DC-Build-Header: pymol 2.4.0+dfsg-3 / 2021-10-26 21:48:32 +0000 DC-Task: type:rebuild-binarch-only source:pymol version:2.4.0+dfsg-3 chroot:unstable esttime:286 logfile:/tmp/pymol_2.4.0+dfsg-3_unstable_clang13.log modes:clang13:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang13 pymol_2.4.0+dfsg-3' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-6-254.eu-central-1.compute.internal +==============================================================================+ | pymol 2.4.0+dfsg-3 (amd64) Tue, 26 Oct 2021 21:48:32 +0000 | +==============================================================================+ Package: pymol Version: 2.4.0+dfsg-3 Source Version: 2.4.0+dfsg-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-f5c2ef4b-0a97-4e9a-9139-26bc37fca7b9' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang13 ------------ + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=13 + echo 'Install of clang-13' Install of clang-13 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [165 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [47.3 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 Packages T-2021-10-26-2004.40-F-2021-10-26-0202.15.pdiff [55.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main Translation-en [6586 kB] Fetched 6981 kB in 3s (2752 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-13 libomp-13-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc4 libomp5-13 libxml2 libz3-4 Suggested packages: clang-13-doc libomp-13-doc Recommended packages: llvm-13-dev python3 The following NEW packages will be installed: clang-13 lib32gcc-s1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-13-dev libclang-cpp13 libclang1-13 libedit2 libgc1 libgcc-9-dev libicu67 libllvm13 libmd0 libobjc-11-dev libobjc-9-dev libobjc4 libomp-13-dev libomp5-13 libxml2 libz3-4 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 68.5 MB of archives. After this operation, 379 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libmd0 amd64 1.0.4-1 [29.6 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.11.3-1 [108 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20210910-1 [97.5 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.12+dfsg-5 [696 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 libz3-4 amd64 4.8.12-1+b1 [6997 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libllvm13 amd64 1:13.0.0-8 [19.7 MB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libclang-cpp13 amd64 1:13.0.0-8 [10.5 MB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libgc1 amd64 1:8.0.4-3 [239 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 11.2.0-10 [43.2 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libobjc-11-dev amd64 11.2.0-10 [170 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.32-4 [2624 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 11.2.0-10 [49.9 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 11.2.0-10 [601 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-13-dev amd64 1:13.0.0-8 [5730 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libclang1-13 amd64 1:13.0.0-8 [6093 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 clang-13 amd64 1:13.0.0-8 [119 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.4.0-3 [2734 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.4.0-3 [2343 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.4.0-3 [219 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 libomp5-13 amd64 1:13.0.0-8 [377 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libomp-13-dev amd64 1:13.0.0-8 [482 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 68.5 MB in 0s (149 MB/s) Selecting previously unselected package libmd0:amd64. (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 ... 12431 files and directories currently installed.) Preparing to unpack .../00-libmd0_1.0.4-1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../01-libbsd0_0.11.3-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.3-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../02-libedit2_3.1-20210910-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20210910-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../03-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../04-libxml2_2.9.12+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.12+dfsg-5) ... Selecting previously unselected package libz3-4:amd64. Preparing to unpack .../05-libz3-4_4.8.12-1+b1_amd64.deb ... Unpacking libz3-4:amd64 (4.8.12-1+b1) ... Selecting previously unselected package libllvm13:amd64. Preparing to unpack .../06-libllvm13_1%3a13.0.0-8_amd64.deb ... Unpacking libllvm13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libclang-cpp13. Preparing to unpack .../07-libclang-cpp13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-cpp13 (1:13.0.0-8) ... Selecting previously unselected package libgc1:amd64. Preparing to unpack .../08-libgc1_1%3a8.0.4-3_amd64.deb ... Unpacking libgc1:amd64 (1:8.0.4-3) ... Selecting previously unselected package libobjc4:amd64. Preparing to unpack .../09-libobjc4_11.2.0-10_amd64.deb ... Unpacking libobjc4:amd64 (11.2.0-10) ... Selecting previously unselected package libobjc-11-dev:amd64. Preparing to unpack .../10-libobjc-11-dev_11.2.0-10_amd64.deb ... Unpacking libobjc-11-dev:amd64 (11.2.0-10) ... Selecting previously unselected package libc6-i386. Preparing to unpack .../11-libc6-i386_2.32-4_amd64.deb ... Unpacking libc6-i386 (2.32-4) ... Selecting previously unselected package lib32gcc-s1. Preparing to unpack .../12-lib32gcc-s1_11.2.0-10_amd64.deb ... Unpacking lib32gcc-s1 (11.2.0-10) ... Selecting previously unselected package lib32stdc++6. Preparing to unpack .../13-lib32stdc++6_11.2.0-10_amd64.deb ... Unpacking lib32stdc++6 (11.2.0-10) ... Selecting previously unselected package libclang-common-13-dev. Preparing to unpack .../14-libclang-common-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libclang-common-13-dev (1:13.0.0-8) ... Selecting previously unselected package libclang1-13. Preparing to unpack .../15-libclang1-13_1%3a13.0.0-8_amd64.deb ... Unpacking libclang1-13 (1:13.0.0-8) ... Selecting previously unselected package clang-13. Preparing to unpack .../16-clang-13_1%3a13.0.0-8_amd64.deb ... Unpacking clang-13 (1:13.0.0-8) ... Selecting previously unselected package libasan5:amd64. Preparing to unpack .../17-libasan5_9.4.0-3_amd64.deb ... Unpacking libasan5:amd64 (9.4.0-3) ... Selecting previously unselected package libgcc-9-dev:amd64. Preparing to unpack .../18-libgcc-9-dev_9.4.0-3_amd64.deb ... Unpacking libgcc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libobjc-9-dev:amd64. Preparing to unpack .../19-libobjc-9-dev_9.4.0-3_amd64.deb ... Unpacking libobjc-9-dev:amd64 (9.4.0-3) ... Selecting previously unselected package libomp5-13:amd64. Preparing to unpack .../20-libomp5-13_1%3a13.0.0-8_amd64.deb ... Unpacking libomp5-13:amd64 (1:13.0.0-8) ... Selecting previously unselected package libomp-13-dev. Preparing to unpack .../21-libomp-13-dev_1%3a13.0.0-8_amd64.deb ... Unpacking libomp-13-dev (1:13.0.0-8) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libasan5:amd64 (9.4.0-3) ... Setting up libz3-4:amd64 (4.8.12-1+b1) ... Setting up libgc1:amd64 (1:8.0.4-3) ... Setting up libmd0:amd64 (1.0.4-1) ... Setting up libc6-i386 (2.32-4) ... Setting up libomp5-13:amd64 (1:13.0.0-8) ... Setting up libbsd0:amd64 (0.11.3-1) ... Setting up libxml2:amd64 (2.9.12+dfsg-5) ... Setting up libedit2:amd64 (3.1-20210910-1) ... Setting up libobjc4:amd64 (11.2.0-10) ... Setting up libgcc-9-dev:amd64 (9.4.0-3) ... Setting up lib32gcc-s1 (11.2.0-10) ... Setting up lib32stdc++6 (11.2.0-10) ... Setting up libllvm13:amd64 (1:13.0.0-8) ... Setting up libobjc-9-dev:amd64 (9.4.0-3) ... Setting up libclang-common-13-dev (1:13.0.0-8) ... Setting up libomp-13-dev (1:13.0.0-8) ... Setting up libobjc-11-dev:amd64 (11.2.0-10) ... Setting up libclang1-13 (1:13.0.0-8) ... Setting up libclang-cpp13 (1:13.0.0-8) ... Setting up clang-13 (1:13.0.0-8) ... Processing triggers for libc-bin (2.32-4) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10 11' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-13 g++-4.6 + ln -s clang-13 gcc-4.6 + ln -s clang-13 cpp-4.6 + ln -s clang-13 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-13 g++-4.7 + ln -s clang-13 gcc-4.7 + ln -s clang-13 cpp-4.7 + ln -s clang-13 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-13 g++-4.8 + ln -s clang-13 gcc-4.8 + ln -s clang-13 cpp-4.8 + ln -s clang-13 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-13 g++-4.9 + ln -s clang-13 gcc-4.9 + ln -s clang-13 cpp-4.9 + ln -s clang-13 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-13 g++-5 + ln -s clang-13 gcc-5 + ln -s clang-13 cpp-5 + ln -s clang-13 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-13 g++-6 + ln -s clang-13 gcc-6 + ln -s clang-13 cpp-6 + ln -s clang-13 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-13 g++-7 + ln -s clang-13 gcc-7 + ln -s clang-13 cpp-7 + ln -s clang-13 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-13 g++-8 + ln -s clang-13 gcc-8 + ln -s clang-13 cpp-8 + ln -s clang-13 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-13 g++-9 + ln -s clang-13 gcc-9 + ln -s clang-13 cpp-9 + ln -s clang-13 gcc + echo 'gcc-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-13 g++-10 + ln -s clang-13 gcc-10 + ln -s clang-13 cpp-10 + ln -s clang-13 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-11 gcc-11 cpp-11 gcc + ln -s clang++-13 g++-11 + ln -s clang-13 gcc-11 + ln -s clang-13 cpp-11 + ln -s clang-13 gcc + echo 'gcc-11 hold' + dpkg --set-selections + echo 'g++-11 hold' + dpkg --set-selections + cd - /build/pymol-Q9fGgr + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang + cd /usr/bin/ + rm -f clang++ clang + ln -s clang-13 clang++ + ln -s clang-13 clang + clang++ --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + clang --version Debian clang version 13.0.0-8 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/bin + cd - /build/pymol-Q9fGgr + apt install --yes --no-install-recommends --force-yes qt5-qmake WARNING: apt does not have a stable CLI interface. Use with caution in scripts. Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: qt5-qmake-bin qtchooser The following NEW packages will be installed: qt5-qmake qt5-qmake-bin qtchooser 0 upgraded, 3 newly installed, 0 to remove and 0 not upgraded. Need to get 1322 kB of archives. After this operation, 4914 kB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake-bin amd64 5.15.2+dfsg-12 [1046 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 qtchooser amd64 66-2 [26.3 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 qt5-qmake amd64 5.15.2+dfsg-12 [249 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1322 kB in 0s (57.8 MB/s) Selecting previously unselected package qt5-qmake-bin. (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 ... 13528 files and directories currently installed.) Preparing to unpack .../qt5-qmake-bin_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake-bin (5.15.2+dfsg-12) ... Selecting previously unselected package qtchooser. Preparing to unpack .../qtchooser_66-2_amd64.deb ... Unpacking qtchooser (66-2) ... Selecting previously unselected package qt5-qmake:amd64. Preparing to unpack .../qt5-qmake_5.15.2+dfsg-12_amd64.deb ... Unpacking qt5-qmake:amd64 (5.15.2+dfsg-12) ... Setting up qt5-qmake-bin (5.15.2+dfsg-12) ... Setting up qtchooser (66-2) ... Setting up qt5-qmake:amd64 (5.15.2+dfsg-12) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. + cp /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qmake.conf /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/qplatformdefs.h /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ + ls -al /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/ total 16 drwxr-xr-x 2 root root 4096 Oct 26 21:48 . drwxr-xr-x 76 root root 4096 Oct 26 21:48 .. -rw-r--r-- 1 root root 276 Oct 26 21:48 qmake.conf -rw-r--r-- 1 root root 3218 Oct 26 21:48 qplatformdefs.h + cat /usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-g++/qmake.conf # # qmake configuration for linux-clang # MAKEFILE_GENERATOR = UNIX CONFIG += incremental QMAKE_INCREMENTAL_STYLE = sublib include(../common/linux.conf) include(../common/gcc-base-unix.conf) include(../common/clang.conf) QMAKE_LFLAGS += -ccc-gcc-name g++ load(qt_config) + export QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + QMAKESPEC=/usr/lib/x86_64-linux-gnu/qt5/mkspecs/linux-clang/ + sed -i -e 's|compare_problem(2,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + sed -i -e 's|compare_problem(1,|compare_problem(0,|g' /usr/bin/dpkg-gensymbols + grep 'compare_problem(' /usr/bin/dpkg-gensymbols compare_problem(4, g_('new libraries appeared in the symbols file: %s'), "@libs"); compare_problem(3, g_('some libraries disappeared in the symbols file: %s'), "@libs"); compare_problem(0, g_('some new symbols appeared in the symbols file: %s'), compare_problem(0, g_('some symbols or patterns disappeared in the symbols file: %s'), I: Finished running '/tmp/clang13'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/pymol-Q9fGgr/resolver-XcUGHx' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'pymol' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/debichem-team/pymol.git Please use: git clone https://salsa.debian.org/debichem-team/pymol.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 7004 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main pymol 2.4.0+dfsg-3 (dsc) [2267 B] Get:2 http://127.0.0.1:12990/debian sid/main pymol 2.4.0+dfsg-3 (tar) [6945 kB] Get:3 http://127.0.0.1:12990/debian sid/main pymol 2.4.0+dfsg-3 (diff) [56.7 kB] Fetched 7004 kB in 0s (63.1 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/pymol-Q9fGgr/pymol-2.4.0+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/pymol-Q9fGgr' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), dh-python, freeglut3-dev, libfreetype6-dev, libglew-dev, libglm-dev, libnetcdf-dev, libpng-dev, python3-all, python3-all-dev, python3-numpy, python3-opengl, python3-pyqt5, python3-pyqt5.qtopengl, texlive-latex-base, libxml2-dev, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), dh-python, freeglut3-dev, libfreetype6-dev, libglew-dev, libglm-dev, libnetcdf-dev, libpng-dev, python3-all, python3-all-dev, python3-numpy, python3-opengl, python3-pyqt5, python3-pyqt5.qtopengl, texlive-latex-base, libxml2-dev, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [465 B] Get:5 copy:/<>/apt_archive ./ Packages [548 B] Fetched 1970 B in 0s (195 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern freeglut3 freeglut3-dev gettext gettext-base groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libbrotli-dev libbrotli1 libcairo2 libcups2 libcurl3-gnutls libcurl4 libcurl4-openssl-dev libdbus-1-3 libdebhelper-perl libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libegl-dev libegl-mesa0 libegl1 libelf1 libevdev2 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype-dev libfreetype6 libfreetype6-dev libgbm1 libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1 libgles2 libglew-dev libglew2.2 libglib2.0-0 libglm-dev libglu1-mesa libglu1-mesa-dev libglvnd-core-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgraphite2-3 libgudev-1.0-0 libharfbuzz0b libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libice-dev libice6 libicu-dev libinput-bin libinput10 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 libldap-2.4-2 libllvm12 libmagic-mgc libmagic1 libmd4c0 libmpdec3 libmtdev1 libncursesw6 libnetcdf-dev libnetcdf19 libnghttp2-14 libopengl-dev libopengl0 libpaper-utils libpaper1 libpciaccess0 libpcre2-16-0 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5 libptexenc1 libpthread-stubs0-dev libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5 libqt5test5 libqt5widgets5 libqt5xml5 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsigsegv2 libsm-dev libsm6 libsqlite3-0 libssh2-1 libssl-dev libsub-override-perl libsynctex2 libsz2 libteckit0 libtexlua53 libtexluajit2 libtool libuchardet0 libvulkan1 libwacom-common libwacom2 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxi6 libxkbcommon-x11-0 libxkbcommon0 libxml2-dev libxmu6 libxpm4 libxrender1 libxshmfence1 libxt-dev libxt6 libxxf86vm1 libzzip-0-13 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-opengl python3-pkg-resources python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3.9 python3.9-dev python3.9-minimal readline-common sensible-utils shared-mime-info t1utils tex-common texlive-base texlive-binaries texlive-latex-base ucf x11-common x11proto-dev xdg-utils xkb-data xorg-sgml-doctools xtrans-dev zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make flit python3-toml gettext-doc libasprintf-dev libgettextpo-dev groff cups-common libcurl4-doc libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config freetype2-doc glew-utils libhdf5-doc libice-doc icu-doc netcdf-bin netcdf-doc pciutils libthai0 qt5-image-formats-plugins qtwayland5 lm-sensors libsm-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk libx11-doc libxcb-doc libxext-doc libxt-doc m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv gfortran python-numpy-doc python3-numpy-dbg python3-pytest libgle3 python3-setuptools python3.9-venv python3.9-doc binfmt-support readline-doc ghostscript gv | postscript-viewer perl-tk xpdf | pdf-viewer xzdec texlive-latex-base-doc Recommended packages: curl | wget | lynx ca-certificates dbus libarchive-cpio-perl libglib2.0-data xdg-user-dirs javascript-common libldap-common libgpm2 pkg-config libpng-tools publicsuffix qttranslations5-l10n libqt5svg5 qt5-gtk-platformtheme libqt5sql5-sqlite | libqt5sql5-mysql | libqt5sql5-odbc | libqt5sql5-psql | libqt5sql5-tds | libqt5sql5-ibase libsasl2-modules libltdl-dev mesa-vulkan-drivers | vulkan-icd libwacom-bin libmail-sendmail-perl lmodern dvisvgm libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core fonts-lmodern freeglut3 freeglut3-dev gettext gettext-base groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0 libarchive-zip-perl libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libbrotli-dev libbrotli1 libcairo2 libcups2 libcurl3-gnutls libcurl4 libcurl4-openssl-dev libdbus-1-3 libdebhelper-perl libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libegl-dev libegl-mesa0 libegl1 libelf1 libevdev2 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype-dev libfreetype6 libfreetype6-dev libgbm1 libgfortran5 libgl-dev libgl1 libgl1-mesa-dev libgl1-mesa-dri libglapi-mesa libgles-dev libgles1 libgles2 libglew-dev libglew2.2 libglib2.0-0 libglm-dev libglu1-mesa libglu1-mesa-dev libglvnd-core-dev libglvnd-dev libglvnd0 libglx-dev libglx-mesa0 libglx0 libgraphite2-3 libgudev-1.0-0 libharfbuzz0b libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102 libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libice-dev libice6 libicu-dev libinput-bin libinput10 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libjs-sphinxdoc libjs-underscore libkpathsea6 liblapack3 libldap-2.4-2 libllvm12 libmagic-mgc libmagic1 libmd4c0 libmpdec3 libmtdev1 libncursesw6 libnetcdf-dev libnetcdf19 libnghttp2-14 libopengl-dev libopengl0 libpaper-utils libpaper1 libpciaccess0 libpcre2-16-0 libpipeline1 libpixman-1-0 libpng-dev libpng16-16 libpsl5 libptexenc1 libpthread-stubs0-dev libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5 libqt5test5 libqt5widgets5 libqt5xml5 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsigsegv2 libsm-dev libsm6 libsqlite3-0 libssh2-1 libssl-dev libsub-override-perl libsynctex2 libsz2 libteckit0 libtexlua53 libtexluajit2 libtool libuchardet0 libvulkan1 libwacom-common libwacom2 libwayland-client0 libwayland-server0 libx11-6 libx11-data libx11-dev libx11-xcb1 libxau-dev libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev libxext6 libxfixes3 libxi6 libxkbcommon-x11-0 libxkbcommon0 libxml2-dev libxmu6 libxpm4 libxrender1 libxshmfence1 libxt-dev libxt6 libxxf86vm1 libzzip-0-13 m4 man-db media-types po-debconf python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy python3-opengl python3-pkg-resources python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3.9 python3.9-dev python3.9-minimal readline-common sbuild-build-depends-main-dummy sensible-utils shared-mime-info t1utils tex-common texlive-base texlive-binaries texlive-latex-base ucf x11-common x11proto-dev xdg-utils xkb-data xorg-sgml-doctools xtrans-dev zlib1g-dev 0 upgraded, 252 newly installed, 0 to remove and 0 not upgraded. Need to get 153 MB of archives. After this operation, 588 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [972 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdextrautils amd64 2.37.2-4 [143 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-7 [935 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.70.0-3 [1401 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 shared-mime-info amd64 2.0-1 [701 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libdouble-conversion3 amd64 3.1.5-7 [40.1 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libpcre2-16-0 amd64 10.36-2 [231 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 libqt5core5a amd64 5.15.2+dfsg-12 [1829 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.4.1-3 [104 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libfreetype6 amd64 2.11.0+dfsg-1 [453 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libdrm-common all 2.4.107-8 [15.3 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libdrm2 amd64 2.4.107-8 [44.0 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libglvnd0 amd64 1.3.4-2+b1 [51.7 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libwayland-server0 amd64 1.19.0-2+b1 [34.8 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libgbm1 amd64 21.2.4-1 [76.8 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libglapi-mesa amd64 21.2.4-1 [74.9 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 libwayland-client0 amd64 1.19.0-2+b1 [27.3 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 libx11-data all 2:1.7.2-2 [311 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 libx11-6 amd64 2:1.7.2-2+b1 [772 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 libx11-xcb1 amd64 2:1.7.2-2+b1 [203 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 libxcb-dri2-0 amd64 1.14-3 [103 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libxcb-dri3-0 amd64 1.14-3 [102 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libxcb-present0 amd64 1.14-3 [101 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libxcb-sync1 amd64 1.14-3 [105 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 libxcb-xfixes0 amd64 1.14-3 [105 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:41 http://127.0.0.1:12990/debian sid/main amd64 libegl-mesa0 amd64 21.2.4-1 [144 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libegl1 amd64 1.3.4-2+b1 [35.4 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libxcb-glx0 amd64 1.14-3 [118 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libxext6 amd64 2:1.3.4-1 [53.1 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 libxfixes3 amd64 1:5.0.3-2 [22.1 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.107-8 [29.0 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 libpciaccess0 amd64 0.16-1 [53.6 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 libdrm-intel1 amd64 2.4.107-8 [72.5 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.107-8 [27.3 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 libdrm-radeon1 amd64 2.4.107-8 [30.6 kB] Get:53 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.185-2 [172 kB] Get:54 http://127.0.0.1:12990/debian sid/main amd64 libllvm12 amd64 1:12.0.1-15 [19.4 MB] Get:55 http://127.0.0.1:12990/debian sid/main amd64 libsensors-config all 1:3.6.0-7 [32.3 kB] Get:56 http://127.0.0.1:12990/debian sid/main amd64 libsensors5 amd64 1:3.6.0-7 [52.3 kB] Get:57 http://127.0.0.1:12990/debian sid/main amd64 libvulkan1 amd64 1.2.189.0-2 [104 kB] Get:58 http://127.0.0.1:12990/debian sid/main amd64 libgl1-mesa-dri amd64 21.2.4-1 [10.3 MB] Get:59 http://127.0.0.1:12990/debian sid/main amd64 libglx-mesa0 amd64 21.2.4-1 [184 kB] Get:60 http://127.0.0.1:12990/debian sid/main amd64 libglx0 amd64 1.3.4-2+b1 [36.5 kB] Get:61 http://127.0.0.1:12990/debian sid/main amd64 libgl1 amd64 1.3.4-2+b1 [89.6 kB] Get:62 http://127.0.0.1:12990/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:63 http://127.0.0.1:12990/debian sid/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:64 http://127.0.0.1:12990/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:65 http://127.0.0.1:12990/debian sid/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:66 http://127.0.0.1:12990/debian sid/main amd64 libevdev2 amd64 1.11.0+dfsg-1 [34.0 kB] Get:67 http://127.0.0.1:12990/debian sid/main amd64 libmtdev1 amd64 1.1.6-1 [23.0 kB] Get:68 http://127.0.0.1:12990/debian sid/main amd64 libgudev-1.0-0 amd64 237-2 [15.1 kB] Get:69 http://127.0.0.1:12990/debian sid/main amd64 libwacom-common all 1.11-1 [52.2 kB] Get:70 http://127.0.0.1:12990/debian sid/main amd64 libwacom2 amd64 1.11-1 [22.3 kB] Get:71 http://127.0.0.1:12990/debian sid/main amd64 libinput-bin amd64 1.19.1-1 [25.8 kB] Get:72 http://127.0.0.1:12990/debian sid/main amd64 libinput10 amd64 1.19.1-1 [125 kB] Get:73 http://127.0.0.1:12990/debian sid/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:74 http://127.0.0.1:12990/debian sid/main amd64 libmd4c0 amd64 0.4.8-1 [44.2 kB] Get:75 http://127.0.0.1:12990/debian sid/main amd64 libdbus-1-3 amd64 1.12.20-3 [219 kB] Get:76 http://127.0.0.1:12990/debian sid/main amd64 libqt5dbus5 amd64 5.15.2+dfsg-12 [240 kB] Get:77 http://127.0.0.1:12990/debian sid/main amd64 libqt5network5 amd64 5.15.2+dfsg-12 [697 kB] Get:78 http://127.0.0.1:12990/debian sid/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:79 http://127.0.0.1:12990/debian sid/main amd64 libxcb-icccm4 amd64 0.4.1-1.1 [27.4 kB] Get:80 http://127.0.0.1:12990/debian sid/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get:81 http://127.0.0.1:12990/debian sid/main amd64 libxcb-image0 amd64 0.4.0-1+b3 [24.3 kB] Get:82 http://127.0.0.1:12990/debian sid/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get:83 http://127.0.0.1:12990/debian sid/main amd64 libxcb-randr0 amd64 1.14-3 [113 kB] Get:84 http://127.0.0.1:12990/debian sid/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:85 http://127.0.0.1:12990/debian sid/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get:86 http://127.0.0.1:12990/debian sid/main amd64 libxcb-shape0 amd64 1.14-3 [102 kB] Get:87 http://127.0.0.1:12990/debian sid/main amd64 libxcb-xinerama0 amd64 1.14-3 [101 kB] Get:88 http://127.0.0.1:12990/debian sid/main amd64 libxcb-xinput0 amd64 1.14-3 [126 kB] Get:89 http://127.0.0.1:12990/debian sid/main amd64 libxcb-xkb1 amd64 1.14-3 [126 kB] Get:90 http://127.0.0.1:12990/debian sid/main amd64 xkb-data all 2.33-1 [748 kB] Get:91 http://127.0.0.1:12990/debian sid/main amd64 libxkbcommon0 amd64 1.3.1-1 [109 kB] Get:92 http://127.0.0.1:12990/debian sid/main amd64 libxkbcommon-x11-0 amd64 1.3.1-1 [17.5 kB] Get:93 http://127.0.0.1:12990/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:94 http://127.0.0.1:12990/debian sid/main amd64 libqt5gui5 amd64 5.15.2+dfsg-12 [3403 kB] Get:95 http://127.0.0.1:12990/debian sid/main amd64 libpython3.9-minimal amd64 3.9.7-4 [804 kB] Get:96 http://127.0.0.1:12990/debian sid/main amd64 python3.9-minimal amd64 3.9.7-4 [1963 kB] Get:97 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:98 http://127.0.0.1:12990/debian sid/main amd64 media-types all 4.0.0 [30.3 kB] Get:99 http://127.0.0.1:12990/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:100 http://127.0.0.1:12990/debian sid/main amd64 libncursesw6 amd64 6.2+20210905-1 [133 kB] Get:101 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.1-2 [73.8 kB] Get:102 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.1-2 [168 kB] Get:103 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.36.0-2 [815 kB] Get:104 http://127.0.0.1:12990/debian sid/main amd64 libpython3.9-stdlib amd64 3.9.7-4 [1688 kB] Get:105 http://127.0.0.1:12990/debian sid/main amd64 python3.9 amd64 3.9.7-4 [480 kB] Get:106 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:107 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:108 http://127.0.0.1:12990/debian sid/main amd64 tex-common all 6.17 [53.6 kB] Get:109 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get:110 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get:111 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.39-3 [69.1 kB] Get:112 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.21-4 [175 kB] Get:113 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:114 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-5 [204 kB] Get:115 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:116 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get:117 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.5-1 [823 kB] Get:118 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.21-4 [510 kB] Get:119 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 13.5.2 [192 kB] Get:120 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-15 [513 kB] Get:121 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:122 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:123 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:124 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.12.0-2 [26.3 kB] Get:125 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.12.0-2 [15.5 kB] Get:126 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.14-1 [98.3 kB] Get:127 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.21-4 [1311 kB] Get:128 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:129 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:130 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 13.5.2 [1056 kB] Get:131 http://127.0.0.1:12990/debian sid/main amd64 python3-lib2to3 all 3.9.7-1 [79.4 kB] Get:132 http://127.0.0.1:12990/debian sid/main amd64 python3-distutils all 3.9.7-1 [146 kB] Get:133 http://127.0.0.1:12990/debian sid/main amd64 dh-python all 5.20211022.1 [103 kB] Get:134 http://127.0.0.1:12990/debian sid/main amd64 fonts-lmodern all 2.004.5-6.1 [4540 kB] Get:135 http://127.0.0.1:12990/debian sid/main amd64 libxi6 amd64 2:1.8-1 [84.0 kB] Get:136 http://127.0.0.1:12990/debian sid/main amd64 freeglut3 amd64 2.8.1-6 [125 kB] Get:137 http://127.0.0.1:12990/debian sid/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get:138 http://127.0.0.1:12990/debian sid/main amd64 x11proto-dev all 2021.5-1 [599 kB] Get:139 http://127.0.0.1:12990/debian sid/main amd64 libxau-dev amd64 1:1.0.9-1 [22.9 kB] Get:140 http://127.0.0.1:12990/debian sid/main amd64 libxdmcp-dev amd64 1:1.1.2-3 [42.2 kB] Get:141 http://127.0.0.1:12990/debian sid/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get:142 http://127.0.0.1:12990/debian sid/main amd64 libpthread-stubs0-dev amd64 0.4-1 [5344 B] Get:143 http://127.0.0.1:12990/debian sid/main amd64 libxcb1-dev amd64 1.14-3 [176 kB] Get:144 http://127.0.0.1:12990/debian sid/main amd64 libx11-dev amd64 2:1.7.2-2+b1 [844 kB] Get:145 http://127.0.0.1:12990/debian sid/main amd64 libglx-dev amd64 1.3.4-2+b1 [16.9 kB] Get:146 http://127.0.0.1:12990/debian sid/main amd64 libgl-dev amd64 1.3.4-2+b1 [101 kB] Get:147 http://127.0.0.1:12990/debian sid/main amd64 libglvnd-core-dev amd64 1.3.4-2+b1 [14.4 kB] Get:148 http://127.0.0.1:12990/debian sid/main amd64 libegl-dev amd64 1.3.4-2+b1 [20.4 kB] Get:149 http://127.0.0.1:12990/debian sid/main amd64 libgles1 amd64 1.3.4-2+b1 [13.2 kB] Get:150 http://127.0.0.1:12990/debian sid/main amd64 libgles2 amd64 1.3.4-2+b1 [18.3 kB] Get:151 http://127.0.0.1:12990/debian sid/main amd64 libgles-dev amd64 1.3.4-2+b1 [50.9 kB] Get:152 http://127.0.0.1:12990/debian sid/main amd64 libopengl0 amd64 1.3.4-2+b1 [32.0 kB] Get:153 http://127.0.0.1:12990/debian sid/main amd64 libopengl-dev amd64 1.3.4-2+b1 [6428 B] Get:154 http://127.0.0.1:12990/debian sid/main amd64 libglvnd-dev amd64 1.3.4-2+b1 [6188 B] Get:155 http://127.0.0.1:12990/debian sid/main amd64 libgl1-mesa-dev amd64 21.2.4-1 [54.0 kB] Get:156 http://127.0.0.1:12990/debian sid/main amd64 libglu1-mesa amd64 9.0.1-1 [168 kB] Get:157 http://127.0.0.1:12990/debian sid/main amd64 libglu1-mesa-dev amd64 9.0.1-1 [207 kB] Get:158 http://127.0.0.1:12990/debian sid/main amd64 libxext-dev amd64 2:1.3.4-1 [107 kB] Get:159 http://127.0.0.1:12990/debian sid/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:160 http://127.0.0.1:12990/debian sid/main amd64 libice-dev amd64 2:1.0.10-1 [67.1 kB] Get:161 http://127.0.0.1:12990/debian sid/main amd64 libsm-dev amd64 2:1.2.3-1 [38.0 kB] Get:162 http://127.0.0.1:12990/debian sid/main amd64 libxt-dev amd64 1:1.2.0-1 [407 kB] Get:163 http://127.0.0.1:12990/debian sid/main amd64 freeglut3-dev amd64 2.8.1-6 [179 kB] Get:164 http://127.0.0.1:12990/debian sid/main amd64 hdf5-helpers amd64 1.10.7+repack-4 [42.8 kB] Get:165 http://127.0.0.1:12990/debian sid/main amd64 icu-devtools amd64 67.1-7 [201 kB] Get:166 http://127.0.0.1:12990/debian sid/main amd64 libaec0 amd64 1.0.6-1 [20.3 kB] Get:167 http://127.0.0.1:12990/debian sid/main amd64 libsz2 amd64 1.0.6-1 [7492 B] Get:168 http://127.0.0.1:12990/debian sid/main amd64 libaec-dev amd64 1.0.6-1 [18.9 kB] Get:169 http://127.0.0.1:12990/debian sid/main amd64 libavahi-common-data amd64 0.8-5 [124 kB] Get:170 http://127.0.0.1:12990/debian sid/main amd64 libavahi-common3 amd64 0.8-5 [58.4 kB] Get:171 http://127.0.0.1:12990/debian sid/main amd64 libavahi-client3 amd64 0.8-5 [62.1 kB] Get:172 http://127.0.0.1:12990/debian sid/main amd64 libblas3 amd64 3.10.0-1 [156 kB] Get:173 http://127.0.0.1:12990/debian sid/main amd64 libbrotli-dev amd64 1.0.9-2+b2 [288 kB] Get:174 http://127.0.0.1:12990/debian sid/main amd64 libpixman-1-0 amd64 0.40.0-1 [543 kB] Get:175 http://127.0.0.1:12990/debian sid/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:176 http://127.0.0.1:12990/debian sid/main amd64 libcups2 amd64 2.3.3op2-7 [349 kB] Get:177 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get:178 http://127.0.0.1:12990/debian sid/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get:179 http://127.0.0.1:12990/debian sid/main amd64 libldap-2.4-2 amd64 2.4.59+dfsg-1 [232 kB] Get:180 http://127.0.0.1:12990/debian sid/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:181 http://127.0.0.1:12990/debian sid/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:182 http://127.0.0.1:12990/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:183 http://127.0.0.1:12990/debian sid/main amd64 libssh2-1 amd64 1.10.0-2 [178 kB] Get:184 http://127.0.0.1:12990/debian sid/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+b1 [338 kB] Get:185 http://127.0.0.1:12990/debian sid/main amd64 libcurl4 amd64 7.74.0-1.3+b1 [341 kB] Get:186 http://127.0.0.1:12990/debian sid/main amd64 libcurl4-openssl-dev amd64 7.74.0-1.3+b1 [432 kB] Get:187 http://127.0.0.1:12990/debian sid/main amd64 libexpat1-dev amd64 2.4.1-3 [156 kB] Get:188 http://127.0.0.1:12990/debian sid/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2 [190 kB] Get:189 http://127.0.0.1:12990/debian sid/main amd64 libpng-dev amd64 1.6.37-3 [298 kB] Get:190 http://127.0.0.1:12990/debian sid/main amd64 libfreetype-dev amd64 2.11.0+dfsg-1 [614 kB] Get:191 http://127.0.0.1:12990/debian sid/main amd64 libfreetype6-dev amd64 2.11.0+dfsg-1 [109 kB] Get:192 http://127.0.0.1:12990/debian sid/main amd64 libgfortran5 amd64 11.2.0-10 [710 kB] Get:193 http://127.0.0.1:12990/debian sid/main amd64 libglew2.2 amd64 2.2.0-4 [160 kB] Get:194 http://127.0.0.1:12990/debian sid/main amd64 libglew-dev amd64 2.2.0-4 [243 kB] Get:195 http://127.0.0.1:12990/debian sid/main amd64 libglm-dev all 0.9.9.8+ds-2 [183 kB] Get:196 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-103-1 amd64 1.10.7+repack-4 [1236 kB] Get:197 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-cpp-103-1 amd64 1.10.7+repack-4 [145 kB] Get:198 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-fortran-102 amd64 1.10.7+repack-4 [108 kB] Get:199 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-hl-100 amd64 1.10.7+repack-4 [84.1 kB] Get:200 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-hl-fortran-100 amd64 1.10.7+repack-4 [59.2 kB] Get:201 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-hl-cpp-100 amd64 1.10.7+repack-4 [40.2 kB] Get:202 http://127.0.0.1:12990/debian sid/main amd64 libjpeg62-turbo-dev amd64 1:2.0.6-4 [278 kB] Get:203 http://127.0.0.1:12990/debian sid/main amd64 libjpeg-dev amd64 1:2.0.6-4 [67.8 kB] Get:204 http://127.0.0.1:12990/debian sid/main amd64 libssl-dev amd64 1.1.1l-1 [1809 kB] Get:205 http://127.0.0.1:12990/debian sid/main amd64 libhdf5-dev amd64 1.10.7+repack-4 [2495 kB] Get:206 http://127.0.0.1:12990/debian sid/main amd64 libicu-dev amd64 67.1-7 [9597 kB] Get:207 http://127.0.0.1:12990/debian sid/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [315 kB] Get:208 http://127.0.0.1:12990/debian sid/main amd64 libjs-underscore all 1.9.1~dfsg-4 [100 kB] Get:209 http://127.0.0.1:12990/debian sid/main amd64 libjs-sphinxdoc all 4.2.0-5 [137 kB] Get:210 http://127.0.0.1:12990/debian sid/main amd64 libkpathsea6 amd64 2021.20210626.59705-1 [173 kB] Get:211 http://127.0.0.1:12990/debian sid/main amd64 liblapack3 amd64 3.10.0-1 [2213 kB] Get:212 http://127.0.0.1:12990/debian sid/main amd64 libnetcdf19 amd64 1:4.8.1-1 [454 kB] Get:213 http://127.0.0.1:12990/debian sid/main amd64 libnetcdf-dev amd64 1:4.8.1-1 [99.7 kB] Get:214 http://127.0.0.1:12990/debian sid/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:215 http://127.0.0.1:12990/debian sid/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:216 http://127.0.0.1:12990/debian sid/main amd64 libptexenc1 amd64 2021.20210626.59705-1 [65.1 kB] Get:217 http://127.0.0.1:12990/debian sid/main amd64 libpython3.9 amd64 3.9.7-4 [1693 kB] Get:218 http://127.0.0.1:12990/debian sid/main amd64 libpython3.9-dev amd64 3.9.7-4 [4032 kB] Get:219 http://127.0.0.1:12990/debian sid/main amd64 libpython3-dev amd64 3.9.2-3 [21.7 kB] Get:220 http://127.0.0.1:12990/debian sid/main amd64 libpython3-all-dev amd64 3.9.2-3 [1068 B] Get:221 http://127.0.0.1:12990/debian sid/main amd64 libqt5widgets5 amd64 5.15.2+dfsg-12 [2393 kB] Get:222 http://127.0.0.1:12990/debian sid/main amd64 libqt5xml5 amd64 5.15.2+dfsg-12 [150 kB] Get:223 http://127.0.0.1:12990/debian sid/main amd64 libqt5designer5 amd64 5.15.2-5 [2704 kB] Get:224 http://127.0.0.1:12990/debian sid/main amd64 libqt5sql5 amd64 5.15.2+dfsg-12 [150 kB] Get:225 http://127.0.0.1:12990/debian sid/main amd64 libqt5help5 amd64 5.15.2-5 [143 kB] Get:226 http://127.0.0.1:12990/debian sid/main amd64 libqt5opengl5 amd64 5.15.2+dfsg-12 [177 kB] Get:227 http://127.0.0.1:12990/debian sid/main amd64 libqt5printsupport5 amd64 5.15.2+dfsg-12 [231 kB] Get:228 http://127.0.0.1:12990/debian sid/main amd64 libqt5test5 amd64 5.15.2+dfsg-12 [173 kB] Get:229 http://127.0.0.1:12990/debian sid/main amd64 libsynctex2 amd64 2021.20210626.59705-1 [80.5 kB] Get:230 http://127.0.0.1:12990/debian sid/main amd64 libteckit0 amd64 2.5.10+ds1-3 [329 kB] Get:231 http://127.0.0.1:12990/debian sid/main amd64 libtexlua53 amd64 2021.20210626.59705-1 [132 kB] Get:232 http://127.0.0.1:12990/debian sid/main amd64 libtexluajit2 amd64 2021.20210626.59705-1 [267 kB] Get:233 http://127.0.0.1:12990/debian sid/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get:234 http://127.0.0.1:12990/debian sid/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:235 http://127.0.0.1:12990/debian sid/main amd64 libxaw7 amd64 2:1.0.13-1.1 [202 kB] Get:236 http://127.0.0.1:12990/debian sid/main amd64 libxml2-dev amd64 2.9.12+dfsg-5 [792 kB] Get:237 http://127.0.0.1:12990/debian sid/main amd64 libzzip-0-13 amd64 0.13.72+dfsg.1-1.1 [58.3 kB] Get:238 http://127.0.0.1:12990/debian sid/main amd64 python3-all amd64 3.9.2-3 [1056 B] Get:239 http://127.0.0.1:12990/debian sid/main amd64 python3.9-dev amd64 3.9.7-4 [508 kB] Get:240 http://127.0.0.1:12990/debian sid/main amd64 python3-dev amd64 3.9.2-3 [24.8 kB] Get:241 http://127.0.0.1:12990/debian sid/main amd64 python3-all-dev amd64 3.9.2-3 [1064 B] Get:242 http://127.0.0.1:12990/debian sid/main amd64 python3-pkg-resources all 58.2.0-1 [192 kB] Get:243 http://127.0.0.1:12990/debian sid/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:244 http://127.0.0.1:12990/debian sid/main amd64 python3-opengl all 3.1.5+dfsg-1 [610 kB] Get:245 http://127.0.0.1:12990/debian sid/main amd64 python3-pyqt5.sip amd64 12.9.0-3 [55.8 kB] Get:246 http://127.0.0.1:12990/debian sid/main amd64 python3-pyqt5 amd64 5.15.5+dfsg-1 [2472 kB] Get:247 http://127.0.0.1:12990/debian sid/main amd64 python3-pyqt5.qtopengl amd64 5.15.5+dfsg-1 [208 kB] Get:248 http://127.0.0.1:12990/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:249 http://127.0.0.1:12990/debian sid/main amd64 texlive-binaries amd64 2021.20210626.59705-1 [10.1 MB] Get:250 http://127.0.0.1:12990/debian sid/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:251 http://127.0.0.1:12990/debian sid/main amd64 texlive-base all 2021.20210921-1 [21.1 MB] Get:252 http://127.0.0.1:12990/debian sid/main amd64 texlive-latex-base all 2021.20210921-1 [1150 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 153 MB in 1s (137 MB/s) Selecting previously unselected package bsdextrautils. 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Setting up liblapack3:amd64 (3.10.0-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up gettext (0.21-4) ... Setting up libxau-dev:amd64 (1:1.0.9-1) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libice-dev:amd64 (2:1.0.10-1) ... Setting up libtool (2.4.6-15) ... Setting up libreadline8:amd64 (8.1-2) ... Setting up libpng-dev:amd64 (1.6.37-3) ... Setting up libaec-dev:amd64 (1.0.6-1) ... Setting up libavahi-common3:amd64 (0.8-5) ... Setting up libjpeg-dev:amd64 (1:2.0.6-4) ... Setting up libxext6:amd64 (2:1.3.4-1) ... Setting up libldap-2.4-2:amd64 (2.4.59+dfsg-1) ... Setting up m4 (1.4.18-5) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+b1) ... Setting up libqt5network5:amd64 (5.15.2+dfsg-12) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libqt5sql5:amd64 (5.15.2+dfsg-12) ... Setting up libxdmcp-dev:amd64 (1:1.1.2-3) ... Setting up libqt5xml5:amd64 (5.15.2+dfsg-12) ... Setting up libxml2-dev:amd64 (2.9.12+dfsg-5) ... Setting up libptexenc1:amd64 (2021.20210626.59705-1) ... Setting up libfreetype6:amd64 (2.11.0+dfsg-1) ... Setting up libxfixes3:amd64 (1:5.0.3-2) ... Setting up libxkbcommon-x11-0:amd64 (1.3.1-1) ... Setting up ucf (3.0043) ... Setting up libjs-sphinxdoc (4.2.0-5) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.12.0-2) ... Setting up libdrm2:amd64 (2.4.107-8) ... Setting up dwz (0.14-1) ... Setting up groff-base (1.22.4-7) ... Setting up libcurl4:amd64 (7.74.0-1.3+b1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libwacom2:amd64 (1.11-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-5) ... Setting up libpython3.9-stdlib:amd64 (3.9.7-4) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.107-8) ... Setting up automake (1:1.16.5-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libdrm-nouveau2:amd64 (2.4.107-8) ... Setting up libxcb1-dev:amd64 (1.14-3) ... Setting up libxi6:amd64 (2:1.8-1) ... Setting up libgbm1:amd64 (21.2.4-1) ... Setting up libsm-dev:amd64 (2:1.2.3-1) ... Setting up libdrm-radeon1:amd64 (2.4.107-8) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libdrm-intel1:amd64 (2.4.107-8) ... Setting up libgl1-mesa-dri:amd64 (21.2.4-1) ... Setting up libx11-dev:amd64 (2:1.7.2-2+b1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libinput-bin (1.19.1-1) ... Setting up libfreetype-dev:amd64 (2.11.0+dfsg-1) ... Setting up dh-autoreconf (20) ... Setting up tex-common (6.17) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libegl-mesa0:amd64 (21.2.4-1) ... Setting up libpython3.9:amd64 (3.9.7-4) ... Setting up libcurl4-openssl-dev:amd64 (7.74.0-1.3+b1) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libxext-dev:amd64 (2:1.3.4-1) ... Setting up libcups2:amd64 (2.3.3op2-7) ... Setting up libhdf5-103-1:amd64 (1.10.7+repack-4) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.7+repack-4) ... Setting up libegl1:amd64 (1.3.4-2+b1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3.9 (3.9.7-4) ... Setting up libhdf5-hl-100:amd64 (1.10.7+repack-4) ... Setting up libinput10:amd64 (1.19.1-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up libglx-mesa0:amd64 (21.2.4-1) ... Setting up libglx0:amd64 (1.3.4-2+b1) ... Setting up libpython3.9-dev:amd64 (3.9.7-4) ... Setting up debhelper (13.5.2) ... Setting up python3 (3.9.2-3) ... Setting up libxaw7:amd64 (2:1.0.13-1.1) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up libfreetype6-dev:amd64 (2.11.0+dfsg-1) ... Setting up libhdf5-hl-cpp-100:amd64 (1.10.7+repack-4) ... Setting up libgl1:amd64 (1.3.4-2+b1) ... Setting up libxt-dev:amd64 (1:1.2.0-1) ... Setting up libhdf5-fortran-102:amd64 (1.10.7+repack-4) ... Setting up libglew2.2:amd64 (2.2.0-4) ... Setting up libnetcdf19:amd64 (1:4.8.1-1) ... Setting up python3-pyqt5.sip (12.9.0-3) ... Setting up python3.9-dev (3.9.7-4) ... Setting up texlive-binaries (2021.20210626.59705-1) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libhdf5-hl-fortran-100:amd64 (1.10.7+repack-4) ... Setting up libglx-dev:amd64 (1.3.4-2+b1) ... Setting up libglu1-mesa:amd64 (9.0.1-1) ... Setting up python3-lib2to3 (3.9.7-1) ... Setting up texlive-base (2021.20210921-1) ... /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. /usr/bin/which: this version of `which' is deprecated; use `command -v' in scripts instead. tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libgl-dev:amd64 (1.3.4-2+b1) ... Setting up python3-pkg-resources (58.2.0-1) ... Setting up python3-distutils (3.9.7-1) ... Setting up dh-python (5.20211022.1) ... Setting up libpython3-dev:amd64 (3.9.2-3) ... Setting up freeglut3:amd64 (2.8.1-6) ... Setting up libegl-dev:amd64 (1.3.4-2+b1) ... Setting up libqt5gui5:amd64 (5.15.2+dfsg-12) ... Setting up python3-all (3.9.2-3) ... Setting up libqt5widgets5:amd64 (5.15.2+dfsg-12) ... Setting up python3-opengl (3.1.5+dfsg-1) ... Setting up libqt5help5:amd64 (5.15.2-5) ... Setting up libqt5printsupport5:amd64 (5.15.2+dfsg-12) ... Setting up texlive-latex-base (2021.20210921-1) ... Setting up libpython3-all-dev:amd64 (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up libhdf5-dev (1.10.7+repack-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libglu1-mesa-dev:amd64 (9.0.1-1) ... Setting up libnetcdf-dev (1:4.8.1-1) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up libqt5opengl5:amd64 (5.15.2+dfsg-12) ... Setting up libgles-dev:amd64 (1.3.4-2+b1) ... Setting up python3-all-dev (3.9.2-3) ... Setting up libqt5designer5:amd64 (5.15.2-5) ... Setting up libglvnd-dev:amd64 (1.3.4-2+b1) ... Setting up libglew-dev:amd64 (2.2.0-4) ... Setting up libgl1-mesa-dev:amd64 (21.2.4-1) ... Setting up python3-pyqt5 (5.15.5+dfsg-1) ... Setting up python3-pyqt5.qtopengl (5.15.5+dfsg-1) ... Setting up freeglut3-dev:amd64 (2.8.1-6) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.32-4) ... Processing triggers for tex-common (6.17) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.37-7 dpkg-dev_1.20.9 g++-11_11.2.0-10 gcc-11_11.2.0-10 libc6-dev_2.32-4 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 linux-libc-dev_5.14.12-1 Package versions: adduser_3.118 apt_2.3.11 autoconf_2.71-2 automake_1:1.16.5-1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b2 binutils_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-4 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libpixman-1-0_0.40.0-1 libpng-dev_1.6.37-3 libpng16-16_1.6.37-3 libpsl5_0.21.0-1.2 libptexenc1_2021.20210626.59705-1 libpthread-stubs0-dev_0.4-1 libpython3-all-dev_3.9.2-3 libpython3-dev_3.9.2-3 libpython3-stdlib_3.9.2-3 libpython3.9_3.9.7-4 libpython3.9-dev_3.9.7-4 libpython3.9-minimal_3.9.7-4 libpython3.9-stdlib_3.9.7-4 libqt5core5a_5.15.2+dfsg-12 libqt5dbus5_5.15.2+dfsg-12 libqt5designer5_5.15.2-5 libqt5gui5_5.15.2+dfsg-12 libqt5help5_5.15.2-5 libqt5network5_5.15.2+dfsg-12 libqt5opengl5_5.15.2+dfsg-12 libqt5printsupport5_5.15.2+dfsg-12 libqt5sql5_5.15.2+dfsg-12 libqt5test5_5.15.2+dfsg-12 libqt5widgets5_5.15.2+dfsg-12 libqt5xml5_5.15.2+dfsg-12 libquadmath0_11.2.0-10 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.2-2 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsensors-config_1:3.6.0-7 libsensors5_1:3.6.0-7 libsepol1_3.1-1 libsigsegv2_2.13-1 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl-dev_1.1.1l-1 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10 libstdc++6_11.2.0-10 libsub-override-perl_0.09-2 libsynctex2_2021.20210626.59705-1 libsystemd0_249.5-1 libsz2_1.0.6-1 libtasn1-6_4.17.0-2 libteckit0_2.5.10+ds1-3 libtexlua53_2021.20210626.59705-1 libtexluajit2_2021.20210626.59705-1 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-10 libubsan1_11.2.0-10 libuchardet0_0.0.7-1 libudev1_249.5-1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libvulkan1_1.2.189.0-2 libwacom-common_1.11-1 libwacom2_1.11-1 libwayland-client0_1.19.0-2+b1 libwayland-server0_1.19.0-2+b1 libx11-6_2:1.7.2-2+b1 libx11-data_2:1.7.2-2 libx11-dev_2:1.7.2-2+b1 libx11-xcb1_2:1.7.2-2+b1 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxaw7_2:1.0.13-1.1 libxcb-dri2-0_1.14-3 libxcb-dri3-0_1.14-3 libxcb-glx0_1.14-3 libxcb-icccm4_0.4.1-1.1 libxcb-image0_0.4.0-1+b3 libxcb-keysyms1_0.4.0-1+b2 libxcb-present0_1.14-3 libxcb-randr0_1.14-3 libxcb-render-util0_0.3.9-1+b1 libxcb-render0_1.14-3 libxcb-shape0_1.14-3 libxcb-shm0_1.14-3 libxcb-sync1_1.14-3 libxcb-util1_0.4.0-1+b1 libxcb-xfixes0_1.14-3 libxcb-xinerama0_1.14-3 libxcb-xinput0_1.14-3 libxcb-xkb1_1.14-3 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.4-1 libxext6_2:1.3.4-1 libxfixes3_1:5.0.3-2 libxi6_2:1.8-1 libxkbcommon-x11-0_1.3.1-1 libxkbcommon0_1.3.1-1 libxml2_2.9.12+dfsg-5 libxml2-dev_2.9.12+dfsg-5 libxmu6_2:1.1.2-2+b3 libxpm4_1:3.5.12-1 libxrender1_1:0.9.10-1 libxshmfence1_1.3-1 libxt-dev_1:1.2.0-1 libxt6_1:1.2.0-1 libxxf86vm1_1:1.1.4-1+b2 libxxhash0_0.8.0-2 libz3-4_4.8.12-1+b1 libzstd1_1.4.8+dfsg-3 libzzip-0-13_0.13.72+dfsg.1-1.1 linux-libc-dev_5.14.12-1 login_1:4.8.1-1 logsave_1.46.4-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-4 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-all_3.9.2-3 python3-all-dev_3.9.2-3 python3-dev_3.9.2-3 python3-distutils_3.9.7-1 python3-lib2to3_3.9.7-1 python3-minimal_3.9.2-3 python3-numpy_1:1.19.5-1 python3-opengl_3.1.5+dfsg-1 python3-pkg-resources_58.2.0-1 python3-pyqt5_5.15.5+dfsg-1 python3-pyqt5.qtopengl_5.15.5+dfsg-1 python3-pyqt5.sip_12.9.0-3 python3.9_3.9.7-4 python3.9-dev_3.9.7-4 python3.9-minimal_3.9.7-4 qt5-qmake_5.15.2+dfsg-12 qt5-qmake-bin_5.15.2+dfsg-12 qtchooser_66-2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 shared-mime-info_2.0-1 sysvinit-utils_3.00-1 t1utils_1.41-4 tar_1.34+dfsg-1 tex-common_6.17 texlive-base_2021.20210921-1 texlive-binaries_2021.20210626.59705-1 texlive-latex-base_2021.20210921-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.2-4 x11-common_1:7.7+23 x11proto-dev_2021.5-1 xdg-utils_1.1.3-4.1 xkb-data_2.33-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pymol Binary: pymol, python3-pymol, pymol-data Architecture: any all Version: 2.4.0+dfsg-3 Maintainer: Debichem Team Uploaders: Michael Banck Homepage: http://www.pymol.org Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/debichem-team/pymol Vcs-Git: https://salsa.debian.org/debichem-team/pymol.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 12), dh-python, freeglut3-dev, libfreetype6-dev, libglew-dev, libglm-dev, libnetcdf-dev, libpng-dev, python3-all, python3-all-dev, python3-numpy, python3-opengl, python3-pyqt5, python3-pyqt5.qtopengl, texlive-latex-base, libxml2-dev Package-List: pymol deb science optional arch=all pymol-data deb science optional arch=all python3-pymol deb python optional arch=any Checksums-Sha1: dced7aa83bd2a796f3d2ee99445fadda9b26ef29 6945056 pymol_2.4.0+dfsg.orig.tar.xz e6af994852332d3424acc4546194c7f2285a76e8 56680 pymol_2.4.0+dfsg-3.debian.tar.xz Checksums-Sha256: d637798f832189e39a479fb6e688a23680c03d14bbdc215b30bd52fcc1b885b8 6945056 pymol_2.4.0+dfsg.orig.tar.xz 706e3433cfed55c18daeb1aa01fea2d89d987836ca48586cb796f074383fbf00 56680 pymol_2.4.0+dfsg-3.debian.tar.xz Files: f58c9ed287144383453efb4050f61339 6945056 pymol_2.4.0+dfsg.orig.tar.xz 9717f041e40145b2c42b657982cd53fe 56680 pymol_2.4.0+dfsg-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmFdXLQACgkQr8/sjmac 4cKyYRAAmBXfsqQR4EUYAb6r44iku4+dRKOqmgbykMzngQ3PN5RNIHcLCesMkEnm knIkJk3iQat3+nlisXA6wCU0+uOA1suzMFLvlngTFiuf1dQd1QvsAyCgKN9JtGJ2 KcuYRo0LFpYeHZxtMXWWG3GgJNRfkpo6uWe1zoaGttlLWxwO6eLn0QupPSmc4KaZ b8drt6qJqSXDT7pD2BjcepGSbPagSScjdjhJyc+k0Zq5r7gV4mafGUmVKUzk7N5+ +13Y09FcWGYgaYcR0Kv9xKbBGvJWkJOg1RbZhpVzLIUsyXZPJlTCrtwn1uBT/3F2 r2toW6lQgPneDtKKUmPStxpbma2IQHmmVIY+lkfJc/dp9k36/4ZH6tp+J0p/z5sC v4DjMj3DQMdcY2WGi2JXjA62cXjHTGuehDqhh62fZ8pLKlm1roTj0AqevcPuLvWP pqwG4iQPCmUGJ18Ow2oF7k3MqPuW1IDLWdr4K12MtBJJY8xU/A27hIUok/qBlA9w Eng3pX0gWk5gBjPUw6SbZb/8il75ZiQoCQH7fgU0o1iLuxj0Rc+jiCjM8HXRdp0h D1JImxnbYJwZLN7dokSvOBSmVi8BiSGKgxmr4dChNS5z0yn6uz9f2oEQJV9X0LoN PkO9eljFCyPxoDcofIHhX2FZtxZaZOjlEc01OCUjY9AZchgEuGU= =G1ak -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.V_6R6mqi/trustedkeys.kbx': General error gpgv: Signature made Wed Oct 6 08:22:12 2021 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pymol_2.4.0+dfsg-3.dsc dpkg-source: info: extracting pymol in /<> dpkg-source: info: unpacking pymol_2.4.0+dfsg.orig.tar.xz dpkg-source: info: unpacking pymol_2.4.0+dfsg-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 02_test-suite.patch dpkg-source: info: applying 03_povray.patch dpkg-source: info: applying 22_fix_pymol_import.patch dpkg-source: info: applying 27_fix_pymol_path_in_setup.patch dpkg-source: info: applying 28_no_data_install_in_python_path.patch dpkg-source: info: applying 31_fix_format-security.patch dpkg-source: info: applying 32_fix_spelling_lintian_warnings.patch dpkg-source: info: applying 33_fix_relative_paths_in_example_scripts.patch dpkg-source: info: applying 34_fix_examples_add_fetch_instead_of_load.patch dpkg-source: info: applying 40_mstop_movies.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-f5c2ef4b-0a97-4e9a-9139-26bc37fca7b9 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package pymol dpkg-buildpackage: info: source version 2.4.0+dfsg-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Graham Inggs dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.9_pymol/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/<>' rm -f -r build test/tmp test/cmp generated dh_clean debian/pymol.launch debian/pymol-ref-card.* \ Rules.make create_shadertext.pyc make[1]: Leaving directory '/<>' debian/rules build dh build --with python3 --buildsystem pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/Setting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/TextEditor.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/PyMOLMapLoad.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/ColorEditor.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/Demo.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/SetEditor.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/volume.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk copying modules/pmg_tk/PMGApp.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins copying modules/pmg_tk/skins/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/ModalWindow.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins/normal copying modules/pmg_tk/skins/normal/builder.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins/normal creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins/demo copying modules/pmg_tk/skins/demo/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/skins/demo creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/startup copying modules/pmg_tk/startup/apbs_tools.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/startup copying modules/pmg_tk/startup/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_tk/startup creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/file_dialogs.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/pymol_qt_gui.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/mimic_pmg_tk.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/TextEditor.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/keymapping.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/mimic_tk.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/builder.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/pymol_gl_widget.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/properties_dialog.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/volume.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt copying modules/pmg_qt/advanced_settings_gui.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms creating /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/syntax copying modules/pmg_qt/syntax/python.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/syntax copying modules/pmg_qt/syntax/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/syntax copying modules/pmg_qt/syntax/pml.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/syntax copying modules/pmg_qt/syntax/pmlparser.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/syntax creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/constants_palette.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/morphing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/wizarding.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/checking.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/lazyio.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/selecting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/cmd.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/callback.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/api.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/editing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/parser.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/povray.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/__main__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/selector.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/locking.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/keywords.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/helping.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/setting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/vfont.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/moving.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/editor.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/experimenting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/viewing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/xwin.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/completing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/keyboard.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/commanding.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/_gui.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/exporting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/parsing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/util.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/movie.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/menu.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/externing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/gui.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/monitoring.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/constants.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/importing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/colorramping.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/cgo.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/diagnosing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/headering.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/invocation.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/controlling.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/seqalign.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/fitting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/colorprinting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/xray.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/pymolhttpd.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/querying.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/feedingback.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/shortcut.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/rpc.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/computing.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/creating.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/preset.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol copying modules/pymol/internal.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/stereochemistry copying modules/pymol/stereochemistry/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/stereochemistry creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins copying modules/pymol/plugins/legacysupport.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins copying modules/pymol/plugins/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins copying modules/pymol/plugins/installation.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins copying modules/pymol/plugins/managergui.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins copying modules/pymol/plugins/repository.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins copying modules/pymol/plugins/managergui_qt.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/plugins creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/contrib copying modules/pymol/contrib/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/contrib creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl copying modules/pymol/opengl/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl/glut copying modules/pymol/opengl/glut/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl/glut creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl/gl copying modules/pymol/opengl/gl/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl/gl creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl/glu copying modules/pymol/opengl/glu/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/opengl/glu creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/Qt copying modules/pymol/Qt/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/Qt copying modules/pymol/Qt/utils.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/Qt creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/appearance.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/pair_fit.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/renaming.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/annotation.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/sculpting.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/benchmark.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/box.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/message.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/charge.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/command.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/pseudoatom.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/nucmutagenesis.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/dragging.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/openvr.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/security.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/demo.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/toggle.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/measurement.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/stereodemo.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/label.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/fedora.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/mutagenesis.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/cleanup.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/density.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/distance.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard copying modules/pymol/wizard/filter.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol/wizard creating /<>/.pybuild/cpython3_3.9_pymol/build/pymol2 copying modules/pymol2/cmd2.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol2 copying modules/pymol2/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/pymol2 creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/mmd.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/bonds.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/bond_amber.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/dictdb.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/water_residues.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/pdb.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/models.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/arc.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/place.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/brick.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/map.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/gms.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/xyz.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/cif.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/protein_mmff.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/solvate.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/charge.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/protein_residues.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/neighbor.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/protein_amber.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/mass.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/mae.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/mol2.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/pkl.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/mol.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/sdf.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/hetatm.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/water_amber.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/io.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/gamess1.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/lst.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/protein_amber99.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/cpv.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/bond_mmff.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/protein.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy copying modules/chempy/cc1.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy/champ copying modules/chempy/champ/amber99.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/champ copying modules/chempy/champ/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/champ copying modules/chempy/champ/formal_charges.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/champ copying modules/chempy/champ/assign.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/champ creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy/bmin copying modules/chempy/bmin/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/bmin copying modules/chempy/bmin/state.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/bmin copying modules/chempy/bmin/realtime.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/bmin copying modules/chempy/bmin/util.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/bmin copying modules/chempy/bmin/commands.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/bmin creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy/fast copying modules/chempy/fast/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/fast creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy/tinker copying modules/chempy/tinker/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/tinker copying modules/chempy/tinker/state.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/tinker copying modules/chempy/tinker/realtime.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/tinker copying modules/chempy/tinker/keyword.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/tinker copying modules/chempy/tinker/amber.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/tinker creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy/fragments copying modules/chempy/fragments/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/fragments creating /<>/.pybuild/cpython3_3.9_pymol/build/chempy/mmtf copying modules/chempy/mmtf/__init__.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/mmtf copying modules/chempy/mmtf/io.py -> /<>/.pybuild/cpython3_3.9_pymol/build/chempy/mmtf copying modules/pmg_qt/forms/props.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/png.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/save_molecule.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/load_mae.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/save_object.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/movieexport.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/pluginmanager.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/load_map.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/load_mtz.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/load_traj.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/fetch.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/render.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/colors.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/pluginitem.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/load_aln.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms copying modules/pmg_qt/forms/askpartial.ui -> /<>/.pybuild/cpython3_3.9_pymol/build/pmg_qt/forms running build_ext building 'pymol._cmd' extension creating build/temp.linux-x86_64-3.9 creating build/temp.linux-x86_64-3.9/build creating build/temp.linux-x86_64-3.9/build/generated creating build/temp.linux-x86_64-3.9/contrib creating build/temp.linux-x86_64-3.9/contrib/uiuc creating build/temp.linux-x86_64-3.9/contrib/uiuc/plugins creating build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin creating build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src creating build/temp.linux-x86_64-3.9/layer0 creating build/temp.linux-x86_64-3.9/layer1 creating build/temp.linux-x86_64-3.9/layer2 creating build/temp.linux-x86_64-3.9/layer3 creating build/temp.linux-x86_64-3.9/layer4 creating build/temp.linux-x86_64-3.9/layer5 creating build/temp.linux-x86_64-3.9/modules creating build/temp.linux-x86_64-3.9/modules/cealign creating build/temp.linux-x86_64-3.9/modules/cealign/src creating build/temp.linux-x86_64-3.9/ov creating build/temp.linux-x86_64-3.9/ov/src x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include -I/usr/include/freetype2 -I/usr/include/libxml2 -I/usr/include/python3.9 -c -MMD build/generated/ShaderText.cpp -o build/temp.linux-x86_64-3.9/build/generated/ShaderText.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/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 contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:413:14: warning: variable 'len' set but not used [-Wunused-but-set-variable] fio_size_t len = 0; ^ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integers of different signs: 'fio_size_t' (aka 'long') and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] if (rc != iov[i].iov_len) ~~ ^ ~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:532:14: warning: variable 'len' set but not used [-Wunused-but-set-variable] fio_size_t len = 0; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:413:14: warning: variable 'len' set but not used [-Wunused-but-set-variable] fio_size_t len = 0; ^ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integers of different signs: 'fio_size_t' (aka 'long') and 'const size_t' (aka 'const unsigned long') [-Wsign-compare] if (rc != iov[i].iov_len) ~~ ^ ~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:532:14: warning: variable 'len' set but not used [-Wunused-but-set-variable] fio_size_t len = 0; ^ 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: unused function 'get_pte_idx' [-Wunused-function] static int get_pte_idx(const char *label) ^ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:273:8: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] if(ok) { ^ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:271:1: note: previous statement is here if(ok) ok = ok && (molfile_xyzplugin_init() == VMDPLUGIN_SUCCESS); ^ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:413:8: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return ok; ^ contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:411:1: note: previous statement is here if(ok) ok = ok && (molfile_xyzplugin_fini() == VMDPLUGIN_SUCCESS); ^ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:204:54: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:222:26: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] if (input_integer[0] != dcdcordmagic) { ~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:399:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:416:45: warning: comparison of integers of different signs: 'unsigned int' and 'int' [-Wsign-compare] if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] fio_size_t readlen; /* number of bytes actually read */ ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: unused function 'fio_readv' [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: unused function 'fio_read_int32' [-Wunused-function] static int fio_read_int32(fio_fd fd, int *i) { ^ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:609:12: warning: unused function 'fio_write_str' [-Wunused-function] static int fio_write_str(fio_fd fd, const char *str) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: unused function 'swap2_unaligned' [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: unused function 'swap2_aligned' [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: unused function 'fio_readv' [-Wunused-function] static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: unused function 'swap2_unaligned' [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: unused function 'swap4_unaligned' [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: unused function 'swap8_unaligned' [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ 2 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/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/abinitplugin.c:279:19: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (i = 0; i < strlen(line); ++i) { ~ ^ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(data->file, "%*s %f %f %f", &x, &y, &z); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(skip, 1, 8, fp); ^~~~~ ~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1497:10: warning: variable 'bc' set but not used [-Wunused-but-set-variable] int i, bc = 0; ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable 'i' [-Wunused-variable] int i, uid; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] char oldChain[8]; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable 'j' [-Wunused-variable] int i, count, atomdata, pos, idx, xyzcount, j; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable 'bondTable' [-Wunused-variable] int bondTable[32]; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] molfile_atom_t * atom; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] int test = parser->nbonds + bnum; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] char modelNum[8]; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable 'bondTable' [-Wunused-variable] int bondTable[32]; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] int i, pos, j, k; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] char modelNum[8]; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] molfile_atom_t * atom; ^ contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable 'fd' [-Wunused-variable] FILE* fd; ^ 14 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/dlpolyplugin.c -o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:295:5: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] if (NULL == fgets(fbuffer, 1024, data->file)) ^ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:292:3: note: previous statement is here if (NULL == fgets(fbuffer, 1024, data->file)) ^ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:554:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(fbuffer, 1024, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:669:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(fbuffer, 1024, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ 3 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 13 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(fileHeader, sizeof(short), 19, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(brick, sizeof(char), 512, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 7 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(intHeader, sizeof(int), 5, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(floatHeader, sizeof(float), 6, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. 9 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.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:459:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (&len, sizeof(int), 1, fp); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (str, len, 1, fp); ^~~~~ ~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable 'i' [-Wunused-variable] int i,j,k; ^ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 1, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 1, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 2, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 2, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 4, 1, fp); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread (ptr, 8, 1, fp); ^~~~~ ~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/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/basissetplugin.c:42: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (i=0; i>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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/bgfplugin.cpp -o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ 9 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(magicchar,sizeof(char),4,fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&igarb,sizeof(int),1,fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, "%3s", keyWord); ^~~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:109:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %f %f %f %f %f %f", keyWord, ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %f", keyWord, &prod); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %f", keyWord, &plus); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, " %s %f", keyWord, &sigma); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(brick, sizeof(char), 512, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 13 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 9 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable 'type' set but not used [-Wunused-but-set-variable] char *name, *type; ^ contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable 'name' set but not used [-Wunused-but-set-variable] char *name, *type; ^ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ 21 warnings generated. 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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/ccp4plugin.cpp -o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:782:33: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (strlen(atoms[i].type) > fw) { ~~~~~~~~~~~~~~~~~~~~~ ^ ~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28: contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: unused function 'swap2_unaligned' [-Wunused-function] static void swap2_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: unused function 'swap4_unaligned' [-Wunused-function] static void swap4_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: unused function 'swap8_unaligned' [-Wunused-function] static void swap8_unaligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: unused function 'swap2_aligned' [-Wunused-function] static void swap2_aligned(void *v, long ndata) { ^ contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: unused function 'swap8_aligned' [-Wunused-function] static void swap8_aligned(void *v, long ndata) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: unused function 'fort_eat_recmark' [-Wunused-function] static int fort_eat_recmark(FILE *ifp, int recmarklen) { ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: unused function 'fort_get_endian_reclen' [-Wunused-function] static int fort_get_endian_reclen(int reclen, int word0, int word1, ^ contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: unused function 'fortread_4' [-Wunused-function] static int fortread_4(void *dest, int n, int swap, FILE *fd) { ^ contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:304:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(symData, 81, fd); ^~~~~ ~~~~~~~~~~~~~~~ 1 warning generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 9 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:175:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1023, cube->fd); // go on to next line ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1023, cube->fd); // skip second header line ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:326:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1023, cube->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:337:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1023, cube->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:339:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(cube->fd, "%d", &cube->nsets); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:344:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(cube->fd, "%d", &orb); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1023, cube->fd); // gobble up rest of line ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 7 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/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/rst7plugin.c:67:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(title, 82, fd); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:70:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 82, fd); ^~~~~ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:48:11: warning: variable 'timesteprst' set but not used [-Wunused-but-set-variable] double timesteprst; ^ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:224:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ 3 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 10 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:237:60: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:282:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: unused function 'vasp_timestep_unitcell' [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(datablock, total * sizeof(float), 1, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 10 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/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/vaspoutcarplugin.c:87:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:204:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:239:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:242:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ 5 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 7 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: unused function 'vasp_timestep_unitcell' [-Wunused-function] static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/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/uhbdplugin.cpp:102:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&headersize, sizeof(int), 1, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 9 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Deferred.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:69:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:73:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ 12 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Err.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:89:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:92:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:97:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:111:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:121:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, poscar); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:228:27: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 4; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:233:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:237:32: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:252:44: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] for (i = 0; i < 10 - data->version; ++i) fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:283:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ 11 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:86:8: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:92:8: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:139:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:144:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(lineptr, LINESIZE, data->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 5 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Feedback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/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:44:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ^~~~~ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:240:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 13, edm->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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/fs4plugin.cpp -o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:306:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:371:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:241:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:250:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:297:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:365:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:387:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:395:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(nextline, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, bgf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (i=0; ifile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:241:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:278:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:297:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:319:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:357:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mdf->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: unused function 'iswhiteline' [-Wunused-function] static int iswhiteline(char *s) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: unused function 'strtoupper' [-Wunused-function] static char *strtoupper(char *s) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: unused function 'thisline' [-Wunused-function] static void thisline(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: unused function 'whereami' [-Wunused-function] static void whereami(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: unused function 'print_matrix4' [-Wunused-function] static void print_matrix4(const float mat[16]) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1028:12: warning: unused function 'fpexpftoc' [-Wunused-function] static int fpexpftoc(char *ftocstr) { ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:162: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: unused function 'get_pte_label' [-Wunused-function] static const char *get_pte_label(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: unused function 'get_pte_mass' [-Wunused-function] static float get_pte_mass(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: unused function 'get_pte_vdw_radius' [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: unused function 'get_pte_idx' [-Wunused-function] static int get_pte_idx(const char *label) ^ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1002:13: warning: unused function 'print_input_data' [-Wunused-function] static void print_input_data(qmdata_t *data) { ^ 9 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Field.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:74:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:81:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_name ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:82:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); // Read the molecule info ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:91:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); // Read and ignore the mol_type ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, fd); // Read the charge_type ^~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:127:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:138:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:199:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:209:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:289:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, LINESIZE, mol2->file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~ 9 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 11 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:238:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 1024, fd); // go on to next line ^~~~~ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:408:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:442:15: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:444:15: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:446:15: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:448:15: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:450:15: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:473:17: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:508:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(readbuf, 256, xsf->fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (i=0; ifile, "%d", &natm); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:596:25: warning: variable 'hessian_data' set but not used [-Wunused-but-set-variable] molfile_qm_hessian_t *hessian_data; ^ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1165:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(data->file, " Ene= %f\n", &orbenergy); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1166:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(data->file, " Spin= %s\n", spin); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1167:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(data->file, " Occup= %f\n", &occu); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: unused function 'get_pte_label' [-Wunused-function] static const char *get_pte_label(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: unused function 'get_pte_mass' [-Wunused-function] static float get_pte_mass(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: unused function 'get_pte_vdw_radius' [-Wunused-function] static float get_pte_vdw_radius(const int idx) ^ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: unused function 'get_pte_idx' [-Wunused-function] static int get_pte_idx(const char *label) ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: unused function 'symmetry_expand' [-Wunused-function] static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: unused function 'have_keyline' [-Wunused-function] static int have_keyline(FILE *file, const char *keystring1, ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: unused function 'thisline' [-Wunused-function] static void thisline(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: unused function 'whereami' [-Wunused-function] static void whereami(FILE *file) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: unused function 'replace_wavefunction' [-Wunused-function] static void replace_wavefunction(qm_timestep_t *ts, int n) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: unused function 'del_wavefunction' [-Wunused-function] static void del_wavefunction(qm_timestep_t *ts) { ^ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: unused function 'print_matrix4' [-Wunused-function] static void print_matrix4(const float mat[16]) { ^ 9 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.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: unused function 'get_pte_idx_from_string' [-Wunused-function] static int get_pte_idx_from_string(const char *label) { ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Block.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 18 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/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/molemeshplugin.cpp:91:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:116:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:132:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:149:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:155:15: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:161:6: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); //one more read to keep us in sync ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:170:22: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:217:10: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:237:18: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:256:10: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(line, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~ 10 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/File.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/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/namdbinplugin.c:78:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&filen, sizeof(namdbin_int32), 1, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:103:10: warning: variable 'numatoms' set but not used [-Wunused-but-set-variable] int i, numatoms; ^ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:206:55: warning: comparison of integers of different signs: 'unsigned long' and 'int' [-Wsign-compare] if (fwrite(tmp, sizeof(double), 3*n, namdbin->fd) != 3*n) { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ ~~~ 3 warnings generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.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 integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] if (len > sizeof(name)) { ~~~ ^ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:1060:16: warning: comparison of integers of different signs: 'int' and 'unsigned long' [-Wsign-compare] for (i=0; i<(3 * mmtk->atom_numberdim); i++) { ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Crystal.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 13 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/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/graspplugin.cpp:186:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(line3, 1, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:284:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/GenericBuffer.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 : note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:285:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(line, 1, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:291:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:305:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:306:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(line, 1, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:307:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:311:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:313:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:318:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:319:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(line, 1, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:320:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:328:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:329:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(line, 1, 80, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:330:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:354:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:355:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(vertex, 3 * sizeof(float), nvert, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:356:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:357:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:358:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(access, 3 * sizeof(float), nvert, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:359:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:360:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:361:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(normal, 3 * sizeof(float), nvert, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:362:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:371:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:372:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(triangle, 3 * sizeof(int), ntriangles, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:373:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:374:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:375:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(properties, 3 * sizeof(float), nvert, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:394:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:395:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(striangle, sizeof(short), 3 * ntriangles, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:396:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:397:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] TRASH; ^~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:280:15: note: expanded from macro 'TRASH' #define TRASH fread(trash, 4, 1, infile) ^~~~~ ~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(properties, sizeof(float), 3 * nvert, infile); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 34 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/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/parm7plugin.cpp:25: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:79:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, "%s\n", buf); ^~~~~~ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:87:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, "%s\n", buf); ^~~~~~ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:97:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, "%s\n", buf); ^~~~~~ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:204:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, 85, file); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:257:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, 85, file); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:275:7: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, 85, file); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:289:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " %d", &cur); ^~~~~~ ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:368:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(sdum, 512, file); ^~~~~ ~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:371:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, "%s\n", sdum); // "%FLAG" ^~~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:378:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 fscanf(file, "%s\n", sdum); // "TITLE" or "CTITLE" ^~~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:385:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, "%s\n", sdum); // "FORMAT (20a4)" ^~~~~~ ~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:399:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(prm->title, sizeof(prm->title), file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:427:5: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(sdum, sizeof(sdum), file); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:439:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file,parm7, ^~~~~~ ~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:443:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, parm7, ^~~~~~ ~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:447:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, parm7, &prm->Ifpert, &prm->Nbper, &prm->Ngper, ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:451:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file,"%8d",&prm->Numextra); //BB ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:78:9: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, 85, file); ^~~~~ ~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fread(&dataBegin, sizeof(int), 1, fd); ^~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 18 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:2: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fgets(buf, n, mf->f); ^~~~~ ~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Charges[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:444:4: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Masses[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:510:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Rk[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:517:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Req[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:524:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Tk[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:531:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Teq[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:538:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pk[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:545:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Pn[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:552:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Phase[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:559:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Solty[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:567:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn1[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:575:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->Cn2[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:756:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB12[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:763:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &prm->HB6[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:771:11: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT, &H[i]); ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:853:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " " DBLFMT " " DBLFMT " " DBLFMT, ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:867:3: warning: ignoring return value of function declared with 'warn_unused_result' attribute [-Wunused-result] fscanf(file, " %d " DBLFMT " " DBLFMT " " DBLFMT " " DBLFMT, ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Pixmap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 17 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/GraphicsUtil.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Basis.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/PostProcess.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/hash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Isosurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/inthash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontGLUTHel18.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontType.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/ShaderMgr.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer0/Isosurf.cpp:32: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/ButMode.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Movie.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/ButMode.cpp:30: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer1/Movie.cpp:26: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/CGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Map.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/CGO.cpp:32: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Match.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Ortho.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Matrix.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Ortho.cpp:37: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/ShaderPrg.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/P.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/MemoryDebug.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/MyPNG.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Sphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/P.cpp:51: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Parse.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer1/P.cpp:1961:3: warning: 'PyEval_InitThreads' is deprecated [-Wdeprecated-declarations] PyEval_InitThreads(); ^ /usr/include/python3.9/ceval.h:130:1: note: 'PyEval_InitThreads' has been explicitly marked deprecated here Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); ^ /usr/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Tetsurf.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/SceneRender.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer0/Tetsurf.cpp:30: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/PConv.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/SceneRender.cpp:17: In file included from layer3/Editor.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/ScrollBar.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. In file included from layer1/PConv.cpp:28: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Texture.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Picking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Seq.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Pop.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer0/Texture.cpp:35: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Tracker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/PyMOLObject.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Seq.cpp:30: In file included from layer3/Seeker.h:21: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Triangle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Setting.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/PyMOLObject.cpp:37: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Ray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Setting.cpp:32: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Util.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Ray.cpp:34: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Util2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Vector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer0/Vector.cpp:95:26: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] return (rand() / (_1 + RAND_MAX)); ~ ^~~~~~~~ /usr/include/stdlib.h:86:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ layer0/Vector.cpp:202:33: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] x[0] = 0.5F - (rand() / (_1 + RAND_MAX)); ~ ^~~~~~~~ /usr/include/stdlib.h:86:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ layer0/Vector.cpp:203:33: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] x[1] = 0.5F - (rand() / (_1 + RAND_MAX)); ~ ^~~~~~~~ /usr/include/stdlib.h:86:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ layer0/Vector.cpp:204:33: warning: implicit conversion from 'int' to 'float' changes value from 2147483647 to 2147483648 [-Wimplicit-const-int-float-conversion] x[2] = 0.5F - (rand() / (_1 + RAND_MAX)); ~ ^~~~~~~~ /usr/include/stdlib.h:86:18: note: expanded from macro 'RAND_MAX' #define RAND_MAX 2147483647 ^~~~~~~~~~ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/COLLADA.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 4 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/Word.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer0/os_gl.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/CifFile.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Rep.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Character.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Rep.cpp:27: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Scene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Color.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/CifMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Shaker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Scene.cpp:40: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer1/Color.cpp:29: In file included from layer2/ObjectGadgetRamp.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/CifMoleculeReader.cpp:21: In file included from layer2/AssemblyHelpers.h:12: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Symmetry.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Symmetry.cpp:31: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Text.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Control.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Text.cpp:27: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer1/Control.cpp:26: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Extrude.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/ScenePicking.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/Extrude.cpp:22: In file included from layer1/Extrude.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer1/ScenePicking.cpp:10: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/SceneRay.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Font.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontGLUT.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer1/SceneRay.cpp:11: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/CoordSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectGadget.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontGLUT8x13.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/CoordSet.cpp:29: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontGLUT9x15.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontGLUTHel10.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectGadget.cpp:25: In file included from layer2/ObjectGadgetRamp.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/FontGLUTHel12.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepDistDash.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectGadgetRamp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/DistSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectGadgetRamp.cpp:24: In file included from layer2/ObjectGadgetRamp.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/RepDistDash.cpp:33: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/DistSet.cpp:35: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepDistLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectGroup.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/GadgetSet.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepDistLabel.cpp:25: In file included from layer2/RepLabel.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectMap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepDot.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/HydrogenAdder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectMap.cpp:46: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/RepDot.cpp:25: In file included from layer2/RepDot.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/HydrogenAdder.cpp:7: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepEllipsoid.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/MmodTyping.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepEllipsoid.cpp:25: In file included from layer2/RepEllipsoid.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/MmtfMoleculeReader.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepLabel.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/MmtfMoleculeReader.cpp:9: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/Mol2Typing.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepLabel.cpp:25: In file included from layer2/RepLabel.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/TypeFace.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/Mol2Typing.cpp:9: In file included from layer2/Mol2Typing.h:7: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/View.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/MolV3000.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectAlignment.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectMesh.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer1/Wizard.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepMesh.cpp:26: In file included from layer2/RepMesh.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/ObjectAlignment.cpp:27: In file included from layer2/ObjectAlignment.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer1/Wizard.cpp:27: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/ObjectMesh.cpp:35: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepNonbonded.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/AssemblyHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectCGO.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectMolecule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepNonbonded.cpp:24: In file included from layer2/RepNonbonded.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/AssemblyHelpers.cpp:11: In file included from layer2/AssemblyHelpers.h:12: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/AtomInfo.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepNonbondedSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectMolecule.cpp:33: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/AtomInfo.cpp:39: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectCallback.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepNonbondedSphere.cpp:25: In file included from layer2/RepNonbondedSphere.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepRibbon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectCallback.cpp:27: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/AtomInfoHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectDist.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepRibbon.cpp:25: In file included from layer2/RepRibbon.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepSphere.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectDist.cpp:31: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/BondTypeHistory.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/Sculpt.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepSphere.cpp:24: In file included from layer2/RepSphere.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/Seeker.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepSphereGenerate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/Sculpt.cpp:29: In file included from layer3/Editor.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer3/Seeker.cpp:27: In file included from layer3/Seeker.h:21: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/RepSphereGenerate.cpp:16: In file included from layer2/RepSphere.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepSphereImmediate.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/Selector.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/SculptCache.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/SideChainHelper.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepSphereImmediate.cpp:18: In file included from layer2/RepSphere.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer3/Selector.cpp:34: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/SideChainHelper.cpp:10: In file included from layer2/SideChainHelper.h:9: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/VFont.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectMolecule2.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepSurface.cpp:25: In file included from layer2/RepSurface.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/VFont.cpp:23: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/ObjectMolecule2.cpp:31: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/AtomIterators.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/AtomIterators.cpp:9: In file included from layer3/AtomIterators.h:11: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/CifDataValueFormatter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/Editor.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/Editor.cpp:30: In file included from layer3/Editor.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectSlice.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepWireBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectSlice.cpp:36: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/RepWireBond.cpp:22: In file included from layer2/RepWireBond.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/Executive.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectSurface.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVOneToAny.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/Executive.cpp:31: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVOneToOne.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVRandom.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/ov_utility.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 layer3/Executive.cpp:3914:15: warning: unused variable 'object_props' [-Wunused-variable] const char* object_props = args.object_props.c_str(); ^ layer3/Executive.cpp:3915:15: warning: unused variable 'atom_props' [-Wunused-variable] const char* atom_props = args.atom_props.c_str(); ^ layer3/Executive.cpp:3924:8: warning: unused variable 'mimic' [-Wunused-variable] auto mimic = args.mimic; ^ In file included from layer2/ObjectSurface.cpp:35: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/ObjectVolume.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/ObjectVolume.cpp:40: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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/SelectorTmp.cpp -o build/temp.linux-x86_64-3.9/layer3/SelectorTmp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepAngle.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/SelectorTmp.cpp:7: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer2/RepAngle.cpp:33: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepCartoon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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/Cmd.cpp -o build/temp.linux-x86_64-3.9/layer4/Cmd.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepCartoon.cpp:27: In file included from layer2/RepCartoon.h:21: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer4/Cmd.cpp:58: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 4 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/ExecutivePython.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/ExecutivePython.cpp:1: In file included from layer3/ExecutivePython.h:3: In file included from layer3/Executive.h:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/MaeExportHelpers.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/MaeExportHelpers.cpp:11: In file included from layer3/MaeExportHelpers.h:12: In file included from layer3/AtomIterators.h:11: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepCylBond.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/MoleculeExporter.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepCylBond.cpp:26: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer3/MoleculeExporter.cpp:22: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer2/RepDihedral.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer4/Menu.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/MovieScene.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer2/RepDihedral.cpp:33: In file included from layer2/CoordSet.h:25: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer4/Menu.cpp:26: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ In file included from layer3/MovieScene.cpp:12: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer4/PopUp.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. In file included from layer4/PopUp.cpp:31: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer5/PyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer5/PyMOL.cpp:32: In file included from layer3/Selector.h:24: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ layer5/PyMOL.cpp:1798:3: warning: 'PyEval_InitThreads' is deprecated [-Wdeprecated-declarations] PyEval_InitThreads(); ^ /usr/include/python3.9/ceval.h:130:1: note: 'PyEval_InitThreads' has been explicitly marked deprecated here Py_DEPRECATED(3.9) PyAPI_FUNC(void) PyEval_InitThreads(void); ^ /usr/include/python3.9/pyport.h:508:54: note: expanded from macro 'Py_DEPRECATED' #define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__)) ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/PlugIOManager.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/PlugIOManager.cpp:24: In file included from layer3/PlugIOManager.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 2 warnings generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer5/TestPyMOL.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer5/TestPyMOL.cpp:32: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer3/RingFinder.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/layer5/main.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 In file included from layer3/RingFinder.cpp:2: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. In file included from layer5/main.cpp:45: In file included from layer1/P.h:22: layer2/ObjectMolecule.h:173:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage] typedef struct { ^ PDBInfoRec layer2/ObjectMolecule.h:181:3: note: type is not C-compatible due to this member declaration inline bool is_pqr_file() const { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMolecule.h:184:3: note: type is given name 'PDBInfoRec' for linkage purposes by this typedef declaration } PDBInfoRec; ^ 1 warning generated. x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/modules/cealign/src/ccealignmodule.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVContext.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVHeap.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVHeapArray.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -D_PYMOL_LIBPNG -D_PYMOL_FREETYPE -D_PYMOL_VMD_PLUGINS -D_HAVE_LIBXML -D_PYMOL_NO_MSGPACKC -D_PYMOL_NO_MAIN -D_PYMOL_NUMPY -Iinclude -Icontrib/uiuc/plugins/include -Iov/src -Ilayer0 -Ilayer1 -Ilayer2 -Ilayer3 -Ilayer4 -Ilayer5 -Imodules/cealign/src -Ibuild/generated -Icontrib/uiuc/plugins/molfile_plugin/src -I/usr/lib/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-x86_64-3.9/ov/src/OVLexicon.o -Werror=return-type -Wunused-variable -Wno-switch -Wno-narrowing -Wno-char-subscripts -O3 x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.9/build/generated/ShaderText.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/avsplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/binposplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/biomoccaplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/brixplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/carplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/corplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/crdplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/dxplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/edmplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/graspplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/grdplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gridplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/hash.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/inthash.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/jsplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mapplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/msmsplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/offplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/parmplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pbeqplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/phiplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pltplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/plyplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/psfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/raster3dplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/situsplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/stlplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.o build/temp.linux-x86_64-3.9/contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.o build/temp.linux-x86_64-3.9/layer0/Block.o build/temp.linux-x86_64-3.9/layer0/Crystal.o build/temp.linux-x86_64-3.9/layer0/Deferred.o build/temp.linux-x86_64-3.9/layer0/Err.o build/temp.linux-x86_64-3.9/layer0/Feedback.o build/temp.linux-x86_64-3.9/layer0/Field.o build/temp.linux-x86_64-3.9/layer0/File.o build/temp.linux-x86_64-3.9/layer0/GenericBuffer.o build/temp.linux-x86_64-3.9/layer0/GraphicsUtil.o build/temp.linux-x86_64-3.9/layer0/Isosurf.o build/temp.linux-x86_64-3.9/layer0/Map.o build/temp.linux-x86_64-3.9/layer0/Match.o build/temp.linux-x86_64-3.9/layer0/Matrix.o build/temp.linux-x86_64-3.9/layer0/MemoryDebug.o build/temp.linux-x86_64-3.9/layer0/MyPNG.o build/temp.linux-x86_64-3.9/layer0/Parse.o build/temp.linux-x86_64-3.9/layer0/Pixmap.o build/temp.linux-x86_64-3.9/layer0/PostProcess.o build/temp.linux-x86_64-3.9/layer0/ShaderMgr.o build/temp.linux-x86_64-3.9/layer0/ShaderPrg.o build/temp.linux-x86_64-3.9/layer0/Sphere.o build/temp.linux-x86_64-3.9/layer0/Tetsurf.o build/temp.linux-x86_64-3.9/layer0/Texture.o build/temp.linux-x86_64-3.9/layer0/Tracker.o build/temp.linux-x86_64-3.9/layer0/Triangle.o build/temp.linux-x86_64-3.9/layer0/Util.o build/temp.linux-x86_64-3.9/layer0/Util2.o build/temp.linux-x86_64-3.9/layer0/Vector.o build/temp.linux-x86_64-3.9/layer0/Word.o build/temp.linux-x86_64-3.9/layer0/os_gl.o build/temp.linux-x86_64-3.9/layer1/Basis.o build/temp.linux-x86_64-3.9/layer1/ButMode.o build/temp.linux-x86_64-3.9/layer1/CGO.o build/temp.linux-x86_64-3.9/layer1/COLLADA.o build/temp.linux-x86_64-3.9/layer1/Character.o build/temp.linux-x86_64-3.9/layer1/Color.o build/temp.linux-x86_64-3.9/layer1/Control.o build/temp.linux-x86_64-3.9/layer1/Extrude.o build/temp.linux-x86_64-3.9/layer1/Font.o build/temp.linux-x86_64-3.9/layer1/FontGLUT.o build/temp.linux-x86_64-3.9/layer1/FontGLUT8x13.o build/temp.linux-x86_64-3.9/layer1/FontGLUT9x15.o build/temp.linux-x86_64-3.9/layer1/FontGLUTHel10.o build/temp.linux-x86_64-3.9/layer1/FontGLUTHel12.o build/temp.linux-x86_64-3.9/layer1/FontGLUTHel18.o build/temp.linux-x86_64-3.9/layer1/FontType.o build/temp.linux-x86_64-3.9/layer1/Movie.o build/temp.linux-x86_64-3.9/layer1/Ortho.o build/temp.linux-x86_64-3.9/layer1/P.o build/temp.linux-x86_64-3.9/layer1/PConv.o build/temp.linux-x86_64-3.9/layer1/Picking.o build/temp.linux-x86_64-3.9/layer1/Pop.o build/temp.linux-x86_64-3.9/layer1/PyMOLObject.o build/temp.linux-x86_64-3.9/layer1/Ray.o build/temp.linux-x86_64-3.9/layer1/Rep.o build/temp.linux-x86_64-3.9/layer1/Scene.o build/temp.linux-x86_64-3.9/layer1/ScenePicking.o build/temp.linux-x86_64-3.9/layer1/SceneRay.o build/temp.linux-x86_64-3.9/layer1/SceneRender.o build/temp.linux-x86_64-3.9/layer1/ScrollBar.o build/temp.linux-x86_64-3.9/layer1/Seq.o build/temp.linux-x86_64-3.9/layer1/Setting.o build/temp.linux-x86_64-3.9/layer1/Shaker.o build/temp.linux-x86_64-3.9/layer1/Symmetry.o build/temp.linux-x86_64-3.9/layer1/Text.o build/temp.linux-x86_64-3.9/layer1/TypeFace.o build/temp.linux-x86_64-3.9/layer1/View.o build/temp.linux-x86_64-3.9/layer1/Wizard.o build/temp.linux-x86_64-3.9/layer2/AssemblyHelpers.o build/temp.linux-x86_64-3.9/layer2/AtomInfo.o build/temp.linux-x86_64-3.9/layer2/AtomInfoHistory.o build/temp.linux-x86_64-3.9/layer2/BondTypeHistory.o build/temp.linux-x86_64-3.9/layer2/CifFile.o build/temp.linux-x86_64-3.9/layer2/CifMoleculeReader.o build/temp.linux-x86_64-3.9/layer2/CoordSet.o build/temp.linux-x86_64-3.9/layer2/DistSet.o build/temp.linux-x86_64-3.9/layer2/GadgetSet.o build/temp.linux-x86_64-3.9/layer2/HydrogenAdder.o build/temp.linux-x86_64-3.9/layer2/MmodTyping.o build/temp.linux-x86_64-3.9/layer2/MmtfMoleculeReader.o build/temp.linux-x86_64-3.9/layer2/Mol2Typing.o build/temp.linux-x86_64-3.9/layer2/MolV3000.o build/temp.linux-x86_64-3.9/layer2/ObjectAlignment.o build/temp.linux-x86_64-3.9/layer2/ObjectCGO.o build/temp.linux-x86_64-3.9/layer2/ObjectCallback.o build/temp.linux-x86_64-3.9/layer2/ObjectDist.o build/temp.linux-x86_64-3.9/layer2/ObjectGadget.o build/temp.linux-x86_64-3.9/layer2/ObjectGadgetRamp.o build/temp.linux-x86_64-3.9/layer2/ObjectGroup.o build/temp.linux-x86_64-3.9/layer2/ObjectMap.o build/temp.linux-x86_64-3.9/layer2/ObjectMesh.o build/temp.linux-x86_64-3.9/layer2/ObjectMolecule.o build/temp.linux-x86_64-3.9/layer2/ObjectMolecule2.o build/temp.linux-x86_64-3.9/layer2/ObjectSlice.o build/temp.linux-x86_64-3.9/layer2/ObjectSurface.o build/temp.linux-x86_64-3.9/layer2/ObjectVolume.o build/temp.linux-x86_64-3.9/layer2/RepAngle.o build/temp.linux-x86_64-3.9/layer2/RepCartoon.o build/temp.linux-x86_64-3.9/layer2/RepCylBond.o build/temp.linux-x86_64-3.9/layer2/RepDihedral.o build/temp.linux-x86_64-3.9/layer2/RepDistDash.o build/temp.linux-x86_64-3.9/layer2/RepDistLabel.o build/temp.linux-x86_64-3.9/layer2/RepDot.o build/temp.linux-x86_64-3.9/layer2/RepEllipsoid.o build/temp.linux-x86_64-3.9/layer2/RepLabel.o build/temp.linux-x86_64-3.9/layer2/RepMesh.o build/temp.linux-x86_64-3.9/layer2/RepNonbonded.o build/temp.linux-x86_64-3.9/layer2/RepNonbondedSphere.o build/temp.linux-x86_64-3.9/layer2/RepRibbon.o build/temp.linux-x86_64-3.9/layer2/RepSphere.o build/temp.linux-x86_64-3.9/layer2/RepSphereGenerate.o build/temp.linux-x86_64-3.9/layer2/RepSphereImmediate.o build/temp.linux-x86_64-3.9/layer2/RepSurface.o build/temp.linux-x86_64-3.9/layer2/RepWireBond.o build/temp.linux-x86_64-3.9/layer2/Sculpt.o build/temp.linux-x86_64-3.9/layer2/SculptCache.o build/temp.linux-x86_64-3.9/layer2/SideChainHelper.o build/temp.linux-x86_64-3.9/layer2/VFont.o build/temp.linux-x86_64-3.9/layer3/AtomIterators.o build/temp.linux-x86_64-3.9/layer3/CifDataValueFormatter.o build/temp.linux-x86_64-3.9/layer3/Editor.o build/temp.linux-x86_64-3.9/layer3/Executive.o build/temp.linux-x86_64-3.9/layer3/ExecutivePython.o build/temp.linux-x86_64-3.9/layer3/MaeExportHelpers.o build/temp.linux-x86_64-3.9/layer3/MoleculeExporter.o build/temp.linux-x86_64-3.9/layer3/MovieScene.o build/temp.linux-x86_64-3.9/layer3/PlugIOManager.o build/temp.linux-x86_64-3.9/layer3/RingFinder.o build/temp.linux-x86_64-3.9/layer3/Seeker.o build/temp.linux-x86_64-3.9/layer3/Selector.o build/temp.linux-x86_64-3.9/layer3/SelectorTmp.o build/temp.linux-x86_64-3.9/layer4/Cmd.o build/temp.linux-x86_64-3.9/layer4/Menu.o build/temp.linux-x86_64-3.9/layer4/PopUp.o build/temp.linux-x86_64-3.9/layer5/PyMOL.o build/temp.linux-x86_64-3.9/layer5/TestPyMOL.o build/temp.linux-x86_64-3.9/layer5/main.o build/temp.linux-x86_64-3.9/modules/cealign/src/ccealignmodule.o build/temp.linux-x86_64-3.9/ov/src/OVContext.o build/temp.linux-x86_64-3.9/ov/src/OVHeap.o build/temp.linux-x86_64-3.9/ov/src/OVHeapArray.o build/temp.linux-x86_64-3.9/ov/src/OVLexicon.o build/temp.linux-x86_64-3.9/ov/src/OVOneToAny.o build/temp.linux-x86_64-3.9/ov/src/OVOneToOne.o build/temp.linux-x86_64-3.9/ov/src/OVRandom.o build/temp.linux-x86_64-3.9/ov/src/ov_utility.o -lpng -lfreetype -lxml2 -lGL -lGLEW -lnetcdf -o /<>/.pybuild/cpython3_3.9_pymol/build/pymol/_cmd.cpython-39-x86_64-linux-gnu.so building 'chempy.champ._champ' extension creating build/temp.linux-x86_64-3.9/contrib/champ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/champ.c -o build/temp.linux-x86_64-3.9/contrib/champ/champ.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/champ_module.c -o build/temp.linux-x86_64-3.9/contrib/champ/champ_module.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/chiral.c -o build/temp.linux-x86_64-3.9/contrib/champ/chiral.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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/err2.c -o build/temp.linux-x86_64-3.9/contrib/champ/err2.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/champ/feedback2.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/champ/list.o x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/champ/os_memory.o contrib/champ/champ.c:2787:3: error: unterminated function-like macro invocation PRINTFD(FB_smiles_parsing) ^ contrib/champ/feedback2.h:122:61: note: expanded from macro 'PRINTFD' #define PRINTFD(sysmod) {if(feedback_(sysmod,FB_debugging)) fprintf(stderr, ^ /usr/include/x86_64-linux-gnu/bits/stdio2.h:115:11: note: macro 'fprintf' defined here # define fprintf(stream, ...) \ ^ contrib/champ/champ.c:5213:2: error: expected expression } ^ contrib/champ/champ.c:5213:2: error: expected '}' contrib/champ/champ.c:2787:3: note: to match this '{' PRINTFD(FB_smiles_parsing) ^ contrib/champ/feedback2.h:122:25: note: expanded from macro 'PRINTFD' #define PRINTFD(sysmod) {if(feedback_(sysmod,FB_debugging)) fprintf(stderr, ^ contrib/champ/champ.c:5213:2: error: expected '}' } ^ contrib/champ/champ.c:2776:1: note: to match this '{' { ^ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/champ/sort.o 4 errors generated. x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/champ/strblock.o contrib/champ/os_memory.c:55:18: warning: cast to smaller integer type 'int' from 'char *' [-Wpointer-to-int-cast] while(count&&(((int)p)&mask)) { ^~~~~~ contrib/champ/os_memory.c:137:8: warning: cast to smaller integer type 'int' from 'DebugRec *' (aka 'struct DebugRec *') [-Wpointer-to-int-cast] hash=(int)rec; ^~~~~~~~ contrib/champ/os_memory.c:150:8: warning: cast to smaller integer type 'int' from 'DebugRec *' (aka 'struct DebugRec *') [-Wpointer-to-int-cast] hash=(int)rec; ^~~~~~~~ x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -ffile-prefix-map=/<>=. -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-x86_64-3.9/contrib/champ/vla.o 3 warnings generated. error: command '/usr/bin/x86_64-linux-gnu-gcc' failed with exit code 1 E: pybuild pybuild:354: build: plugin distutils failed with: exit code=1: /usr/bin/python3 setup.py build dh_auto_build: error: pybuild --build -i python{version} -p 3.9 returned exit code 13 make: *** [debian/rules:10: build] Error 25 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2021-10-26T21:51:17Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 153508 Build-Time: 95 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 48 Job: pymol_2.4.0+dfsg-3 Machine Architecture: amd64 Package: pymol Package-Time: 165 Source-Version: 2.4.0+dfsg-3 Space: 153508 Status: attempted Version: 2.4.0+dfsg-3 -------------------------------------------------------------------------------- Finished at 2021-10-26T21:51:17Z Build needed 00:02:45, 153508k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 166.684275536s DC-Time-Estimation: 166.684275536 versus expected 286 (r/m: 0.7158187182343455 ; m: 166.684275536)