Diff of the two buildlogs: -- --- b1/build.log 2025-09-09 12:44:22.256637878 +0000 +++ b2/build.log 2025-09-09 12:45:01.960685946 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Sep 9 00:43:52 -12 2025 -I: pbuilder-time-stamp: 1757421832 +I: Current time: Tue Oct 13 09:07:25 +14 2026 +I: pbuilder-time-stamp: 1791832045 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -24,53 +24,85 @@ dpkg-source: info: applying gcc-15 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/971298/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2740470/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Oct 12 19:07 /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/2740470/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2740470/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='arm64' - 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='cbf2c0a6d3234fd1be2fbbbd52f98bc6' - 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='971298' - PS1='# ' - PS2='> ' + INVOCATION_ID=67e4f9d4765b44b3871b390ce208dfab + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2740470 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.eWBnVKzq/pbuilderrc_gbPa --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.eWBnVKzq/b1 --logfile b1/build.log mafft_7.525-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.eWBnVKzq/pbuilderrc_GCRu --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.eWBnVKzq/b2 --logfile b2/build.log mafft_7.525-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-cloud-arm64 #1 SMP Debian 6.12.43-1 (2025-08-27) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/971298/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2740470/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -135,7 +167,7 @@ Get: 27 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.26 [939 kB] -Fetched 11.0 MB in 0s (223 MB/s) +Fetched 11.0 MB in 0s (87.7 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 ... 20012 files and directories currently installed.) @@ -266,7 +298,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mafft-7.525/ && 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 > ../mafft_7.525-1_source.changes +I: user script /srv/workspace/pbuilder/2740470/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2740470/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mafft-7.525/ && 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 > ../mafft_7.525-1_source.changes dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.525-1 dpkg-buildpackage: info: source distribution unstable @@ -315,10 +351,6 @@ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c -mltaln9.c: In function 'check_guidetreefile': -mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2850 | fgets( string, sizeof(string) / sizeof(char), fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rna.c: In function 'rnaalifoldcall': rna.c:225:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | system( cmd ); @@ -329,6 +361,11 @@ rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 285 | system( cmd ); | ^~~~~~~~~~~~~ +In file included from constants.c:7: +blosum.c: In function 'overridematrix': +blosum.c:372:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 372 | fgets( buf, 499, fp ); + | ^~~~~~~~~~~~~~~~~~~~~ io.c: In function 'PreRead': io.c:1120:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1120 | fgets( b, B-1, fp ); *locnjob = atoi( b ); @@ -424,8 +461,6 @@ 3173 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadSsearch': -In file included from constants.c:7: -blosum.c: In function 'overridematrix': io.c:3192:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3192 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ @@ -470,30 +505,14 @@ io.c:3656:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3656 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ -mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': io.c: In function 'ReadFasta34m10': io.c:3769:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3769 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ -blosum.c:372:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 372 | fgets( buf, 499, fp ); - | ^~~~~~~~~~~~~~~~~~~~~ io.c:3793:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3793 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nucbk': -mltaln9.c:15688:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] -15688 | fread( &size, sizeof( int ), 1, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mltaln9.c:15689:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] -15689 | fread( &opt, sizeof( double ), 1, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mltaln9.c:15692:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] -15692 | fread( m, size*sizeof( int ), 3, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mltaln9.c:15728:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] -15728 | fread( &c, sizeof( char ), 1, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:3896:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3896 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ @@ -582,6 +601,23 @@ io.c:6397:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 6397 | fgets( buf, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c: In function 'check_guidetreefile': +mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2850 | fgets( string, sizeof(string) / sizeof(char), fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': +mltaln9.c:15688:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] +15688 | fread( &size, sizeof( int ), 1, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c:15689:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] +15689 | fread( &opt, sizeof( double ), 1, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c:15692:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] +15692 | fread( m, size*sizeof( int ), 3, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c:15728:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] +15728 | fread( &c, sizeof( char ), 1, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c @@ -605,7 +641,6 @@ 326 | system( com ); | ^~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dndblast.o dndblast.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c dndblast.c: In function 'main': dndblast.c:201:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | system( com ); @@ -613,50 +648,50 @@ dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | system( com ); | ^~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c -mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave': -mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] - 6494 | int *mem = calloc( sizeof( int ), nseq ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from mltaln.h:13, - from mltaln9.c:1: -/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here - 675 | extern void *calloc (size_t __nmemb, size_t __size) - | ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c +gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread +pairash.c: In function 'prepareash': pairlocalalign.c: In function 'calllast_once': +pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 639 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1056:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1056 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1092:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1092 | system( command ); | ^~~~~~~~~~~~~~~~~ -pairash.c: In function 'prepareash': -pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 639 | fgets( line, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:681:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 681 | fgets( line, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx': pairlocalalign.c:608:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 608 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ +pairash.c:681:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 681 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +pairlocalalign.c: In function 'calllast_fast': +pairlocalalign.c:981:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 981 | system( command ); + | ^~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash': pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 485 | system( com ); | ^~~~~~~~~~~~~ +pairlocalalign.c: In function 'lastcallthread': +pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 872 | system( command ); + | ^~~~~~~~~~~~~~~~~ pairash.c: In function 'readrash': pairash.c:277:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ -pairlocalalign.c: In function 'calllast_fast': pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ @@ -666,13 +701,10 @@ pairash.c:294:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 294 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ -pairlocalalign.c:981:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 981 | system( command ); - | ^~~~~~~~~~~~~~~~~ -pairlocalalign.c: In function 'lastcallthread': -pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 872 | system( command ); - | ^~~~~~~~~~~~~~~~~ +pairlocalalign.c: In function 'readlastresx_singleq': +pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 374 | fgets( gett, 9999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'preparetmalign': pairash.c:530:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fgets( line, 999, fp ); @@ -683,10 +715,6 @@ pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 587 | system( command ); | ^~~~~~~~~~~~~~~~~ -pairlocalalign.c: In function 'readlastresx_singleq': -pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 374 | fgets( gett, 9999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'checkcbeta': pairash.c:321:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 321 | fgets( linec, 999, fp ); @@ -779,7 +807,10 @@ pairlocalalign.c:3474:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3474 | system( fn ); | ^~~~~~~~~~~~ -gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread +maffttext2hex.c: In function 'main': +maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 55 | fgets( (char *)buf, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash.isra': pairash.c:428:43: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 428 | sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); @@ -809,10 +840,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -maffttext2hex.c: In function 'main': -maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 55 | fgets( (char *)buf, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c pairash.c: In function 'calltmalign.isra': pairash.c:346:41: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] 346 | sprintf( com, "mkdir -p %s", cachedir ); @@ -839,31 +869,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c splittbfast.c: In function 'main': splittbfast.c:3236:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3236 | system( com ); | ^~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c disttbfast.c: In function 'disttbfast': disttbfast.c:4387:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 4387 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c tbfast.c: In function 'main': tbfast.c:3260:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3260 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c f2cl.c: In function 'main': f2cl.c:297:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 297 | fgets( gett, B-1, orderfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c mccaskillwrap.c: In function 'main': mccaskillwrap.c:372:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 372 | system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran @@ -885,15 +911,17 @@ mccaskillwrap.c:46:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 46 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c contrafoldwrap.c: In function 'readcontrafold': contrafoldwrap.c:57:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c +gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c regtable2seq.c: In function 'readereg': regtable2seq.c:69:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets( gett, 999, regfp ); @@ -905,7 +933,6 @@ regtable2seq.c:120:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c @@ -924,6 +951,15 @@ sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb +mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave': +mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] + 6494 | int *mem = calloc( sizeof( int ), nseq ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from mltaln.h:13, + from mltaln9.c:1: +/usr/include/stdlib.h:675:14: note: in a call to allocation function 'calloc' declared here + 675 | extern void *calloc (size_t __nmemb, size_t __size) + | ^~~~~~ gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread @@ -1073,12 +1109,14 @@ 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/2740470/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2740470/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/971298 and its subdirectories -I: Current time: Tue Sep 9 00:44:21 -12 2025 -I: pbuilder-time-stamp: 1757421861 +I: removing directory /srv/workspace/pbuilder/2740470 and its subdirectories +I: Current time: Tue Oct 13 09:08:01 +14 2026 +I: pbuilder-time-stamp: 1791832081