Diff of the two buildlogs: -- --- b1/build.log 2025-09-07 12:19:27.799318728 +0000 +++ b2/build.log 2025-09-07 12:20:17.931390207 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Sep 7 00:18:23 -12 2025 -I: pbuilder-time-stamp: 1757247503 +I: Current time: Sun Oct 11 08:42:28 +14 2026 +I: pbuilder-time-stamp: 1791657748 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/4032743/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2287704/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 Oct 10 18:42 /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/2287704/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2287704/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]="2" [2]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=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='960d66b90963480c8de42539b8783d3a' - 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='4032743' - PS1='# ' - PS2='> ' + INVOCATION_ID=6b26393ec1f84c4f8c267f7610bec383 + 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=2287704 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.3OV1NWbZ/pbuilderrc_Pjvl --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.3OV1NWbZ/b1 --logfile b1/build.log mafft_7.525-1.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://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.3OV1NWbZ/pbuilderrc_i6O1 --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.3OV1NWbZ/b2 --logfile b2/build.log mafft_7.525-1.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 ionos11-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 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/4032743/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2287704/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 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 13.26 [939 kB] -Fetched 11.2 MB in 0s (80.1 MB/s) +Fetched 11.2 MB in 0s (29.0 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 ... 19897 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/2287704/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2287704/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 @@ -276,7 +312,7 @@ debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core - cd core && make -j40 clean + cd core && make -j42 clean make[1]: Entering directory '/build/reproducible-path/mafft-7.525/core' rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno make[1]: Leaving directory '/build/reproducible-path/mafft-7.525/core' @@ -299,7 +335,7 @@ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-z,relro -Wl,-z,now" - cd core && make -j40 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + cd core && make -j42 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/mafft-7.525/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl @@ -343,29 +379,53 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c -dndfast7.c: In function 'main': -dndfast7.c:326:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 326 | 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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c 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 'prepareash': +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 ); + | ^~~~~~~~~~~~~ +rna.c:245:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 245 | fgets( gett, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 285 | system( cmd ); + | ^~~~~~~~~~~~~ +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 ); + | ^~~~~~~~~~~~~ +dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 382 | system( com ); + | ^~~~~~~~~~~~~ +dndfast7.c: In function 'main': dvtditr.c: In function 'main': +dndfast7.c:326:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 326 | system( com ); + | ^~~~~~~~~~~~~ +dvtditr.c:1020:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 1020 | system( "cp infile.tree GuideTree" ); // tekitou + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 ); | ^~~~~~~~~~~~~~~~~~~~~~ -dvtditr.c:1020:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 1020 | system( "cp infile.tree GuideTree" ); // tekitou - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash': +In file included from constants.c:7: +blosum.c: In function 'overridematrix': pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 485 | system( com ); | ^~~~~~~~~~~~~ +blosum.c:372:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 372 | fgets( buf, 499, fp ); + | ^~~~~~~~~~~~~~~~~~~~~ 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 ); @@ -413,7 +473,12 @@ pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 238 | fgets( line, nlenmax*2, 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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c 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 ); @@ -431,10 +496,6 @@ io.c:1255:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1255 | fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ | ^~~~~~~~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~ pairlocalalign.c: In function 'calllast_once': pairlocalalign.c:1056:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1056 | system( command ); @@ -442,12 +503,6 @@ pairlocalalign.c:1092:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1092 | system( command ); | ^~~~~~~~~~~~~~~~~ -rna.c:245:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 245 | fgets( gett, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ -rna.c:285:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 285 | system( cmd ); - | ^~~~~~~~~~~~~ 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 ); @@ -464,14 +519,7 @@ pairlocalalign.c:374:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 374 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ -pairlocalalign.c: In function 'readhat4': io.c: In function 'readhat2_doublehalf_part_pointer': -pairlocalalign.c:1532:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1532 | fgets( oneline, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -pairlocalalign.c:1544:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1544 | fgets( oneline, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:2708:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2708 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ @@ -481,6 +529,13 @@ io.c:2716:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2716 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ +pairlocalalign.c: In function 'readhat4': +pairlocalalign.c:1532:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1532 | fgets( oneline, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ +pairlocalalign.c:1544:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1544 | fgets( oneline, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_pointer': io.c:2746:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2746 | fgets( b, B, fp ); @@ -491,10 +546,6 @@ io.c:2752:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2752 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ -pairlocalalign.c: In function 'recalllara': -pairlocalalign.c:1245:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 1245 | fgets( com, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf': io.c:2780:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2780 | fgets( b, B, fp ); @@ -505,26 +556,40 @@ io.c:2782:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2782 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ -pairlocalalign.c: In function 'callmxscarna_giving_bpp': +pairlocalalign.c: In function 'recalllara': +pairlocalalign.c:1245:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 1245 | fgets( com, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_double': io.c:2810:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2810 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ +io.c:2811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2811 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); + | ^~~~~~~~~~~~~~~~~ +io.c:2812:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2812 | fgets( b, B, fp ); + | ^~~~~~~~~~~~~~~~~ +io.c: In function 'readhat2_int': +pairlocalalign.c: In function 'callmxscarna_giving_bpp': +io.c:2840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2840 | fgets( b, B, fp ); + | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1408:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1408 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1410:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1410 | system( com ); | ^~~~~~~~~~~~~ -io.c:2811:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2811 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); - | ^~~~~~~~~~~~~~~~~ -io.c:2812:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2812 | fgets( b, B, fp ); +io.c:2841:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2841 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1430:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1430 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ +io.c:2842:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2842 | fgets( b, B, fp ); + | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1451:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1451 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ @@ -537,35 +602,35 @@ pairlocalalign.c:1487:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1487 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ -io.c: In function 'readhat2_int': -io.c:2840:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2840 | fgets( b, B, fp ); +io.c: In function 'readhat2_pointer': +io.c:2871:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2871 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ -io.c:2841:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2841 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); +io.c:2872:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2872 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ -io.c:2842:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2842 | fgets( b, B, fp ); +io.c:2873:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2873 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ -io.c: In function 'readhat2_pointer': +io.c: In function 'readhat2': pairlocalalign.c: In function 'calldafs_giving_bpp': pairlocalalign.c:1291:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1291 | system( com ); | ^~~~~~~~~~~~~ +io.c:2901:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2901 | fgets( b, B, fp ); + | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1293:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1293 | system( com ); | ^~~~~~~~~~~~~ -io.c:2871:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2871 | fgets( b, B, fp ); +io.c:2902:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2902 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1313:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1313 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ -io.c:2872:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2872 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); - | ^~~~~~~~~~~~~~~~~ -io.c:2873:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2873 | fgets( b, B, fp ); +io.c:2903:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 2903 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1334:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1334 | system( com ); // for cygwin, wakaran @@ -582,33 +647,23 @@ pairlocalalign.c:1368:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1368 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ -io.c: In function 'readhat2': -io.c:2901:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2901 | fgets( b, B, fp ); - | ^~~~~~~~~~~~~~~~~ -io.c:2902:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2902 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); - | ^~~~~~~~~~~~~~~~~ -io.c:2903:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 2903 | fgets( b, B, fp ); - | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'pairalign_node': +io.c: In function 'ReadFasta_sub': pairlocalalign.c:3468:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3468 | system( "rm -rf hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~~ -pairlocalalign.c:3469:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 3469 | system( "mkdir hat3dir" ); // toriaezu - | ^~~~~~~~~~~~~~~~~~~~~~~~~ -pairlocalalign.c:3474:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 3474 | system( fn ); - | ^~~~~~~~~~~~ -io.c: In function 'ReadFasta_sub': io.c:3158:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3158 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ +pairlocalalign.c:3469:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 3469 | system( "mkdir hat3dir" ); // toriaezu + | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:3173:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3173 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ +pairlocalalign.c:3474:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 3474 | system( fn ); + | ^~~~~~~~~~~~ io.c: In function 'ReadSsearch': io.c:3192:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3192 | fgets( b, B-1, fp ); @@ -713,13 +768,9 @@ io.c:5596:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5596 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ -dndblast.c: In function 'main': io.c:5619:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5619 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ -dndblast.c:201:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 201 | system( com ); - | ^~~~~~~~~~~~~ io.c: In function 'readsubalignmentstable': io.c:5775:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5775 | fgets( line, linelen-1, fp ); @@ -734,6 +785,7 @@ io.c:5860:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5860 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ +tbfast.c: In function 'main': io.c: In function 'readpairfoldalign': io.c:5919:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5919 | fgets( gett, 999, fp ); @@ -750,25 +802,23 @@ io.c:5959:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5959 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ -dndblast.c:382:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 382 | system( com ); - | ^~~~~~~~~~~~~ +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 + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readexternalanchors': io.c:6397:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 6397 | fgets( buf, 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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c -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 ); - | ^~~~~~~~~~~~~~~~~~~~~ -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ); @@ -798,18 +848,23 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ); @@ -836,27 +891,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.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 @@ -878,13 +917,14 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c score.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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.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 ); @@ -896,21 +936,17 @@ 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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c -restoreu.c: In function 'main': -restoreu.c:185:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 185 | fgets( gett, 999, dlfp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ gcc -o version version.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread 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 +restoreu.c: In function 'main': +restoreu.c:185:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 185 | fgets( gett, 999, dlfp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ setdirection.c: In function 'main': setdirection.c:132:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 132 | fgets( line, 99, difp ); @@ -967,7 +1003,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/mafft-7.525' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft - cd core && make -j40 install DESTDIR=/build/reproducible-path/mafft-7.525/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft + cd core && make -j42 install DESTDIR=/build/reproducible-path/mafft-7.525/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft make[2]: Entering directory '/build/reproducible-path/mafft-7.525/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* @@ -1069,12 +1105,14 @@ 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/2287704/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2287704/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/4032743 and its subdirectories -I: Current time: Sun Sep 7 00:19:27 -12 2025 -I: pbuilder-time-stamp: 1757247567 +I: removing directory /srv/workspace/pbuilder/2287704 and its subdirectories +I: Current time: Sun Oct 11 08:43:17 +14 2026 +I: pbuilder-time-stamp: 1791657797