Diff of the two buildlogs: -- --- b1/build.log 2024-11-07 21:42:50.544800687 +0000 +++ b2/build.log 2024-11-07 22:07:14.868763270 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Nov 7 09:25:58 -12 2024 -I: pbuilder-time-stamp: 1731014758 +I: Current time: Fri Nov 8 11:44:43 +14 2024 +I: pbuilder-time-stamp: 1731015883 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying 40_mstop_movies.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1156/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Nov 7 21:45 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="32" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='2ae25c2b0557477eb7af2ab797553e8d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1156' - PS1='# ' - PS2='> ' + INVOCATION_ID=f63e1951ceae48278e0cf87b2de66a58 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=10614 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0BEmS9bI/pbuilderrc_I9hB --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0BEmS9bI/b1 --logfile b1/build.log pymol_3.0.0+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='103' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0BEmS9bI/pbuilderrc_hI7t --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0BEmS9bI/b2 --logfile b2/build.log pymol_3.0.0+dfsg-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64z 6.1.0-26-arm64 #1 SMP Debian 6.1.112-1 (2024-09-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-armmp-lpae #1 SMP Debian 6.1.112-1 (2024-09-30) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1156/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -441,7 +473,7 @@ Get: 292 http://deb.debian.org/debian trixie/main armhf xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 293 http://deb.debian.org/debian trixie/main armhf texlive-base all 2024.20240829-2 [22.7 MB] Get: 294 http://deb.debian.org/debian trixie/main armhf texlive-latex-base all 2024.20240829-2 [1273 kB] -Fetched 174 MB in 2s (80.0 MB/s) +Fetched 174 MB in 4s (48.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:armhf. (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 ... 19690 files and directories currently installed.) @@ -1398,8 +1430,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Nov 7 21:27:20 UTC 2024. -Universal Time is now: Thu Nov 7 21:27:20 UTC 2024. +Local time is now: Thu Nov 7 21:48:22 UTC 2024. +Universal Time is now: Thu Nov 7 21:48:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:armhf (1.17.0-2+b1) ... @@ -1671,7 +1703,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/pymol-3.0.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../pymol_3.0.0+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/pymol-3.0.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../pymol_3.0.0+dfsg-1_source.changes dpkg-buildpackage: info: source package pymol dpkg-buildpackage: info: source version 3.0.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -1699,6 +1735,20 @@ I: pybuild base:311: python3.12 setup.py config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build +contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function 'PlugIOManagerInitAll': +contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:271:1: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 271 | if(ok) ok = ok && (molfile_xyzplugin_init() == VMDPLUGIN_SUCCESS); + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:273:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 273 | if(ok) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function 'PlugIOManagerFreeAll': +contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:411:1: warning: this 'if' clause does not guard... [-Wmisleading-indentation] + 411 | if(ok) ok = ok && (molfile_xyzplugin_fini() == VMDPLUGIN_SUCCESS); + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:413:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' + 413 | return ok; + | ^~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_config_structure': contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:292:3: warning: this 'if' clause does not guard... [-Wmisleading-indentation] 292 | if (NULL == fgets(fbuffer, 1024, data->file)) @@ -1714,28 +1764,10 @@ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:554:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 554 | fgets(fbuffer, 1024, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function 'PlugIOManagerInitAll': -contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:271:1: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 271 | if(ok) ok = ok && (molfile_xyzplugin_init() == VMDPLUGIN_SUCCESS); - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:273:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 273 | if(ok) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c: In function 'PlugIOManagerFreeAll': -contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:411:1: warning: this 'if' clause does not guard... [-Wmisleading-indentation] - 411 | if(ok) ok = ok && (molfile_xyzplugin_fini() == VMDPLUGIN_SUCCESS); - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c:413:8: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' - 413 | return ok; - | ^~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_config_structure': contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:362:5: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] 362 | strncpy(atom->name, buf, sizeof(atom->name)); | ^ -contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_structure': -contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:267:5: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] - 267 | strncpy(atom->name, buf, sizeof(atom->name)); - | ^ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'void* open_plt_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fread(intHeader, sizeof(int), 5, fd); @@ -1743,10 +1775,41 @@ contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:82:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 82 | fread(floatHeader, sizeof(float), 6, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c: In function 'read_dlpoly_structure': +contrib/uiuc/plugins/molfile_plugin/src/dlpolyplugin.c:267:5: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 4095 [-Wstringop-truncation] + 267 | strncpy(atom->name, buf, sizeof(atom->name)); + | ^ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_readline': contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:279:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 279 | for (i = 0; i < strlen(line); ++i) { | ^ +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'DEN_read_volumetric_data': +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 970 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 971 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'POT_read_volumetric_data': +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1113 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1114 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_header': +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1511 | fread(skip, 1, 8, fp); + | ^~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'GEO_read_next_timestep': +contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 619 | fscanf(data->file, "%*s %f %f %f", &x, &y, &z); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] + 160 | static int get_pte_idx_from_string(const char *label) { + | ^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_bonds(void*, int*, int**, int**, float**, int**, int*, char***)': contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:278:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 278 | fgets(line, LINESIZE, mdf->file); @@ -1777,41 +1840,6 @@ contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:183:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 183 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'DEN_read_volumetric_data': -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:970:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 970 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:971:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 971 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'POT_read_volumetric_data': -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1113:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1113 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1114:5: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1114 | fread(recordmarker, 1, data->hdr->bintype.recordmarker, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_header': -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:1511:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1511 | fread(skip, 1, 8, fp); - | ^~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'GEO_read_next_timestep': -contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:619:5: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 619 | fscanf(data->file, "%*s %f %f %f", &x, &y, &z); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:70: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: At top level: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] - 160 | static int get_pte_idx_from_string(const char *label) { - | ^~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'int read_dsn6_data(void*, int, float*, float*)': -contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 233 | fread(brick, sizeof(char), 512, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'void* open_dsn6_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 91 | fread(fileHeader, sizeof(short), 19, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/plyplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void put_element_ply(PlyFile*, void*)': contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:459:7: warning: unused variable 'i' [-Wunused-variable] @@ -1825,6 +1853,45 @@ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable 'i' [-Wunused-variable] 1541 | int i,j,k; | ^ +contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'int read_dsn6_data(void*, int, float*, float*)': +contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:233:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 233 | fread(brick, sizeof(char), 512, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp: In function 'void* open_dsn6_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/dsn6plugin.cpp:91:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 91 | fread(fileHeader, sizeof(short), 19, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1629 | fread (&len, sizeof(int), 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1631 | fread (str, len, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void get_binary_item(FILE*, int, int*, unsigned int*, double*)': +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2057 | fread (ptr, 1, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2063 | fread (ptr, 1, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2069 | fread (ptr, 2, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2075 | fread (ptr, 2, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2081 | fread (ptr, 4, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2087 | fread (ptr, 4, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2093 | fread (ptr, 4, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 2099 | fread (ptr, 8, 1, fp); + | ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp: In function 'int read_mol2_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:275:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 275 | fgets(line, LINESIZE, mol2->file); @@ -1862,37 +1929,6 @@ contrib/uiuc/plugins/molfile_plugin/src/mol2plugin.cpp:92:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(line, LINESIZE, fd); // Read the charge_type | ~~~~~^~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1629:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1629 | fread (&len, sizeof(int), 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1631:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1631 | fread (str, len, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void get_binary_item(FILE*, int, int*, unsigned int*, double*)': -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2057:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2057 | fread (ptr, 1, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2063:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2063 | fread (ptr, 1, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2069:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2069 | fread (ptr, 2, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2075:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2075 | fread (ptr, 2, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2081:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2081 | fread (ptr, 4, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2087:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2087 | fread (ptr, 4, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2093:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2093 | fread (ptr, 4, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:2099:13: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 2099 | fread (ptr, 8, 1, fp); - | ~~~~~~^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'char* recreate_command_line(int, char**)': contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1334:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 1334 | line[0] = '\0'; @@ -1999,37 +2035,6 @@ contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:140:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 58 [-Wstringop-truncation] 140 | strncpy(resid, record+22, 4); resid[4] = 0; | ^ -contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: In function 'write_psf_structure': -contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:782:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] - 782 | if (strlen(atoms[i].type) > fw) { - | ^ -In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: -contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At top level: -contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: 'fortread_4' defined but not used [-Wunused-function] - 103 | static int fortread_4(void *dest, int n, int swap, FILE *fd) { - | ^~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'fort_get_endian_reclen' defined but not used [-Wunused-function] - 55 | static int fort_get_endian_reclen(int reclen, int word0, int word1, - | ^~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'fort_eat_recmark' defined but not used [-Wunused-function] - 36 | static int fort_eat_recmark(FILE *ifp, int recmarklen) { - | ^~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28: -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'swap8_aligned' defined but not used [-Wunused-function] - 124 | static void swap8_aligned(void *v, long ndata) { - | ^~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] - 96 | static void swap2_aligned(void *v, long ndata) { - | ^~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] - 65 | static void swap8_unaligned(void *v, long ndata) { - | ^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function] - 46 | static void swap4_unaligned(void *v, long ndata) { - | ^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] - 32 | static void swap2_unaligned(void *v, long ndata) { - | ^~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] @@ -2048,55 +2053,24 @@ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1006:12: warning: 'have_keyline' defined but not used [-Wunused-function] 1006 | static int have_keyline(FILE *file, const char *keystring1, | ^~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)': -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:91:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 91 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:962:12: warning: 'goto_keyline' defined but not used [-Wunused-function] 962 | static int goto_keyline(FILE *file, ...) { | ^~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:901:14: warning: 'strtoupper' defined but not used [-Wunused-function] 901 | static char *strtoupper(char *s) { | ^~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:116:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 116 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:132:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 132 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:149:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 149 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:895:12: warning: 'iswhiteline' defined but not used [-Wunused-function] 895 | static int iswhiteline(char *s) { | ^~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:155:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 155 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:161:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 161 | fgets(line, 80, infile); //one more read to keep us in sync - | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:846:13: warning: 'eatwhitelines' defined but not used [-Wunused-function] 846 | static void eatwhitelines(FILE *file) { | ^~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:170:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 170 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:835:13: warning: 'eatline' defined but not used [-Wunused-function] 835 | static void eatline(FILE * fd, int n) | ^~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:217:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 217 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:237:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:711:12: warning: 'symmetry_expand' defined but not used [-Wunused-function] 711 | static int symmetry_expand(qm_atom_t **atoms, int numunique, int natoms, | ^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:256:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 256 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: 'print_matrix4' defined but not used [-Wunused-function] 585 | static void print_matrix4(const float mat[16]) { | ^~~~~~~~~~~~~ @@ -2115,6 +2089,37 @@ contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:437:18: warning: 'init_qmdata' defined but not used [-Wunused-function] 437 | static qmdata_t* init_qmdata() { | ^~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: In function 'write_psf_structure': +contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:782:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare] + 782 | if (strlen(atoms[i].type) > fw) { + | ^ +In file included from contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:30: +contrib/uiuc/plugins/molfile_plugin/src/fortread.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/fortread.h:103:12: warning: 'fortread_4' defined but not used [-Wunused-function] + 103 | static int fortread_4(void *dest, int n, int swap, FILE *fd) { + | ^~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/fortread.h:55:12: warning: 'fort_get_endian_reclen' defined but not used [-Wunused-function] + 55 | static int fort_get_endian_reclen(int reclen, int word0, int word1, + | ^~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/fortread.h:36:12: warning: 'fort_eat_recmark' defined but not used [-Wunused-function] + 36 | static int fort_eat_recmark(FILE *ifp, int recmarklen) { + | ^~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/fortread.h:28: +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:124:13: warning: 'swap8_aligned' defined but not used [-Wunused-function] + 124 | static void swap8_aligned(void *v, long ndata) { + | ^~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] + 96 | static void swap2_aligned(void *v, long ndata) { + | ^~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] + 65 | static void swap8_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function] + 46 | static void swap4_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] + 32 | static void swap2_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:243:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 243 | fgets(line, LINESIZE, bgf->file); @@ -2146,6 +2151,37 @@ contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 59 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)': +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:91:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 91 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:116:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 116 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:132:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 132 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:149:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 149 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:155:20: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 155 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:161:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 161 | fgets(line, 80, infile); //one more read to keep us in sync + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:170:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 170 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:217:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 217 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:237:23: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/molemeshplugin.cpp:256:15: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 256 | fgets(line, 80, infile); + | ~~~~~^~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c: In function 'read_next_timestep': contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:103:10: warning: variable 'numatoms' set but not used [-Wunused-but-set-variable] 103 | int i, numatoms; @@ -2158,12 +2194,13 @@ contrib/uiuc/plugins/molfile_plugin/src/namdbinplugin.c:78:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fread(&filen, sizeof(namdbin_int32), 1, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/14/map:62, - from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:58: -/usr/include/c++/14/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]': -/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator' changed in GCC 7.1 - 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function 'open_binpos_read': +contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 64 | fread(magicchar,sizeof(char),4,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 72 | fread(&igarb,sizeof(int),1,fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_structure': contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:730:15: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 730 | if (len > sizeof(name)) { @@ -2172,6 +2209,12 @@ contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:1060:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare] 1060 | for (i=0; i<(3 * mmtk->atom_numberdim); i++) { | ^ +In file included from /usr/include/c++/14/map:62, + from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:58: +/usr/include/c++/14/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]': +/usr/include/c++/14/bits/stl_tree.h:2206:5: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator' changed in GCC 7.1 + 2206 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, {anonymous}::Blob>; _KeyOfValue = std::_Select1st, {anonymous}::Blob> >; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]': /usr/include/c++/14/bits/stl_tree.h:2454:7: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator' changed in GCC 7.1 2454 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -2185,6 +2228,47 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'int read_brix_data(void*, int, float*, float*)': +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 247 | fread(brick, sizeof(char), 512, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'void* open_brix_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 79 | fscanf(fd, "%3s", keyWord); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 86 | fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 100 | fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:109:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 109 | fscanf(fd, " %s %f %f %f %f %f %f", keyWord, + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 110 | &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 123 | fscanf(fd, " %s %f", keyWord, &prod); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 128 | fscanf(fd, " %s %f", keyWord, &plus); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 135 | fscanf(fd, " %s %f", keyWord, &sigma); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function 'open_rst_read': +contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:48:11: warning: variable 'timesteprst' set but not used [-Wunused-but-set-variable] + 48 | double timesteprst; + | ^~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:67:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 67 | fgets(title, 82, fd); + | ^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:70:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 70 | fgets(line, 82, fd); + | ^~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'void DDmkdir(const std::string&, mode_t, int, int)': contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:714:23: warning: '%03x' directive writing between 3 and 8 bytes into a region of size 6 [-Wformat-overflow=] 714 | sprintf(sub, "%03x/", i); @@ -2220,23 +2304,93 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function 'open_binpos_read': -contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:64:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 64 | fread(magicchar,sizeof(char),4,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c:72:3: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 72 | fread(&igarb,sizeof(int),1,fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c: In function 'open_rst_read': -contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:48:11: warning: variable 'timesteprst' set but not used [-Wunused-but-set-variable] - 48 | double timesteprst; - | ^~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:67:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 67 | fgets(title, 82, fd); - | ^~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/rst7plugin.c:70:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 70 | fgets(line, 82, fd); - | ^~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_timestep': +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 339 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 344 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 349 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 363 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 373 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_structure': +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 266 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 268 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 272 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 295 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 305 | fgets(line, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'open_car_read': +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 169 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 179 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 182 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 210 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 213 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 224 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 226 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 230 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 234 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 245 | fgets(line, LINESIZE, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_structure': +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:29: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] + 127 | sprintf(atom->resname, "%d", resid); + | ^~ +In function 'read_car_structure_line', + inlined from 'read_car_structure' at contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: +contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:28: note: directive argument in the range [-2147483648, 9999999] + 127 | sprintf(atom->resname, "%d", resid); + | ^~~~ +In file included from /usr/include/stdio.h:970, + from contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:85: +In function 'sprintf', + inlined from 'read_car_structure_line' at contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:5, + inlined from 'read_car_structure' at contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 8 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp: In function 'std::string framefile(const std::string&, size_t, size_t, int, int)': contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:675:35: warning: '__builtin___sprintf_chk' may write a terminating nul past the end of the destination [-Wformat-overflow=] 675 | sprintf(answer, "%03x/", d1); @@ -2348,37 +2502,14 @@ contrib/uiuc/plugins/molfile_plugin/src/ReadPARM7.h:97:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fscanf(file, "%s\n", buf); | ~~~~~~^~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'int read_brix_data(void*, int, float*, float*)': -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:247:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 247 | fread(brick, sizeof(char), 512, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp: In function 'void* open_brix_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:79:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 79 | fscanf(fd, "%3s", keyWord); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:86:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 86 | fscanf(fd, " %s %d %d %d", keyWord, &org_x, &org_y, &org_z); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:93:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf(fd, " %s %d %d %d", keyWord, &ext_x, &ext_y, &ext_z); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:100:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 100 | fscanf(fd, " %s %f %f %f", keyWord, &grid_x, &grid_y, &grid_z); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:109:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 109 | fscanf(fd, " %s %f %f %f %f %f %f", keyWord, - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 110 | &cell_x, &cell_y, &cell_z, &cell_alpha, &cell_beta, &cell_gamma); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:123:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 123 | fscanf(fd, " %s %f", keyWord, &prod); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:128:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 128 | fscanf(fd, " %s %f", keyWord, &plus); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/brixplugin.cpp:135:9: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 135 | fscanf(fd, " %s %f", keyWord, &sigma); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function 'void* open_ccp4_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 304 | fgets(symData, 81, fd); + | ~~~~~^~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function 'int read_spider_data(void*, int, float*, float*)': +contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 286 | fread(datablock, total * sizeof(float), 1, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/parmplugin.cpp:24: contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h: In member function 'int {anonymous}::ReadPARM::readparm(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/ReadPARM.h:435:17: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2438,97 +2569,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 869 | &prm->Xcap, &prm->Ycap, &prm->Zcap); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp: In function 'int read_spider_data(void*, int, float*, float*)': -contrib/uiuc/plugins/molfile_plugin/src/spiderplugin.cpp:286:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 286 | fread(datablock, total * sizeof(float), 1, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_timestep': -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:326:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:339:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 339 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:344:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 344 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:349:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 349 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:363:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 363 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:373:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 373 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_structure': -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:266:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 266 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:268:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 268 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:272:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 272 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:295:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 295 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:305:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 305 | fgets(line, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'open_car_read': -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:169:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 169 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:179:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 179 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:182:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 182 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:210:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 210 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:213:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 213 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:224:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 224 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:226:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 226 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:230:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 230 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:234:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 234 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:245:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 245 | fgets(line, LINESIZE, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c: In function 'read_car_structure': -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:29: warning: '%d' directive writing between 1 and 11 bytes into a region of size 8 [-Wformat-overflow=] - 127 | sprintf(atom->resname, "%d", resid); - | ^~ -In function 'read_car_structure_line', - inlined from 'read_car_structure' at contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: -contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:28: note: directive argument in the range [-2147483648, 9999999] - 127 | sprintf(atom->resname, "%d", resid); - | ^~~~ -In file included from /usr/include/stdio.h:970, - from contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:85: -In function 'sprintf', - inlined from 'read_car_structure_line' at contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:127:5, - inlined from 'read_car_structure' at contrib/uiuc/plugins/molfile_plugin/src/carplugin.c:277:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:10: note: '__builtin___sprintf_chk' output between 2 and 12 bytes into a destination of size 8 - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)': contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 96 | fgets(line, 80, infile); @@ -2551,6 +2591,10 @@ contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 171 | fgets(line, 80, infile); | ~~~~~^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c: In function 'read_tinker_structure': +contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:103:5: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] + 103 | strncpy(atom->name, buffer, sizeof(atom->name)); + | ^ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::__cxx11::basic_string; _Tp = {anonymous}::Blob; _Compare = std::less >; _Alloc = std::allocator, {anonymous}::Blob> >]', inlined from 'int handle_posn_momentum_v1({anonymous}::BlobMap&, uint32_t, bool, const float*, molfile_timestep_t*)' at contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:1496:19: /usr/include/c++/14/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::pair, {anonymous}::Blob>, std::_Select1st, {anonymous}::Blob> >, std::less >, std::allocator, {anonymous}::Blob> > >::const_iterator' changed in GCC 7.1 @@ -2596,14 +2640,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp: In function 'void* open_ccp4_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/ccp4plugin.cpp:304:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 304 | fgets(symData, 81, fd); - | ~~~~~^~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c: In function 'read_tinker_structure': -contrib/uiuc/plugins/molfile_plugin/src/tinkerplugin.c:103:5: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] - 103 | strncpy(atom->name, buffer, sizeof(atom->name)); - | ^ contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 102 | fread(&headersize, sizeof(int), 1, fd); @@ -2672,149 +2708,6 @@ contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { | ^~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] - 133 | static int get_pte_idx(const char *label) - | ^~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:31: -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function 'read_next_timestep': -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:144:5: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 52 [-Wstringop-truncation] - 144 | strncpy(numstr, record + 30, 8); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:149:5: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 44 [-Wstringop-truncation] - 149 | strncpy(numstr+10, record + 38, 8); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:154:5: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 36 [-Wstringop-truncation] - 154 | strncpy(numstr+20, record + 46, 8); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] - 159 | strncpy(numstr+30, record + 54, 6); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] - 164 | strncpy(numstr+40, record + 60, 6); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function 'read_pdb_structure': -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:299:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 70 [-Wstringop-truncation] - 299 | strncpy(name, record + 12, 4); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:304:3: warning: '__builtin_strncpy' output may be truncated copying 1 byte from a string of length 66 [-Wstringop-truncation] - 304 | strncpy(altloc, record + 16, 1); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:308:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 65 [-Wstringop-truncation] - 308 | strncpy(resname, record + 17, 4); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:317:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 60 [-Wstringop-truncation] - 317 | strncpy(resid, record + 22, 4); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] - 159 | strncpy(numstr+30, record + 54, 6); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] - 164 | strncpy(numstr+40, record + 60, 6); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:330:5: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 10 [-Wstringop-truncation] - 330 | strncpy(segname, record + 72, 4); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:339:5: warning: '__builtin_strncpy' output may be truncated copying 2 bytes from a string of length 6 [-Wstringop-truncation] - 339 | strncpy(elementsymbol, record + 76, 2); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_data': -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:237:60: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:282:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 282 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_metadata': -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 150 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'open_vaspchgcar_read': -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 71 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 75 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 81 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 92 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 103 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: -contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: -contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] - 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) - | ^~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function 'open_pdb_read': -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:190:5: warning: '__builtin_strncpy' output may be truncated copying 9 bytes from a string of length 32 [-Wstringop-truncation] - 190 | strncpy(date, record + 50, 9); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:200:5: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 20 [-Wstringop-truncation] - 200 | strncpy(pdbcode, record + 62, 4); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'int getUniqueResID(char*, int)': -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable 'i' [-Wunused-variable] - 443 | int i, uid; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)': -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable 'j' [-Wunused-variable] - 484 | int i, count, atomdata, pos, idx, xyzcount, j; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] - 503 | char oldChain[8]; - | ^~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'bool readAngleBonds(molfile_atom_t*, pdbxParser*)': -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable 'bondTable' [-Wunused-variable] - 803 | int bondTable[32]; - | ^~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] - 807 | int i, pos, j, k; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] - 811 | char modelNum[8]; - | ^~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] - 822 | molfile_atom_t * atom; - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] - 884 | int test = parser->nbonds + bnum; - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'bool readRMSDBonds(molfile_atom_t*, pdbxParser*)': -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable 'bondTable' [-Wunused-variable] - 984 | int bondTable[32]; - | ^~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] - 988 | int i, pos, j, k; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] - 991 | char modelNum[8]; - | ^~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] - 1002 | molfile_atom_t * atom; - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'void* open_file_write(const char*, const char*, int)': -contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable 'fd' [-Wunused-variable] - 1409 | FILE* fd; - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_timestep': -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:239:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 239 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:242:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 242 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_structure': -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:204:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 204 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp: In function 'void* open_cube_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:175:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 175 | fgets(readbuf, 1023, cube->fd); // go on to next line @@ -2837,47 +2730,62 @@ contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 349 | fgets(readbuf, 1023, cube->fd); // gobble up rest of line | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'open_vaspoutcar_read': -contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:87:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 87 | 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: At top level: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] - 160 | static int get_pte_idx_from_string(const char *label) { - | ^~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_data': -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 238 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_data': +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:237:60: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_metadata': -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:282:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 282 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'read_vaspchgcar_metadata': +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:150:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 150 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'open_vaspparchg_read': -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c: In function 'open_vaspchgcar_read': +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:71:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 71 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:75:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 75 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:81:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:92:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 92 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:103:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 103 | fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] +contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:131:44: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspchgcarplugin.c:41: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) | ^~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] + 133 | static int get_pte_idx(const char *label) + | ^~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:31: +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function 'read_next_timestep': +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:144:5: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 52 [-Wstringop-truncation] + 144 | strncpy(numstr, record + 30, 8); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:149:5: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 44 [-Wstringop-truncation] + 149 | strncpy(numstr+10, record + 38, 8); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:154:5: warning: '__builtin_strncpy' output may be truncated copying 8 bytes from a string of length 36 [-Wstringop-truncation] + 154 | strncpy(numstr+20, record + 46, 8); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] + 159 | strncpy(numstr+30, record + 54, 6); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] + 164 | strncpy(numstr+40, record + 60, 6); + | ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_fread': contrib/uiuc/plugins/molfile_plugin/src/fastio.h:435:35: warning: format '%ld' expects argument of type 'long int', but argument 2 has type 'fio_size_t' {aka 'long long int'} [-Wformat=] @@ -2923,6 +2831,26 @@ | ~~~~~~ | | | fio_size_t {aka long long int} +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_timestep': +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:239:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 239 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:242:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 242 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'read_vaspoutcar_structure': +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:204:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 204 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c: In function 'open_vaspoutcar_read': +contrib/uiuc/plugins/molfile_plugin/src/vaspoutcarplugin.c:87:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 87 | 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: At top level: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] + 160 | static int get_pte_idx_from_string(const char *label) { + | ^~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdheader': contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] 191 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { @@ -2966,6 +2894,114 @@ contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: 'fio_readv' defined but not used [-Wunused-function] 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { | ^~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function 'read_pdb_structure': +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:299:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 70 [-Wstringop-truncation] + 299 | strncpy(name, record + 12, 4); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:304:3: warning: '__builtin_strncpy' output may be truncated copying 1 byte from a string of length 66 [-Wstringop-truncation] + 304 | strncpy(altloc, record + 16, 1); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:308:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 65 [-Wstringop-truncation] + 308 | strncpy(resname, record + 17, 4); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:317:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 60 [-Wstringop-truncation] + 317 | strncpy(resid, record + 22, 4); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:159:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 28 [-Wstringop-truncation] + 159 | strncpy(numstr+30, record + 54, 6); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:164:5: warning: '__builtin_strncpy' output may be truncated copying 6 bytes from a string of length 22 [-Wstringop-truncation] + 164 | strncpy(numstr+40, record + 60, 6); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:330:5: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 10 [-Wstringop-truncation] + 330 | strncpy(segname, record + 72, 4); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:339:5: warning: '__builtin_strncpy' output may be truncated copying 2 bytes from a string of length 6 [-Wstringop-truncation] + 339 | strncpy(elementsymbol, record + 76, 2); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h: In function 'open_pdb_read': +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:190:5: warning: '__builtin_strncpy' output may be truncated copying 9 bytes from a string of length 32 [-Wstringop-truncation] + 190 | strncpy(date, record + 50, 9); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/readpdb.h:200:5: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 20 [-Wstringop-truncation] + 200 | strncpy(pdbcode, record + 62, 4); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_data': +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:238:60: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 238 | for (n = 0; n < data->numatoms + data->version + 5; ++n) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'read_vaspparchg_metadata': +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:150:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 150 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c: In function 'open_vaspparchg_read': +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:71:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 71 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:75:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 75 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:81:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 81 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:92:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 92 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:103:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 103 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:131:44: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 131 | for (i = 0; i < data->numatoms + 2; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: +contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h:111:13: warning: 'vasp_timestep_unitcell' defined but not used [-Wunused-function] + 111 | static void vasp_timestep_unitcell(molfile_timestep_t *ts, vasp_plugindata_t *data) + | ^~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'int getUniqueResID(char*, int)': +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:443:7: warning: unused variable 'i' [-Wunused-variable] + 443 | int i, uid; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'int parseStructureFaster(molfile_atom_t*, int*, pdbxParser*)': +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:484:47: warning: unused variable 'j' [-Wunused-variable] + 484 | int i, count, atomdata, pos, idx, xyzcount, j; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:503:8: warning: unused variable 'oldChain' [-Wunused-variable] + 503 | char oldChain[8]; + | ^~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'bool readAngleBonds(molfile_atom_t*, pdbxParser*)': +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:803:7: warning: unused variable 'bondTable' [-Wunused-variable] + 803 | int bondTable[32]; + | ^~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:807:15: warning: unused variable 'j' [-Wunused-variable] + 807 | int i, pos, j, k; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:811:8: warning: unused variable 'modelNum' [-Wunused-variable] + 811 | char modelNum[8]; + | ^~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:822:20: warning: unused variable 'atom' [-Wunused-variable] + 822 | molfile_atom_t * atom; + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:884:7: warning: unused variable 'test' [-Wunused-variable] + 884 | int test = parser->nbonds + bnum; + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'bool readRMSDBonds(molfile_atom_t*, pdbxParser*)': +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:984:7: warning: unused variable 'bondTable' [-Wunused-variable] + 984 | int bondTable[32]; + | ^~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:988:15: warning: unused variable 'j' [-Wunused-variable] + 988 | int i, pos, j, k; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:991:8: warning: unused variable 'modelNum' [-Wunused-variable] + 991 | char modelNum[8]; + | ^~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1002:20: warning: unused variable 'atom' [-Wunused-variable] + 1002 | molfile_atom_t * atom; + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp: In function 'void* open_file_write(const char*, const char*, int)': +contrib/uiuc/plugins/molfile_plugin/src/pdbxplugin.cpp:1409:9: warning: unused variable 'fd' [-Wunused-variable] + 1409 | FILE* fd; + | ^~ contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'write_vaspposcar_timestep': contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:360:40: warning: argument to 'sizeof' in 'strncpy' call is the same expression as the source; did you mean to use the size of the destination? [-Wsizeof-pointer-memaccess] 360 | strncpy(tmptype, atom->type, sizeof(atom->type)); @@ -3208,13 +3244,13 @@ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1422:5: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] 1422 | strncat(data->basis_string, &data->gbasis[3], 1); | ^ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1411:5: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] + 1411 | strncat(data->basis_string, &data->gbasis[2], 1); + | ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function 'void eatline(FILE*)': contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:238:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 238 | fgets(readbuf, 1024, fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1411:5: warning: '__builtin___strncat_chk' output may be truncated copying 1 byte from a string of length 9 [-Wstringop-truncation] - 1411 | strncat(data->basis_string, &data->gbasis[2], 1); - | ^ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp: In function 'void* open_xsf_read(const char*, const char*, int*)': contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:408:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 408 | fgets(readbuf, 256, xsf->fd); @@ -3592,27 +3628,6 @@ /usr/include/c++/14/bits/stl_pair.h:1132:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 1132 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -layer2/ObjectSurface.cpp: In function 'void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)': -layer2/ObjectSurface.cpp:269:30: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] - 269 | " ObjectSurfaceDump: %s written to %s\n", I->Name, fname ENDFB(I->G); - | ^~ -In file included from layer2/ObjectSurface.cpp:45: -layer0/Feedback.h:274:15: note: 'snprintf' output 34 or more bytes (assuming 289) into a destination of size 255 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectSurface.cpp:268:7: note: in expansion of macro 'PRINTFB' - 268 | PRINTFB(I->G, FB_ObjectSurface, FB_Actions) - | ^~~~~~~ -layer2/ObjectSurface.cpp: In member function 'virtual void ObjectSurface::update()': -layer2/ObjectSurface.cpp:494:43: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] - 494 | " ObjectSurface: updating \"%s\".\n", I->Name ENDFB(I->G); - | ^~ -layer0/Feedback.h:274:15: note: 'snprintf' output between 30 and 285 bytes into a destination of size 255 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectSurface.cpp:493:13: note: in expansion of macro 'PRINTFB' - 493 | PRINTFB(I->G, FB_ObjectSurface, FB_Details) - | ^~~~~~~ layer1/SymOp.cpp: In member function 'std::string pymol::SymOp::to_string() const': layer1/SymOp.cpp:37:32: warning: '%d' directive output may be truncated writing between 1 and 4 bytes into a region of size between 0 and 5 [-Wformat-truncation=] 37 | std::snprintf(code, 8, "%u_%d%d%d", index + 1, x + 5, y + 5, z + 5); @@ -3637,6 +3652,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +layer2/ObjectSurface.cpp: In function 'void ObjectSurfaceDump(ObjectSurface*, const char*, int, int)': +layer2/ObjectSurface.cpp:269:30: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 235 [-Wformat-truncation=] + 269 | " ObjectSurfaceDump: %s written to %s\n", I->Name, fname ENDFB(I->G); + | ^~ +In file included from layer2/ObjectSurface.cpp:45: +layer0/Feedback.h:274:15: note: 'snprintf' output 34 or more bytes (assuming 289) into a destination of size 255 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectSurface.cpp:268:7: note: in expansion of macro 'PRINTFB' + 268 | PRINTFB(I->G, FB_ObjectSurface, FB_Actions) + | ^~~~~~~ +layer2/ObjectSurface.cpp: In member function 'virtual void ObjectSurface::update()': +layer2/ObjectSurface.cpp:494:43: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] + 494 | " ObjectSurface: updating \"%s\".\n", I->Name ENDFB(I->G); + | ^~ +layer0/Feedback.h:274:15: note: 'snprintf' output between 30 and 285 bytes into a destination of size 255 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectSurface.cpp:493:13: note: in expansion of macro 'PRINTFB' + 493 | PRINTFB(I->G, FB_ObjectSurface, FB_Details) + | ^~~~~~~ layer2/ObjectVolume.cpp: In function 'ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)': layer2/ObjectVolume.cpp:80:33: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 230 [-Wformat-truncation=] 80 | "ObjectVolume-Error: map '%s' has been deleted.\n", vs->MapName @@ -3886,6 +3922,33 @@ layer3/Editor.cpp:341:12: note: 'sprintf' output between 12 and 267 bytes into a destination of size 256 341 | sprintf(buffer, "(byobject %s)", name); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer3/Selector.cpp: In function 'int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)': +layer3/Selector.cpp:1717:70: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] + 1717 | " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", + | ^~ +In file included from /usr/include/stdio.h:970, + from /usr/include/c++/14/cstdio:42, + from /usr/include/c++/14/ext/string_conversions.h:45, + from /usr/include/c++/14/bits/basic_string.h:4154, + from /usr/include/c++/14/string:54, + from layer3/Selector.cpp:20: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)' at layer3/Selector.cpp:1716:19: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 59 and 324 bytes into a destination of size 255 + 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 69 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 70 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +In file included from layer1/Setting.h:27, + from layer1/PyMOLObject.h:25, + from layer3/Executive.h:25, + from layer3/Executive.cpp:37: +layer0/Result.h: In constructor 'pymol::Result::Result(type) [with ResultT = std::pair]': +layer0/Result.h:99:3: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 99 | Result(type r) : m_result(std::move(r)) {} + | ^~~~~~ layer2/ObjectSlice.cpp: In member function 'virtual void ObjectSlice::update()': layer2/ObjectSlice.cpp:639:42: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 225 [-Wformat-truncation=] 639 | "ObjectSliceUpdate-Error: map '%s' has been deleted.\n", oss->MapName @@ -3906,33 +3969,6 @@ layer2/ObjectSlice.cpp:649:11: note: in expansion of macro 'PRINTFB' 649 | PRINTFB(I->G, FB_ObjectSlice, FB_Blather) | ^~~~~~~ -In file included from layer1/Setting.h:27, - from layer1/PyMOLObject.h:25, - from layer3/Executive.h:25, - from layer3/Executive.cpp:37: -layer0/Result.h: In constructor 'pymol::Result::Result(type) [with ResultT = std::pair]': -layer0/Result.h:99:3: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 99 | Result(type r) : m_result(std::move(r)) {} - | ^~~~~~ -layer3/Selector.cpp: In function 'int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)': -layer3/Selector.cpp:1717:70: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 207 [-Wformat-truncation=] - 1717 | " AssignSS-Warning: Ignoring incomplete residue /%s/%s/%s/%d%c ...\n", - | ^~ -In file included from /usr/include/stdio.h:970, - from /usr/include/c++/14/cstdio:42, - from /usr/include/c++/14/ext/string_conversions.h:45, - from /usr/include/c++/14/bits/basic_string.h:4154, - from /usr/include/c++/14/string:54, - from layer3/Selector.cpp:20: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int SelectorAssignSS(PyMOLGlobals*, int, int, int, int, ObjectMolecule*, int)' at layer3/Selector.cpp:1716:19: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 59 and 324 bytes into a destination of size 255 - 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 69 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 70 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function 'pymol::Result<> ExecutiveRemoveAtoms(PyMOLGlobals*, const char*, int)': layer3/Executive.cpp:9017:58: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 207 and 217 [-Wformat-truncation=] 9017 | " Remove: eliminated %d atoms in model \"%s\".\n", @@ -4487,8 +4523,8 @@ dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'pymol' in '../pymol_3.0.0+dfsg-1_all.deb'. -dpkg-deb: building package 'python3-pymol-dbgsym' in '../python3-pymol-dbgsym_3.0.0+dfsg-1_armhf.deb'. dpkg-deb: building package 'python3-pymol' in '../python3-pymol_3.0.0+dfsg-1_armhf.deb'. +dpkg-deb: building package 'python3-pymol-dbgsym' in '../python3-pymol-dbgsym_3.0.0+dfsg-1_armhf.deb'. dpkg-deb: building package 'pymol-data' in '../pymol-data_3.0.0+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../pymol_3.0.0+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../pymol_3.0.0+dfsg-1_armhf.changes @@ -4497,12 +4533,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10614/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1156 and its subdirectories -I: Current time: Thu Nov 7 09:42:46 -12 2024 -I: pbuilder-time-stamp: 1731015766 +I: removing directory /srv/workspace/pbuilder/10614 and its subdirectories +I: Current time: Fri Nov 8 12:07:08 +14 2024 +I: pbuilder-time-stamp: 1731017228