-overflow=] sprintf(buffer, "(byres %s)", name); ^~~~~~~~~~~~ ~~~~ layer3/Editor.cpp:335:12: note: ‘sprintf’ output between 9 and 264 bytes into a destination of size 256 sprintf(buffer, "(byres %s)", name); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp:337:21: warning: ‘%s’ directive writing up to 255 bytes into a region of size 247 [-Wformat-overflow=] sprintf(buffer, "(bychain %s)", name); ^~~~~~~~~~~~~~ ~~~~ layer3/Editor.cpp:337:12: note: ‘sprintf’ output between 11 and 266 bytes into a destination of size 256 sprintf(buffer, "(bychain %s)", name); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp:339:21: warning: ‘%s’ directive writing up to 255 bytes into a region of size 246 [-Wformat-overflow=] sprintf(buffer, "(byobject %s)", name); ^~~~~~~~~~~~~~~ ~~~~ layer3/Editor.cpp:339:12: note: ‘sprintf’ output between 12 and 267 bytes into a destination of size 256 sprintf(buffer, "(byobject %s)", name); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Executive.cpp -o build/temp.linux-x86_64-3.6/layer3/Executive.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/RepWireBond.cpp -o build/temp.linux-x86_64-3.6/layer2/RepWireBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveIsosurfaceEtc(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int, int, int)’: layer3/Executive.cpp:1046:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveIsomeshEtc(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int, int, float)’: layer3/Executive.cpp:1191:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveVolume(PyMOLGlobals*, const char*, const char*, float, const char*, float, int, float, int, int)’: layer3/Executive.cpp:1364:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveLoad(PyMOLGlobals*, const ExecutiveLoadArgs&)’: layer3/Executive.cpp:3914:15: warning: unused variable ‘object_props’ [-Wunused-variable] const char* object_props = args.object_props.c_str(); ^~~~~~~~~~~~ layer3/Executive.cpp:3915:15: warning: unused variable ‘atom_props’ [-Wunused-variable] const char* atom_props = args.atom_props.c_str(); ^~~~~~~~~~ layer3/Executive.cpp:3924:8: warning: unused variable ‘mimic’ [-Wunused-variable] auto mimic = args.mimic; ^~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveMapSet(PyMOLGlobals*, const char*, int, const char*, int, int, int, int)’: layer3/Executive.cpp:6368:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(obj->State.size() > max_n_state) ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ layer3/Executive.cpp:6479:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(src_state < obj->State.size()) { ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘float ExecutiveRMSPairs(PyMOLGlobals*, const std::vector&, int, bool)’: layer3/Executive.cpp:11201:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for(a = 0; a < pairs; a++) { ~~^~~~~~~ layer3/Executive.cpp:11206:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] if(a < (pairs - 1)) ~~^~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveColor(PyMOLGlobals*, const char*, const char*, int, int)’: layer3/Executive.cpp:12555:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] int ok = false; ^~ layer3/Executive.cpp: In function ‘void ExecutiveSymExp(PyMOLGlobals*, const char*, const char*, const char*, float, int, int)’: layer3/Executive.cpp:14097:28: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(a = 0; a < nsymmat; a++) { ~~^~~~~~~~~ In file included from layer0/OOMac.h:22, from layer3/Executive.cpp:30: layer3/Executive.cpp: In function ‘void ExecutiveFree(PyMOLGlobals*)’: layer3/Executive.cpp:16361:14: warning: deleting object of polymorphic class type ‘CExecutive’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Executive); ^~~~~~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSliceNew(PyMOLGlobals*, const char*, const char*, int, int)’: layer3/Executive.cpp:16674:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if(map_state >= mapObj->State.size()) ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from layer3/Executive.h:37, from layer3/Executive.cpp:31: layer0/TrackerList.h: In instantiation of ‘pymol::TrackerAdapter::TrackerAdapterIterator::TrackerAdapterIterator(CTracker*, int) [with bool IsConst = false; T = SpecRec]’: layer0/TrackerList.h:99:29: required from ‘pymol::TrackerAdapter::iterator pymol::TrackerAdapter::begin() [with T = SpecRec; pymol::TrackerAdapter::iterator = pymol::TrackerAdapter::TrackerAdapterIterator]’ layer3/Executive.cpp:263:62: required from here layer0/TrackerList.h:80:15: warning: ‘pymol::TrackerAdapter::TrackerAdapterIterator::m_tracker’ will be initialized after [-Wreorder] CTracker* m_tracker; ^~~~~~~~~ layer0/TrackerList.h:79:22: warning: ‘int pymol::TrackerAdapter::TrackerAdapterIterator::m_iter_id’ [-Wreorder] int m_iter_id = -1; ^ layer0/TrackerList.h:35:14: warning: when initialized here [-Wreorder] explicit TrackerAdapterIterator(CTracker* tracker, int list_id) ^~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/Sculpt.cpp -o build/temp.linux-x86_64-3.6/layer2/Sculpt.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘int ExecutiveSetBondSettingFromString(PyMOLGlobals*, int, const char*, const char*, const char*, int, int, int)’: layer3/Executive.cpp:11590:17: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11590:17: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 560 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11589:15: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘PyObject* ExecutiveGetBondSetting(PyMOLGlobals*, int, char*, const char*, int, int, int)’: layer3/Executive.cpp:11672:8: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Getting: %s for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11672:8: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 38 and 556 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11671:6: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetBondSetting(PyMOLGlobals*, int, PyObject*, const char*, const char*, int, int, int)’: layer3/Executive.cpp:11775:19: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11775:19: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 560 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11774:17: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:11794:7: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 236 [-Wformat-truncation=] " Setting-Warning: '%s' is not a bond-level setting\n", name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 50 and 304 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11793:5: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Setting, FB_Warnings) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveUnsetBondSetting(PyMOLGlobals*, int, const char*, const char*, int, int, int)’: layer3/Executive.cpp:11851:15: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s unset for %d bonds in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, nSet, rec->obj->Name ENDF(G); ~~~~ layer3/Executive.cpp:11851:15: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 44 and 562 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11850:13: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetSetting(PyMOLGlobals*, int, PyObject*, const char*, int, int, int)’: layer3/Executive.cpp:12089:9: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 236 [-Wformat-truncation=] " Setting-Warning: '%s' is a %s-level setting\n", name, SettingLevelGetName(G, index) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output 42 or more bytes (assuming 296) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12088:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Setting, FB_Warnings) ^~~~~~~ layer3/Executive.cpp:11945:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects, state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value, nObj, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:11945:21: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1339 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11944:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:11942:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects.\n", name, value, nObj ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1321 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11941:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12034:27: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d atoms in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, op.i4, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 561 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12033:25: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12066:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value, rec->obj->Name, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12066:25: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12065:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12059:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12058:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:11901:18: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] PRINTF " Setting: %s set to %s.\n", name, value ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:11901:11: note: in expansion of macro ‘PRINTF’ PRINTF " Setting: %s set to %s.\n", name, value ENDF(G); ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetSettingFromString(PyMOLGlobals*, int, const char*, const char*, int, int, int)’: layer3/Executive.cpp:12251:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects, state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, nObj, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12251:21: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1339 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12250:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12248:21: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in %d objects.\n", name, value2, nObj ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1321 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12247:19: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12283:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set for %d atoms in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, op.i4, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 42 and 561 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12282:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12315:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, rec->obj->Name, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12315:25: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12314:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12307:25: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, rec->obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12306:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12211:18: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12211:11: note: in expansion of macro ‘PRINTF’ PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetObjSettingFromString(PyMOLGlobals*, int, const char*, CObject*, int, int, int)’: layer3/Executive.cpp:12380:19: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, obj->Name, state + 1 ENDF(G); ~~~~ layer3/Executive.cpp:12380:19: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 43 and 1584 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12379:17: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12372:19: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] " Setting: %s set to %s in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name, value2, obj->Name ENDF(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 34 and 1566 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12371:17: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12351:18: warning: ‘%s’ directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output between 21 and 1298 bytes into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12351:11: note: in expansion of macro ‘PRINTF’ PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); ^~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveUnsetSetting(PyMOLGlobals*, int, const char*, int, int, int)’: layer3/Executive.cpp:12490:23: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 215 [-Wformat-truncation=] " Setting: %s unset for %d atoms in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output 44 or more bytes (assuming 299) into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12489:21: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12515:25: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 227 [-Wformat-truncation=] " Setting: %s unset in object \"%s\", state %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:12515:25: note: directive argument in the range [1, 2147483647] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output 41 or more bytes (assuming 305) into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12514:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp:12509:25: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 227 [-Wformat-truncation=] " Setting: %s unset in object \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:282:53: note: ‘snprintf’ output 32 or more bytes (assuming 287) into a destination of size 255 #define PRINTF { FeedbackLineType _FBstr; (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:12508:23: note: in expansion of macro ‘PRINTF’ PRINTF ^~~~~~ layer3/Executive.cpp: In function ‘bool ExecutiveSetSymmetry(PyMOLGlobals*, pymol::zstring_view, int, const CSymmetry&, bool)’: layer3/Executive.cpp:6023:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 202 [-Wformat-truncation=] " %s-Details: Updated symmetry for '%s'\n", __func__, obj->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 56 and 311 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:6022:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Details) ^~~~~~~ layer3/Executive.cpp:6014:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 199 [-Wformat-truncation=] " %s-Warning: Cannot set symmetry for '%s' (type %s)\n", __func__, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 76 and 331 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:6013:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/SculptCache.cpp -o build/temp.linux-x86_64-3.6/layer2/SculptCache.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/SideChainHelper.cpp -o build/temp.linux-x86_64-3.6/layer2/SideChainHelper.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer1/PyMOLObject.h:26, from layer2/ObjectMolecule.h:24, from layer2/SideChainHelper.h:9, from layer2/SideChainHelper.cpp:10: layer1/Setting.h: In function ‘V AtomSettingGetWD(PyMOLGlobals*, T*, int, V) [with V = bool; T = const AtomInfoType]’: layer1/Setting.h:421:11: warning: ‘out’ is used uninitialized in this function [-Wuninitialized] int i = *out; ^~~~ In file included from layer2/ObjectMolecule.h:25, from layer2/SideChainHelper.h:9, from layer2/SideChainHelper.cpp:10: layer2/AtomInfo.h:500:5: note: ‘out’ was declared here V out; ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer2/VFont.cpp -o build/temp.linux-x86_64-3.6/layer2/VFont.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘void ExecutiveManageObject(PyMOLGlobals*, CObject*, int, int)’: layer3/Executive.cpp:14515:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] " Executive-Warning: name \"%s\" collides with a selection language keyword.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 73 and 328 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14514:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ layer3/Executive.cpp:14510:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] " Executive: object name \"%s\" is illegal -- renamed to 'all_'.\n", obj->Name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 61 and 316 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14509:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ layer3/Executive.cpp:14535:13: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] " Executive: object \"%s\" created.\n", obj->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 32 and 287 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14534:11: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveGroup(PyMOLGlobals*, const char*, const char*, int, int)’: layer3/Executive.cpp:2366:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] " Executive: adding '%s' to group '%s'.\n", rec->name, rec->group_name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 36 and 546 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:2365:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveSetSession(PyMOLGlobals*, PyObject*, int, int)’: layer3/Executive.cpp:5145:13: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 213 [-Wformat-truncation=] " Executive: skipping unrecognized object \"%s\" of type %d.\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 56 and 321 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:5144:11: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Errors) ^~~~~~~ layer3/Executive.cpp:5170:11: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 210 [-Wformat-truncation=] "ExectiveSetNamedEntries-Error: after object \"%s\".\n", rec->name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 49 and 304 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:5169:9: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Errors) ^~~~~~~ layer3/Executive.cpp: In function ‘void ExecutiveSelectRect(PyMOLGlobals*, BlockRect*, int)’: layer3/Executive.cpp:7355:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7355:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7341:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7341:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7331:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7331:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7323:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7323:20: note: ‘sprintf’ output between 28 and 1308 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp:7314:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 751 and 1008 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"(%s)\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~ layer3/Executive.cpp:7314:20: note: ‘sprintf’ output between 30 and 1310 bytes into a destination of size 1024 sprintf(buf2, "%scmd.select(\"%s\",\"(%s)\",enable=1)\n", prefix, selName, ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buffer); ~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveCopy(PyMOLGlobals*, const char*, const char*, int)’: layer3/Executive.cpp:9799:5: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] " Executive: object %s created.\n", oDst->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 30 and 285 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9798:3: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/AtomIterators.cpp -o build/temp.linux-x86_64-3.6/layer3/AtomIterators.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘void ExecutiveSymExp(PyMOLGlobals*, const char*, const char*, const char*, float, int, int)’: layer3/Executive.cpp:14181:21: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 238 [-Wformat-truncation=] "new_name before: %s\n", new_name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 19 and 1042 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14180:19: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Blather) ^~~~~~~ layer3/Executive.cpp:14184:21: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 236 [-Wformat-truncation=] "Making new object: %s from name=%s, a=%d, x=%d, y=%d, z=%d\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ new_name, name, (int)a, x, y, z ENDFB(G); ~~~~~~~~ layer3/Executive.cpp:14184:21: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:14184:21: note: directive argument in the range [-1, 2] layer3/Executive.cpp:14184:21: note: directive argument in the range [-1, 2] layer3/Executive.cpp:14184:21: note: directive argument in the range [-1, 2] In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output 52 or more bytes (assuming 1078) into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:14183:19: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Blather) ^~~~~~~ layer3/Executive.cpp: In function ‘int ExecutiveProcessPDBFile(PyMOLGlobals*, CObject*, const char*, const char*, const char*, int, int, int, char*, int, int, int, int)’: layer3/Executive.cpp:4344:35: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4344:35: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4344:24: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4342:35: warning: ‘%04d’ directive writing between 4 and 10 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, model_number); ^~~~~~~~~ layer3/Executive.cpp:4342:35: note: directive argument in the range [1, 2147483647] layer3/Executive.cpp:4342:24: note: ‘sprintf’ output between 6 and 267 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, model_number); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4331:35: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4331:35: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4331:24: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4322:33: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4322:33: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4322:22: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4320:33: warning: ‘%04d’ directive writing between 4 and 10 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, model_number); ^~~~~~~~~ layer3/Executive.cpp:4320:33: note: directive argument in the range [1, 2147483647] layer3/Executive.cpp:4320:22: note: ‘sprintf’ output between 6 and 267 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, model_number); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp:4309:33: warning: ‘%04d’ directive writing between 4 and 11 bytes into a region of size between 0 and 255 [-Wformat-overflow=] sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ^~~~~~~~~ layer3/Executive.cpp:4309:33: note: using the range [-2147483648, 2147483647] for directive argument layer3/Executive.cpp:4309:22: note: ‘sprintf’ output between 6 and 268 bytes into a destination of size 256 sprintf(pdb_name, "%s_%04d", cur_name, n_processed + 1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In member function ‘virtual int CExecutive::drag(int, int, int)’: layer3/Executive.cpp:15534:42: warning: ‘%s’ directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order_input, (location == -2) ? "upper" : "current"); ~~~~~~~~~~~ layer3/Executive.cpp:15534:26: note: ‘sprintf’ output between 32 and 1057 bytes into a destination of size 1024 sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ order_input, (location == -2) ? "upper" : "current"); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveSetName(PyMOLGlobals*, const char*, const char*)’: layer3/Executive.cpp:3623:7: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 222 [-Wformat-truncation=] " Warning: Invalid characters in '%s' have been replaced or stripped\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ name ENDFB(G); ~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 67 and 322 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:3622:5: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Warnings) ^~~~~~~ layer3/AtomIterators.cpp: In member function ‘virtual bool SeleAtomIterator::next()’: layer3/AtomIterators.cpp:61:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while ((++a) < I->Table.size()) { ~~~~~~^~~~~~~~~~~~~~~~~ layer3/AtomIterators.cpp: In member function ‘virtual bool SeleCoordIterator::next()’: layer3/AtomIterators.cpp:129:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for (a++; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/CifDataValueFormatter.cpp -o build/temp.linux-x86_64-3.6/layer3/CifDataValueFormatter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveRemoveAtoms(PyMOLGlobals*, const char*, int)’: layer3/Executive.cpp:9162:17: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 207 and 217 [-Wformat-truncation=] " Remove: eliminated %d atoms in model \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 42 and 307 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9161:15: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveBond(PyMOLGlobals*, const char*, const char*, int, int, int)’: layer3/Executive.cpp:9508:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 200 and 210 [-Wformat-truncation=] " Valence: %d bond valences adjusted in model \"%s\".\n", cnt, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 49 and 314 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9507:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp:9495:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 214 and 224 [-Wformat-truncation=] " Bond: %d bonds added to model \"%s\".\n", cnt, rec->obj->Name ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 35 and 300 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9494:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp:9520:19: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size between 208 and 218 [-Wformat-truncation=] " Unbond: %d bonds removed from model \"%s\".\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 41 and 306 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:9519:17: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Editor, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result<> ExecutiveLoad(PyMOLGlobals*, const ExecutiveLoadArgs&)’: layer3/Executive.cpp:4132:7: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 255 [-Wformat-truncation=] "%s", buf ENDFB(G); ^~~~ ~~~ In file included from layer1/Ortho.h:32, from layer3/Executive.h:30, from layer3/Executive.cpp:31: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 1 and 1024 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer3/Executive.cpp:4131:5: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ layer3/Executive.cpp: In function ‘pymol::Result > ExecutiveSpectrum(PyMOLGlobals*, const char*, const char*, float, float, int, int, const char*, int, int, int)’: layer3/Executive.cpp:4839:24: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 8 equals destination size [-Wstringop-truncation] strncpy(value_s, raw_ptr, sizeof(value_e)); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/ExecutivePython.cpp -o build/temp.linux-x86_64-3.6/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveSetRawAlignment(PyMOLGlobals*, pymol::zstring_view, PyObject*, pymol::zstring_view, int, int)’: layer3/ExecutivePython.cpp:175:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] for(size_t c = 0; c < n_cols; ++c) { ~~^~~~~~~~ layer3/ExecutivePython.cpp:184:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] for(size_t i = 0; i < n_idx; ++i) { ~~^~~~~~~ layer3/ExecutivePython.cpp: In function ‘pymol::Result<> ExecutiveLoadObject(PyMOLGlobals*, const char*, PyObject*, int, int, int, int, int, int)’: layer3/ExecutivePython.cpp:150:5: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 255 [-Wformat-truncation=] "%s", buf ENDFB(G); ^~~~ ~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from layer3/Executive.h:20, from layer3/ExecutivePython.h:3, from layer3/ExecutivePython.cpp:1: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin_snprintf’ output between 1 and 1024 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/MaeExportHelpers.cpp -o build/temp.linux-x86_64-3.6/layer3/MaeExportHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer2/AtomInfo.h:23, from layer3/MaeExportHelpers.h:11, from layer3/MaeExportHelpers.cpp:11: layer1/Setting.h: In function ‘int MaeExportGetAtomStyle(PyMOLGlobals*, const SeleCoordIterator&)’: layer1/Setting.h:421:11: warning: ‘out’ may be used uninitialized in this function [-Wmaybe-uninitialized] int i = *out; ^~~~ In file included from layer3/MaeExportHelpers.h:11, from layer3/MaeExportHelpers.cpp:11: layer2/AtomInfo.h:500:5: note: ‘out’ was declared here V out; ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/MoleculeExporter.cpp -o build/temp.linux-x86_64-3.6/layer3/MoleculeExporter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/MovieScene.cpp -o build/temp.linux-x86_64-3.6/layer3/MovieScene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/PlugIOManager.cpp -o build/temp.linux-x86_64-3.6/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/PlugIOManager.cpp: In function ‘ObjectMap* PlugIOManagerLoadVol(PyMOLGlobals*, ObjectMap*, const char*, int, int, const char*)’: layer3/PlugIOManager.cpp:403:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(obj->State.size() <= state) { ~~~~~~~~~~~~~~~~~~^~~~~~~~ layer3/PlugIOManager.cpp: In function ‘CObject* PlugIOManagerLoad(PyMOLGlobals*, CObject**, const char*, int, int, const char*, int)’: layer3/PlugIOManager.cpp:939:9: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 200 [-Wformat-truncation=] " PlugIOManagerLoad: can't load trajectory into object '%s'\n", obj->Name ENDFB(G); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer3/PlugIOManager.cpp:20: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 58 and 313 bytes into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/RingFinder.cpp -o build/temp.linux-x86_64-3.6/layer3/RingFinder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/RingFinder.cpp: In member function ‘void AbstractRingFinder::recursion(int, int)’: layer3/RingFinder.cpp:24:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] } else if (depth < m_indices.size() - 1) { ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Seeker.cpp -o build/temp.linux-x86_64-3.6/layer3/Seeker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: layer3/Seeker.cpp:1207:23: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(row->len < min_pad) { ~~~~~~~~~^~~~~~~~~ layer3/Seeker.cpp:1243:23: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(row->len < min_pad) { ~~~~~~~~~^~~~~~~~~ layer3/Seeker.cpp: In lambda function: layer3/Seeker.cpp:1305:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for(int i = 0; i < str_size; i++){ ~~^~~~~~~~~~ layer3/Seeker.cpp: In function ‘void SeekerUpdate(PyMOLGlobals*)’: layer3/Seeker.cpp:1989:27: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] if(row->ext_len < stop) ~~~~~~~~~~~~~^~~~~~ layer3/Seeker.cpp: In function ‘void SeekerSelectionToggle(PyMOLGlobals*, CSeqRow*, int, int, int, int)’: layer3/Seeker.cpp:232:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer3/Seeker.cpp:20: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 28 and 1308 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Seeker.cpp: In function ‘void SeekerSelectionToggleRange(PyMOLGlobals*, CSeqRow*, int, int, int, int, int)’: layer3/Seeker.cpp:148:27: warning: ‘%s’ directive writing up to 1023 bytes into a region of size between 752 and 1009 [-Wformat-overflow=] sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ buf1); ~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/malloc.h:24, from layer0/os_predef.h:86, from layer0/os_python.h:21, from layer3/Seeker.cpp:20: /usr/include/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 28 and 1308 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/Selector.cpp -o build/temp.linux-x86_64-3.6/layer3/Selector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer3/Selector.cpp: In member function ‘virtual bool SelectorAtomIterator::next()’: layer3/Selector.cpp:212:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] if ((++a) >= selector->Table.size()) ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘bool SelectorIsSelectionDiscrete(PyMOLGlobals*, SelectorID_t, bool)’: layer3/Selector.cpp:1055:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorClassifyAtoms(PyMOLGlobals*, int, int, ObjectMolecule*)’: layer3/Selector.cpp:1184:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(a < I->Table.size()) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:1208:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(a1 < I->Table.size()) { ~~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘const char* SelectorGetNameFromIndex(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:1625:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 1; a < I->Info.size(); a++) { ~~^~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: layer3/Selector.cpp:1760:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:1788:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(a1 < I->Table.size()) { ~~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:1982:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘PyObject* SelectorColorectionGet(PyMOLGlobals*, const char*)’: layer3/Selector.cpp:2795:18: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(b = 0; b < n_used; b++) { ~~^~~~~~~~ layer3/Selector.cpp:2811:16: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(a = 0; a < n_used; a++) { ~~^~~~~~~~ layer3/Selector.cpp:2823:18: warning: comparison of integer expressions of different signedness: ‘ov_size’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] for(b = 0; b < n_used; b++) { ~~^~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorColorectionApply(PyMOLGlobals*, PyObject*, const char*)’: layer3/Selector.cpp:2871:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] for(b = 0; b < n_used; b++) { /* update selection indices */ ~~^~~~~~~~ layer3/Selector.cpp:2876:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:2880:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ov_size’ {aka ‘long unsigned int’} [-Wsign-compare] for(b = 0; b < n_used; b++) { ~~^~~~~~~~ layer3/Selector.cpp: In function ‘PyObject* SelectorSecretsAsPyList(PyMOLGlobals*)’: layer3/Selector.cpp:2981:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = 0; a < I->Info.size(); a++) { ~~^~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘PyObject* SelectorAsPyList(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3060:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCountStates(PyMOLGlobals*, int)’: layer3/Selector.cpp:3554:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCheckIntersection(PyMOLGlobals*, int, int)’: layer3/Selector.cpp:3578:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCountAtoms(PyMOLGlobals*, int, int)’: layer3/Selector.cpp:3596:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘void SelectorSetDeleteFlagOnSelectionInObject(PyMOLGlobals*, int, ObjectMolecule*, signed char)’: layer3/Selector.cpp:3611:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int* SelectorGetIndexVLAImpl(PyMOLGlobals*, CSelector*, SelectorID_t)’: layer3/Selector.cpp:3697:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘void SelectorLogSele(PyMOLGlobals*, const char*)’: layer3/Selector.cpp:3757:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetSingleObjectMolecule(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3922:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘ObjectMolecule* SelectorGetFirstObjectMolecule(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3952:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘ObjectMolecule** SelectorGetObjectMoleculeVLA(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:3976:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSubdivide(PyMOLGlobals*, const char*, SelectorID_t, SelectorID_t, SelectorID_t, SelectorID_t, const char*, const char*, int*)’: layer3/Selector.cpp:4434:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorGetSeleNCSet(PyMOLGlobals*, SelectorID_t)’: layer3/Selector.cpp:4800:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorGetArrayNCSet(PyMOLGlobals*, const sele_array_t&, int)’: layer3/Selector.cpp:4830:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = start; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorMapMaskVDW(PyMOLGlobals*, int, ObjectMapState*, float, int)’: layer3/Selector.cpp:4991:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorMapGaussian(PyMOLGlobals*, int, ObjectMapState*, float, int, int, int, int, float)’: layer3/Selector.cpp:5348:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:5392:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorMapCoulomb(PyMOLGlobals*, int, ObjectMapState*, float, int, int, int, float)’: layer3/Selector.cpp:5600:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorCreateObjectMolecule(PyMOLGlobals*, SelectorID_t, const char*, int, int, int, int, int, int, int)’: layer3/Selector.cpp:6288:3: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ob) ^~ layer3/Selector.cpp:6292:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ SelectorUpdateTable(G, source, -1); ^~~~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6303:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In lambda function: layer3/Selector.cpp:6329:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6359:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyModels; a < I->Obj.size(); a++) { /* find bonds wholly contained in the selection */ ~~^~~~~~~~~~~~~~~ layer3/Selector.cpp:6385:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:6452:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) /* any selected atoms in this state? */ ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorEmbedSelection(PyMOLGlobals*, const int*, pymol::zstring_view, ObjectMolecule*, int, int)’: layer3/Selector.cpp:6892:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = start; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘sele_array_t SelectorSelectFromTagDict(PyMOLGlobals*, const std::unordered_map&)’: layer3/Selector.cpp:6987:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(int a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorModulate1(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:7548:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7570:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; ok && a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7613:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; ok && a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7642:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7679:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; ok && a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7720:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSelect0(PyMOLGlobals*, EvalElem*)’: layer3/Selector.cpp:7753:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7765:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7770:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7777:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7781:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7785:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7789:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7793:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7802:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7819:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7824:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7829:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7834:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7839:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7844:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7849:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7853:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7857:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7862:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7867:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7874:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7890:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7896:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7905:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7917:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:7938:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘pymol::Result<> SelectorSelect1(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:8643:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyModels; a < I->Obj.size(); a++) ~~^~~~~~~~~~~~~~~ layer3/Selector.cpp:8653:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] else if(model > I->Obj.size()) ~~~~~~^~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSelect2(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:8735:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8739:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8787:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8798:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8809:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8820:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8835:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8846:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8857:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8868:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8883:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8894:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8905:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:8916:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorSelect3(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:8948:1: warning: label ‘ok_except1’ defined but not used [-Wunused-label] ok_except1: ^~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorLogic1(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:9415:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:9446:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorOperator22(PyMOLGlobals*, EvalElem*, int)’: layer3/Selector.cpp:9707:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] for(a = 0; a < table_size; a++) { ~~^~~~~~~~~~~~ layer3/Selector.cpp:9729:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:9759:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = 0; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:9764:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘pymol::Result > SelectorEvaluate(PyMOLGlobals*, std::vector >&, int, int)’: layer3/Selector.cpp:9913:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] while(ok && c < word.size()) { ~~^~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘DistSet* SelectorGetDistSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, float, float*)’: layer3/Selector.cpp:10503:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘DistSet* SelectorGetAngleSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, float*, int*)’: layer3/Selector.cpp:10786:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:10799:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:10827:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘DistSet* SelectorGetDihedralSet(PyMOLGlobals*, DistSet*, int, int, int, int, int, int, int, int, int, float*, int*)’: layer3/Selector.cpp:11032:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:11084:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp:11130:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] for(a = cNDummyAtoms; a < I->Table.size(); a++) { ~~^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: At global scope: layer3/Selector.cpp:173:13: warning: ‘void SelectorCleanImpl(PyMOLGlobals*, CSelector*)’ declared ‘static’ but never defined [-Wunused-function] static void SelectorCleanImpl(PyMOLGlobals * G, CSelector *I); ^~~~~~~~~~~~~~~~~ layer3/Selector.cpp: In function ‘int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)’: layer3/Selector.cpp:1830:21: warning: ‘%s’ directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/c++/8/cstdio:42, from /usr/include/c++/8/ext/string_conversions.h:43, from /usr/include/c++/8/bits/basic_string.h:6400, from /usr/include/c++/8/string:52, from /usr/include/c++/8/stdexcept:39, from /usr/include/c++/8/array:39, from /usr/include/c++/8/tuple:39, from /usr/include/c++/8/functional:54, from layer3/Selector.cpp:19: /usr/include/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output 59 or more bytes (assuming 314) into a destination of size 255 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer3/SelectorTmp.cpp -o build/temp.linux-x86_64-3.6/layer3/SelectorTmp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer4/Cmd.cpp -o build/temp.linux-x86_64-3.6/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer4/Cmd.cpp: In function ‘PyObject* CmdPushUndo(PyObject*, PyObject*)’: layer4/Cmd.cpp:2339:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if(ok) ^~ layer4/Cmd.cpp:2341:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ if(s0[0]) ^~ layer4/Cmd.cpp: In function ‘PyObject* Cmd_New(PyObject*, PyObject*)’: layer4/Cmd.cpp:3599:11: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] int ok = true; ^~ layer4/Cmd.cpp: In function ‘PyObject* CmdGetMinMax(PyObject*, PyObject*)’: layer4/Cmd.cpp:4648:7: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] int ok = false; ^~ In file included from layer4/Cmd.cpp:74: layer1/PConv.h: In instantiation of ‘PyObject* PConvToPyObject(const std::array<_Tp, _Nm>&) [with T = float; long unsigned int N = 3; PyObject = _object]’: layer4/Cmd.cpp:377:27: required from ‘PyObject* APIResult(PyMOLGlobals*, pymol::Result&) [with T = std::array; PyObject = _object; PyMOLGlobals = _PyMOLGlobals]’ layer4/Cmd.cpp:4212:29: required from here layer1/PConv.h:248:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] for (int i = 0; i < N; ++i) { ~~^~~ layer4/Cmd.cpp: In function ‘PyObject* CmdLoadTraj(PyObject*, PyObject*)’: layer4/Cmd.cpp:5883:9: warning: ‘%s’ directive output may be truncated writing up to 1023 bytes into a region of size 255 [-Wformat-truncation=] "%s", buf ENDFB(G); ^~~~ ~~~ In file included from layer1/Ortho.h:32, from layer1/ButMode.h:20, from layer4/Cmd.cpp:56: layer0/Feedback.h:274:15: note: ‘snprintf’ output between 1 and 1024 bytes into a destination of size 255 (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, ^ layer4/Cmd.cpp:5882:7: note: in expansion of macro ‘PRINTFB’ PRINTFB(G, FB_Executive, FB_Actions) ^~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer4/Menu.cpp -o build/temp.linux-x86_64-3.6/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer4/PopUp.cpp -o build/temp.linux-x86_64-3.6/layer4/PopUp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from layer0/OOMac.h:22, from layer4/PopUp.cpp:23: layer4/PopUp.cpp: In function ‘void PopUpFree(Block*)’: layer4/PopUp.cpp:390:11: warning: deleting object of polymorphic class type ‘CPopUp’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(I); ^ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer5/PyMOL.cpp -o build/temp.linux-x86_64-3.6/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer5/PyMOL.cpp: In function ‘PyMOLreturn_status Loader(CPyMOL*, const char*, const char*, int, const char*, const char*, int, int, int, int, int, int)’: layer5/PyMOL.cpp:1541:27: warning: comparison of integer expressions of different signedness: ‘long int’ and ‘long unsigned int’ [-Wsign-compare] if((stop - start) >= sizeof(WordType)) ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from layer5/PyMOL.cpp:23: layer5/PyMOL.cpp: In function ‘void PyMOL_Stop(CPyMOL*)’: layer5/PyMOL.cpp:2061:14: warning: deleting object of polymorphic class type ‘CMovie’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] DeleteP(G->Movie); ^~~~~ layer0/MemoryDebug.h:74:39: note: in definition of macro ‘DeleteP’ #define DeleteP(ptr) {if(ptr) {delete ptr;ptr=NULL;}} ^~~ layer5/PyMOL.cpp: In function ‘char* PyMOL_GetClickString(CPyMOL*, int)’: layer5/PyMOL.cpp:2717:19: warning: ‘%s’ directive writing up to 255 bytes into a region of size between 137 and 914 [-Wformat-overflow=] "type=object:molecule\nobject=%s\nindex=%d\nrank=%d\nid=%d\nsegi=%s\nchain=%s\nresn=%s\nresi=%d%s\nname=%s\nalt=%s\nclick=%s\nmod_keys=%s\nx=%d\ny=%d\n%s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer5/PyMOL.cpp:2727:70: ai->alt, butstr, modstr, I->ClickedX, I->ClickedY, posstr); ~~~~~~ layer5/PyMOL.cpp:2716:18: note: ‘sprintf’ output 112 or more bytes (assuming 1144) into a destination of size 1025 sprintf(result, ~~~~~~~^~~~~~~~ "type=object:molecule\nobject=%s\nindex=%d\nrank=%d\nid=%d\nsegi=%s\nchain=%s\nresn=%s\nresi=%d%s\nname=%s\nalt=%s\nclick=%s\nmod_keys=%s\nx=%d\ny=%d\n%s", ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ I->ClickedObject, ~~~~~~~~~~~~~~~~~ I->ClickedIndex + 1, ~~~~~~~~~~~~~~~~~~~~ ai->rank, ~~~~~~~~~ ai->id, ~~~~~~~ LexStr(I->G, ai->segi), ~~~~~~~~~~~~~~~~~~~~~~~ LexStr(I->G, ai->chain), ~~~~~~~~~~~~~~~~~~~~~~~~ LexStr(I->G, ai->resn), ~~~~~~~~~~~~~~~~~~~~~~~ ai->resv, inscode_str, ~~~~~~~~~~~~~~~~~~~~~~ LexStr(I->G, ai->name), ~~~~~~~~~~~~~~~~~~~~~~~ ai->alt, butstr, modstr, I->ClickedX, I->ClickedY, posstr); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer5/TestPyMOL.cpp -o build/temp.linux-x86_64-3.6/layer5/TestPyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD layer5/main.cpp -o build/temp.linux-x86_64-3.6/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 layer5/main.cpp: In function ‘int MainCreateWindow(const char*)’: layer5/main.cpp:882:24: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] hint->res_name = "pymol"; ^~~~~~~ layer5/main.cpp:883:25: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] hint->res_class = "Pymol"; ^~~~~~~ layer5/main.cpp: In function ‘void launch(CPyMOLOptions*, int)’: layer5/main.cpp:1330:31: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings] char *myArgv[8] = {"pymol"}; ^ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-x86_64-3.6/modules/cealign/src/ccealignmodule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 In file included from modules/cealign/src/tnt/tnt.h:49, from modules/cealign/src/ccealignmodule.cpp:38: modules/cealign/src/tnt/tnt_array2d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Array2D&)’: modules/cealign/src/tnt/tnt_array2d_utils.h:62:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=0; i>(std::istream&, TNT::Array3D&)’: modules/cealign/src/tnt/tnt_array3d_utils.h:47:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=0; i>(std::istream&, TNT::Fortran_Array2D&)’: modules/cealign/src/tnt/tnt_fortran_array2d_utils.h:61:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=1; i<=M; i++) ^~~ modules/cealign/src/tnt/tnt_fortran_array2d_utils.h:67:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ A = B; ^ In file included from modules/cealign/src/tnt/tnt.h:57, from modules/cealign/src/ccealignmodule.cpp:38: modules/cealign/src/tnt/tnt_fortran_array3d_utils.h: In function ‘std::istream& TNT::operator>>(std::istream&, TNT::Fortran_Array3D&)’: modules/cealign/src/tnt/tnt_fortran_array3d_utils.h:65:5: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] for (int i=1; i<=M; i++) ^~~ modules/cealign/src/tnt/tnt_fortran_array3d_utils.h:70:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ A = B; ^ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVContext.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 ov/src/OVContext.cpp: In function ‘void OVContext_Del(OVContext*)’: ov/src/OVContext.cpp:21:13: warning: variable ‘heap’ set but not used [-Wunused-but-set-variable] OVHeap *heap = I->heap; ^~~~ g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVHeap.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVHeap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVHeapArray.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVHeapArray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVLexicon.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVLexicon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVOneToAny.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVOneToAny.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVOneToOne.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVOneToOne.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/OVRandom.cpp -o build/temp.linux-x86_64-3.6/ov/src/OVRandom.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -DMMTF_MSGPACK_USE_CPP11 -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -Icontrib/mmtf-c -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.6m -c -MMD ov/src/ov_utility.cpp -o build/temp.linux-x86_64-3.6/ov/src/ov_utility.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O2 g++ -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.6/build/generated/ShaderText.o build/temp.linux-x86_64-3.6/contrib/mmtf-c/mmtf_parser.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/hash.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/inthash.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o build/temp.linux-x86_64-3.6/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o build/temp.linux-x86_64-3.6/layer0/Block.o build/temp.linux-x86_64-3.6/layer0/Crystal.o build/temp.linux-x86_64-3.6/layer0/Deferred.o build/temp.linux-x86_64-3.6/layer0/Err.o build/temp.linux-x86_64-3.6/layer0/Feedback.o build/temp.linux-x86_64-3.6/layer0/Field.o build/temp.linux-x86_64-3.6/layer0/File.o build/temp.linux-x86_64-3.6/layer0/GenericBuffer.o build/temp.linux-x86_64-3.6/layer0/GraphicsUtil.o build/temp.linux-x86_64-3.6/layer0/Isosurf.o build/temp.linux-x86_64-3.6/layer0/Map.o build/temp.linux-x86_64-3.6/layer0/Match.o build/temp.linux-x86_64-3.6/layer0/Matrix.o build/temp.linux-x86_64-3.6/layer0/MemoryDebug.o build/temp.linux-x86_64-3.6/layer0/MyPNG.o build/temp.linux-x86_64-3.6/layer0/Parse.o build/temp.linux-x86_64-3.6/layer0/Pixmap.o build/temp.linux-x86_64-3.6/layer0/PostProcess.o build/temp.linux-x86_64-3.6/layer0/ShaderMgr.o build/temp.linux-x86_64-3.6/layer0/ShaderPrg.o build/temp.linux-x86_64-3.6/layer0/Sphere.o build/temp.linux-x86_64-3.6/layer0/Tetsurf.o build/temp.linux-x86_64-3.6/layer0/Texture.o build/temp.linux-x86_64-3.6/layer0/Tracker.o build/temp.linux-x86_64-3.6/layer0/Triangle.o build/temp.linux-x86_64-3.6/layer0/Util.o build/temp.linux-x86_64-3.6/layer0/Util2.o build/temp.linux-x86_64-3.6/layer0/Vector.o build/temp.linux-x86_64-3.6/layer0/Word.o build/temp.linux-x86_64-3.6/layer0/os_gl.o build/temp.linux-x86_64-3.6/layer1/Basis.o build/temp.linux-x86_64-3.6/layer1/ButMode.o build/temp.linux-x86_64-3.6/layer1/CGO.o build/temp.linux-x86_64-3.6/layer1/COLLADA.o build/temp.linux-x86_64-3.6/layer1/Character.o build/temp.linux-x86_64-3.6/layer1/Color.o build/temp.linux-x86_64-3.6/layer1/Control.o build/temp.linux-x86_64-3.6/layer1/Extrude.o build/temp.linux-x86_64-3.6/layer1/Font.o build/temp.linux-x86_64-3.6/layer1/FontGLUT.o build/temp.linux-x86_64-3.6/layer1/FontGLUT8x13.o build/temp.linux-x86_64-3.6/layer1/FontGLUT9x15.o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel10.o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel12.o build/temp.linux-x86_64-3.6/layer1/FontGLUTHel18.o build/temp.linux-x86_64-3.6/layer1/FontType.o build/temp.linux-x86_64-3.6/layer1/Movie.o build/temp.linux-x86_64-3.6/layer1/Ortho.o build/temp.linux-x86_64-3.6/layer1/P.o build/temp.linux-x86_64-3.6/layer1/PConv.o build/temp.linux-x86_64-3.6/layer1/Picking.o build/temp.linux-x86_64-3.6/layer1/Pop.o build/temp.linux-x86_64-3.6/layer1/PyMOLObject.o build/temp.linux-x86_64-3.6/layer1/Ray.o build/temp.linux-x86_64-3.6/layer1/Rep.o build/temp.linux-x86_64-3.6/layer1/Scene.o build/temp.linux-x86_64-3.6/layer1/ScenePicking.o build/temp.linux-x86_64-3.6/layer1/SceneRay.o build/temp.linux-x86_64-3.6/layer1/SceneRender.o build/temp.linux-x86_64-3.6/layer1/ScrollBar.o build/temp.linux-x86_64-3.6/layer1/Seq.o build/temp.linux-x86_64-3.6/layer1/Setting.o build/temp.linux-x86_64-3.6/layer1/Shaker.o build/temp.linux-x86_64-3.6/layer1/Symmetry.o build/temp.linux-x86_64-3.6/layer1/Text.o build/temp.linux-x86_64-3.6/layer1/TypeFace.o build/temp.linux-x86_64-3.6/layer1/View.o build/temp.linux-x86_64-3.6/layer1/Wizard.o build/temp.linux-x86_64-3.6/layer2/AssemblyHelpers.o build/temp.linux-x86_64-3.6/layer2/AtomInfo.o build/temp.linux-x86_64-3.6/layer2/AtomInfoHistory.o build/temp.linux-x86_64-3.6/layer2/BondTypeHistory.o build/temp.linux-x86_64-3.6/layer2/CifFile.o build/temp.linux-x86_64-3.6/layer2/CifMoleculeReader.o build/temp.linux-x86_64-3.6/layer2/CoordSet.o build/temp.linux-x86_64-3.6/layer2/DistSet.o build/temp.linux-x86_64-3.6/layer2/GadgetSet.o build/temp.linux-x86_64-3.6/layer2/HydrogenAdder.o build/temp.linux-x86_64-3.6/layer2/MmodTyping.o build/temp.linux-x86_64-3.6/layer2/MmtfMoleculeReader.o build/temp.linux-x86_64-3.6/layer2/Mol2Typing.o build/temp.linux-x86_64-3.6/layer2/MolV3000.o build/temp.linux-x86_64-3.6/layer2/ObjectAlignment.o build/temp.linux-x86_64-3.6/layer2/ObjectCGO.o build/temp.linux-x86_64-3.6/layer2/ObjectCallback.o build/temp.linux-x86_64-3.6/layer2/ObjectDist.o build/temp.linux-x86_64-3.6/layer2/ObjectGadget.o build/temp.linux-x86_64-3.6/layer2/ObjectGadgetRamp.o build/temp.linux-x86_64-3.6/layer2/ObjectGroup.o build/temp.linux-x86_64-3.6/layer2/ObjectMap.o build/temp.linux-x86_64-3.6/layer2/ObjectMesh.o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule.o build/temp.linux-x86_64-3.6/layer2/ObjectMolecule2.o build/temp.linux-x86_64-3.6/layer2/ObjectSlice.o build/temp.linux-x86_64-3.6/layer2/ObjectSurface.o build/temp.linux-x86_64-3.6/layer2/ObjectVolume.o build/temp.linux-x86_64-3.6/layer2/RepAngle.o build/temp.linux-x86_64-3.6/layer2/RepCartoon.o build/temp.linux-x86_64-3.6/layer2/RepCylBond.o build/temp.linux-x86_64-3.6/layer2/RepDihedral.o build/temp.linux-x86_64-3.6/layer2/RepDistDash.o build/temp.linux-x86_64-3.6/layer2/RepDistLabel.o build/temp.linux-x86_64-3.6/layer2/RepDot.o build/temp.linux-x86_64-3.6/layer2/RepEllipsoid.o build/temp.linux-x86_64-3.6/layer2/RepLabel.o build/temp.linux-x86_64-3.6/layer2/RepMesh.o build/temp.linux-x86_64-3.6/layer2/RepNonbonded.o build/temp.linux-x86_64-3.6/layer2/RepNonbondedSphere.o build/temp.linux-x86_64-3.6/layer2/RepRibbon.o build/temp.linux-x86_64-3.6/layer2/RepSphere.o build/temp.linux-x86_64-3.6/layer2/RepSphereGenerate.o build/temp.linux-x86_64-3.6/layer2/RepSphereImmediate.o build/temp.linux-x86_64-3.6/layer2/RepSurface.o build/temp.linux-x86_64-3.6/layer2/RepWireBond.o build/temp.linux-x86_64-3.6/layer2/Sculpt.o build/temp.linux-x86_64-3.6/layer2/SculptCache.o build/temp.linux-x86_64-3.6/layer2/SideChainHelper.o build/temp.linux-x86_64-3.6/layer2/VFont.o build/temp.linux-x86_64-3.6/layer3/AtomIterators.o build/temp.linux-x86_64-3.6/layer3/CifDataValueFormatter.o build/temp.linux-x86_64-3.6/layer3/Editor.o build/temp.linux-x86_64-3.6/layer3/Executive.o build/temp.linux-x86_64-3.6/layer3/ExecutivePython.o build/temp.linux-x86_64-3.6/layer3/MaeExportHelpers.o build/temp.linux-x86_64-3.6/layer3/MoleculeExporter.o build/temp.linux-x86_64-3.6/layer3/MovieScene.o build/temp.linux-x86_64-3.6/layer3/PlugIOManager.o build/temp.linux-x86_64-3.6/layer3/RingFinder.o build/temp.linux-x86_64-3.6/layer3/Seeker.o build/temp.linux-x86_64-3.6/layer3/Selector.o build/temp.linux-x86_64-3.6/layer3/SelectorTmp.o build/temp.linux-x86_64-3.6/layer4/Cmd.o build/temp.linux-x86_64-3.6/layer4/Menu.o build/temp.linux-x86_64-3.6/layer4/PopUp.o build/temp.linux-x86_64-3.6/layer5/PyMOL.o build/temp.linux-x86_64-3.6/layer5/TestPyMOL.o build/temp.linux-x86_64-3.6/layer5/main.o build/temp.linux-x86_64-3.6/modules/cealign/src/ccealignmodule.o build/temp.linux-x86_64-3.6/ov/src/OVContext.o build/temp.linux-x86_64-3.6/ov/src/OVHeap.o build/temp.linux-x86_64-3.6/ov/src/OVHeapArray.o build/temp.linux-x86_64-3.6/ov/src/OVLexicon.o build/temp.linux-x86_64-3.6/ov/src/OVOneToAny.o build/temp.linux-x86_64-3.6/ov/src/OVOneToOne.o build/temp.linux-x86_64-3.6/ov/src/OVRandom.o build/temp.linux-x86_64-3.6/ov/src/ov_utility.o -L/usr/lib64 -L/usr/lib -L/usr/lib64 -lpng -lfreetype -lxml2 -lGL -lGLEW -lglut -lnetcdf -lpython3.6m -o build/lib.linux-x86_64-3.6/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so building 'chempy.champ._champ' extension creating build/temp.linux-x86_64-3.6/contrib/champ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/champ.c -o build/temp.linux-x86_64-3.6/contrib/champ/champ.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/chiral.c -o build/temp.linux-x86_64-3.6/contrib/champ/chiral.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/err2.c -o build/temp.linux-x86_64-3.6/contrib/champ/err2.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/feedback2.c -o build/temp.linux-x86_64-3.6/contrib/champ/feedback2.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/list.c -o build/temp.linux-x86_64-3.6/contrib/champ/list.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/os_memory.c -o build/temp.linux-x86_64-3.6/contrib/champ/os_memory.o contrib/champ/os_memory.c: In function ‘OSMemoryZero’: contrib/champ/os_memory.c:55:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] while(count&&(((int)p)&mask)) { ^ contrib/champ/os_memory.c: In function ‘OSMemoryHashAdd’: contrib/champ/os_memory.c:137:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] hash=(int)rec; ^ contrib/champ/os_memory.c: In function ‘OSMemoryHashRemove’: contrib/champ/os_memory.c:150:8: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] hash=(int)rec; ^ gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/sort.c -o build/temp.linux-x86_64-3.6/contrib/champ/sort.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/strblock.c -o build/temp.linux-x86_64-3.6/contrib/champ/strblock.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/vla.c -o build/temp.linux-x86_64-3.6/contrib/champ/vla.o gcc -pthread -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -Icontrib/champ -I/usr/include/python3.6m -c -MMD contrib/champ/champ_module.c -o build/temp.linux-x86_64-3.6/contrib/champ/champ_module.o gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection build/temp.linux-x86_64-3.6/contrib/champ/champ.o build/temp.linux-x86_64-3.6/contrib/champ/champ_module.o build/temp.linux-x86_64-3.6/contrib/champ/chiral.o build/temp.linux-x86_64-3.6/contrib/champ/err2.o build/temp.linux-x86_64-3.6/contrib/champ/feedback2.o build/temp.linux-x86_64-3.6/contrib/champ/list.o build/temp.linux-x86_64-3.6/contrib/champ/os_memory.o build/temp.linux-x86_64-3.6/contrib/champ/sort.o build/temp.linux-x86_64-3.6/contrib/champ/strblock.o build/temp.linux-x86_64-3.6/contrib/champ/vla.o -L/usr/lib64 -lpython3.6m -o build/lib.linux-x86_64-3.6/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so + sleep 1 + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.WlAhnr + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 ++ dirname /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 + cd pymol-open-source-2.4.0 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection' + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + /usr/bin/python3.6 setup.py install -O1 --skip-build --root /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 --use-msgpackc=c++11 --glut --pymol-path=/usr/lib64/python3.6/site-packages/pymol running install running install_lib creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64 creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6 creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/commands.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/realtime.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/state.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin copying build/lib.linux-x86_64-3.6/chempy/bmin/util.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/amber99.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/assign.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ copying build/lib.linux-x86_64-3.6/chempy/champ/formal_charges.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fast copying build/lib.linux-x86_64-3.6/chempy/fast/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fast creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments copying build/lib.linux-x86_64-3.6/chempy/fragments/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf copying build/lib.linux-x86_64-3.6/chempy/mmtf/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf copying build/lib.linux-x86_64-3.6/chempy/mmtf/io.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/keyword.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/realtime.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/tinker/state.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker copying build/lib.linux-x86_64-3.6/chempy/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/arc.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/bond_amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/bond_mmff.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/bonds.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/brick.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/cc1.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/charge.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/cif.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/cpv.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/dictdb.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/gamess1.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/gms.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/hetatm.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/io.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/lst.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mae.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/map.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mass.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mmd.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/models.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mol.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/mol2.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/neighbor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/pdb.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/pkl.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/place.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_amber99.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_mmff.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/protein_residues.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/sdf.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/solvate.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/water_amber.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/water_residues.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy copying build/lib.linux-x86_64-3.6/chempy/xyz.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/askpartial.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/colors.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/fetch.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_aln.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_mae.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_map.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_mtz.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/load_traj.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/movieexport.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/pluginitem.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/pluginmanager.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/png.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/props.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/render.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/save_molecule.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/save_object.ui -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms copying build/lib.linux-x86_64-3.6/pmg_qt/forms/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/pml.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/pmlparser.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/syntax/python.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax copying build/lib.linux-x86_64-3.6/pmg_qt/TextEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/advanced_settings_gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/builder.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/file_dialogs.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/keymapping.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/mimic_pmg_tk.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/mimic_tk.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/properties_dialog.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/pymol_gl_widget.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/pymol_qt_gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt copying build/lib.linux-x86_64-3.6/pmg_qt/volume.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo copying build/lib.linux-x86_64-3.6/pmg_tk/skins/demo/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/normal/ModalWindow.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/normal/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/normal/builder.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal copying build/lib.linux-x86_64-3.6/pmg_tk/skins/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup copying build/lib.linux-x86_64-3.6/pmg_tk/startup/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup copying build/lib.linux-x86_64-3.6/pmg_tk/startup/apbs_tools.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup copying build/lib.linux-x86_64-3.6/pmg_tk/ColorEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/Demo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/PyMOLMapLoad.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/SetEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/Setting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/TextEditor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/volume.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk copying build/lib.linux-x86_64-3.6/pmg_tk/PMGApp.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt copying build/lib.linux-x86_64-3.6/pymol/Qt/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt copying build/lib.linux-x86_64-3.6/pymol/Qt/utils.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/contrib copying build/lib.linux-x86_64-3.6/pymol/contrib/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/contrib creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/gl copying build/lib.linux-x86_64-3.6/pymol/opengl/gl/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/gl creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glu copying build/lib.linux-x86_64-3.6/pymol/opengl/glu/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glu creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glut copying build/lib.linux-x86_64-3.6/pymol/opengl/glut/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glut copying build/lib.linux-x86_64-3.6/pymol/opengl/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/installation.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/legacysupport.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/managergui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/managergui_qt.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins copying build/lib.linux-x86_64-3.6/pymol/plugins/repository.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry copying build/lib.linux-x86_64-3.6/pymol/stereochemistry/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/annotation.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/appearance.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/benchmark.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/box.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/charge.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/cleanup.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/command.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/demo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/density.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/distance.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/dragging.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/fedora.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/filter.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/label.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/measurement.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/message.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/mutagenesis.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/nucmutagenesis.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/openvr.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/pair_fit.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/pseudoatom.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/renaming.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/sculpting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/security.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/stereodemo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/wizard/toggle.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard copying build/lib.linux-x86_64-3.6/pymol/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/__main__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/_gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/api.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/callback.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/cgo.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/checking.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/cmd.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/colorprinting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/colorramping.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/commanding.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/completing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/computing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/constants.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/constants_palette.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/controlling.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/creating.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/diagnosing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/editing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/editor.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/experimenting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/exporting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/externing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/feedingback.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/fitting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/gui.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/headering.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/helping.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/importing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/internal.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/invocation.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/keyboard.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/keywords.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/lazyio.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/locking.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/menu.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/monitoring.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/morphing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/movie.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/moving.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/parser.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/parsing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/povray.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/preset.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/pymolhttpd.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/querying.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/rpc.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/selecting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/selector.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/seqalign.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/setting.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/shortcut.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/util.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/vfont.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/viewing.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/wizarding.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/xray.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying build/lib.linux-x86_64-3.6/pymol/xwin.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2 copying build/lib.linux-x86_64-3.6/pymol2/__init__.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2 copying build/lib.linux-x86_64-3.6/pymol2/cmd2.py -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2 byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/commands.py to commands.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/realtime.py to realtime.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/state.py to state.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bmin/util.py to util.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/amber99.py to amber99.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/assign.py to assign.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/formal_charges.py to formal_charges.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fast/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/fragments/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmtf/io.py to io.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/amber.py to amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/keyword.py to keyword.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/realtime.py to realtime.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/tinker/state.py to state.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/arc.py to arc.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bond_amber.py to bond_amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bond_mmff.py to bond_mmff.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/bonds.py to bonds.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/brick.py to brick.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/cc1.py to cc1.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/charge.py to charge.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/cif.py to cif.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/cpv.py to cpv.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/dictdb.py to dictdb.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/gamess1.py to gamess1.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/gms.py to gms.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/hetatm.py to hetatm.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/io.py to io.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/lst.py to lst.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mae.py to mae.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/map.py to map.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mass.py to mass.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mmd.py to mmd.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/models.py to models.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mol.py to mol.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/mol2.py to mol2.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/neighbor.py to neighbor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/pdb.py to pdb.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/pkl.py to pkl.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/place.py to place.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein.py to protein.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_amber.py to protein_amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_amber99.py to protein_amber99.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_mmff.py to protein_mmff.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/protein_residues.py to protein_residues.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/sdf.py to sdf.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/solvate.py to solvate.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/water_amber.py to water_amber.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/water_residues.py to water_residues.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/xyz.py to xyz.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/forms/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/pml.py to pml.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/pmlparser.py to pmlparser.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/syntax/python.py to python.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/TextEditor.py to TextEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/advanced_settings_gui.py to advanced_settings_gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/builder.py to builder.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/file_dialogs.py to file_dialogs.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/keymapping.py to keymapping.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/mimic_pmg_tk.py to mimic_pmg_tk.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/mimic_tk.py to mimic_tk.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/properties_dialog.py to properties_dialog.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/pymol_gl_widget.py to pymol_gl_widget.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/pymol_qt_gui.py to pymol_qt_gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_qt/volume.py to volume.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/demo/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal/ModalWindow.py to ModalWindow.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/normal/builder.py to builder.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/skins/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/startup/apbs_tools.py to apbs_tools.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/ColorEditor.py to ColorEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/Demo.py to Demo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/PyMOLMapLoad.py to PyMOLMapLoad.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/SetEditor.py to SetEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/Setting.py to Setting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/TextEditor.py to TextEditor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/volume.py to volume.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pmg_tk/PMGApp.py to PMGApp.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/Qt/utils.py to utils.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/contrib/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/gl/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glu/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/glut/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/opengl/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/installation.py to installation.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/legacysupport.py to legacysupport.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/managergui.py to managergui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/managergui_qt.py to managergui_qt.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/plugins/repository.py to repository.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/stereochemistry/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/annotation.py to annotation.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/appearance.py to appearance.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/benchmark.py to benchmark.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/box.py to box.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/charge.py to charge.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/cleanup.py to cleanup.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/command.py to command.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/demo.py to demo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/density.py to density.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/distance.py to distance.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/dragging.py to dragging.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/fedora.py to fedora.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/filter.py to filter.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/label.py to label.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/measurement.py to measurement.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/message.py to message.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/mutagenesis.py to mutagenesis.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/nucmutagenesis.py to nucmutagenesis.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/openvr.py to openvr.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/pair_fit.py to pair_fit.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/pseudoatom.py to pseudoatom.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/renaming.py to renaming.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/sculpting.py to sculpting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/security.py to security.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/stereodemo.py to stereodemo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizard/toggle.py to toggle.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/__main__.py to __main__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/_gui.py to _gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/api.py to api.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/callback.py to callback.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/cgo.py to cgo.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/checking.py to checking.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/cmd.py to cmd.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/colorprinting.py to colorprinting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/colorramping.py to colorramping.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/commanding.py to commanding.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/completing.py to completing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/computing.py to computing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/constants.py to constants.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/constants_palette.py to constants_palette.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/controlling.py to controlling.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/creating.py to creating.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/diagnosing.py to diagnosing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/editing.py to editing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/editor.py to editor.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/experimenting.py to experimenting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/exporting.py to exporting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/externing.py to externing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/feedingback.py to feedingback.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/fitting.py to fitting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/gui.py to gui.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/headering.py to headering.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/helping.py to helping.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/importing.py to importing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/internal.py to internal.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/invocation.py to invocation.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/keyboard.py to keyboard.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/keywords.py to keywords.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/lazyio.py to lazyio.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/locking.py to locking.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/menu.py to menu.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/monitoring.py to monitoring.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/morphing.py to morphing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/movie.py to movie.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/moving.py to moving.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/parser.py to parser.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/parsing.py to parsing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/povray.py to povray.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/preset.py to preset.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymolhttpd.py to pymolhttpd.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/querying.py to querying.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/rpc.py to rpc.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/selecting.py to selecting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/selector.py to selector.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/seqalign.py to seqalign.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/setting.py to setting.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/shortcut.py to shortcut.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/util.py to util.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/vfont.py to vfont.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/viewing.py to viewing.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/wizarding.py to wizarding.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/xray.py to xray.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/xwin.py to xwin.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2/__init__.py to __init__.cpython-36.pyc byte-compiling /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol2/cmd2.py to cmd2.cpython-36.pyc writing byte-compilation script '/tmp/tmp8v33nx_6.py' /usr/bin/python3.6 /tmp/tmp8v33nx_6.py removing /tmp/tmp8v33nx_6.py running install_egg_info Writing /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol-2.4.0-py3.6.egg-info copying LICENSE -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol copying data -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/data copying test -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test copying examples -> /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples creating /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/bin + echo '#!/bin/sh' + echo 'export PYMOL_PATH=/usr/lib64/python3.6/site-packages/pymol' + echo 'exec /usr/bin/python3.6 /usr/lib64/python3.6/site-packages/pymol/__init__.py "$@"' + cp -a data examples test /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/ + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/link_demo.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/particle01.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/examples/devel/particle02.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B03.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B05.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/inp/B11.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/test/ref/T01.log + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/link_demo.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/particle01.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/examples/devel/particle02.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B03.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B05.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/inp/B11.py + rm -f /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/pymol_path/test/ref/T01.log + mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/bin + install -p -m 755 pymol /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/bin/ + desktop-file-install --vendor= --dir=/builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/applications /builddir/build/SOURCES/pymol.desktop + mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/pixmaps + install -p -m 644 /builddir/build/SOURCES/pymol.png /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/pixmaps/ + mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/metainfo + install -p -m 644 /builddir/build/SOURCES/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/metainfo/ + appstream-util validate-relax --nonet /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64//usr/share/metainfo/pymol.appdata.xml /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64//usr/share/metainfo/pymol.appdata.xml: GLib-GIO-Message: 14:06:15.078: Using the 'memory' GSettings backend. Your settings will not be saved or shared with other applications. OK + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 2.4.0-4.1.el8.ors --unique-debug-suffix -2.4.0-4.1.el8.ors.x86_64 --unique-debug-src-base pymol-2.4.0-4.1.el8.ors.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/pymol-open-source-2.4.0 extracting debug info from /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/chempy/champ/_champ.cpython-36m-x86_64-linux-gnu.so extracting debug info from /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6/site-packages/pymol/_cmd.cpython-36m-x86_64-linux-gnu.so /usr/lib/rpm/sepdebugcrcfix: Updated 2 CRC32s, 0 CRC32s did match. 51223 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile '' 1 Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib/debug/usr/lib64/python3.6 using /usr/libexec/platform-python Bytecompiling .py files below /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/lib64/python3.6 using /usr/libexec/platform-python + /usr/lib/rpm/brp-python-hardlink + PYTHON3=/usr/bin/python3.6 + /usr/lib/rpm/redhat/brp-mangle-shebangs *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer3/MaeExportHelpers.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer3/MaeExportHelpers.cpp is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer0/GraphicsUtil.h is executable but has no shebang, removing executable bit *** WARNING: ./usr/src/debug/pymol-2.4.0-4.1.el8.ors.x86_64/layer0/GraphicsUtil.cpp is executable but has no shebang, removing executable bit Processing files: pymol-2.4.0-4.1.el8.ors.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.F9LyI4 + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + DOCDIR=/builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr AUTHORS /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr DEVELOPERS /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr README.md /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + cp -pr ChangeLog /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/doc/pymol + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.xlsS5H + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + LICENSEDIR=/builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/licenses/pymol + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/licenses/pymol + cp -pr LICENSE /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64/usr/share/licenses/pymol + exit 0 Provides: PyMOL(x86-64) = 0:2.4.0-4.1.el8.ors application() application(pymol.desktop) metainfo() metainfo(pymol.appdata.xml) pymol = 2.4.0-4.1.el8.ors pymol(x86-64) = 2.4.0-4.1.el8.ors python3.6dist(pymol) = 2.4.0 python3dist(pymol) = 2.4.0 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /bin/csh /bin/sh /usr/bin/python3.6 libGL.so.1()(64bit) libGLEW.so.2.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libfreetype.so.6()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libglut.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.27)(64bit) libnetcdf.so.15()(64bit) libpng16.so.16()(64bit) libpng16.so.16(PNG16_0)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) libpython3.6m.so.1.0()(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.5)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.18)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libxml2.so.2()(64bit) libxml2.so.2(LIBXML2_2.4.30)(64bit) libxml2.so.2(LIBXML2_2.6.0)(64bit) libxml2.so.2(LIBXML2_2.6.3)(64bit) python(abi) = 3.6 rtld(GNU_HASH) Processing files: pymol-debugsource-2.4.0-4.1.el8.ors.x86_64 Provides: pymol-debugsource = 2.4.0-4.1.el8.ors pymol-debugsource(x86-64) = 2.4.0-4.1.el8.ors Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: pymol-debuginfo-2.4.0-4.1.el8.ors.x86_64 Provides: debuginfo(build-id) = 10490c069cc3d2ed2b634bb0482291c280b65ac6 debuginfo(build-id) = 6f4c8b18c2f4d709ad3a82130e6ac834c599c448 pymol-debuginfo = 2.4.0-4.1.el8.ors pymol-debuginfo(x86-64) = 2.4.0-4.1.el8.ors Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: pymol-debugsource(x86-64) = 2.4.0-4.1.el8.ors Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 Wrote: /builddir/build/RPMS/pymol-2.4.0-4.1.el8.ors.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debugsource-2.4.0-4.1.el8.ors.x86_64.rpm Wrote: /builddir/build/RPMS/pymol-debuginfo-2.4.0-4.1.el8.ors.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.THI2V7 + umask 022 + cd /builddir/build/BUILD + cd pymol-open-source-2.4.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/pymol-2.4.0-4.1.el8.ors.x86_64 + exit 0 Child return code was: 0