Diff of the two buildlogs: -- --- b1/build.log 2024-04-08 14:47:31.800498763 +0000 +++ b2/build.log 2024-04-08 14:48:10.582849200 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 8 02:46:22 -12 2024 -I: pbuilder-time-stamp: 1712587582 +I: Current time: Mon May 12 11:10:33 +14 2025 +I: pbuilder-time-stamp: 1746997833 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,54 +27,86 @@ dpkg-source: info: unpacking mafft_7.505-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/28830/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/129680/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +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 May 11 21:10 /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/129680/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/129680/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='5686f6e9d95847c8bee8e85246b8f785' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='28830' - PS1='# ' - PS2='> ' + INVOCATION_ID=69fe8a827e094de48449b7e19e96579a + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=129680 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.wzHx4V5V/pbuilderrc_IQsE --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wzHx4V5V/b1 --logfile b1/build.log mafft_7.505-1.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + 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.wzHx4V5V/pbuilderrc_lw3h --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.wzHx4V5V/b2 --logfile b2/build.log mafft_7.505-1.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 7 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/28830/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 11 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/129680/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -140,7 +172,7 @@ Get: 28 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 debhelper all 13.15.3 [901 kB] -Fetched 19.3 MB in 0s (46.1 MB/s) +Fetched 19.3 MB in 1s (25.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed 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 ... 19875 files and directories currently installed.) @@ -275,7 +307,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/mafft-7.505/ && 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_7.505-1_source.changes +I: user script /srv/workspace/pbuilder/129680/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/129680/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/mafft-7.505/ && 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_7.505-1_source.changes dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.505-1 dpkg-buildpackage: info: source distribution unstable @@ -285,7 +321,7 @@ debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core - cd core && make -j11 clean + cd core && make -j21 clean make[1]: Entering directory '/build/reproducible-path/mafft-7.505/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-7.505/core' @@ -308,7 +344,7 @@ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-z,relro -Wl,-z,now" - cd core && make -j11 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" + cd core && make -j21 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/reproducible-path/mafft-7.505/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl @@ -323,6 +359,25 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c +dvtditr.c: In function 'main': +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 + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from constants.c:7: +blosum.c: In function 'overridematrix': +blosum.c:370:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 370 | fgets( buf, 499, 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 ); @@ -333,11 +388,6 @@ 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:370:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 370 | 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 ); @@ -577,6 +627,7 @@ mltaln9.c:2850:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2850 | fgets( string, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': mltaln9.c:15685:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15685 | fread( &size, sizeof( int ), 1, fp ); @@ -603,49 +654,16 @@ /usr/include/i386-linux-gnu/bits/stdio2.h:209:1: note: in a call to function 'fgets' declared with attribute 'access (write_only, 1, 2)' 209 | fgets (char *__restrict __s, int __n, FILE *__restrict __stream) | ^~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c -dvtditr.c: In function 'main': -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 - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c -mltaln9.c: In function 'createchain': -mltaln9.c:2113:31: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] - 2113 | instanttree = calloc( treelen, sizeof( char ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from mltaln.h:13: -/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here - 556 | extern void *calloc (size_t __nmemb, size_t __size) - | ^~~~~~ -mltaln9.c:2124:17: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] - 2124 | order = calloc( nseq, sizeof( int ) ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here - 556 | extern void *calloc (size_t __nmemb, size_t __size) - | ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.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 ); | ^~~~~~~~~~~~~ -In function 'fgets', - inlined from 'check_guidetreefile' at mltaln9.c:2850:2: -/usr/include/i386-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] - 215 | return __fgets_chk_warn (__s, sz, __n, __stream); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 ); @@ -653,7 +671,6 @@ 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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c @@ -661,6 +678,8 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c +gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread 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 ); @@ -680,6 +699,7 @@ pairlocalalign.c:872:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 872 | system( command ); | ^~~~~~~~~~~~~~~~~ +gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread 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 ); @@ -752,6 +772,10 @@ pairlocalalign.c:3473:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3473 | system( fn ); | ^~~~~~~~~~~~ +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': pairash.c:639:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 639 | fgets( line, 999, fp ); @@ -810,7 +834,14 @@ 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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c +splittbfast.c: In function 'main': +splittbfast.c:3218:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 3218 | system( com ); + | ^~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c 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 ); @@ -840,18 +871,15 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread -mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave': -mltaln9.c:6494:28: warning: argument 2 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] - 6494 | int *mem = calloc( sizeof( int ), nseq ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here - 556 | extern void *calloc (size_t __nmemb, size_t __size) - | ^~~~~~ -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 -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c +disttbfast.c: In function 'disttbfast': +disttbfast.c:4583:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 4583 | system( "cp infile.tree GuideTree" ); // tekitou + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tbfast.c: In function 'main': +tbfast.c:3254:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 3254 | system( "cp infile.tree GuideTree" ); // tekitou + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ); @@ -878,30 +906,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c -splittbfast.c: In function 'main': -splittbfast.c:3218:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 3218 | system( com ); - | ^~~~~~~~~~~~~ -disttbfast.c: In function 'disttbfast': -disttbfast.c:4583:41: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 4583 | system( "cp infile.tree GuideTree" ); // tekitou - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c -tbfast.c: In function 'main': -tbfast.c:3254:33: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 3254 | system( "cp infile.tree GuideTree" ); // tekitou - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c -f2cl.c: In function 'main': -f2cl.c:287:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 287 | fgets( gett, B-1, orderfp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 @@ -919,20 +926,24 @@ mccaskillwrap.c:155:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | system( com ); | ^~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c mccaskillwrap.c: In function 'readrawmccaskill': 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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c +f2cl.c: In function 'main': +f2cl.c:287:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 287 | fgets( gett, B-1, orderfp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 ); @@ -940,29 +951,54 @@ regtable2seq.c:97:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c regtable2seq.c: In function 'readreg': 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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c gcc -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c +mltaln9.c: In function 'createchain': +mltaln9.c:2113:31: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] + 2113 | instanttree = calloc( treelen, sizeof( char ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from mltaln.h:13: +/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here + 556 | extern void *calloc (size_t __nmemb, size_t __size) + | ^~~~~~ +mltaln9.c:2124:17: warning: argument 1 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] + 2124 | order = calloc( nseq, sizeof( int ) ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here + 556 | extern void *calloc (size_t __nmemb, size_t __size) + | ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c -gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ -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 +gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~ +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 +In function 'fgets', + inlined from 'check_guidetreefile' at mltaln9.c:2850:2: +/usr/include/i386-linux-gnu/bits/stdio2.h:215:12: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] + 215 | return __fgets_chk_warn (__s, sz, __n, __stream); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c: In function 'fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave': +mltaln9.c:6494:28: warning: argument 2 range [2147483648, 4294967295] exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] + 6494 | int *mem = calloc( sizeof( int ), nseq ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/stdlib.h:556:14: note: in a call to allocation function 'calloc' declared here + 556 | 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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/reproducible-path/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread @@ -1007,7 +1043,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/mafft-7.505' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft - cd core && make -j11 install DESTDIR=/build/reproducible-path/mafft-7.505/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 -j21 install DESTDIR=/build/reproducible-path/mafft-7.505/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-7.505/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* @@ -1113,12 +1149,14 @@ 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/129680/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/129680/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/28830 and its subdirectories -I: Current time: Mon Apr 8 02:47:31 -12 2024 -I: pbuilder-time-stamp: 1712587651 +I: removing directory /srv/workspace/pbuilder/129680 and its subdirectories +I: Current time: Mon May 12 11:11:07 +14 2025 +I: pbuilder-time-stamp: 1746997867