Diff of the two buildlogs: -- --- b1/build.log 2025-03-05 19:31:06.189608184 +0000 +++ b2/build.log 2025-03-05 19:33:37.278772841 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Mar 5 07:27:09 -12 2025 -I: pbuilder-time-stamp: 1741202829 +I: Current time: Wed Apr 8 15:54:08 +14 2026 +I: pbuilder-time-stamp: 1775613248 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying cometsearch-makefile-to-handle-lib-debian-way-of-doing-things.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/203406/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2328305/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 Apr 8 01:54 /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/2328305/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2328305/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' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + 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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(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=42 ' + 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='733f66f6686343749c7633da44ac59b9' - 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='203406' - PS1='# ' - PS2='> ' + INVOCATION_ID=1b5b077af327497599318385dd5d3e93 + 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=2328305 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.czqpWoUb/pbuilderrc_I8l3 --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.czqpWoUb/b1 --logfile b1/build.log comet-ms_2019015+cleaned1-4.1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.czqpWoUb/pbuilderrc_qnnC --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.czqpWoUb/b2 --logfile b2/build.log comet-ms_2019015+cleaned1-4.1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/203406/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2328305/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -155,7 +187,7 @@ Get: 41 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libmstoolkit-dev amd64 82-7.2 [140 kB] -Fetched 25.0 MB in 0s (62.2 MB/s) +Fetched 25.0 MB in 3s (7595 kB/s) Preconfiguring packages ... Selecting previously unselected package sgml-base. (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 ... 19800 files and directories currently installed.) @@ -350,7 +382,11 @@ fakeroot is already the newest version (1.37-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && 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 > ../comet-ms_2019015+cleaned1-4.1_source.changes +I: user script /srv/workspace/pbuilder/2328305/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2328305/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/comet-ms-2019015+cleaned1/ && 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 > ../comet-ms_2019015+cleaned1-4.1_source.changes dpkg-buildpackage: info: source package comet-ms dpkg-buildpackage: info: source version 2019015+cleaned1-4.1 dpkg-buildpackage: info: source distribution unstable @@ -406,7 +442,7 @@ make[1]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' docbook-to-man debian/comet-ms.sgml > debian/comet-ms.1 dh_auto_build - make -j20 "INSTALL=install --strip-program=true" + make -j42 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1' cd CometSearch ; make make[3]: Entering directory '/build/reproducible-path/comet-ms-2019015+cleaned1/CometSearch' @@ -423,26 +459,6 @@ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometWriteTxt.cpp -c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometSearchManager.cpp -c g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/comet-ms-2019015+cleaned1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -fpermissive -Wall -Wextra -Wno-char-subscripts -DCURL_STATICLIB -DHTTP_ONLY -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I/usr/include/libmstoolkit -ICometSearch -O3 -fpermissive -Wall -Wextra -Wno-write-strings -std=c++11 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D__LINUX__ -I. -I/usr/include/libmstoolkit CometCheckForUpdates.cpp -c -CometMassSpecUtils.cpp: In static member function 'static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)': -CometMassSpecUtils.cpp:136:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 136 | fread(&lSize, sizeof(long), 1, fpdb); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometMassSpecUtils.cpp:141:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 141 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometMassSpecUtils.cpp:148:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 148 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometMassSpecUtils.cpp:155:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 155 | fscanf(fpdb, "%99s", szProteinName); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometWritePepXML.cpp: In static member function 'static bool CometWritePepXML::WritePepXMLHeader(FILE*, CometSearchManager&)': -CometWritePepXML.cpp:100:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 100 | realpath(g_staticParams.inputFile.szBaseName, resolvedPathBaseName); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometWritePepXML.cpp:101:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 101 | realpath(szRunSummaryBaseName, szRunSummaryResolvedPath); - | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometCheckForUpdates.cpp: In static member function 'static void CometCheckForUpdates::SendAnalyticsHit()': CometCheckForUpdates.cpp:161:11: warning: '%s' directive output may be truncated writing up to 1023 bytes into a region of size between 895 and 898 [-Wformat-truncation=] 161 | "%s\r\n", host, (int)strlen(postData), postData); @@ -464,6 +480,37 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +CometWritePepXML.cpp: In static member function 'static bool CometWritePepXML::WritePepXMLHeader(FILE*, CometSearchManager&)': +CometWritePepXML.cpp:100:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 100 | realpath(g_staticParams.inputFile.szBaseName, resolvedPathBaseName); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometWritePepXML.cpp:101:12: warning: ignoring return value of 'char* realpath(const char*, char*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 101 | realpath(szRunSummaryBaseName, szRunSummaryResolvedPath); + | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from CometSearch.cpp:19: +ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': +ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' + 69 | new ThreadManager(this); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:138:66: required from here + 138 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/); + | ^ +ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] + 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometMassSpecUtils.cpp: In static member function 'static void CometMassSpecUtils::GetProteinName(FILE*, comet_fileoffset_t, char*)': +CometMassSpecUtils.cpp:136:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 136 | fread(&lSize, sizeof(long), 1, fpdb); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometMassSpecUtils.cpp:141:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 141 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fpdb); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometMassSpecUtils.cpp:148:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 148 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fpdb); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometMassSpecUtils.cpp:155:13: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 155 | fscanf(fpdb, "%99s", szProteinName); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometPreprocess.h:21, from CometPreprocess.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PreprocessThreadData*]': @@ -476,17 +523,66 @@ ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from CometSearch.cpp:19: -ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = SearchThreadData*]': -ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = SearchThreadData*; ThreadProc = void (*)(SearchThreadData*)]' - 69 | new ThreadManager(this); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:138:66: required from here - 138 | minNumThreads, maxNumThreads, 1 /*maxNumParamsToQueue*/); - | ^ -ThreadPool.h:257:13: warning: cast between incompatible function types from 'uint32_t (*)(void*)' {aka 'unsigned int (*)(void*)'} to 'ThreadProc' {aka 'void* (*)(void*)'} [-Wcast-function-type] - 257 | reinterpret_cast(ThreadManager::ThreadRoutingFunction), - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)': +CometSearch.cpp:312:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 312 | fgets(szPeffLine, iLenSzLine, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:329:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 329 | fgets(szPeffLine+(int)strlen(szPeffLine), iLenSzLine - (int)strlen(szPeffLine), fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:673:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 673 | fgets(szBuf, sizeof(szBuf), fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp: In member function 'void CometSearch::ReadOBO(char*, std::vector*)': +CometSearch.cpp:725:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 725 | fgets(szLineOBO, SIZE_BUF, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:777:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 777 | fgets(szLineOBO, SIZE_BUF, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp: In member function 'bool CometSearch::IndexSearch()': +CometSearch.cpp:1159:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1159 | fread(&lEndOfStruct, sizeof(comet_fileoffset_t), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1166:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1166 | fread(&iMinMass, sizeof(int), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1167:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1167 | fread(&iMaxMass, sizeof(int), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1168:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1168 | fread(&tNumPeptides, sizeof(uint64_t), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1185:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1185 | fread(lReadIndex, sizeof(comet_fileoffset_t), iMaxPeptideMass10, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1224:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1224 | fread(&sDBI, sizeof(struct DBIndex), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1229:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1229 | fread(&lSize, sizeof(long), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1233:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1233 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1266:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1266 | fread(&sDBI, sizeof(struct DBIndex), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1269:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1269 | fread(&lSize, sizeof(long), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1273:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1273 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1311:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1311 | fread(&lSize, sizeof(long), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1316:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1316 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +CometSearch.cpp:1323:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1323 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fp); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ CometWriteOut.cpp: In static member function 'static bool CometWriteOut::PrintResults(int, bool, FILE*)': CometWriteOut.cpp:124:32: warning: '%.5d' directive writing between 5 and 11 bytes into a region of size between 0 and 1022 [-Wformat-overflow=] 124 | sprintf(szOutput, "%s/%s.%.5d.%.5d.%d.out", @@ -549,66 +645,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -CometSearch.cpp: In static member function 'static bool CometSearch::RunSearch(int, int, int, int)': -CometSearch.cpp:312:27: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 312 | fgets(szPeffLine, iLenSzLine, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:329:30: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 329 | fgets(szPeffLine+(int)strlen(szPeffLine), iLenSzLine - (int)strlen(szPeffLine), fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:673:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 673 | fgets(szBuf, sizeof(szBuf), fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp: In member function 'void CometSearch::ReadOBO(char*, std::vector*)': -CometSearch.cpp:725:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 725 | fgets(szLineOBO, SIZE_BUF, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:777:18: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 777 | fgets(szLineOBO, SIZE_BUF, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp: In member function 'bool CometSearch::IndexSearch()': -CometSearch.cpp:1159:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1159 | fread(&lEndOfStruct, sizeof(comet_fileoffset_t), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1166:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1166 | fread(&iMinMass, sizeof(int), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1167:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1167 | fread(&iMaxMass, sizeof(int), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1168:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1168 | fread(&tNumPeptides, sizeof(uint64_t), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1185:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1185 | fread(lReadIndex, sizeof(comet_fileoffset_t), iMaxPeptideMass10, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1224:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1224 | fread(&sDBI, sizeof(struct DBIndex), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1229:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1229 | fread(&lSize, sizeof(long), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1233:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1233 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1266:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1266 | fread(&sDBI, sizeof(struct DBIndex), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1269:12: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1269 | fread(&lSize, sizeof(long), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1273:15: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1273 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1311:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1311 | fread(&lSize, sizeof(long), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1316:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1316 | fread(&tmpoffset, sizeof(comet_fileoffset_t), 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -CometSearch.cpp:1323:21: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1323 | fread(szTmp, sizeof(char)*WIDTH_REFERENCE, 1, fp); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from CometPostAnalysis.cpp:19: ThreadPool.h: In instantiation of 'ThreadManager::ThreadManager(ThreadPool*) [with T = PostAnalysisThreadData*]': ThreadPool.h:69:10: required from 'ThreadPool::ThreadPool(ThreadProc, int, int, int) [with T = PostAnalysisThreadData*; ThreadProc = void (*)(PostAnalysisThreadData*)]' @@ -1243,7 +1279,7 @@ make[2]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1' make[1]: Leaving directory '/build/reproducible-path/comet-ms-2019015+cleaned1' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-63wj24Fj + rm -fr -- /tmp/dh-xdg-rundir-sr193hCj create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/comet-ms.substvars @@ -1329,12 +1365,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2328305/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2328305/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/203406 and its subdirectories -I: Current time: Wed Mar 5 07:31:05 -12 2025 -I: pbuilder-time-stamp: 1741203065 +I: removing directory /srv/workspace/pbuilder/2328305 and its subdirectories +I: Current time: Wed Apr 8 15:56:36 +14 2026 +I: pbuilder-time-stamp: 1775613396