Diff of the two buildlogs: -- --- b1/build.log 2024-11-06 18:25:19.603613033 +0000 +++ b2/build.log 2024-11-06 18:29:55.041821705 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 9 12:44:24 -12 2025 -I: pbuilder-time-stamp: 1765327464 +I: Current time: Thu Nov 7 08:25:23 +14 2024 +I: pbuilder-time-stamp: 1730917523 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,51 +36,83 @@ 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/2726436/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3347977/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +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 6 18:25 /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/3347977/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3347977/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='amd64' - DEBIAN_FRONTEND='noninteractive' + 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]="x86_64-pc-linux-gnu") + 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=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='f8313b215aca42b4929d96c19ed60de1' - 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='2726436' - PS1='# ' - PS2='> ' + INVOCATION_ID=157dd6d67ea0435e88c95f0901aca62a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3347977 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.nis98BYn/pbuilderrc_zOHY --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.nis98BYn/b1 --logfile b1/build.log pymol_3.0.0+dfsg-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.nis98BYn/pbuilderrc_btnw --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.nis98BYn/b2 --logfile b2/build.log pymol_3.0.0+dfsg-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2726436/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3347977/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -442,7 +474,7 @@ Get: 294 http://deb.debian.org/debian trixie/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get: 295 http://deb.debian.org/debian trixie/main amd64 texlive-base all 2024.20240829-2 [22.7 MB] Get: 296 http://deb.debian.org/debian trixie/main amd64 texlive-latex-base all 2024.20240829-2 [1273 kB] -Fetched 191 MB in 2s (93.7 MB/s) +Fetched 191 MB in 5s (36.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19970 files and directories currently installed.) @@ -1406,8 +1438,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Dec 10 00:45:50 UTC 2025. -Universal Time is now: Wed Dec 10 00:45:50 UTC 2025. +Local time is now: Wed Nov 6 18:27:30 UTC 2024. +Universal Time is now: Wed Nov 6 18:27:30 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -1680,7 +1712,11 @@ 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/3347977/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3347977/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 @@ -1723,51 +1759,6 @@ 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/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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 252 | fgets(line, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_bonds_aux(void*, int*, int**, int**, float**)': -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 328 | fgets(line, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 346 | fgets(line, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 355 | fgets(nextline, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 419 | fgets(line, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_structure(void*, int*, molfile_atom_t*)': -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 194 | fgets(line, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 203 | fgets(line, LINESIZE, bgf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'void* open_bgf_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 59 | fgets(line, LINESIZE, 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; @@ -1778,10 +1769,6 @@ 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/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)); - | ^ 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] @@ -1841,10 +1828,78 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 869 | &prm->Xcap, &prm->Ycap, &prm->Zcap); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:252:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 252 | fgets(line, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_bonds_aux(void*, int*, int**, int**, float**)': +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:328:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 328 | fgets(line, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:346:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 346 | fgets(line, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:355:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 355 | fgets(nextline, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:419:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 419 | fgets(line, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'int read_bgf_structure(void*, int*, molfile_atom_t*)': +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:194:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 194 | fgets(line, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:203:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 203 | fgets(line, LINESIZE, bgf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp: In function 'void* open_bgf_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/bgfplugin.cpp:59:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 59 | fgets(line, LINESIZE, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +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/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_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/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/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 102 | fread(&headersize, sizeof(int), 1, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function 'void* open_fs4_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 79 | fread(&dataBegin, sizeof(int), 1, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'void* open_plt_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | fread(intHeader, sizeof(int), 5, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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/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; @@ -1857,26 +1912,11 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp: In function 'void* open_fs4_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/fs4plugin.cpp:79:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 79 | fread(&dataBegin, sizeof(int), 1, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp: In function 'void* open_plt_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/pltplugin.cpp:69:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | fread(intHeader, sizeof(int), 5, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/gromacsplugin.cpp:30: contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h: In function 'int mdio_readline(md_file*, char*, int, int)': contrib/uiuc/plugins/molfile_plugin/src/Gromacs.h:426:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 426 | fgets(buf, n, mf->f); | ~~~~~^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp: In function 'void* open_uhbd_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/uhbdplugin.cpp:102:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 102 | fread(&headersize, sizeof(int), 1, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c: In function 'abinit_readline': contrib/uiuc/plugins/molfile_plugin/src/abinitplugin.c:279:19: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 279 | for (i = 0; i < strlen(line); ++i) { @@ -1889,25 +1929,51 @@ 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/vasp5xdatcarplugin.c: In function 'read_vasp5xdatcar_timestep': +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:224:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 224 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 545 | for (i=0; ihdr->bintype.recordmarker, data->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function 'read_vasp5xdatcar_structure': +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 174 | for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 180 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 189 | for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 194 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 204 | for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function 'open_vasp5xdatcar_read': +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 72 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 77 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: 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/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/gamessplugin.c: In function 'have_gamess': -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1106:8: warning: variable 'word' set but not used [-Wunused-but-set-variable] - 1106 | char word[3][BUFSIZ]; - | ^~~~ 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); @@ -1917,22 +1983,48 @@ 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/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/gamessplugin.c: In function 'get_basis_stats': 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 'long unsigned int' [-Wsign-compare] 730 | if (len > sizeof(name)) { | ^ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:2264:8: warning: variable 'word' set but not used [-Wunused-but-set-variable] - 2264 | char word[7][BUFSIZ]; - | ^~~~ contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c: In function 'read_mmtk_cdf_timestep': contrib/uiuc/plugins/molfile_plugin/src/netcdfplugin.c:1060:16: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] 1060 | for (i=0; i<(3 * mmtk->atom_numberdim); i++) { | ^ +In file included from contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:160: +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 545 | for (i=0; ifile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function 'read_vasp5xdatcar_structure': -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:174:27: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 174 | for (i = 0; i < 2; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:180:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 180 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:189:26: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 189 | for (i = 0; i < 3; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:194:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 194 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:204:26: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 204 | for (i = 0; i < 8; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c: In function 'open_vasp5xdatcar_read': -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:69:27: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:72:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 72 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:77:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 77 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/vasp5xdatcarplugin.c:40: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: 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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:297:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 297 | fgets(line, LINESIZE, mdf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:319:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 319 | fgets(line, LINESIZE, mdf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:357:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 357 | fgets(line, LINESIZE, mdf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/binposplugin.c: In function 'open_binpos_read': -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_structure(void*, int*, molfile_atom_t*)': -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:223:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 223 | fgets(line, LINESIZE, mdf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/mdfplugin.cpp:241:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 241 | fgets(line, LINESIZE, mdf->file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -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/mdfplugin.cpp: In function 'void* open_mdf_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:164:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 164 | fgets(line, LINESIZE, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:176:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 176 | fgets(line, LINESIZE, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:183:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 183 | fgets(line, LINESIZE, 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] - 459 | int i,j,k; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void ascii_get_element(PlyFile*, char*)': -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1407:7: warning: unused variable 'i' [-Wunused-variable] - 1407 | int i,j,k; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h: In function 'void binary_get_element(PlyFile*, char*)': -contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1541:7: warning: unused variable 'i' [-Wunused-variable] - 1541 | int i,j,k; - | ^ contrib/uiuc/plugins/molfile_plugin/src/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); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -2092,27 +2106,6 @@ 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/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/gamessplugin.c: In function 'read_gamess_rundata': -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:615:3: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] - 615 | strncpy(sys_data->basis_string, data->basis_string, - | ^ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:620:3: warning: '__builtin_strncpy' output may be truncated copying 4096 bytes from a string of length 8191 [-Wstringop-truncation] - 620 | strncpy(sys_data->runtitle, data->runtitle, sizeof(sys_data->runtitle)); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:621:3: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] - 621 | strncpy(sys_data->geometry, data->geometry, sizeof(sys_data->geometry)); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:622:3: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] - 622 | strncpy(sys_data->version_string, data->version_string, - | ^ 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); @@ -2155,15 +2148,111 @@ contrib/uiuc/plugins/molfile_plugin/src/ply_c.h:1333:26: note: destination object of size 0 allocated by 'malloc' 1333 | line = (char *) malloc (sizeof(char) * len); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'read_gamess_rundata': +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:615:3: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] + 615 | strncpy(sys_data->basis_string, data->basis_string, + | ^ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:620:3: warning: '__builtin_strncpy' output may be truncated copying 4096 bytes from a string of length 8191 [-Wstringop-truncation] + 620 | strncpy(sys_data->runtitle, data->runtitle, sizeof(sys_data->runtitle)); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:621:3: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] + 621 | strncpy(sys_data->geometry, data->geometry, sizeof(sys_data->geometry)); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:622:3: warning: '__builtin_strncpy' output may be truncated copying 81 bytes from a string of length 8191 [-Wstringop-truncation] + 622 | strncpy(sys_data->version_string, data->version_string, + | ^ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_coordinates': contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] 1618 | strncpy(atm->type, atname, sizeof(atm->type)); | ^ contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1618:5: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] +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/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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:297:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 297 | fgets(line, LINESIZE, mdf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:319:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 319 | fgets(line, LINESIZE, mdf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:357:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 357 | fgets(line, LINESIZE, mdf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'int read_mdf_structure(void*, int*, molfile_atom_t*)': +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:223:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 223 | fgets(line, LINESIZE, mdf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:241:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 241 | fgets(line, LINESIZE, mdf->file); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp: In function 'void* open_mdf_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:164:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 164 | fgets(line, LINESIZE, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:176:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 176 | fgets(line, LINESIZE, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/mdfplugin.cpp:183:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 183 | fgets(line, LINESIZE, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_basis_options': +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/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/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 + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 181 | fgets(readbuf, 1023, cube->fd); // skip second header line + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:326:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | fgets(readbuf, 1023, cube->fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:337:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 337 | fgets(readbuf, 1023, cube->fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:339:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 339 | fscanf(cube->fd, "%d", &cube->nsets); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:344:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 344 | fscanf(cube->fd, "%d", &orb); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 349 | fgets(readbuf, 1023, cube->fd); // gobble up rest of line + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +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) + | ^~~~~~~~~~~ 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); @@ -2201,55 +2290,6 @@ 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/gamessplugin.c: In function 'get_basis_options': -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/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/stlplugin.cpp: In function 'int read_rawgraphics(void*, int*, const molfile_graphics_t**)': -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:96:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 96 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:104:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 104 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:119:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 119 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:131:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 131 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:153:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 153 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:162:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 162 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/stlplugin.cpp:171:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 171 | fgets(line, 80, infile); - | ~~~~~^~~~~~~~~~~~~~~~~~ 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); @@ -2281,10 +2321,6 @@ 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/gamessplugin.c: In function 'get_input_structure': -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1682:5: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] - 1682 | strncpy(atm->type, atname, sizeof(atm->type)); - | ^ 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); @@ -2314,71 +2350,9 @@ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspparchgplugin.c:41: contrib/uiuc/plugins/molfile_plugin/src/vaspplugin.h: At top level: -In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': contrib/uiuc/plugins/molfile_plugin/src/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/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 545 | for (i=0; ifile, " Ene= %f\n", &orbenergy); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1166:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1166 | fscanf(data->file, " Spin= %s\n", spin); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1167:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 1167 | fscanf(data->file, " Occup= %f\n", &occu); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'eatline': -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 840 | fgets(readbuf, 1024, fd); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'open_molden_read': -contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:224:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 224 | fscanf(data->file, "%d", &natm); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: At top level: -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: 'whereami' defined but not used [-Wunused-function] - 1097 | static void whereami(FILE *file) { - | ^~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: 'thisline' defined but not used [-Wunused-function] - 1077 | static void thisline(FILE *file) { - | ^~~~~~~~ -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/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/qmplugin.h:585:13: warning: 'print_matrix4' defined but not used [-Wunused-function] - 585 | static void print_matrix4(const float mat[16]) { - | ^~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: 'del_wavefunction' defined but not used [-Wunused-function] - 507 | static void del_wavefunction(qm_timestep_t *ts) { - | ^~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: 'replace_wavefunction' defined but not used [-Wunused-function] - 490 | static void replace_wavefunction(qm_timestep_t *ts, int n) { - | ^~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] - 133 | static int get_pte_idx(const char *label) - | ^~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'get_pte_vdw_radius' defined but not used [-Wunused-function] - 109 | static float get_pte_vdw_radius(const int idx) - | ^~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'get_pte_mass' defined but not used [-Wunused-function] - 102 | static float get_pte_mass(const int idx) - | ^~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function] - 95 | static const char *get_pte_label(const int idx) - | ^~~~~~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp: In function 'int read_parm7_structure(void*, int*, molfile_atom_t*)': contrib/uiuc/plugins/molfile_plugin/src/parm7plugin.cpp:78:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 78 | fgets(buf, 85, file); @@ -2457,10 +2431,179 @@ 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/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 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/gamessplugin.c: In function 'get_input_structure': +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1682:5: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 8191 [-Wstringop-truncation] + 1682 | strncpy(atm->type, atname, sizeof(atm->type)); | ^ +In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:51: +contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': +contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 519 | if (rc != iov[i].iov_len) + | ^~ +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)); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_timestep': +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 232 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 237 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 246 | for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 249 | if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 256 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_structure': +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 195 | for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 198 | if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 203 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'open_vaspposcar_read': +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 69 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:73:27: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 73 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 87 | fgets(lineptr, LINESIZE, data->file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: 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/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/dcdplugin.c: In function 'read_dcdheader': +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 191 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:204:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 204 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:222:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 222 | if (input_integer[0] != dcdcordmagic) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:399:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 399 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:416:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] + 416 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdstep': +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:621:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] + 621 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:625:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] + 625 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] + 546 | fio_size_t readlen; /* number of bytes actually read */ + | ^~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:96:13: warning: 'swap2_aligned' defined but not used [-Wunused-function] + 96 | static void swap2_aligned(void *v, long ndata) { + | ^~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] + 32 | static void swap2_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/fastio.h:609:12: warning: 'fio_write_str' defined but not used [-Wunused-function] + 609 | static int fio_write_str(fio_fd fd, const char *str) { + | ^~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: 'fio_read_int32' defined but not used [-Wunused-function] + 605 | static int fio_read_int32(fio_fd fd, int *i) { + | ^~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: 'fio_readv' defined but not used [-Wunused-function] + 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { + | ^~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:49: +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 545 | for (i=0; ifile); @@ -2527,10 +2670,68 @@ 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); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/pdbplugin.c:32: +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'read_molden_rundata': +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:596:25: warning: variable 'hessian_data' set but not used [-Wunused-but-set-variable] + 596 | molfile_qm_hessian_t *hessian_data; + | ^~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'count_orbitals': +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1165:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1165 | fscanf(data->file, " Ene= %f\n", &orbenergy); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1166:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1166 | fscanf(data->file, " Spin= %s\n", spin); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:1167:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 1167 | fscanf(data->file, " Occup= %f\n", &occu); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'eatline': +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 840 | fgets(readbuf, 1024, fd); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c: In function 'open_molden_read': +contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:224:11: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 224 | fscanf(data->file, "%d", &natm); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: 'whereami' defined but not used [-Wunused-function] + 1097 | static void whereami(FILE *file) { + | ^~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1077:13: warning: 'thisline' defined but not used [-Wunused-function] + 1077 | static void thisline(FILE *file) { + | ^~~~~~~~ +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/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/qmplugin.h:585:13: warning: 'print_matrix4' defined but not used [-Wunused-function] + 585 | static void print_matrix4(const float mat[16]) { + | ^~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: 'del_wavefunction' defined but not used [-Wunused-function] + 507 | static void del_wavefunction(qm_timestep_t *ts) { + | ^~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: 'replace_wavefunction' defined but not used [-Wunused-function] + 490 | static void replace_wavefunction(qm_timestep_t *ts, int n) { + | ^~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:48: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:133:12: warning: 'get_pte_idx' defined but not used [-Wunused-function] 133 | static int get_pte_idx(const char *label) | ^~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:109:14: warning: 'get_pte_vdw_radius' defined but not used [-Wunused-function] + 109 | static float get_pte_vdw_radius(const int idx) + | ^~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:102:14: warning: 'get_pte_mass' defined but not used [-Wunused-function] + 102 | static float get_pte_mass(const int idx) + | ^~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:95:20: warning: 'get_pte_label' defined but not used [-Wunused-function] + 95 | static const char *get_pte_label(const int idx) + | ^~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: +contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': +contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 519 | if (rc != iov[i].iov_len) + | ^~ 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); @@ -2552,6 +2753,71 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +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/pqrplugin.c: In function 'get_atom_radius': +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:16: warning: variable 'type' set but not used [-Wunused-but-set-variable] + 166 | char *name, *type; + | ^~~~ +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable 'name' set but not used [-Wunused-but-set-variable] + 166 | char *name, *type; + | ^~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] + 65 | static void swap8_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function] + 46 | static void swap4_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] + 32 | static void swap2_unaligned(void *v, long ndata) { + | ^~~~~~~~~~~~~~~ +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/moldenplugin.c: In function 'read_molden_structure': contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:350:7: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 350 | strncpy(atom->type, atname, sizeof(atom->type)); @@ -2565,114 +2831,6 @@ contrib/uiuc/plugins/molfile_plugin/src/moldenplugin.c:326:7: warning: '__builtin_strncpy' output may be truncated copying 11 bytes from a string of length 1023 [-Wstringop-truncation] 326 | strncpy(data->atoms[i].type, atname, sizeof(data->atoms[i].type)); | ^ -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)); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_timestep': -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 232 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:237:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 237 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:246:43: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 246 | for (i = 0; i < data->version - 2; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:249:35: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 249 | if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:256:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 256 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'read_vaspposcar_structure': -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:195:42: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 195 | for (i = 0; i < data->version + 3; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:198:34: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 198 | if (tolower(lineptr[0]) == 's') fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:203:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 203 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function 'get_atom_radius': -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c: In function 'open_vaspposcar_read': -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:69:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 69 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:73:27: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 73 | for (i = 0; i < 5; ++i) fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:87:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 87 | fgets(lineptr, LINESIZE, data->file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/vaspposcarplugin.c:40: -contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h: 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/pqrplugin.c:166:16: warning: variable 'type' set but not used [-Wunused-but-set-variable] - 166 | char *name, *type; - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:166:9: warning: variable 'name' set but not used [-Wunused-but-set-variable] - 166 | char *name, *type; - | ^~~~ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c: In function 'get_contrl': -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1981:3: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] - 1981 | strncpy(data->geometry, trimright(temp+7), sizeof(data->geometry)); - | ^ -In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:79: -contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': -contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 519 | if (rc != iov[i].iov_len) - | ^~ -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 - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:181:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 181 | fgets(readbuf, 1023, cube->fd); // skip second header line - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:326:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | fgets(readbuf, 1023, cube->fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:337:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 337 | fgets(readbuf, 1023, cube->fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:339:11: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 339 | fscanf(cube->fd, "%d", &cube->nsets); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:344:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 344 | fscanf(cube->fd, "%d", &orb); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/cubeplugin.cpp:349:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 349 | fgets(readbuf, 1023, cube->fd); // gobble up rest of line - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -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/gamessplugin.c: In function 'get_contrl_firefly': -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1818:3: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] - 1818 | strncpy(data->geometry, trimright(temp+7), sizeof(data->geometry)); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function 'read_pqr_timestep': -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:109:3: warning: '__builtin_strncpy' output may be truncated copying 80 bytes from a string of length 81 [-Wstringop-truncation] - 109 | strncpy(tmp, record, PQR_RECORD_LENGTH); - | ^ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp: In function 'int read_xbgf_timestep(void*, int, molfile_timestep_t*)': contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:288:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 288 | fgets(line, LINESIZE, bgf->file); @@ -2693,6 +2851,11 @@ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:455:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 455 | fgets(line, LINESIZE, bgf->file); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] + 545 | for (i=0; ifile); @@ -2704,77 +2867,6 @@ contrib/uiuc/plugins/molfile_plugin/src/xbgfplugin.cpp:72:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 72 | fgets(line, LINESIZE, fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from contrib/uiuc/plugins/molfile_plugin/src/jsplugin.c:89: -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At top level: -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:65:13: warning: 'swap8_unaligned' defined but not used [-Wunused-function] - 65 | static void swap8_unaligned(void *v, long ndata) { - | ^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:46:13: warning: 'swap4_unaligned' defined but not used [-Wunused-function] - 46 | static void swap4_unaligned(void *v, long ndata) { - | ^~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h:32:13: warning: 'swap2_unaligned' defined but not used [-Wunused-function] - 32 | static void swap2_unaligned(void *v, long ndata) { - | ^~~~~~~~~~~~~~~ -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/pqrplugin.c: In function 'read_pqr_structure': -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:137:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 68 [-Wstringop-truncation] - 137 | strncpy(name, record+12, 4); name[4] = 0; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:138:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 63 [-Wstringop-truncation] - 138 | strncpy(resname, record+17, 4); resname[4] = 0; - | ^ -contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:139:3: warning: '__builtin_strncpy' output may be truncated copying 1 byte from a string of length 59 [-Wstringop-truncation] - 139 | strncpy(chain, record+21, 1); chain[1] = 0; - | ^ -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/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/gamessplugin.c: In function 'get_proc_mem.isra': -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1279:5: warning: '__builtin_strncpy' output may be truncated copying 256 bytes from a string of length 8191 [-Wstringop-truncation] - 1279 | strncpy(data->memory,&word[2][0],sizeof(data->memory)); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1272:5: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] - 1272 | strncpy(data->memory,trimright(temp),sizeof(data->memory)); - | ^ -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); - | ^ -In file included from contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c:42: -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'angular_momentum_expon': -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:545:14: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 545 | for (i=0; i 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/gamessplugin.c: In function 'get_contrl': +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1981:3: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] + 1981 | strncpy(data->geometry, trimright(temp+7), sizeof(data->geometry)); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function 'read_pqr_timestep': +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:109:3: warning: '__builtin_strncpy' output may be truncated copying 80 bytes from a string of length 81 [-Wstringop-truncation] + 109 | strncpy(tmp, record, PQR_RECORD_LENGTH); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c: In function 'read_pqr_structure': +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:137:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 68 [-Wstringop-truncation] + 137 | strncpy(name, record+12, 4); name[4] = 0; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:138:3: warning: '__builtin_strncpy' output may be truncated copying 4 bytes from a string of length 63 [-Wstringop-truncation] + 138 | strncpy(resname, record+17, 4); resname[4] = 0; + | ^ +contrib/uiuc/plugins/molfile_plugin/src/pqrplugin.c:139:3: warning: '__builtin_strncpy' output may be truncated copying 1 byte from a string of length 59 [-Wstringop-truncation] + 139 | strncpy(chain, record+21, 1); chain[1] = 0; + | ^ +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/gamessplugin.c: In function 'get_contrl_firefly': +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1818:3: warning: '__builtin_strncpy' specified bound 8192 equals destination size [-Wstringop-truncation] + 1818 | strncpy(data->geometry, trimright(temp+7), sizeof(data->geometry)); + | ^ +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/gamessplugin.c: In function 'get_proc_mem.isra': +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1279:5: warning: '__builtin_strncpy' output may be truncated copying 256 bytes from a string of length 8191 [-Wstringop-truncation] + 1279 | strncpy(data->memory,&word[2][0],sizeof(data->memory)); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/gamessplugin.c:1272:5: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation] + 1272 | strncpy(data->memory,trimright(temp),sizeof(data->memory)); + | ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c: In function 'read_vaspxdatcar_timestep': contrib/uiuc/plugins/molfile_plugin/src/vaspxdatcarplugin.c:283:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 283 | fgets(lineptr, LINESIZE, data->file); @@ -2893,102 +2990,41 @@ 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/dcdplugin.c:51: -contrib/uiuc/plugins/molfile_plugin/src/fastio.h: In function 'fio_readv': -contrib/uiuc/plugins/molfile_plugin/src/fastio.h:519:14: warning: comparison of integer expressions of different signedness: 'fio_size_t' {aka 'long int'} and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 519 | if (rc != iov[i].iov_len) - | ^~ -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/dcdplugin.c: In function 'read_dcdheader': -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:191:57: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 191 | } else if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:204:54: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 204 | if (input_integer[0] == 84 && input_integer[1] == dcdcordmagic) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:222:26: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 222 | if (input_integer[0] != dcdcordmagic) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:399:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 399 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:416:45: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] - 416 | if ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4) { - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c: In function 'read_dcdstep': -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:621:23: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] - 621 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:625:43: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare] - 625 | if ((tmpbuf[2*i]+tmpbuf[2*i+1]) != sizeof(float)*N) return DCD_BADFORMAT; - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:546:16: warning: variable 'readlen' set but not used [-Wunused-but-set-variable] - 546 | fio_size_t readlen; /* number of bytes actually read */ - | ^~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'get_traj_frame.isra': -contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:819:5: warning: '__builtin_strncpy' output may be truncated copying 10 bytes from a string of length 10 [-Wstringop-truncation] - 819 | strncpy((*atoms)[i].type, (*atoms)[indexmap[i]].type, 10); - | ^ -In file included from contrib/uiuc/plugins/molfile_plugin/src/dcdplugin.c:60: -contrib/uiuc/plugins/molfile_plugin/src/endianswap.h: At top level: +contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c: In function 'write_psf_structure': +contrib/uiuc/plugins/molfile_plugin/src/psfplugin.c:782:33: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] + 782 | if (strlen(atoms[i].type) > fw) { + | ^ +In file included from contrib/uiuc/plugins/molfile_plugin/src/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/fastio.h:609:12: warning: 'fio_write_str' defined but not used [-Wunused-function] - 609 | static int fio_write_str(fio_fd fd, const char *str) { - | ^~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/fastio.h:605:12: warning: 'fio_read_int32' defined but not used [-Wunused-function] - 605 | static int fio_read_int32(fio_fd fd, int *i) { - | ^~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/fastio.h:459:19: warning: 'fio_readv' defined but not used [-Wunused-function] - 459 | static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) { - | ^~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h: In function 'get_traj_frame.isra': +contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:819:5: warning: '__builtin_strncpy' output may be truncated copying 10 bytes from a string of length 10 [-Wstringop-truncation] + 819 | strncpy((*atoms)[i].type, (*atoms)[indexmap[i]].type, 10); + | ^ contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c: In function 'read_vaspxml_structure': contrib/uiuc/plugins/molfile_plugin/src/vaspxmlplugin.c:139:7: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 139 | fgets(lineptr, LINESIZE, data->file); @@ -3037,6 +3073,13 @@ contrib/uiuc/plugins/molfile_plugin/src/xsfplugin.cpp:508:16: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 508 | fgets(readbuf, 256, xsf->fd); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +layer0/MemoryUsage.cpp: In function 'size_t pymol::memory_usage()': +layer0/MemoryUsage.cpp:38:21: warning: use of assignment suppression and length modifier together in gnu_scanf format [-Wformat=] + 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); + | ^~~~~~~~~ +layer0/MemoryUsage.cpp:38:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -3068,17 +3111,6 @@ 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/vtfplugin.c: In function 'vtf_read_bonds': -contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:147:48: warning: '%s' directive argument is null [-Wformat-overflow=] - 147 | sprintf(message, "vtfplugin:%d: error: %s: \"%s\"\n", - | ^~ -contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function 'vtf_open_file_read': -contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:538:9: warning: '__builtin___strncat_chk' output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] - 538 | strncat(msg, keyword, 200); - | ^ -contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:629:7: warning: '__builtin___strncat_chk' output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] - 629 | strncat(msg, keyword, 200); - | ^ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp: In function 'void line3(FILE*, GRASSP*)': contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:186:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 186 | fread(line3, 1, 80, infile); @@ -3249,6 +3281,17 @@ contrib/uiuc/plugins/molfile_plugin/src/graspplugin.cpp:398:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 398 | fread(properties, sizeof(float), 3 * nvert, infile); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function 'vtf_read_bonds': +contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:147:48: warning: '%s' directive argument is null [-Wformat-overflow=] + 147 | sprintf(message, "vtfplugin:%d: error: %s: \"%s\"\n", + | ^~ +contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c: In function 'vtf_open_file_read': +contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:538:9: warning: '__builtin___strncat_chk' output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] + 538 | strncat(msg, keyword, 200); + | ^ +contrib/uiuc/plugins/molfile_plugin/src/vtfplugin.c:629:7: warning: '__builtin___strncat_chk' output may be truncated copying 200 bytes from a string of length 254 [-Wstringop-truncation] + 629 | strncat(msg, keyword, 200); + | ^ In file included from contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:57: contrib/uiuc/plugins/molfile_plugin/src/periodic_table.h:160:12: warning: 'get_pte_idx_from_string' defined but not used [-Wunused-function] 160 | static int get_pte_idx_from_string(const char *label) { @@ -3257,10 +3300,6 @@ contrib/uiuc/plugins/molfile_plugin/src/xyzplugin.c:133:7: warning: '__builtin_strncpy' output may be truncated copying 16 bytes from a string of length 1023 [-Wstringop-truncation] 133 | strncpy(atom->name, buffer, sizeof(atom->name)); | ^ -layer0/MemoryUsage.cpp: In function 'size_t pymol::memory_usage()': -layer0/MemoryUsage.cpp:38:21: warning: use of assignment suppression and length modifier together in gnu_scanf format [-Wformat=] - 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); - | ^~~~~~~~~ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp: In function 'int read_vtk_data_ex(void*, molfile_volumetric_readwrite_t*)': contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:371:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 371 | fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); @@ -3269,9 +3308,10 @@ contrib/uiuc/plugins/molfile_plugin/src/vtkplugin.cpp:306:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] 306 | fscanf(fd, "%lf %lf %lf", &vx, &vy, &vz); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer0/MemoryUsage.cpp:38:16: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 38 | std::fscanf(fp, "%*zu%zu", &vmRSS); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function 'void* open_grid_read(const char*, const char*, int*)': +contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 84 | fread(&dataBegin, sizeof(int), 1, fd); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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); @@ -3307,10 +3347,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp: In function 'void* open_grid_read(const char*, const char*, int*)': -contrib/uiuc/plugins/molfile_plugin/src/gridplugin.cpp:84:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 84 | fread(&dataBegin, sizeof(int), 1, fd); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function 'int {anonymous}::write_structure(void*, int, const molfile_atom_t*)': +contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1904:9: warning: unused variable 'last_ctnumber' [-Wunused-variable] + 1904 | int last_ctnumber = -1; + | ^~~~~~~~~~~~~ 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); @@ -3344,10 +3384,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function 'int {anonymous}::write_structure(void*, int, const molfile_atom_t*)': -contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp:1904:9: warning: unused variable 'last_ctnumber' [-Wunused-variable] - 1904 | int last_ctnumber = -1; - | ^~~~~~~~~~~~~ In file included from contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:71: In function 'void swap4_unaligned(void*, long int)', inlined from 'void {anonymous}::Blob::get_float(float*) const' at contrib/uiuc/plugins/molfile_plugin/src/dtrplugin.cpp:615:36, @@ -3745,6 +3781,14 @@ contrib/uiuc/plugins/molfile_plugin/src/edmplugin.cpp:44:8: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 44 | fgets(readbuf, 1024, fd); // go on to next line | ~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from include/tnt/tnt.h:45, + from layer0/ccealignmodule.cpp:39: +In member function 'void TNT::Array1D::set_(T*, T*, const T&) [with T = double]', + inlined from 'TNT::Array1D::Array1D(int, const T&) [with T = double]' at include/tnt/tnt_array1d.h:119:6, + inlined from 'PyObject* findBest(pcePoint, pcePoint, pathCache, int, int, int)' at layer0/ccealignmodule.cpp:506:28: +include/tnt/tnt_array1d.h:283:20: warning: 'void* __builtin_memset(void*, int, long unsigned int)' specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] + 283 | *p = a; + | ~~~^~~ layer1/SceneMouse.cpp: In function 'void SceneClickTransformObject(PyMOLGlobals*, pymol::CObject*, const NamedPicking&, int, bool)': layer1/SceneMouse.cpp:453:32: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 237 [-Wformat-truncation=] 453 | " You clicked %s -> (%s)\n", buffer.c_str(), name ENDFB(G); @@ -3770,14 +3814,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -In file included from include/tnt/tnt.h:45, - from layer0/ccealignmodule.cpp:39: -In member function 'void TNT::Array1D::set_(T*, T*, const T&) [with T = double]', - inlined from 'TNT::Array1D::Array1D(int, const T&) [with T = double]' at include/tnt/tnt_array1d.h:119:6, - inlined from 'PyObject* findBest(pcePoint, pcePoint, pathCache, int, int, int)' at layer0/ccealignmodule.cpp:506:28: -include/tnt/tnt_array1d.h:283:20: warning: 'void* __builtin_memset(void*, int, long unsigned int)' specified bound between 18446744056529682432 and 18446744073709551608 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] - 283 | *p = a; - | ~~~^~~ layer1/Ray.cpp: In function 'void RayRenderVRML2(CRay*, int, int, char**, float, float, float, float, float)': layer1/Ray.cpp:1535:20: warning: '%s' directive writing up to 1023 bytes into a region of size between 0 and 914 [-Wformat-overflow=] 1535 | "%s" @@ -3859,17 +3895,24 @@ 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 - | ^~ +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); + | ^~ +layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132] + 37 | std::snprintf(code, 8, "%u_%d%d%d", index + 1, x + 5, y + 5, z + 5); + | ^~~~~~~~~~~ +layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132] In file included from /usr/include/stdio.h:970, - from /usr/include/python3.12/Python.h:24, - from layer0/os_python.h:34, - from layer2/ObjectVolume.cpp:20: + 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 layer1/SymOp.h:9, + from layer1/SymOp.cpp:7: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)' at layer2/ObjectVolume.cpp:79:5: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 46 and 301 bytes into a destination of size 255 + inlined from 'std::string pymol::SymOp::to_string() const' at layer1/SymOp.cpp:37:16: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 6 and 17 bytes into a destination of size 8 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, @@ -3887,54 +3930,23 @@ layer2/ObjectMolecule.cpp:7602:3: note: in expansion of macro 'PRINTFB' 7602 | PRINTFB(G, FB_ObjectMolecule, FB_Blather) | ^~~~~~~ -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); - | ^~ -layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132] - 37 | std::snprintf(code, 8, "%u_%d%d%d", index + 1, x + 5, y + 5, z + 5); - | ^~~~~~~~~~~ -layer1/SymOp.cpp:37:26: note: directive argument in the range [-123, 132] +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 + | ^~ 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 layer1/SymOp.h:9, - from layer1/SymOp.cpp:7: + from /usr/include/python3.12/Python.h:24, + from layer0/os_python.h:34, + from layer2/ObjectVolume.cpp:20: In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'std::string pymol::SymOp::to_string() const' at layer1/SymOp.cpp:37:16: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 6 and 17 bytes into a destination of size 8 + inlined from 'ObjectMapState* ObjectVolumeStateGetMapState(ObjectVolumeState*)' at layer2/ObjectVolume.cpp:79:5: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 46 and 301 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 ()); | ~~~~~~~~~~~~~~~~~ -layer2/ObjectMolecule.cpp: In member function 'virtual void ObjectMolecule::update()': -layer2/ObjectMolecule.cpp:10629:82: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] -10629 | " ObjectMolecule-DEBUG: updating representations for state %d of \"%s\".\n", - | ^~ -layer0/Feedback.h:274:15: note: 'snprintf' output between 68 and 333 bytes into a destination of size 255 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectMolecule.cpp:10628:13: note: in expansion of macro 'PRINTFB' -10628 | PRINTFB(G, FB_ObjectMolecule, FB_Blather) - | ^~~~~~~ -layer2/ObjectMolecule.cpp: In function 'int ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, const float*, int, int)': -layer2/ObjectMolecule.cpp:10755:43: warning: '%s' directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] -10755 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", - | ^~ -10756 | buffer, v[0], v[1], v[2], state + 1, mode, 0); - | ~~~~~~ -layer2/ObjectMolecule.cpp:10755:21: note: directive argument in the range [-2147483647, 2147483647] -10755 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -layer2/ObjectMolecule.cpp:10755:14: note: 'sprintf' output between 78 and 2036 bytes into a destination of size 1024 -10755 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -10756 | buffer, v[0], v[1], v[2], state + 1, mode, 0); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Editor.cpp: In function 'void EditorPrepareDrag(PyMOLGlobals*, pymol::CObject*, int, int, int, int)': layer3/Editor.cpp:1935:29: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 236 [-Wformat-truncation=] 1935 | " Editor: grabbing (%s).", name ENDFB(G); @@ -3965,6 +3977,30 @@ 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); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMolecule.cpp: In member function 'virtual void ObjectMolecule::update()': +layer2/ObjectMolecule.cpp:10629:82: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 181 and 191 [-Wformat-truncation=] +10629 | " ObjectMolecule-DEBUG: updating representations for state %d of \"%s\".\n", + | ^~ +layer0/Feedback.h:274:15: note: 'snprintf' output between 68 and 333 bytes into a destination of size 255 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectMolecule.cpp:10628:13: note: in expansion of macro 'PRINTFB' +10628 | PRINTFB(G, FB_ObjectMolecule, FB_Blather) + | ^~~~~~~ +layer2/ObjectMolecule.cpp: In function 'int ObjectMoleculeMoveAtom(ObjectMolecule*, int, int, const float*, int, int)': +layer2/ObjectMolecule.cpp:10755:43: warning: '%s' directive writing up to 1023 bytes into a region of size 1004 [-Wformat-overflow=] +10755 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", + | ^~ +10756 | buffer, v[0], v[1], v[2], state + 1, mode, 0); + | ~~~~~~ +layer2/ObjectMolecule.cpp:10755:21: note: directive argument in the range [-2147483647, 2147483647] +10755 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +layer2/ObjectMolecule.cpp:10755:14: note: 'sprintf' output between 78 and 2036 bytes into a destination of size 1024 +10755 | sprintf(line, "cmd.translate_atom(\"%s\",%15.9f,%15.9f,%15.9f,%d,%d,%d)\n", + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +10756 | buffer, v[0], v[1], v[2], state + 1, mode, 0); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer2/ObjectMap.cpp: In function 'void ObjectMapDump(const ObjectMap*, const char*, int, int)': layer2/ObjectMap.cpp:5983:24: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 239 [-Wformat-truncation=] 5983 | " ObjectMapDump: %s written to %s\n", om->Name, fname ENDFB(om->G); @@ -4068,23 +4104,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -layer2/ObjectMolecule2.cpp: In function 'int ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, const char*, const char*, const char*, const char*, const char*, const char*, float, int, float, float, const char*, const float*, int, int, int, int)': -layer2/ObjectMolecule2.cpp:335:27: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] - 335 | " ObjMol: created %s/%s/%s/%s`%d%c/%s\n", - | ^~ -In file included from /usr/include/stdio.h:970, - from /usr/include/python3.12/Python.h:24, - from layer0/os_python.h:34, - from layer2/ObjectMolecule2.cpp:24: -In function 'int snprintf(char*, size_t, const char*, ...)', - inlined from 'int ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, const char*, const char*, const char*, const char*, const char*, const char*, float, int, float, float, const char*, const float*, int, int, int, int)' at layer2/ObjectMolecule2.cpp:334:7: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 26 and 291 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", @@ -4186,25 +4205,6 @@ layer3/Executive.cpp:12213:11: note: in expansion of macro 'PRINTF' 12213 | PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); | ^~~~~~ -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/x86_64-linux-gnu/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 'int ExecutiveSetSettingFromString(PyMOLGlobals*, int, const char*, const char*, int, int, int)': layer3/Executive.cpp:12145:36: warning: '%s' directive output may be truncated writing up to 254 bytes into a region of size 245 [-Wformat-truncation=] 12145 | " Setting: %s set for %d atoms in object \"%s\".\n", @@ -4278,6 +4278,23 @@ layer3/Executive.cpp:12073:11: note: in expansion of macro 'PRINTF' 12073 | PRINTF " Setting: %s set to %s.\n", name, value2 ENDF(G); | ^~~~~~ +layer2/ObjectMolecule2.cpp: In function 'int ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, const char*, const char*, const char*, const char*, const char*, const char*, float, int, float, float, const char*, const float*, int, int, int, int)': +layer2/ObjectMolecule2.cpp:335:27: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 238 [-Wformat-truncation=] + 335 | " ObjMol: created %s/%s/%s/%s`%d%c/%s\n", + | ^~ +In file included from /usr/include/stdio.h:970, + from /usr/include/python3.12/Python.h:24, + from layer0/os_python.h:34, + from layer2/ObjectMolecule2.cpp:24: +In function 'int snprintf(char*, size_t, const char*, ...)', + inlined from 'int ObjectMoleculeAddPseudoatom(ObjectMolecule*, int, const char*, const char*, const char*, const char*, const char*, const char*, float, int, float, float, const char*, const float*, int, int, int, int)' at layer2/ObjectMolecule2.cpp:334:7: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: '__builtin___snprintf_chk' output between 26 and 291 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 'bool ExecutiveSetSymmetry(PyMOLGlobals*, pymol::zstring_view, int, const CSymmetry&, bool)': layer3/Executive.cpp:5952:46: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 199 [-Wformat-truncation=] 5952 | " %s-Warning: Cannot set symmetry for '%s' (type %s)\n", __func__, @@ -4306,6 +4323,25 @@ layer3/Executive.cpp:5951:7: note: in expansion of macro 'PRINTFB' 5951 | PRINTFB(G, FB_Executive, FB_Warnings) | ^~~~~~~ +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/x86_64-linux-gnu/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<> ExecutiveBond(PyMOLGlobals*, const char*, const char*, int, int, int, pymol::zstring_view)': layer3/Executive.cpp:9381:67: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size between 200 and 210 [-Wformat-truncation=] 9381 | " Valence: %d bond valences adjusted in model \"%s\".\n", cnt, @@ -4365,6 +4401,17 @@ layer3/Executive.cpp:12369:23: note: in expansion of macro 'PRINTF' 12369 | PRINTF | ^~~~~~ +layer3/Executive.cpp: In member function 'virtual int CExecutive::drag(int, int, int)': +layer3/Executive.cpp:15489:55: warning: '%s' directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] +15489 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", + | ^~ +15490 | order_input, (location == -2) ? "upper" : "current"); + | ~~~~~~~~~~~ +layer3/Executive.cpp:15489:26: note: 'sprintf' output between 32 and 1057 bytes into a destination of size 1024 +15489 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +15490 | order_input, (location == -2) ? "upper" : "current"); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/PlugIOManager.cpp: In function 'pymol::CObject* PlugIOManagerLoad(PyMOLGlobals*, pymol::CObject**, const char*, int, int, const char*, int)': layer3/PlugIOManager.cpp:941:65: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 200 [-Wformat-truncation=] 941 | " PlugIOManagerLoad: can't load trajectory into object '%s'\n", obj->Name ENDFB(G); @@ -4382,37 +4429,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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 - | ^~ -In file included from layer2/ObjectSlice.cpp:44: -layer0/Feedback.h:274:15: note: 'snprintf' output between 51 and 306 bytes into a destination of size 255 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectSlice.cpp:638:9: note: in expansion of macro 'PRINTFB' - 638 | PRINTFB(I->G, FB_ObjectSlice, FB_Errors) - | ^~~~~~~ -layer2/ObjectSlice.cpp:650:39: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 231 [-Wformat-truncation=] - 650 | " ObjectSlice: updating \"%s\".\n", I->Name ENDFB(I->G); - | ^~ -layer0/Feedback.h:274:15: note: 'snprintf' output between 28 and 283 bytes into a destination of size 255 - 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, - | ^ -layer2/ObjectSlice.cpp:649:11: note: in expansion of macro 'PRINTFB' - 649 | PRINTFB(I->G, FB_ObjectSlice, FB_Blather) - | ^~~~~~~ -layer3/Executive.cpp: In member function 'virtual int CExecutive::drag(int, int, int)': -layer3/Executive.cpp:15489:55: warning: '%s' directive writing up to 1023 bytes into a region of size 1013 [-Wformat-overflow=] -15489 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", - | ^~ -15490 | order_input, (location == -2) ? "upper" : "current"); - | ~~~~~~~~~~~ -layer3/Executive.cpp:15489:26: note: 'sprintf' output between 32 and 1057 bytes into a destination of size 1024 -15489 | sprintf(I->ReorderLog, "cmd.order(\"%s\",location=\"%s\")\n", - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -15490 | order_input, (location == -2) ? "upper" : "current"); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ layer3/Executive.cpp: In function 'pymol::Result<> ExecutiveSetSetting(PyMOLGlobals*, int, PyObject*, pymol::zstring_view, int, int, int)': layer3/Executive.cpp:11893:70: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 217 [-Wformat-truncation=] 11893 | " Setting: %s set for %d atoms in object \"%s\".\n", @@ -4484,6 +4500,26 @@ layer3/Executive.cpp:11760:11: note: in expansion of macro 'PRINTF' 11760 | PRINTF " Setting: %s set to %s.\n", name, value ENDF(G); | ^~~~~~ +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 + | ^~ +In file included from layer2/ObjectSlice.cpp:44: +layer0/Feedback.h:274:15: note: 'snprintf' output between 51 and 306 bytes into a destination of size 255 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectSlice.cpp:638:9: note: in expansion of macro 'PRINTFB' + 638 | PRINTFB(I->G, FB_ObjectSlice, FB_Errors) + | ^~~~~~~ +layer2/ObjectSlice.cpp:650:39: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 231 [-Wformat-truncation=] + 650 | " ObjectSlice: updating \"%s\".\n", I->Name ENDFB(I->G); + | ^~ +layer0/Feedback.h:274:15: note: 'snprintf' output between 28 and 283 bytes into a destination of size 255 + 274 | (snprintf)( _FBstr, FEEDBACK_MAX_OUTPUT, + | ^ +layer2/ObjectSlice.cpp:649:11: note: in expansion of macro 'PRINTFB' + 649 | PRINTFB(I->G, FB_ObjectSlice, FB_Blather) + | ^~~~~~~ layer3/Executive.cpp: In function 'void ExecutiveManageObject(PyMOLGlobals*, pymol::CObject*, int, int)': layer3/Executive.cpp:14465:37: warning: '%s' directive output may be truncated writing up to 255 bytes into a region of size 229 [-Wformat-truncation=] 14465 | " Executive-Warning: name \"%s\" collides with a selection language keyword.\n", @@ -4713,12 +4749,14 @@ 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/3347977/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3347977/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/2726436 and its subdirectories -I: Current time: Tue Dec 9 12:48:18 -12 2025 -I: pbuilder-time-stamp: 1765327698 +I: removing directory /srv/workspace/pbuilder/3347977 and its subdirectories +I: Current time: Thu Nov 7 08:29:54 +14 2024 +I: pbuilder-time-stamp: 1730917794