Diff of the two buildlogs: -- --- b1/build.log 2025-10-28 05:19:49.857944525 +0000 +++ b2/build.log 2025-10-28 05:21:00.206033222 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Oct 27 17:19:07 -12 2025 -I: pbuilder-time-stamp: 1761628747 +I: Current time: Tue Dec 1 01:42:52 +14 2026 +I: pbuilder-time-stamp: 1796038972 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -30,53 +30,85 @@ dpkg-source: info: applying cppflags.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1304721/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2021630/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-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 30 11:43 /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/2021630/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2021630/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=40 ' - DISTRIBUTION='forky' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(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=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='78929f5a199849bbad227182d598ae78' - 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='1304721' - PS1='# ' - PS2='> ' + INVOCATION_ID=4b5de75ae246482f887c9edb3389804e + 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=2021630 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.Dnf5VOGr/pbuilderrc_nefp --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Dnf5VOGr/b1 --logfile b1/build.log soapaligner_2.20-6.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - 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.Dnf5VOGr/pbuilderrc_eFJN --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Dnf5VOGr/b2 --logfile b2/build.log soapaligner_2.20-6.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + 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 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1304721/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2021630/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -141,7 +173,7 @@ Get: 27 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] -Fetched 11.2 MB in 0s (160 MB/s) +Fetched 11.2 MB in 0s (126 MB/s) Preconfiguring packages ... Selecting previously unselected package sensible-utils. (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 ... 19902 files and directories currently installed.) @@ -278,7 +310,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/soapaligner-2.20/ && 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 > ../soapaligner_2.20-6_source.changes +I: user script /srv/workspace/pbuilder/2021630/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2021630/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/soapaligner-2.20/ && 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 > ../soapaligner_2.20-6_source.changes dpkg-buildpackage: info: source package soapaligner dpkg-buildpackage: info: source version 2.20-6 dpkg-buildpackage: info: source distribution unstable @@ -288,7 +324,7 @@ debian/rules clean dh clean dh_auto_clean - make -j40 clean + make -j42 clean make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20' rm -f *.o soap make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20' @@ -311,7 +347,7 @@ dh_autoreconf dh_auto_configure dh_auto_build - make -j40 INSTALL="install --strip-program=true" + make -j42 INSTALL="install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/soapaligner-2.20' cc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" SeqIO.c -o SeqIO.o cc -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/soapaligner-2.20=. -flto=auto -ffat-lto-objects -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -funroll-loops -maccumulate-outgoing-args -fomit-frame-pointer -DPTHREADS -DMAKE_TIME=\""SOURCE_DATE_EPOCH"\" MiscUtilities.c -o MiscUtilities.o @@ -334,31 +370,6 @@ r250.c:33:41: warning: overflow in conversion from 'long int' to 'int' changes value from '548781581296767' to '724984959' [-Woverflow] 33 | static int quotient1 = LONG_MAX / 16807L; | ^~~~~~~~ -MemManager.c: In function 'MMBulkLoad': -MemManager.c:1043:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1043 | fread(&mmBulk->itemSize, sizeof(unsigned int), 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1044:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1044 | fread(&mmBulk->itemPerAllocationInPowerOf2, sizeof(unsigned int), 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1045:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1045 | fread(&mmBulk->boundaryCushionSize, sizeof(unsigned int), 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1046:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1046 | fread(&mmBulk->currentDirectoryEntry, sizeof(unsigned int), 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1047:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1047 | fread(&mmBulk->nextUnusedItem, sizeof(unsigned int), 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1048:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1048 | fread(&mmBulk->directorySize, sizeof(unsigned int), 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1065:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1065 | fread(mmBulk->directory[i], mmBulk->itemSize << mmBulk->itemPerAllocationInPowerOf2, 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -MemManager.c:1079:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] - 1079 | fread(mmBulk->directory[i], mmBulk->itemSize * mmBulk->nextUnusedItem, 1, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ TextConverter.c: In function 'ReadCharMap': TextConverter.c:85:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 85 | fscanf(inputFile, " %c %u \n", &c, &v); @@ -385,18 +396,35 @@ TextConverter.c:895:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 895 | fread(textOutput, sizeof(unsigned char), textLenForThisLoad, textFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c: In function 'MMBulkLoad': TextConverter.c: In function 'LoadTextIncFromEnd': TextConverter.c:913:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 913 | fread(textOutput, sizeof(unsigned char), textLengthPerLoad, textFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from BWTAln.h:23, - from BWTAln.c:1: -extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined - 84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int); - | ^~~~~~~~~~~ -extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined - 83 | inline int altCalMM(unsigned int x); - | ^~~~~~~~ +MemManager.c:1043:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1043 | fread(&mmBulk->itemSize, sizeof(unsigned int), 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1044:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1044 | fread(&mmBulk->itemPerAllocationInPowerOf2, sizeof(unsigned int), 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1045:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1045 | fread(&mmBulk->boundaryCushionSize, sizeof(unsigned int), 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1046:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1046 | fread(&mmBulk->currentDirectoryEntry, sizeof(unsigned int), 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1047:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1047 | fread(&mmBulk->nextUnusedItem, sizeof(unsigned int), 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1048:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1048 | fread(&mmBulk->directorySize, sizeof(unsigned int), 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1065:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1065 | fread(mmBulk->directory[i], mmBulk->itemSize << mmBulk->itemPerAllocationInPowerOf2, 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +MemManager.c:1079:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] + 1079 | fread(mmBulk->directory[i], mmBulk->itemSize * mmBulk->nextUnusedItem, 1, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from extratools.c:1: extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined 83 | inline int altCalMM(unsigned int x); @@ -445,6 +473,49 @@ extratools.c:91:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 91 | fread((unsigned int *)&((*hashTable).occList[i]),sizeof(unsigned int),1,inFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +HSP.c: In function 'HSPLoad': +HSP.c:89:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 89 | fscanf(annotationFile, "%u\t%d\t%d\n", &numOfChar, &chrNum, &FASTARandomSeed); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +HSP.c:94:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 94 | fscanf(annotationFile, "%u\t", &nameLen); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +HSP.c:96:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 96 | fscanf(annotationFile, "%s\n", hsp->chrName[i]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +HSP.c:98:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 98 | fscanf(annotationFile, "%d\n", &(hsp->numOfBlock)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +HSP.c:104:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 104 | fscanf(annotationFile, "%d\t%u\t%u\t%u\n", &(p->chrID), &(p->blockStart), &(p->blockEnd), &(p->ori)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from Match.c:17: +Match.h:130:12: warning: inline function 'CheckIns' declared but never defined + 130 | inline int CheckIns(HITITEM *, HITITEM *, PEAUX *); + | ^~~~~~~~ +In file included from BWTAln.h:23, + from Match.h:23: +extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined + 84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int); + | ^~~~~~~~~~~ +extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined + 83 | inline int altCalMM(unsigned int x); + | ^~~~~~~~ +In file included from soap.c:24: +Match.h:132:13: warning: inline function 'PickupHit' declared but never defined + 132 | inline void PickupHit(ALNSEQ *, const int ,int *, HITTABLE *,const unsigned int *, const unsigned int, unsigned short * ); + | ^~~~~~~~~ +Match.h:130:12: warning: inline function 'CheckIns' declared but never defined + 130 | inline int CheckIns(HITITEM *, HITITEM *, PEAUX *); + | ^~~~~~~~ +In file included from BWTAln.h:23, + from Match.h:23: +extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined + 84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int); + | ^~~~~~~~~~~ +extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined + 83 | inline int altCalMM(unsigned int x); + | ^~~~~~~~ BWT.c: In function 'BWTLoad': BWT.c:155:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | fread(&bwt->inverseSa0, sizeof(unsigned int), 1, bwtCodeFile); @@ -503,61 +574,26 @@ BWT.c:272:17: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 272 | fread(bwt->saIndexRange, sizeof(SaIndexRange), numOfSaIndexRange, saIndexRangeFile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from soapio.h:21, - from soapio.c:17: -extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined - 84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int); - | ^~~~~~~~~~~ -extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined - 83 | inline int altCalMM(unsigned int x); - | ^~~~~~~~ -In file included from Match.c:17: -Match.h:130:12: warning: inline function 'CheckIns' declared but never defined - 130 | inline int CheckIns(HITITEM *, HITITEM *, PEAUX *); - | ^~~~~~~~ In file included from BWTAln.h:23, - from Match.h:23: + from BWTAln.c:1: extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined 84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int); | ^~~~~~~~~~~ extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined 83 | inline int altCalMM(unsigned int x); | ^~~~~~~~ -In file included from PairMatch.c:19: -Match.h:132:13: warning: inline function 'PickupHit' declared but never defined - 132 | inline void PickupHit(ALNSEQ *, const int ,int *, HITTABLE *,const unsigned int *, const unsigned int, unsigned short * ); - | ^~~~~~~~~ -In file included from BWTAln.h:23, - from Match.h:23: +In file included from soapio.h:21, + from soapio.c:17: extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined 84 | inline int CalMismatch(const char *,const unsigned int *,const unsigned int , const unsigned int, const unsigned int); | ^~~~~~~~~~~ extratools.h:83:12: warning: inline function 'altCalMM' declared but never defined 83 | inline int altCalMM(unsigned int x); | ^~~~~~~~ -HSP.c: In function 'HSPLoad': -HSP.c:89:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 89 | fscanf(annotationFile, "%u\t%d\t%d\n", &numOfChar, &chrNum, &FASTARandomSeed); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -HSP.c:94:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 94 | fscanf(annotationFile, "%u\t", &nameLen); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -HSP.c:96:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 96 | fscanf(annotationFile, "%s\n", hsp->chrName[i]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -HSP.c:98:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 98 | fscanf(annotationFile, "%d\n", &(hsp->numOfBlock)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -HSP.c:104:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 104 | fscanf(annotationFile, "%d\t%u\t%u\t%u\n", &(p->chrID), &(p->blockStart), &(p->blockEnd), &(p->ori)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from soap.c:24: +In file included from PairMatch.c:19: Match.h:132:13: warning: inline function 'PickupHit' declared but never defined 132 | inline void PickupHit(ALNSEQ *, const int ,int *, HITTABLE *,const unsigned int *, const unsigned int, unsigned short * ); | ^~~~~~~~~ -Match.h:130:12: warning: inline function 'CheckIns' declared but never defined - 130 | inline int CheckIns(HITITEM *, HITITEM *, PEAUX *); - | ^~~~~~~~ In file included from BWTAln.h:23, from Match.h:23: extratools.h:84:12: warning: inline function 'CalMismatch' declared but never defined @@ -586,7 +622,7 @@ | ^ make[1]: Leaving directory '/build/reproducible-path/soapaligner-2.20' dh_auto_test - rm -fr -- /tmp/dh-xdg-rundir-p6O6hnvz + rm -fr -- /tmp/dh-xdg-rundir-5eL4JZa9 create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/soapaligner.substvars @@ -665,8 +701,8 @@ dh_builddeb dpkg-deb --root-owner-group --build debian/soapaligner .. dpkg-deb --root-owner-group --build debian/.debhelper/soapaligner/dbgsym-root .. -dpkg-deb: building package 'soapaligner' in '../soapaligner_2.20-6_amd64.deb'. dpkg-deb: building package 'soapaligner-dbgsym' in '../soapaligner-dbgsym_2.20-6_amd64.deb'. +dpkg-deb: building package 'soapaligner' in '../soapaligner_2.20-6_amd64.deb'. dpkg-genbuildinfo --build=binary -O../soapaligner_2.20-6_amd64.buildinfo dpkg-genchanges --build=binary -O../soapaligner_2.20-6_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -674,12 +710,14 @@ 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/2021630/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2021630/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/1304721 and its subdirectories -I: Current time: Mon Oct 27 17:19:49 -12 2025 -I: pbuilder-time-stamp: 1761628789 +I: removing directory /srv/workspace/pbuilder/2021630 and its subdirectories +I: Current time: Tue Dec 1 01:43:58 +14 2026 +I: pbuilder-time-stamp: 1796039038