Diff of the two buildlogs: -- --- b1/build.log 2025-09-10 05:48:03.642259112 +0000 +++ b2/build.log 2025-09-10 05:49:05.270340839 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 13 00:09:22 -12 2026 -I: pbuilder-time-stamp: 1791893362 +I: Current time: Wed Sep 10 19:48:04 +14 2025 +I: pbuilder-time-stamp: 1757483284 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -34,53 +34,85 @@ dpkg-source: info: applying fixup-implicit-function-declaration.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2806415/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/603800/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 Sep 10 05:48 /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/603800/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/603800/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=42 ' - 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=40 ' + 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='3d256417a1cb4bd8b54cd59432bf71af' - 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='2806415' - PS1='# ' - PS2='> ' + INVOCATION_ID=0d314000a1814af2bd50c36eb6ca5640 + 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=603800 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.fB8EnyJc/pbuilderrc_ZsBh --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.fB8EnyJc/b1 --logfile b1/build.log lagan_2.0-10.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.fB8EnyJc/pbuilderrc_jfVU --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.fB8EnyJc/b2 --logfile b2/build.log lagan_2.0-10.dsc' + SUDO_GID=110 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2806415/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/603800/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -149,7 +181,7 @@ Get: 29 http://deb.debian.org/debian forky/main amd64 debhelper all 13.26 [939 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libboost1.83-dev amd64 1.83.0-4.2 [10.6 MB] Get: 31 http://deb.debian.org/debian forky/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] -Fetched 21.8 MB in 2s (10.7 MB/s) +Fetched 21.8 MB in 1s (17.6 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 ... 19898 files and directories currently installed.) @@ -288,7 +320,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/lagan-2.0/ && 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 > ../lagan_2.0-10_source.changes +I: user script /srv/workspace/pbuilder/603800/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/603800/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/lagan-2.0/ && 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 > ../lagan_2.0-10_source.changes dpkg-buildpackage: info: source package lagan dpkg-buildpackage: info: source version 2.0-10 dpkg-buildpackage: info: source distribution unstable @@ -300,7 +336,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_clean - make -j42 clean + make -j40 clean make[2]: Entering directory '/build/reproducible-path/lagan-2.0' rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay make -C src clean @@ -323,7 +359,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/lagan-2.0' dh_auto_build --sourcedirectory=src - cd src && make -j42 "INSTALL=install --strip-program=true" + cd src && make -j40 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../anchors anchors.c skiplist.c -Wl,-z,relro gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG -Wl,-z,relro @@ -349,53 +385,7 @@ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -o ../utils/overlay utils/overlay.c -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ -fchaos.c: In function 'readfile': -fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] - 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mlagan.c: In function 'readfile': -mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] - 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 81 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 344 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ -utils/rc.c: In function 'main': -utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | fgets(temp, 255, stdin); - | ^~~~~~~~~~~~~~~~~~~~~~~ -anchors.c: In function 'anchors_getline': -anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 232 | fgets(temp, 1024, infile); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -order.c: In function 'readfile': -fchaos.c: In function 'readSubstMatrix': utils/contigorder.c: In function 'getFileInfo': -order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 63 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 627 | fscanf (file, "%d", &gappenstart); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 628 | fscanf (file, "%d", &gappenext); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -order.c: In function 'readSubstMatrix': -order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 151 | fscanf (file, "%d", &gapstart); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 152 | fscanf (file, "%d", &gapcont); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:15:57: warning: format '%s' expects a matching 'char *' argument [-Wformat=] 15 | fprintf (stderr, "contigorder: Error opening file: %s\n"); | ~^ @@ -414,10 +404,6 @@ | | | char * utils/contigorder.c: In function 'getFileInfo': -utils/getlength.c: In function 'main': -utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 20 | fgets (buffer, BUF_SIZE, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c:19:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fscanf (file, "numContigs = %d\n", numContigs); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -427,10 +413,6 @@ utils/contigorder.c:26:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 26 | fscanf (file, "%&d", &dummy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/getbounds.c: In function 'getLength': -utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 18 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/contigorder.c: In function 'getScores': utils/contigorder.c:56:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 56 | fscanf (file, "numContigs = %*d\n"); @@ -441,10 +423,38 @@ utils/contigorder.c:63:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 63 | fscanf (file, "%d", &((*score)[i][j])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/rc.c: In function 'main': +utils/rc.c:39:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | fgets(temp, 255, stdin); + | ^~~~~~~~~~~~~~~~~~~~~~~ +utils/cextract.c: In function 'getLength': +utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +anchors.c: In function 'anchors_getline': +anchors.c:232:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 232 | fgets(temp, 1024, infile); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +utils/getbounds.c: In function 'getLength': +utils/getbounds.c:18:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 18 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/cextract.c: In function 'readfile': +utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 41 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/seqmerge.c: In function 'main': utils/seqmerge.c:19:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 19 | fgets (buffer, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/getcontigpos.c: In function 'getLength': +utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 16 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/getcontigpos.c: In function 'readfile': +utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 41 | fgets (buffer, 1024, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~ utils/fa2xfa.c: In function 'getLength': utils/fa2xfa.c:30:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 30 | fgets (buffer, 1024, file); @@ -457,47 +467,42 @@ prolagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/getcontigpos.c: In function 'getLength': -utils/getcontigpos.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/getcontigpos.c: In function 'readfile': -utils/getcontigpos.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 41 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +mlagan.c: In function 'readfile': +mlagan.c:95:25: warning: too many arguments for format [-Wformat-extra-args] + 95 | fprintf(stderr, "Warning: %c converted to 'N'\n", currchar, alpha); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c: In function 'readfile': +fchaos.c:357:25: warning: too many arguments for format [-Wformat-extra-args] + 357 | fprintf(stderr, "WARNING %c converted to N\n", currchar, alpha); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorecontigs.c: In function 'main': utils/scorecontigs.c:385:38: warning: format '%s' expects argument of type 'char *', but argument 6 has type 'char (*)[1024]' [-Wformat=] 385 | if (fscanf (filelist, "%d %d %d %s\n", &(num[numseqs]), &(offs1[numseqs]), &(offs2[numseqs]), &(contignames[numseqs])) == 4){ | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | char * char (*)[1024] -utils/scorecontigs.c: In function 'cntlets': -utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 56 | fgets(temp, 1024, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -utils/scorecontigs.c: In function 'readseq': -utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 82 | fgets (temp, 1024, input); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ prolagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ -utils/overlay.c: In function 'read_align': -utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 110 | fgets(temp, 255, input); +mlagan.c:81:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 81 | fgets(temp, 255, input); | ^~~~~~~~~~~~~~~~~~~~~~~ -utils/cextract.c: In function 'getLength': +utils/scorecontigs.c: In function 'cntlets': utils/scorealign.c: In function 'getSequence': +utils/scorecontigs.c:56:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 56 | fgets(temp, 1024, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c:266:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 266 | fgets (line, 1024, file); | ^~~~~~~~~~~~~~~~~~~~~~~~ -utils/cextract.c:16:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 16 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/cextract.c: In function 'readfile': -utils/cextract.c:41:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 41 | fgets (buffer, 1024, file); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/getlength.c: In function 'main': +utils/getlength.c:20:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 20 | fgets (buffer, BUF_SIZE, file); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/scorecontigs.c: In function 'readseq': +utils/scorecontigs.c:82:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 82 | fgets (temp, 1024, input); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ utils/scorealign.c: In function 'readScoreMatrix': utils/scorealign.c:415:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 415 | fgets (line, 1024, file); @@ -511,6 +516,45 @@ utils/scorealign.c:430:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 430 | fscanf (file, "%d%d", &gapopen, &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/overlay.c: In function 'read_align': +utils/overlay.c:110:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 110 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ +order.c: In function 'readfile': +order.c:63:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 63 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ +order.c: In function 'readSubstMatrix': +order.c:147:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 147 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +order.c:151:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 151 | fscanf (file, "%d", &gapstart); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +order.c:152:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 152 | fscanf (file, "%d", &gapcont); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c:344:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 344 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c: In function 'readSubstMatrix': +fchaos.c:622:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 622 | fscanf (file, "%d", &(substmatrix[(unsigned char) symbs[i]][(unsigned char) symbs[j]])); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c:627:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 627 | fscanf (file, "%d", &gappenstart); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +fchaos.c:628:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 628 | fscanf (file, "%d", &gappenext); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +utils/cstat.c: In function 'cntlets': +utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 45 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ +utils/cstat.c: In function 'readseq': +utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 68 | fgets(temp, 255, input); + | ^~~~~~~~~~~~~~~~~~~~~~~ utils/dotplot.cpp: In function 'int main(int, char**)': utils/dotplot.cpp:37:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 37 | fgets (buffer, 105, file); @@ -521,14 +565,6 @@ utils/dotplot.cpp:97:11: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets (buffer, 105, file); | ~~~~~~^~~~~~~~~~~~~~~~~~~ -utils/cstat.c: In function 'cntlets': -utils/cstat.c:45:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 45 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ -utils/cstat.c: In function 'readseq': -utils/cstat.c:68:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 68 | fgets(temp, 255, input); - | ^~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); @@ -546,6 +582,19 @@ utils/Glue.cpp:72:22: note: in expansion of macro 'NUCLEOTIDE_MATRIX_FILE' 72 | readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); | ^~~~~~~~~~~~~~~~~~~~~~ +utils/Glue.cpp: In function 'void readScoreMatrix(char*)': +utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 44 | fgets (line, 1024, file); + | ~~~~~~^~~~~~~~~~~~~~~~~~ +utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 52 | fscanf (file, "%1s", &(line[0])); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 54 | fscanf (file, "%d", &k); + | ~~~~~~~^~~~~~~~~~~~~~~~ +utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] + 59 | fscanf (file, "%d%d", &gapopen, &gapcont); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ @@ -564,28 +613,18 @@ multial.c:563:10: warning: 'matchcache' is static but used in inline function 'scoreOpp' which is not static 563 | return matchcache[v(other->cnts[0][ow]) | | ^~~~~~~~~~ -multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static - 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | - | ^~~~~~~~ -multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static - 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | - | ^~~~~~~~~~ -multial.c: In function 'readSubstMatrix': -multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 478 | fscanf (file, "%d", &k); - | ^~~~~~~~~~~~~~~~~~~~~~~ -multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 486 | fscanf (file, "%d", &gapstart); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 487 | fscanf (file, "%d", &gapcont); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:603:9: warning: 'gapcache' is static but used in inline function 'openGap' which is not static 603 | sav = gapcache[(v(ali->numseq - (alopen + ali->cnts[CNTS_CB][w]) + other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ +multial.c:556:5: warning: 'gapcache' is static but used in inline function 'matchscore' which is not static + 556 | gapcache[v(a->cnts[CNTS_GS][ai] + b->cnts[CNTS_GS][bi]) | + | ^~~~~~~~ multial.c:586:10: warning: 'gapcache' is static but used in inline function 'contGap' which is not static 586 | return gapcache[(v(other->cnts[CNTS_GS][ow])) | | ^~~~~~~~ +multial.c:552:5: warning: 'matchcache' is static but used in inline function 'matchscore' which is not static + 552 | matchcache[v(a->cnts[0][ai] + b->cnts[0][bi]) | + | ^~~~~~~~~~ multial.c:581:10: warning: 'gapcache' is static but used in inline function 'endGap2' which is not static 581 | return gapcache[(v((a->numseq - a->cnts[CNTS_GS][ai] - a->cnts[CNTS_GC][ai]) + b->cnts[CNTS_GE][bi])<<12) | | ^~~~~~~~ @@ -608,25 +647,22 @@ multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 478 | fscanf (file, "%d", &k); | ^~~~~~~~~~~~~~~~~~~~~~~ +multial.c: In function 'readSubstMatrix': +multial.c:478:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 478 | fscanf (file, "%d", &k); + | ^~~~~~~~~~~~~~~~~~~~~~~ +multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 486 | fscanf (file, "%d", &gapstart); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:486:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 486 | fscanf (file, "%d", &gapstart); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 487 | fscanf (file, "%d", &gapcont); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -utils/Glue.cpp: In function 'void readScoreMatrix(char*)': -utils/Glue.cpp:44:9: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 44 | fgets (line, 1024, file); - | ~~~~~~^~~~~~~~~~~~~~~~~~ -utils/Glue.cpp:52:12: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 52 | fscanf (file, "%1s", &(line[0])); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -utils/Glue.cpp:54:14: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 54 | fscanf (file, "%d", &k); - | ~~~~~~~^~~~~~~~~~~~~~~~ -utils/Glue.cpp:59:10: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 59 | fscanf (file, "%d%d", &gapopen, &gapcont); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +multial.c:487:3: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 487 | fscanf (file, "%d", &gapcont); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ skiplist.c: In function 'printSLE': skiplist.c:12:19: warning: format '%x' expects argument of type 'unsigned int', but argument 3 has type 'void *' [-Wformat=] 12 | printf(" %d %x\n", tbp->index, tbp->myelem); @@ -654,12 +690,12 @@ g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c io.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c rightinfluence.cpp -Wl,-z,relro g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c leftinfluence.cpp -Wl,-z,relro -cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ g++ -Wno-deprecated -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lagan-2.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fsigned-char -O3 -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I./ -c score.cpp -Wl,-z,relro cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ +cc1plus: warning: '-Werror=' argument '-Werror=implicit-function-declaration' is not valid for C++ io.cpp: In function 'long long int getline(FILE*, hll*)': io.cpp:60:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 60 | fgets(temp, 1024, infile); @@ -669,7 +705,7 @@ make[2]: Leaving directory '/build/reproducible-path/lagan-2.0/src' make[1]: Leaving directory '/build/reproducible-path/lagan-2.0' dh_auto_test - make -j42 test + make -j40 test make[1]: Entering directory '/build/reproducible-path/lagan-2.0' make -C src make[2]: Entering directory '/build/reproducible-path/lagan-2.0/src' @@ -710,8 +746,8 @@ dpkg-gencontrol: warning: package lagan: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-deb: building package 'lagan' in '../lagan_2.0-10_amd64.deb'. +dpkg-deb: building package 'lagan-dbgsym' in '../lagan-dbgsym_2.0-10_amd64.deb'. dpkg-genbuildinfo --build=binary -O../lagan_2.0-10_amd64.buildinfo dpkg-genchanges --build=binary -O../lagan_2.0-10_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -719,12 +755,14 @@ 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/603800/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/603800/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/2806415 and its subdirectories -I: Current time: Tue Oct 13 00:11:03 -12 2026 -I: pbuilder-time-stamp: 1791893463 +I: removing directory /srv/workspace/pbuilder/603800 and its subdirectories +I: Current time: Wed Sep 10 19:49:04 +14 2025 +I: pbuilder-time-stamp: 1757483344