Diff of the two buildlogs: -- --- b1/build.log 2024-01-07 18:37:08.721637341 +0000 +++ b2/build.log 2024-01-07 18:43:17.059252542 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 7 06:34:40 -12 2024 -I: pbuilder-time-stamp: 1704652480 +I: Current time: Sun Feb 9 15:00:12 +14 2025 +I: pbuilder-time-stamp: 1739062812 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./pymol_2.4.0+dfsg-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.PROYxcwL/trustedkeys.kbx': General error +gpgv: keyblock resource '/tmp/dpkg-verify-sig.iQ0tyf42/trustedkeys.kbx': General error gpgv: Signature made Sat May 22 11:26:38 2021 gpgv: using RSA key 9CA877749FAB2E4FA96862ECDC686A27B43481B0 gpgv: Can't check signature: No public key @@ -38,49 +38,80 @@ dpkg-source: info: applying 40_mstop_movies.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2370122/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 9 01:00 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=12 ' - DISTRIBUTION='bullseye' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bullseye + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='ca89265e253541e1be8634502c3fb12e' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2370122' - PS1='# ' - PS2='> ' + INVOCATION_ID=62f8657b50504cc69bcdb3b6471802f8 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2462350 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6OUf2Hxo/pbuilderrc_Zv3T --distribution bullseye --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6OUf2Hxo/b1 --logfile b1/build.log pymol_2.4.0+dfsg-2.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6OUf2Hxo/pbuilderrc_396I --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6OUf2Hxo/b2 --logfile b2/build.log pymol_2.4.0+dfsg-2.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink02-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Mar 27 2022 bash @@ -140,7 +171,7 @@ -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 7 09:23 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 9 01:00 sh -> /bin/bash -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty -rwsr-xr-x 1 root root 67776 Jan 20 2022 su @@ -166,7 +197,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/2370122/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -484,7 +515,7 @@ Get: 250 http://deb.debian.org/debian bullseye/main arm64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 251 http://deb.debian.org/debian bullseye/main arm64 texlive-base all 2020.20210202-3 [20.8 MB] Get: 252 http://deb.debian.org/debian bullseye/main arm64 texlive-latex-base all 2020.20210202-3 [1120 kB] -Fetched 150 MB in 1s (128 MB/s) +Fetched 150 MB in 2s (84.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17734 files and directories currently installed.) @@ -1289,8 +1320,8 @@ Setting up tzdata (2021a-1+deb11u10) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 7 18:35:14 UTC 2024. -Universal Time is now: Sun Jan 7 18:35:14 UTC 2024. +Local time is now: Sun Feb 9 01:01:33 UTC 2025. +Universal Time is now: Sun Feb 9 01:01:33 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up xtrans-dev (1.4.0-1) ... @@ -1544,7 +1575,11 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/pymol-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pymol_2.4.0+dfsg-2_source.changes +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bullseye +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pymol-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pymol_2.4.0+dfsg-2_source.changes dpkg-buildpackage: info: source package pymol dpkg-buildpackage: info: source version 2.4.0+dfsg-2 dpkg-buildpackage: info: source distribution unstable @@ -1837,15 +1872,14 @@ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mapplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 48 | double timesteprst; | ^~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 292 | if (NULL == fgets(fbuffer, 1024, data->file)) @@ -1884,29 +1918,26 @@ 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] 59 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ -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] - 271 | 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' - 273 | 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] - 411 | 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' - 413 | return ok; - | ^~~~~~ +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] + 304 | fgets(symData, 81, fd); + | ~~~~~^~~~~~~~~~~~~~~~~ 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] 79 | fread(&dataBegin, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 69 | fread(intHeader, sizeof(int), 5, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 435 | fscanf(file, " " DBLFMT, &prm->Charges[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 82 | fread(floatHeader, sizeof(float), 6, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 444 | fscanf(file, " " DBLFMT, &prm->Masses[i]); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -1961,42 +1992,40 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 869 | &prm->Xcap, &prm->Ycap, &prm->Zcap); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 304 | fgets(symData, 81, fd); - | ~~~~~^~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:34: -In function 'strncpy', - inlined from 'read_dlpoly_config_structure' at contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:362:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 426 | fgets(buf, n, mf->f); | ~~~~~^~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 102 | fread(&headersize, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 69 | 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] - 82 | fread(floatHeader, sizeof(float), 6, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In file included from /usr/include/string.h:495, + from contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:34: In function 'strncpy', - inlined from 'read_dlpoly_structure' at contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:267:5: + inlined from 'read_dlpoly_config_structure' at contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:362:5: /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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] + 271 | 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' + 273 | 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] + 411 | 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' + 413 | return ok; + | ^~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 103 | int i, numatoms; @@ -2005,9 +2034,6 @@ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:206:55: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 206 | if (fwrite(tmp, sizeof(double), 3*n, namdbin->fd) != 3*n) { | ^~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 278 | fgets(line, LINESIZE, mdf->file); @@ -2025,16 +2051,6 @@ 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] 223 | fgets(line, LINESIZE, mdf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 545 | for (i=0; ifile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2048,30 +2064,27 @@ 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] 183 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ -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] - 1106 | char word[3][BUFSIZ]; - | ^~~~ +In function 'strncpy', + inlined from 'read_dlpoly_structure' at contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:267:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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] + 459 | 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] 1407 | int i,j,k; | ^ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 1541 | int i,j,k; | ^ -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] - 2264 | 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] - 3573 | char word[6][BUFSIZ]; - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_readline': -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:279:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 279 | for (i = 0; i < strlen(line); ++i) { - | ^ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/situsplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 1629 | fread (&len, sizeof(int), 1, fp); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2103,11 +2116,95 @@ 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] 2099 | fread (ptr, 8, 1, fp); | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_structure': +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:730:15: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] + 730 | if (len > sizeof(name)) { + | ^ +contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_timestep': +contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:1060:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 1060 | for (i=0; i<(3 * mmtk->atom_numberdim); i++) { + | ^ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_readline': +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:279:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 279 | for (i = 0; i < strlen(line); ++i) { + | ^ +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] + 160 | static int get_pte_idx_from_string(const char *label) { + | ^~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ +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] + 275 | 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] + 289 | 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] + 199 | 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] + 209 | 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] + 127 | 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] + 138 | 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] + 74 | 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] + 81 | 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] + 82 | 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] + 91 | 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] + 92 | fgets(line, LINESIZE, fd); // Read the charge_type + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 545 | for (i=0; i sizeof(name)) { - | ^ -contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_timestep': -contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:1060:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 1060 | for (i=0; i<(3 * mmtk->atom_numberdim); i++) { - | ^ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'char* recreate_command_line(int, char**)': contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1334:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1334 | line[0] = '\0'; @@ -2176,118 +2248,21 @@ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1333:26: note: at offset 0 to an object with size 0 allocated by 'malloc' here 1333 | line = (char *) malloc (sizeof(char) * len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/corplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -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] - 275 | 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] - 289 | 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] - 199 | 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] - 209 | 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] - 127 | 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] - 138 | 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] - 74 | 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] - 81 | 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] - 82 | 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] - 91 | 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] - 92 | fgets(line, LINESIZE, fd); // Read the charge_type - | ~~~~~^~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 286 | fread(datablock, total * sizeof(float), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:155: -In function 'strncpy', - inlined from 'read_gamess_structure' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:477:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 16 equals destination size [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'read_gamess_structure' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:478:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 16 equals destination size [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In function 'strncpy', - inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:615:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:620:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4096 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:621:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:622:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) | ^~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In function 'strncpy', - inlined from 'get_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -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] - 96 | 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] - 104 | 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] - 119 | 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] - 131 | 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] - 153 | 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] - 162 | 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] - 171 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/crdplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] @@ -2333,54 +2308,6 @@ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function] 95 | static const char *get_pte_label(const int idx) | ^~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -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] - 247 | 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] - 79 | 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] - 86 | 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] - 93 | 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] - 100 | 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] - 109 | fscanf(fd, " %s %f %f %f %f %f %f", keyWord, - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 110 | &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] - 123 | 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] - 128 | 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] - 135 | fscanf(fd, " %s %f", keyWord, &sigma); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] - 160 | static int get_pte_idx_from_string(const char *label) { - | ^~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In function 'strncat', - inlined from 'get_basis_options' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1422:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:136:10: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] - 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncat', - inlined from 'get_basis_options' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1411:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:136:10: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] - 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from /usr/include/string.h:495, from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:34: @@ -2405,14 +2332,62 @@ 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, - from contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:41: + from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:155: In function 'strncpy', - inlined from 'read_tinker_structure' at contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:103:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] + inlined from 'read_gamess_structure' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:477:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 16 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In function 'strncpy', + inlined from 'read_gamess_structure' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:478:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 16 equals destination size [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/offplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In function 'strncpy', + inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:615:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:620:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4096 bytes from a string of length 8191 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:621:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'read_gamess_rundata' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:622:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 96 | 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] + 104 | 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] + 119 | 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] + 131 | 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] + 153 | 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] + 162 | 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] + 171 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 175 | fgets(readbuf, 1023, cube->fd); // go on to next line @@ -2435,16 +2410,57 @@ 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] 349 | fgets(readbuf, 1023, cube->fd); // gobble up rest of line | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 360 | strncpy(tmptype, atom->type, sizeof(atom->type)); - | ^ -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: -At top level: +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] + 247 | 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] + 79 | 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] + 86 | 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] + 93 | 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] + 100 | 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] + 109 | fscanf(fd, " %s %f %f %f %f %f %f", keyWord, + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 110 | &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] + 123 | 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] + 128 | 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] + 135 | fscanf(fd, " %s %f", keyWord, &sigma); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:40: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/carplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In file included from /usr/include/string.h:495, + from contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:41: +In function 'strncpy', + inlined from 'read_tinker_structure' at contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:103:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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=] 127 | sprintf(atom->resname, "%d", resid); @@ -2459,19 +2475,34 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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] + 360 | strncpy(tmptype, atom->type, sizeof(atom->type)); + | ^ +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: +At top level: +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/inthash.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/inthash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] + 160 | static int get_pte_idx_from_string(const char *label) { + | ^~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: -contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] - 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) - | ^~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_fmoxyz' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1682:5, - inlined from 'get_input_structure' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1537:12: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: +contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': +contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'const long unsigned int'} [-Wsign-compare] + 519 | if (rc != iov[i].iov_len) + | ^~ +In function 'strncat', + inlined from 'get_basis_options' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1422:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:136:10: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] + 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncat', + inlined from 'get_basis_options' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1411:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:136:10: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] + 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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] 78 | fgets(buf, 85, file); @@ -2489,10 +2520,20 @@ 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] 275 | fgets(buf, 85, file); | ~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdheader': 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] 289 | fscanf(file, " %d", &cur); | ~~~~~~^~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 191 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:204:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 204 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:222:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 222 | if (input_integer[0] != dcdcordmagic) { + | ^~ 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] 368 | fgets(sdum, 512, file); @@ -2540,6 +2581,9 @@ 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] 451 | fscanf(file,"%8d",&prm->Numextra); //BB | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:399:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 399 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { + | ^~ 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] 79 | fscanf(file, "%s\n", buf); @@ -2550,7 +2594,40 @@ 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] 97 | fscanf(file, "%s\n", buf); | ~~~~~~^~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/hash.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:416:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 416 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdstep': +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:621:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] + 621 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:625:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] + 625 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] + 546 | 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] + 96 | 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] + 32 | 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] + 609 | 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] + 605 | 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] + 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { + | ^~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 288 | fgets(line, LINESIZE, bgf->file); @@ -2558,7 +2635,6 @@ 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] 297 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 365 | fgets(line, LINESIZE, bgf->file); @@ -2583,80 +2659,32 @@ 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] 72 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_proc_mem.isra' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1279:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 256 bytes from a string of length 8191 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_proc_mem.isra' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1272:5: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: +In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'const long unsigned int'} [-Wsign-compare] 519 | if (rc != iov[i].iov_len) | ^~ -In function 'strncpy', - inlined from 'get_contrl' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1981:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdheader': -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 191 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:204:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 204 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:222:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 222 | if (input_integer[0] != dcdcordmagic) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:399:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 399 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:416:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 416 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdstep': -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:621:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] - 621 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:625:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] - 625 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] - 546 | fio_size_t readlen; /* number of bytes actually read */ - | ^~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: +contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] + 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) + | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: At top level: -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] - 96 | 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] + 65 | 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] + 46 | 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] 32 | 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] - 609 | 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] - 605 | static int fio_read_int32(fio_fd fd, int *i) { - | ^~~~~~~~~~~~~~ +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] 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/inthash.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/inthash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Deferred.cpp -o build/temp.linux-arm64-3.9/layer0/Deferred.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] - 160 | static int get_pte_idx_from_string(const char *label) { - | ^~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 166 | char *name, *type; @@ -2664,10 +2692,11 @@ contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable 'name' set but not used [-Wunused-but-set-variable] 166 | char *name, *type; | ^~~~ -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] - 133 | static int get_pte_idx(const char *label) - | ^~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:40: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] + 160 | static int get_pte_idx_from_string(const char *label) { + | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:34: In function 'strncpy', @@ -2676,47 +2705,7 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 80 bytes from a string of length 81 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/string.h:495, - from contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:23, - from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:31: -In function 'strncpy', - inlined from 'get_pdb_cryst1' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:119:3, - inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:277:9: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 80 bytes from a string of length 82 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:144:5, - inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 52 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:149:5, - inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 44 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:154:5, - inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 36 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5, - inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5, - inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/GenericBuffer.cpp -o build/temp.linux-arm64-3.9/layer0/GenericBuffer.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In function 'strncpy', inlined from 'get_pqr_fields' at contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:137:3, inlined from 'read_pqr_structure' at contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:268:7: @@ -2741,49 +2730,45 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 58 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: -contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': -contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'const long unsigned int'} [-Wsign-compare] - 519 | if (rc != iov[i].iov_len) - | ^~ -In function 'strncpy', - inlined from 'get_contrl_firefly' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1818:3: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Deferred.cpp -o build/temp.linux-arm64-3.9/layer0/Deferred.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/GenericBuffer.cpp -o build/temp.linux-arm64-3.9/layer0/GenericBuffer.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Err.cpp -o build/temp.linux-arm64-3.9/layer0/Err.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In function 'strncpy', - inlined from 'get_pdb_header' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:190:5, - inlined from 'open_pdb_read' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:79:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 9 bytes from a string of length 32 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_header' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:200:5, - inlined from 'open_pdb_read' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:79:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 20 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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] + 91 | 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] + 116 | 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] + 132 | 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] + 149 | 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] + 155 | 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] + 161 | 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] + 170 | 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] + 217 | 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] + 237 | 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] + 256 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: In function 'write_psf_structure': contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:782:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] 782 | if (strlen(atoms[i].type) > fw) { | ^ -In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: -At top level: -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] - 65 | 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] - 46 | 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] - 32 | 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] - 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { - | ^~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: At top level: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: 'fortread_4' defined but not used [-Wunused-function] @@ -2812,58 +2797,12 @@ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] 32 | static void swap2_unaligned(void *v, long ndata) { | ^~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -In function 'strncpy', - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:299:3, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 70 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:304:3, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 1 byte from a string of length 66 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:308:3, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 65 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'strncpy', - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:317:3, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 60 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5, - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:326:3, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5, - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:326:3, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:330:5, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 10 [-Wstringop-truncation] - 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'strncpy', - inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:339:5, - inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 2 bytes from a string of length 6 [-Wstringop-truncation] + inlined from 'get_fmoxyz' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1682:5, + inlined from 'get_input_structure' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1537:12: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] @@ -2918,11 +2857,29 @@ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:437:18: warning: 'init_qmdata' defined but not used [-Wunused-function] 437 | static qmdata_t* init_qmdata() { | ^~~~~~~~~~~ +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Matrix.cpp -o build/temp.linux-arm64-3.9/layer0/Matrix.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:47: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Err.cpp -o build/temp.linux-arm64-3.9/layer0/Err.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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] + 133 | static int get_pte_idx(const char *label) + | ^~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_proc_mem.isra' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1279:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 256 bytes from a string of length 8191 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_proc_mem.isra' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1272:5: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:43: In function 'strncpy', @@ -2930,89 +2887,10 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 16 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -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] - 443 | 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] - 484 | int i, count, atomdata, pos, idx, xyzcount, j; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] - 503 | 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] - 803 | int bondTable[32]; - | ^~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] - 807 | int i, pos, j, k; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] - 811 | char modelNum[8]; - | ^~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] - 822 | molfile_atom_t * atom; - | ^~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] - 884 | 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] - 984 | int bondTable[32]; - | ^~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] - 988 | int i, pos, j, k; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] - 991 | char modelNum[8]; - | ^~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] - 1002 | 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] - 1409 | FILE* fd; - | ^~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Matrix.cpp -o build/temp.linux-arm64-3.9/layer0/Matrix.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -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] - 91 | 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] - 116 | 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] - 132 | 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] - 149 | 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] - 155 | 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] - 161 | 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] - 170 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ 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] 238 | fgets(readbuf, 1024, fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~ -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] - 217 | 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] - 237 | 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] - 256 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ 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] 408 | fgets(readbuf, 256, xsf->fd); @@ -3038,11 +2916,113 @@ 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] 508 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_contrl' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1981:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/string.h:495, + from contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:23, + from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:31: +In function 'strncpy', + inlined from 'get_pdb_cryst1' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:119:3, + inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:277:9: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 80 bytes from a string of length 82 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:144:5, + inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 52 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:149:5, + inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 44 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:154:5, + inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 36 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5, + inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5, + inlined from 'read_next_timestep' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:270:9: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/PostProcess.cpp -o build/temp.linux-arm64-3.9/layer0/PostProcess.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In function 'strncpy', - inlined from 'symmetry_expand' at contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:819:5, - inlined from 'get_traj_frame.constprop' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2931:7: -/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 10 bytes from a string of length 10 [-Wstringop-truncation] + inlined from 'get_pdb_header' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:190:5, + inlined from 'open_pdb_read' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:79:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 9 bytes from a string of length 32 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_header' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:200:5, + inlined from 'open_pdb_read' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:79:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 20 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Texture.cpp -o build/temp.linux-arm64-3.9/layer0/Texture.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In function 'strncpy', + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:299:3, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 70 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:304:3, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 1 byte from a string of length 66 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:308:3, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 65 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:317:3, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 60 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5, + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:326:3, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_coordinates' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5, + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:326:3, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:330:5, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 10 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'strncpy', + inlined from 'get_pdb_fields' at contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:339:5, + inlined from 'read_pdb_structure' at contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:151:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 2 bytes from a string of length 6 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, @@ -3056,7 +3036,11 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Texture.cpp -o build/temp.linux-arm64-3.9/layer0/Texture.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In function 'strncpy', + inlined from 'get_contrl_firefly' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1818:3: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:495, from contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:32: In function 'strncat', @@ -3075,13 +3059,12 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:136:10: warning: '__builtin___strncat_chk' output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] 136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Feedback.cpp -o build/temp.linux-arm64-3.9/layer0/Feedback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from /usr/include/string.h:495, from contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:53: In function 'strncpy', @@ -3094,10 +3077,54 @@ /usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 16 equals destination size [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Block.cpp -o build/temp.linux-arm64-3.9/layer0/Block.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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] + 443 | 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] + 484 | int i, count, atomdata, pos, idx, xyzcount, j; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] + 503 | 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] + 803 | int bondTable[32]; + | ^~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] + 807 | int i, pos, j, k; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] + 811 | char modelNum[8]; + | ^~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] + 822 | molfile_atom_t * atom; + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] + 884 | 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] + 984 | int bondTable[32]; + | ^~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] + 988 | int i, pos, j, k; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] + 991 | char modelNum[8]; + | ^~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] + 1002 | 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] + 1409 | FILE* fd; + | ^~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Feedback.cpp -o build/temp.linux-arm64-3.9/layer0/Feedback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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:371:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 371 | fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); @@ -3107,8 +3134,77 @@ 306 | fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Vector.cpp -o build/temp.linux-arm64-3.9/layer0/Vector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/GraphicsUtil.cpp -o build/temp.linux-arm64-3.9/layer0/GraphicsUtil.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/CGO.cpp -o build/temp.linux-arm64-3.9/layer1/CGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +In function 'strncpy', + inlined from 'symmetry_expand' at contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:819:5, + inlined from 'get_traj_frame.constprop' at contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2931:7: +/usr/include/aarch64-linux-gnu/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 10 bytes from a string of length 10 [-Wstringop-truncation] + 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/GraphicsUtil.cpp -o build/temp.linux-arm64-3.9/layer0/GraphicsUtil.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/phiplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Extrude.cpp -o build/temp.linux-arm64-3.9/layer1/Extrude.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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:714:16: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] + 714 | sprintf(sub, "%03x/", i); + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:15: note: directive argument in the range [0, 2147483646] + 714 | sprintf(sub, "%03x/", i); + | ^~~~~~~ +In file included from /usr/include/stdio.h:867, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] + 722 | sprintf(subsub, "%03x", j); + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:22: note: directive argument in the range [0, 2147483646] + 722 | sprintf(subsub, "%03x", j); + | ^~~~~~ +In file included from /usr/include/stdio.h:867, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/ShaderMgr.cpp -o build/temp.linux-arm64-3.9/layer0/ShaderMgr.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Crystal.cpp -o build/temp.linux-arm64-3.9/layer0/Crystal.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'std::string framefile(const string&, size_t, size_t, int, int)': +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] + 675 | sprintf(answer, "%03x/", d1); + | ^ +In file included from /usr/include/stdio.h:867, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:28: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] + 673 | sprintf(answer, "%03x/%03x/", d1, d2); + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:22: note: directive argument in the range [0, 2147483646] + 673 | sprintf(answer, "%03x/%03x/", d1, d2); + | ^~~~~~~~~~~~ +In file included from /usr/include/stdio.h:867, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 + 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 37 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Isosurf.cpp -o build/temp.linux-arm64-3.9/layer0/Isosurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Field.cpp -o build/temp.linux-arm64-3.9/layer0/Field.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 186 | fread(line3, 1, 80, infile); @@ -3279,104 +3375,46 @@ 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] 398 | fread(properties, sizeof(float), 3 * nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Extrude.cpp -o build/temp.linux-arm64-3.9/layer1/Extrude.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Field.cpp -o build/temp.linux-arm64-3.9/layer0/Field.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +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] + 1902 | int last_ctnumber = -1; + | ^~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/grdplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/ShaderMgr.cpp -o build/temp.linux-arm64-3.9/layer0/ShaderMgr.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Isosurf.cpp -o build/temp.linux-arm64-3.9/layer0/Isosurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -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:714:16: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] - 714 | sprintf(sub, "%03x/", i); - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:15: note: directive argument in the range [0, 2147483646] - 714 | sprintf(sub, "%03x/", i); - | ^~~~~~~ -In file included from /usr/include/stdio.h:867, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 6 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] - 722 | sprintf(subsub, "%03x", j); - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:722:22: note: directive argument in the range [0, 2147483646] - 722 | sprintf(subsub, "%03x", j); - | ^~~~~~ -In file included from /usr/include/stdio.h:867, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 9 bytes into a destination of size 6 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Tracker.cpp -o build/temp.linux-arm64-3.9/layer0/Tracker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] 84 | fread(&dataBegin, sizeof(int), 1, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Word.cpp -o build/temp.linux-arm64-3.9/layer0/Word.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUTHel10.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUTHel10.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'std::string framefile(const string&, size_t, size_t, int, int)': -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:28: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] - 675 | sprintf(answer, "%03x/", d1); - | ^ -In file included from /usr/include/stdio.h:867, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 5 and 10 bytes into a destination of size 9 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:28: warning: '%03x' directive writing between 3 and 8 bytes into a region of size between 0 and 5 [-Wformat-overflow=] - 673 | sprintf(answer, "%03x/%03x/", d1, d2); - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:673:22: note: directive argument in the range [0, 2147483646] - 673 | sprintf(answer, "%03x/%03x/", d1, d2); - | ^~~~~~~~~~~~ -In file included from /usr/include/stdio.h:867, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.hxx:56, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:47: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 9 and 19 bytes into a destination of size 9 - 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 37 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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] - 1902 | int last_ctnumber = -1; - | ^~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Crystal.cpp -o build/temp.linux-arm64-3.9/layer0/Crystal.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUTHel12.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUTHel12.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Tracker.cpp -o build/temp.linux-arm64-3.9/layer0/Tracker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Word.cpp -o build/temp.linux-arm64-3.9/layer0/Word.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUTHel18.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUTHel18.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontType.cpp -o build/temp.linux-arm64-3.9/layer1/FontType.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/File.cpp -o build/temp.linux-arm64-3.9/layer0/File.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Triangle.cpp -o build/temp.linux-arm64-3.9/layer0/Triangle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Ortho.cpp -o build/temp.linux-arm64-3.9/layer1/Ortho.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUTHel18.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUTHel18.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/File.cpp -o build/temp.linux-arm64-3.9/layer0/File.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontType.cpp -o build/temp.linux-arm64-3.9/layer1/FontType.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/PyMOLObject.cpp -o build/temp.linux-arm64-3.9/layer1/PyMOLObject.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/os_gl.cpp -o build/temp.linux-arm64-3.9/layer0/os_gl.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Basis.cpp -o build/temp.linux-arm64-3.9/layer1/Basis.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Font.cpp -o build/temp.linux-arm64-3.9/layer1/Font.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Movie.cpp -o build/temp.linux-arm64-3.9/layer1/Movie.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUT.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUT.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/MemoryDebug.cpp -o build/temp.linux-arm64-3.9/layer0/MemoryDebug.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Font.cpp -o build/temp.linux-arm64-3.9/layer1/Font.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/MyPNG.cpp -o build/temp.linux-arm64-3.9/layer0/MyPNG.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Map.cpp -o build/temp.linux-arm64-3.9/layer0/Map.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUT.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUT.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Parse.cpp -o build/temp.linux-arm64-3.9/layer0/Parse.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Movie.cpp -o build/temp.linux-arm64-3.9/layer1/Movie.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Pixmap.cpp -o build/temp.linux-arm64-3.9/layer0/Pixmap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Map.cpp -o build/temp.linux-arm64-3.9/layer0/Map.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUT8x13.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUT8x13.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Util.cpp -o build/temp.linux-arm64-3.9/layer0/Util.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/SceneRay.cpp -o build/temp.linux-arm64-3.9/layer1/SceneRay.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Ray.cpp -o build/temp.linux-arm64-3.9/layer1/Ray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUT8x13.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUT8x13.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/FontGLUT9x15.cpp -o build/temp.linux-arm64-3.9/layer1/FontGLUT9x15.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/SceneRay.cpp -o build/temp.linux-arm64-3.9/layer1/SceneRay.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/ButMode.cpp -o build/temp.linux-arm64-3.9/layer1/ButMode.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Shaker.cpp -o build/temp.linux-arm64-3.9/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Match.cpp -o build/temp.linux-arm64-3.9/layer0/Match.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/dxplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Util2.cpp -o build/temp.linux-arm64-3.9/layer0/Util2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/P.cpp -o build/temp.linux-arm64-3.9/layer1/P.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp -o build/temp.linux-arm64-3.9/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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] @@ -3386,15 +3424,11 @@ 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] 44 | fgets(readbuf, 1024, fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Shaker.cpp -o build/temp.linux-arm64-3.9/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Match.cpp -o build/temp.linux-arm64-3.9/layer0/Match.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/ButMode.cpp -o build/temp.linux-arm64-3.9/layer1/ButMode.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Wizard.cpp -o build/temp.linux-arm64-3.9/layer1/Wizard.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Util2.cpp -o build/temp.linux-arm64-3.9/layer0/Util2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/P.cpp -o build/temp.linux-arm64-3.9/layer1/P.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/CifFile.cpp -o build/temp.linux-arm64-3.9/layer2/CifFile.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/HydrogenAdder.cpp -o build/temp.linux-arm64-3.9/layer2/HydrogenAdder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Symmetry.cpp -o build/temp.linux-arm64-3.9/layer1/Symmetry.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectAlignment.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectAlignment.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/HydrogenAdder.cpp -o build/temp.linux-arm64-3.9/layer2/HydrogenAdder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer1/P.cpp: In function 'void PSetupEmbedded(PyMOLGlobals*, int, char**)': layer1/P.cpp:1961:22: warning: 'void PyEval_InitThreads()' is deprecated [-Wdeprecated-declarations] 1961 | PyEval_InitThreads(); @@ -3405,9 +3439,7 @@ /usr/include/python3.9/ceval.h:130:37: note: declared here 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); | ^~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectGadgetRamp.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectGadgetRamp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/AssemblyHelpers.cpp -o build/temp.linux-arm64-3.9/layer2/AssemblyHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Text.cpp -o build/temp.linux-arm64-3.9/layer1/Text.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer1/Ray.cpp: In function 'void RayRenderVRML2(CRay*, int, int, char**, float, float, float, float, float)': layer1/Ray.cpp:1538:20: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 914 [-Wformat-overflow=] 1538 | "%s" @@ -3438,24 +3470,31 @@ | ~~~~~~~~~~~~~~~~~~ 1543 | vert2[2] - mid[2], axis[0], axis[1], axis[2], angle, geometry); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Text.cpp -o build/temp.linux-arm64-3.9/layer1/Text.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/PConv.cpp -o build/temp.linux-arm64-3.9/layer1/PConv.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/MmodTyping.cpp -o build/temp.linux-arm64-3.9/layer2/MmodTyping.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectAlignment.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectAlignment.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/SceneRender.cpp -o build/temp.linux-arm64-3.9/layer1/SceneRender.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectGadgetRamp.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectGadgetRamp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/CifMoleculeReader.cpp -o build/temp.linux-arm64-3.9/layer2/CifMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/PConv.cpp -o build/temp.linux-arm64-3.9/layer1/PConv.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMolecule2.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/AssemblyHelpers.cpp -o build/temp.linux-arm64-3.9/layer2/AssemblyHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/MmtfMoleculeReader.cpp -o build/temp.linux-arm64-3.9/layer2/MmtfMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/AtomInfo.cpp -o build/temp.linux-arm64-3.9/layer2/AtomInfo.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectGroup.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectGroup.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/Mol2Typing.cpp -o build/temp.linux-arm64-3.9/layer2/Mol2Typing.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/ShaderPrg.cpp -o build/temp.linux-arm64-3.9/layer0/ShaderPrg.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectCGO.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectCGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Picking.cpp -o build/temp.linux-arm64-3.9/layer1/Picking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMap.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/MolV3000.cpp -o build/temp.linux-arm64-3.9/layer2/MolV3000.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/AtomInfo.cpp -o build/temp.linux-arm64-3.9/layer2/AtomInfo.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectGroup.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectGroup.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Pop.cpp -o build/temp.linux-arm64-3.9/layer1/Pop.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/MolV3000.cpp -o build/temp.linux-arm64-3.9/layer2/MolV3000.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/ScrollBar.cpp -o build/temp.linux-arm64-3.9/layer1/ScrollBar.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepCartoon.cpp -o build/temp.linux-arm64-3.9/layer2/RepCartoon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/ShaderPrg.cpp -o build/temp.linux-arm64-3.9/layer0/ShaderPrg.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMap.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Rep.cpp -o build/temp.linux-arm64-3.9/layer1/Rep.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepDot.cpp -o build/temp.linux-arm64-3.9/layer2/RepDot.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectCGO.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectCGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Seq.cpp -o build/temp.linux-arm64-3.9/layer1/Seq.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/AtomInfoHistory.cpp -o build/temp.linux-arm64-3.9/layer2/AtomInfoHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Scene.cpp -o build/temp.linux-arm64-3.9/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 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:313:27: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] 313 | " ObjMol: created %s/%s/%s/%s`%d%c/%s\n", @@ -3471,19 +3510,14 @@ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Sphere.cpp -o build/temp.linux-arm64-3.9/layer0/Sphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Seq.cpp -o build/temp.linux-arm64-3.9/layer1/Seq.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepEllipsoid.cpp -o build/temp.linux-arm64-3.9/layer2/RepEllipsoid.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectCallback.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectCallback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/AtomInfoHistory.cpp -o build/temp.linux-arm64-3.9/layer2/AtomInfoHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer0/Tetsurf.cpp -o build/temp.linux-arm64-3.9/layer0/Tetsurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Rep.cpp -o build/temp.linux-arm64-3.9/layer1/Rep.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepEllipsoid.cpp -o build/temp.linux-arm64-3.9/layer2/RepEllipsoid.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectDist.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectDist.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectSlice.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectSlice.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Setting.cpp -o build/temp.linux-arm64-3.9/layer1/Setting.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/BondTypeHistory.cpp -o build/temp.linux-arm64-3.9/layer2/BondTypeHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Scene.cpp -o build/temp.linux-arm64-3.9/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepLabel.cpp -o build/temp.linux-arm64-3.9/layer2/RepLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepNonbondedSphere.cpp -o build/temp.linux-arm64-3.9/layer2/RepNonbondedSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Setting.cpp -o build/temp.linux-arm64-3.9/layer1/Setting.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectDist.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectDist.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepLabel.cpp -o build/temp.linux-arm64-3.9/layer2/RepLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer2/ObjectMap.cpp: In function 'void ObjectMapDump(const ObjectMap*, const char*, int, int)': layer2/ObjectMap.cpp:5982:24: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 239 [-Wformat-truncation=] 5982 | " ObjectMapDump: %s written to %s\n", om->Name, fname ENDFB(om->G); @@ -3498,8 +3532,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectSlice.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectSlice.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepRibbon.cpp -o build/temp.linux-arm64-3.9/layer2/RepRibbon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepSurface.cpp -o build/temp.linux-arm64-3.9/layer2/RepSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectGadget.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectGadget.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepMesh.cpp -o build/temp.linux-arm64-3.9/layer2/RepMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer2/ObjectSlice.cpp: In member function 'virtual void ObjectSlice::update()': layer2/ObjectSlice.cpp:639:42: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 225 [-Wformat-truncation=] 639 | "ObjectSliceUpdate-Error: map '%s' has been deleted.\n", oss->MapName @@ -3525,125 +3562,8 @@ layer2/ObjectSlice.cpp:649:11: note: in expansion of macro 'PRINTFB' 649 | PRINTFB(I->G, FB_ObjectSlice, FB_Blather) | ^~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepRibbon.cpp -o build/temp.linux-arm64-3.9/layer2/RepRibbon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectSurface.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/VFont.cpp -o build/temp.linux-arm64-3.9/layer2/VFont.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepMesh.cpp -o build/temp.linux-arm64-3.9/layer2/RepMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer2/ObjectMap.cpp: In function 'ObjectMap* ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int)': -layer2/ObjectMap.cpp:2977:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] - 2977 | " PHIStrToMap: %s\n", cc ENDFB(I->G); - | ^~ ~~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer2/ObjectMap.cpp:2986:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] - 2986 | " PHIStrToMap: %s\n", cc ENDFB(I->G); - | ^~ ~~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer2/ObjectMap.cpp:2992:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] - 2992 | " PHIStrToMap: %s\n", cc ENDFB(I->G); - | ^~ ~~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer2/ObjectMap.cpp:3074:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] - 3074 | " PHIStrToMap: %s\n", cc ENDFB(I->G); - | ^~ ~~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepCylBond.cpp -o build/temp.linux-arm64-3.9/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/TypeFace.cpp -o build/temp.linux-arm64-3.9/layer1/TypeFace.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/View.cpp -o build/temp.linux-arm64-3.9/layer1/View.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepSphere.cpp -o build/temp.linux-arm64-3.9/layer2/RepSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/AtomIterators.cpp -o build/temp.linux-arm64-3.9/layer3/AtomIterators.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer2/ObjectSurface.cpp: In function 'void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)': -layer2/ObjectSurface.cpp:264:30: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] - 264 | " 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 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectSurface.cpp:263:7: note: in expansion of macro 'PRINTFB' - 263 | PRINTFB(I->G, FB_ObjectSurface, FB_Actions) - | ^~~~~~~ -layer2/ObjectMap.cpp: In function 'int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)': -layer2/ObjectMap.cpp:4297:18: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] - 4297 | " ObjectMap: %s\n", cc ENDFB(I->G); - | ^~ ~~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 14 and 1037 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer2/ObjectMap.cpp:4297:18: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] - 4297 | " ObjectMap: %s\n", cc ENDFB(I->G); - | ^~ ~~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 14 and 1037 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/CoordSet.cpp -o build/temp.linux-arm64-3.9/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer2/ObjectSurface.cpp: In member function 'virtual void ObjectSurface::update()': -layer2/ObjectSurface.cpp:493:43: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] - 493 | " 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 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectSurface.cpp:492:13: note: in expansion of macro 'PRINTFB' - 492 | PRINTFB(I->G, FB_ObjectSurface, FB_Details) - | ^~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/CifDataValueFormatter.cpp -o build/temp.linux-arm64-3.9/layer3/CifDataValueFormatter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/ExecutivePython.cpp -o build/temp.linux-arm64-3.9/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectVolume.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectVolume.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepCylBond.cpp -o build/temp.linux-arm64-3.9/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer1/Scene.cpp: In function 'int SceneClick(Block*, int, int, int, int, double)': layer1/Scene.cpp:4227:36: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 242 [-Wformat-truncation=] 4227 | PRINTF " You clicked %s", buffer ENDF(G); @@ -3846,35 +3766,133 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4405 | sel_mode_kw, buf1); | ~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMesh.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Editor.cpp -o build/temp.linux-arm64-3.9/layer3/Editor.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepSphereGenerate.cpp -o build/temp.linux-arm64-3.9/layer2/RepSphereGenerate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepNonbonded.cpp -o build/temp.linux-arm64-3.9/layer2/RepNonbonded.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepDihedral.cpp -o build/temp.linux-arm64-3.9/layer2/RepDihedral.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer2/CoordSet.cpp: In member function 'void CoordSet::update(int)': -layer2/CoordSet.cpp:1240:72: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 223 [-Wformat-truncation=] - 1240 | PRINTFB(G, FB_CoordSet, FB_Blather) " CoordSetUpdate-Entered: object %s state %d cset %p\n", - | ^~ +layer2/ObjectMap.cpp: In function 'ObjectMap* ObjectMapLoadPHI(PyMOLGlobals*, ObjectMap*, const char*, int, int, int, int)': +layer2/ObjectMap.cpp:2977:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] + 2977 | " PHIStrToMap: %s\n", cc ENDFB(I->G); + | ^~ ~~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMap.cpp:2986:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] + 2986 | " PHIStrToMap: %s\n", cc ENDFB(I->G); + | ^~ ~~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMap.cpp:2992:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] + 2992 | " PHIStrToMap: %s\n", cc ENDFB(I->G); + | ^~ ~~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMap.cpp:3074:22: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 241 [-Wformat-truncation=] + 3074 | " PHIStrToMap: %s\n", cc ENDFB(I->G); + | ^~ ~~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 16 and 1039 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/VFont.cpp -o build/temp.linux-arm64-3.9/layer2/VFont.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectSurface.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/ScenePicking.cpp -o build/temp.linux-arm64-3.9/layer1/ScenePicking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepSphereImmediate.cpp -o build/temp.linux-arm64-3.9/layer2/RepSphereImmediate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/DistSet.cpp -o build/temp.linux-arm64-3.9/layer2/DistSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer2/ObjectVolume.cpp: In function 'ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)': -layer2/ObjectVolume.cpp:74:33: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] - 74 | "ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName - | ^~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepSphereGenerate.cpp -o build/temp.linux-arm64-3.9/layer2/RepSphereGenerate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +layer2/ObjectMap.cpp: In function 'int ObjectMapGRDStrToMap(ObjectMap*, char*, int, int, int)': +layer2/ObjectMap.cpp:4297:18: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] + 4297 | " ObjectMap: %s\n", cc ENDFB(I->G); + | ^~ ~~ In file included from /usr/include/stdio.h:867, 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 46 and 301 bytes into a destination of size 255 + from layer2/ObjectMap.cpp:21: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 14 and 1037 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMap.cpp:4297:18: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size 243 [-Wformat-truncation=] + 4297 | " ObjectMap: %s\n", cc ENDFB(I->G); + | ^~ ~~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 14 and 1037 bytes into a destination of size 255 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/TypeFace.cpp -o build/temp.linux-arm64-3.9/layer1/TypeFace.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/AtomIterators.cpp -o build/temp.linux-arm64-3.9/layer3/AtomIterators.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/View.cpp -o build/temp.linux-arm64-3.9/layer1/View.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +layer2/ObjectSurface.cpp: In function 'void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)': +layer2/ObjectSurface.cpp:264:30: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] + 264 | " 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 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectSurface.cpp:263:7: note: in expansion of macro 'PRINTFB' + 263 | PRINTFB(I->G, FB_ObjectSurface, FB_Actions) + | ^~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepDihedral.cpp -o build/temp.linux-arm64-3.9/layer2/RepDihedral.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMesh.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/ExecutivePython.cpp -o build/temp.linux-arm64-3.9/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepNonbonded.cpp -o build/temp.linux-arm64-3.9/layer2/RepNonbonded.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +layer2/ObjectSurface.cpp: In member function 'virtual void ObjectSurface::update()': +layer2/ObjectSurface.cpp:493:43: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] + 493 | " 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 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectSurface.cpp:492:13: note: in expansion of macro 'PRINTFB' + 492 | PRINTFB(I->G, FB_ObjectSurface, FB_Details) + | ^~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/CifDataValueFormatter.cpp -o build/temp.linux-arm64-3.9/layer3/CifDataValueFormatter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepSphereImmediate.cpp -o build/temp.linux-arm64-3.9/layer2/RepSphereImmediate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/CoordSet.cpp -o build/temp.linux-arm64-3.9/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/RingFinder.cpp -o build/temp.linux-arm64-3.9/layer3/RingFinder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/MaeExportHelpers.cpp -o build/temp.linux-arm64-3.9/layer3/MaeExportHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Editor.cpp -o build/temp.linux-arm64-3.9/layer3/Editor.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectVolume.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectVolume.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Seeker.cpp -o build/temp.linux-arm64-3.9/layer3/Seeker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer4/Menu.cpp -o build/temp.linux-arm64-3.9/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepDistDash.cpp -o build/temp.linux-arm64-3.9/layer2/RepDistDash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-arm64-3.9/modules/cealign/src/ccealignmodule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer2/ObjectMesh.cpp: In function 'void ObjectMeshDump(ObjectMesh*, const char*, int, int)': layer2/ObjectMesh.cpp:329:27: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] 329 | " ObjectMeshDump: %s written to %s\n", I->Name, fname ENDFB(I->G); @@ -3888,6 +3906,11 @@ layer2/ObjectMesh.cpp:328:7: note: in expansion of macro 'PRINTFB' 328 | PRINTFB(I->G, FB_ObjectMesh, FB_Actions) | ^~~~~~~ +layer2/CoordSet.cpp: In member function 'void CoordSet::update(int)': +layer2/CoordSet.cpp:1240:72: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 223 [-Wformat-truncation=] + 1240 | PRINTFB(G, FB_CoordSet, FB_Blather) " CoordSetUpdate-Entered: object %s state %d cset %p\n", + | ^~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer4/PopUp.cpp -o build/temp.linux-arm64-3.9/layer4/PopUp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer2/ObjectMesh.cpp: In member function 'virtual void ObjectMesh::update()': layer2/ObjectMesh.cpp:507:41: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 226 [-Wformat-truncation=] 507 | "ObjectMeshUpdate-Error: map '%s' has been deleted.\n", ms->MapName @@ -3913,6 +3936,22 @@ layer2/ObjectMesh.cpp:539:13: note: in expansion of macro 'PRINTFB' 539 | PRINTFB(G, FB_ObjectMesh, FB_Details) | ^~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/MaeExportHelpers.cpp -o build/temp.linux-arm64-3.9/layer3/MaeExportHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/DistSet.cpp -o build/temp.linux-arm64-3.9/layer2/DistSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +layer2/ObjectVolume.cpp: In function 'ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)': +layer2/ObjectVolume.cpp:74:33: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] + 74 | "ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName + | ^~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 46 and 301 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp: In function 'void EditorPrepareDrag(PyMOLGlobals*, CObject*, int, int, int, int)': layer3/Editor.cpp:1944:29: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] 1944 | " Editor: grabbing (%s).", name ENDFB(G); @@ -3926,37 +3965,6 @@ layer3/Editor.cpp:1943:7: note: in expansion of macro 'PRINTFB' 1943 | PRINTFB(G, FB_Editor, FB_Blather) | ^~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Seeker.cpp -o build/temp.linux-arm64-3.9/layer3/Seeker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer3/Editor.cpp: In function 'void EditorDefineExtraPks(PyMOLGlobals*)': -layer3/Editor.cpp:335:29: warning: '%s' directive writing up to 255 bytes into a region of size 249 [-Wformat-overflow=] - 335 | sprintf(buffer, "(byres %s)", name); - | ^~ ~~~~ -layer3/Editor.cpp:335:12: note: 'sprintf' output between 9 and 264 bytes into a destination of size 256 - 335 | sprintf(buffer, "(byres %s)", name); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer3/Editor.cpp:337:31: warning: '%s' directive writing up to 255 bytes into a region of size 247 [-Wformat-overflow=] - 337 | sprintf(buffer, "(bychain %s)", name); - | ^~ ~~~~ -layer3/Editor.cpp:337:12: note: 'sprintf' output between 11 and 266 bytes into a destination of size 256 - 337 | sprintf(buffer, "(bychain %s)", name); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer3/Editor.cpp:339:32: warning: '%s' directive writing up to 255 bytes into a region of size 246 [-Wformat-overflow=] - 339 | sprintf(buffer, "(byobject %s)", name); - | ^~ ~~~~ -layer3/Editor.cpp:339:12: note: 'sprintf' output between 12 and 267 bytes into a destination of size 256 - 339 | sprintf(buffer, "(byobject %s)", name); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer4/Menu.cpp -o build/temp.linux-arm64-3.9/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD modules/cealign/src/ccealignmodule.cpp -o build/temp.linux-arm64-3.9/modules/cealign/src/ccealignmodule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMolecule.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMolecule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/COLLADA.cpp -o build/temp.linux-arm64-3.9/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/MoleculeExporter.cpp -o build/temp.linux-arm64-3.9/layer3/MoleculeExporter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/GadgetSet.cpp -o build/temp.linux-arm64-3.9/layer2/GadgetSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepWireBond.cpp -o build/temp.linux-arm64-3.9/layer2/RepWireBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepDistLabel.cpp -o build/temp.linux-arm64-3.9/layer2/RepDistLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer4/PopUp.cpp -o build/temp.linux-arm64-3.9/layer4/PopUp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Executive.cpp -o build/temp.linux-arm64-3.9/layer3/Executive.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepAngle.cpp -o build/temp.linux-arm64-3.9/layer2/RepAngle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer3/Seeker.cpp: In function 'void SeekerSelectionToggleRange(PyMOLGlobals*, CSeqRow*, int, int, int, int, int)': layer3/Seeker.cpp:148:50: warning: '%s' directive writing up to 1023 bytes into a region of size between 754 and 1009 [-Wformat-overflow=] 148 | sprintf(buf2, "%scmd.select(\"%s\",\"%s\",enable=1)\n", prefix, selName, @@ -3989,8 +3997,52 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer3/Editor.cpp: In function 'void EditorDefineExtraPks(PyMOLGlobals*)': +layer3/Editor.cpp:335:29: warning: '%s' directive writing up to 255 bytes into a region of size 249 [-Wformat-overflow=] + 335 | sprintf(buffer, "(byres %s)", name); + | ^~ ~~~~ +layer3/Editor.cpp:335:12: note: 'sprintf' output between 9 and 264 bytes into a destination of size 256 + 335 | sprintf(buffer, "(byres %s)", name); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer3/Editor.cpp:337:31: warning: '%s' directive writing up to 255 bytes into a region of size 247 [-Wformat-overflow=] + 337 | sprintf(buffer, "(bychain %s)", name); + | ^~ ~~~~ +layer3/Editor.cpp:337:12: note: 'sprintf' output between 11 and 266 bytes into a destination of size 256 + 337 | sprintf(buffer, "(bychain %s)", name); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer3/Editor.cpp:339:32: warning: '%s' directive writing up to 255 bytes into a region of size 246 [-Wformat-overflow=] + 339 | sprintf(buffer, "(byobject %s)", name); + | ^~ ~~~~ +layer3/Editor.cpp:339:12: note: 'sprintf' output between 12 and 267 bytes into a destination of size 256 + 339 | sprintf(buffer, "(byobject %s)", name); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/ObjectMolecule.cpp -o build/temp.linux-arm64-3.9/layer2/ObjectMolecule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepDistLabel.cpp -o build/temp.linux-arm64-3.9/layer2/RepDistLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/COLLADA.cpp -o build/temp.linux-arm64-3.9/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer5/PyMOL.cpp -o build/temp.linux-arm64-3.9/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/GadgetSet.cpp -o build/temp.linux-arm64-3.9/layer2/GadgetSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Selector.cpp -o build/temp.linux-arm64-3.9/layer3/Selector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/MoleculeExporter.cpp -o build/temp.linux-arm64-3.9/layer3/MoleculeExporter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVContext.cpp -o build/temp.linux-arm64-3.9/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVHeap.cpp -o build/temp.linux-arm64-3.9/ov/src/OVHeap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVHeapArray.cpp -o build/temp.linux-arm64-3.9/ov/src/OVHeapArray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Executive.cpp -o build/temp.linux-arm64-3.9/layer3/Executive.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVLexicon.cpp -o build/temp.linux-arm64-3.9/ov/src/OVLexicon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVOneToAny.cpp -o build/temp.linux-arm64-3.9/ov/src/OVOneToAny.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +layer5/PyMOL.cpp: In function 'void init_python(int, char**)': +layer5/PyMOL.cpp:1798:22: warning: 'void PyEval_InitThreads()' is deprecated [-Wdeprecated-declarations] + 1798 | PyEval_InitThreads(); + | ^ +In file included from /usr/include/python3.9/Python.h:145, + from layer0/os_python.h:32, + from layer5/PyMOL.cpp:17: +/usr/include/python3.9/ceval.h:130:37: note: declared here + 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); + | ^~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVOneToOne.cpp -o build/temp.linux-arm64-3.9/ov/src/OVOneToOne.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepWireBond.cpp -o build/temp.linux-arm64-3.9/layer2/RepWireBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/RepAngle.cpp -o build/temp.linux-arm64-3.9/layer2/RepAngle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVRandom.cpp -o build/temp.linux-arm64-3.9/ov/src/OVRandom.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer3/Executive.cpp: In function 'pymol::Result<> ExecutiveLoad(PyMOLGlobals*, const ExecutiveLoadArgs&)': layer3/Executive.cpp:3914:15: warning: unused variable 'object_props' [-Wunused-variable] 3914 | const char* object_props = args.object_props.c_str(); @@ -4001,16 +4053,10 @@ layer3/Executive.cpp:3924:8: warning: unused variable 'mimic' [-Wunused-variable] 3924 | auto mimic = args.mimic; | ^~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer5/PyMOL.cpp -o build/temp.linux-arm64-3.9/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVRandom.cpp -o build/temp.linux-arm64-3.9/ov/src/OVRandom.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/Selector.cpp -o build/temp.linux-arm64-3.9/layer3/Selector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/ov_utility.cpp -o build/temp.linux-arm64-3.9/ov/src/ov_utility.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVContext.cpp -o build/temp.linux-arm64-3.9/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Character.cpp -o build/temp.linux-arm64-3.9/layer1/Character.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVHeap.cpp -o build/temp.linux-arm64-3.9/ov/src/OVHeap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/Sculpt.cpp -o build/temp.linux-arm64-3.9/layer2/Sculpt.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVHeapArray.cpp -o build/temp.linux-arm64-3.9/ov/src/OVHeapArray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/OVLexicon.cpp -o build/temp.linux-arm64-3.9/ov/src/OVLexicon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD ov/src/ov_utility.cpp -o build/temp.linux-arm64-3.9/ov/src/ov_utility.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Color.cpp -o build/temp.linux-arm64-3.9/layer1/Color.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer5/TestPyMOL.cpp -o build/temp.linux-arm64-3.9/layer5/TestPyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer2/ObjectMolecule.cpp: In function 'CoordSet* ObjectMoleculeMOLStr2CoordSet.constprop(PyMOLGlobals*, const char*, AtomInfoType**, const char**)': layer2/ObjectMolecule.cpp:7785:37: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 224 [-Wformat-truncation=] 7785 | " ObjMolMOLStr2CoordSet: title '%s'\n", nameTmp ENDFB(G) @@ -4023,19 +4069,10 @@ layer2/ObjectMolecule.cpp:7784:3: note: in expansion of macro 'PRINTFB' 7784 | PRINTFB(G, FB_ObjectMolecule, FB_Blather) | ^~~~~~~ -layer5/PyMOL.cpp: In function 'void init_python(int, char**)': -layer5/PyMOL.cpp:1798:22: warning: 'void PyEval_InitThreads()' is deprecated [-Wdeprecated-declarations] - 1798 | PyEval_InitThreads(); - | ^ -In file included from /usr/include/python3.9/Python.h:145, - from layer0/os_python.h:32, - from layer5/PyMOL.cpp:17: -/usr/include/python3.9/ceval.h:130:37: note: declared here - 130 | Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); - | ^~~~~~~~~~~~~~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Color.cpp -o build/temp.linux-arm64-3.9/layer1/Color.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer5/TestPyMOL.cpp -o build/temp.linux-arm64-3.9/layer5/TestPyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/Sculpt.cpp -o build/temp.linux-arm64-3.9/layer2/Sculpt.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer5/main.cpp -o build/temp.linux-arm64-3.9/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/MovieScene.cpp -o build/temp.linux-arm64-3.9/layer3/MovieScene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Control.cpp -o build/temp.linux-arm64-3.9/layer1/Control.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer3/Executive.cpp: In function 'pymol::Result<> ExecutiveRemoveAtoms(PyMOLGlobals*, const char*, int)': layer3/Executive.cpp:9162:58: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 207 and 217 [-Wformat-truncation=] 9162 | " Remove: eliminated %d atoms in model \"%s\".\n", @@ -4392,36 +4429,6 @@ layer3/Executive.cpp:12508:23: note: in expansion of macro 'PRINTF' 12508 | PRINTF | ^~~~~~ -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/SculptCache.cpp -o build/temp.linux-arm64-3.9/layer2/SculptCache.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer1/Control.cpp -o build/temp.linux-arm64-3.9/layer1/Control.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer5/main.cpp -o build/temp.linux-arm64-3.9/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/SideChainHelper.cpp -o build/temp.linux-arm64-3.9/layer2/SideChainHelper.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 -layer2/ObjectMolecule.cpp: In member function 'virtual void ObjectMolecule::update()': -layer2/ObjectMolecule.cpp:10827:82: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] -10827 | " 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 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectMolecule.cpp:10826:13: note: in expansion of macro 'PRINTFB' -10826 | PRINTFB(G, FB_ObjectMolecule, FB_Blather) - | ^~~~~~~ -layer2/ObjectMolecule.cpp: In function 'int ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, const float*, int, int)': -layer2/ObjectMolecule.cpp:10955:43: warning: '%s' directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] -10955 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", - | ^~ -10956 | buffer, v[0], v[1], v[2], state + 1, mode, 0); - | ~~~~~~ -layer2/ObjectMolecule.cpp:10955:21: note: directive argument in the range [-2147483647, 2147483647] -10955 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer2/ObjectMolecule.cpp:10955:14: note: 'sprintf' output between 78 and 2036 bytes into a destination of size 1024 -10955 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -10956 | buffer, v[0], v[1], v[2], state + 1, mode, 0); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function 'bool ExecutiveSetSymmetry(PyMOLGlobals*, pymol::zstring_view, int, const CSymmetry&, bool)': layer3/Executive.cpp:6023:43: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 202 [-Wformat-truncation=] 6023 | " %s-Details: Updated symmetry for '%s'\n", __func__, obj->Name ENDFB(G); @@ -4447,6 +4454,21 @@ layer3/Executive.cpp:6013:7: note: in expansion of macro 'PRINTFB' 6013 | PRINTFB(G, FB_Executive, FB_Warnings) | ^~~~~~~ +layer3/Selector.cpp: In function 'int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)': +layer3/Selector.cpp:1830:70: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] + 1830 | " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", + | ^~ +In file included from /usr/include/stdio.h:867, + from /usr/include/c++/10/cstdio:42, + from /usr/include/c++/10/ext/string_conversions.h:43, + from /usr/include/c++/10/bits/basic_string.h:6545, + from /usr/include/c++/10/string:55, + from layer3/Selector.cpp:20: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 59 and 324 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function 'pymol::Result<> ExecutiveBond(PyMOLGlobals*, const char*, const char*, int, int, int)': layer3/Executive.cpp:9495:53: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 214 and 224 [-Wformat-truncation=] 9495 | " Bond: %d bonds added to model \"%s\".\n", cnt, rec->obj->Name @@ -4484,21 +4506,34 @@ layer3/Executive.cpp:9519:17: note: in expansion of macro 'PRINTFB' 9519 | PRINTFB(G, FB_Editor, FB_Actions) | ^~~~~~~ -layer3/Selector.cpp: In function 'int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)': -layer3/Selector.cpp:1830:70: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] - 1830 | " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", - | ^~ -In file included from /usr/include/stdio.h:867, - from /usr/include/c++/10/cstdio:42, - from /usr/include/c++/10/ext/string_conversions.h:43, - from /usr/include/c++/10/bits/basic_string.h:6545, - from /usr/include/c++/10/string:55, - from layer3/Selector.cpp:20: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 59 and 324 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/SculptCache.cpp -o build/temp.linux-arm64-3.9/layer2/SculptCache.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 +layer2/ObjectMolecule.cpp: In member function 'virtual void ObjectMolecule::update()': +layer2/ObjectMolecule.cpp:10827:82: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] +10827 | " 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 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectMolecule.cpp:10826:13: note: in expansion of macro 'PRINTFB' +10826 | PRINTFB(G, FB_ObjectMolecule, FB_Blather) + | ^~~~~~~ +layer2/ObjectMolecule.cpp: In function 'int ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, const float*, int, int)': +layer2/ObjectMolecule.cpp:10955:43: warning: '%s' directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] +10955 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", + | ^~ +10956 | buffer, v[0], v[1], v[2], state + 1, mode, 0); + | ~~~~~~ +layer2/ObjectMolecule.cpp:10955:21: note: directive argument in the range [-2147483647, 2147483647] +10955 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMolecule.cpp:10955:14: note: 'sprintf' output between 78 and 2036 bytes into a destination of size 1024 +10955 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +10956 | buffer, v[0], v[1], v[2], state + 1, mode, 0); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer2/SideChainHelper.cpp -o build/temp.linux-arm64-3.9/layer2/SideChainHelper.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 aarch64-linux-gnu-g++ -pthread -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD layer3/PlugIOManager.cpp -o build/temp.linux-arm64-3.9/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer3/Executive.cpp: In function 'void ExecutiveManageObject(PyMOLGlobals*, CObject*, int, int)': layer3/Executive.cpp:14515:37: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] @@ -4614,20 +4649,6 @@ | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 7315 | buffer); | ~~~~~~~ -layer3/PlugIOManager.cpp: In function 'CObject* PlugIOManagerLoad(PyMOLGlobals*, CObject**, const char*, int, int, const char*, int)': -layer3/PlugIOManager.cpp:939:65: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 200 [-Wformat-truncation=] - 939 | " PlugIOManagerLoad: can't load trajectory into object '%s'\n", obj->Name ENDFB(G); - | ^~ -In file included from /usr/include/stdio.h:867, - 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 58 and 313 bytes into a destination of size 255 - 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 68 | __bos (__s), __fmt, __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function 'pymol::Result<> ExecutiveCopy(PyMOLGlobals*, const char*, const char*, int)': layer3/Executive.cpp:9799:25: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] 9799 | " Executive: object %s created.\n", oDst->Name ENDFB(G); @@ -4674,6 +4695,20 @@ layer3/Executive.cpp:14183:19: note: in expansion of macro 'PRINTFB' 14183 | PRINTFB(G, FB_Executive, FB_Blather) | ^~~~~~~ +layer3/PlugIOManager.cpp: In function 'CObject* PlugIOManagerLoad(PyMOLGlobals*, CObject**, const char*, int, int, const char*, int)': +layer3/PlugIOManager.cpp:939:65: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 200 [-Wformat-truncation=] + 939 | " PlugIOManagerLoad: can't load trajectory into object '%s'\n", obj->Name ENDFB(G); + | ^~ +In file included from /usr/include/stdio.h:867, + 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/aarch64-linux-gnu/bits/stdio2.h:67:35: note: '__builtin___snprintf_chk' output between 58 and 313 bytes into a destination of size 255 + 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 68 | __bos (__s), __fmt, __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In member function 'virtual int CExecutive::drag(int, int, int)': layer3/Executive.cpp:15534:55: warning: '%s' directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] 15534 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", @@ -4712,8 +4747,8 @@ aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/feedback2.c -o build/temp.linux-arm64-3.9/contrib/champ/feedback2.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/list.c -o build/temp.linux-arm64-3.9/contrib/champ/list.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/os_memory.c -o build/temp.linux-arm64-3.9/contrib/champ/os_memory.o -aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/strblock.c -o build/temp.linux-arm64-3.9/contrib/champ/strblock.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/sort.c -o build/temp.linux-arm64-3.9/contrib/champ/sort.o +aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/strblock.c -o build/temp.linux-arm64-3.9/contrib/champ/strblock.o aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/reproducible-path/pymol-2.4.0+dfsg=. -specs=/usr/share/dpkg/no-pie-compile.specs -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -Icontrib/champ -I/usr/include/python3.9 -c -MMD contrib/champ/vla.c -o build/temp.linux-arm64-3.9/contrib/champ/vla.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] @@ -5407,10 +5442,10 @@ dpkg-gencontrol: warning: package python3-pymol: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild -dpkg-deb: building package 'python3-pymol' in '../python3-pymol_2.4.0+dfsg-2_arm64.deb'. -dpkg-deb: building package 'pymol' in '../pymol_2.4.0+dfsg-2_all.deb'. dpkg-deb: building package 'python3-pymol-dbgsym' in '../python3-pymol-dbgsym_2.4.0+dfsg-2_arm64.deb'. +dpkg-deb: building package 'pymol' in '../pymol_2.4.0+dfsg-2_all.deb'. dpkg-deb: building package 'pymol-data' in '../pymol-data_2.4.0+dfsg-2_all.deb'. +dpkg-deb: building package 'python3-pymol' in '../python3-pymol_2.4.0+dfsg-2_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pymol_2.4.0+dfsg-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -5418,12 +5453,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2462350/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/2370122 and its subdirectories -I: Current time: Sun Jan 7 06:37:07 -12 2024 -I: pbuilder-time-stamp: 1704652627 +I: removing directory /srv/workspace/pbuilder/2462350 and its subdirectories +I: Current time: Sun Feb 9 15:06:15 +14 2025 +I: pbuilder-time-stamp: 1739063175