Diff of the two buildlogs: -- --- b1/build.log 2023-04-19 11:15:03.340210879 +0000 +++ b2/build.log 2023-04-19 11:15:49.314171925 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 18 23:13:57 -12 2023 -I: pbuilder-time-stamp: 1681902837 +I: Current time: Wed May 22 07:38:05 +14 2024 +I: pbuilder-time-stamp: 1716313085 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./mafft_7.505.orig.tar.gz] I: copying [./mafft_7.505-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Sat Jun 25 07:18:48 2022 -12 +gpgv: Signature made Sun Jun 26 09:18:48 2022 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key @@ -26,135 +26,167 @@ 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/2085893/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1213750/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 May 22 07:38 /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/1213750/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1213750/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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=15' - DISTRIBUTION='bookworm' - 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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=16' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='07424a8f2f0b4410a090014cf745dcdb' - 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='2085893' - PS1='# ' - PS2='> ' + INVOCATION_ID=9da51cd9d88b4ec4ab0e6c3b272b71b8 + 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=1213750 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.5KywjEyf/pbuilderrc_pkau --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5KywjEyf/b1 --logfile b1/build.log mafft_7.505-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.5KywjEyf/pbuilderrc_jbGn --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.5KywjEyf/b2 --logfile b2/build.log --extrapackages usrmerge mafft_7.505-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 ionos11-amd64 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:05 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2085893/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 May 22 07:38 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/1213750/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -220,7 +252,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] -Fetched 18.7 MB in 0s (48.2 MB/s) +Fetched 18.7 MB in 0s (88.8 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 ... 19596 files and directories currently installed.) @@ -354,8 +386,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/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/1213750/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/1213750/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/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 @@ -365,7 +408,7 @@ debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core - cd core && make -j15 clean + cd core && make -j16 clean make[1]: Entering directory '/build/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/mafft-7.505/core' @@ -388,7 +431,7 @@ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -ffile-prefix-map=/build/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 -j15 "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/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 -j16 "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/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/mafft-7.505/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl @@ -407,11 +450,7 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c -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 ); - | ^~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c 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 ); @@ -422,6 +461,15 @@ 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 ); + | ^~~~~~~~~~~~~~~~~~~~~ +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, 999, 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 ); @@ -653,15 +701,6 @@ io.c:5902:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5902 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ -io.c: In function 'readexternalanchors': -io.c:6340:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 6340 | 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, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.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 ); @@ -675,6 +714,10 @@ mltaln9.c:15725:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15725 | fread( &c, sizeof( char ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +io.c: In function 'readexternalanchors': +io.c:6340:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 6340 | fgets( buf, 9999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'check_guidetreefile': mltaln9.c:2850:9: warning: 'fgets' writing 999 bytes into a region of size 100 overflows the destination [-Wstringop-overflow=] 2850 | fgets( string, 999, fp ); @@ -693,20 +736,20 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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 ); | ^~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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] @@ -723,6 +766,11 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ); @@ -730,10 +778,34 @@ 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: In function 'callrash': +pairash.c:485:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 485 | system( com ); + | ^~~~~~~~~~~~~ +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 ); + | ^~~~~~~~~~~~~~~~~~~~~~ +pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 284 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +pairash.c:289:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 289 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +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: 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 ); @@ -742,10 +814,44 @@ 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 'preparetmalign': +pairash.c:530:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 530 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +pairash.c:576:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 576 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 587 | system( command ); + | ^~~~~~~~~~~~~~~~~ +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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~ +pairash.c: In function 'calltmalign': +pairash.c:347:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] + 347 | system( com ); + | ^~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx_singleq': +pairash.c:356:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 356 | fgets( com, 100, fp ); + | ^~~~~~~~~~~~~~~~~~~~~ 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 'readtmalign': +pairash.c:228:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 228 | fgets( line, 999, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~ +pairash.c:232:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 232 | fgets( line, nlenmax*2, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +pairash.c:235:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 235 | fgets( line, nlenmax*2, fp ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] + 238 | fgets( line, nlenmax*2, 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 ); @@ -804,7 +910,6 @@ pairlocalalign.c:1368:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1368 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ -gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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 'pairalign_node': pairlocalalign.c:3467:9: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3467 | system( "rm -rf hat3dir" ); // toriaezu @@ -815,69 +920,8 @@ pairlocalalign.c:3473:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3473 | system( fn ); | ^~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:284:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 284 | fgets( line, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:289:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 289 | fgets( line, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:294:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 294 | fgets( line, 999, 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 ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:576:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 576 | fgets( line, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:587:25: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 587 | system( command ); - | ^~~~~~~~~~~~~~~~~ -maffttext2hex.c: In function 'main': -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~~ -pairash.c: In function 'calltmalign': -pairash.c:347:17: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] - 347 | system( com ); - | ^~~~~~~~~~~~~ -pairash.c:356:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 356 | fgets( com, 100, fp ); - | ^~~~~~~~~~~~~~~~~~~~~ -pairash.c: In function 'readtmalign': -pairash.c:228:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 228 | fgets( line, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~ -pairash.c:232:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 232 | fgets( line, nlenmax*2, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -pairash.c:235:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 235 | fgets( line, nlenmax*2, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -pairash.c:238:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 238 | fgets( line, nlenmax*2, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 -ffile-prefix-map=/build/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c pairash.c: In function 'callrash.constprop': 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 ); @@ -907,8 +951,9 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c pairash.c: In function 'calltmalign.constprop': 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 ); @@ -935,27 +980,39 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.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 ); | ^~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.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 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mltaln9.c: In function 'createchain': +mltaln9.c:2113:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-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 [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -979,24 +1036,15 @@ | ^~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c +In function 'fgets', + inlined from 'check_guidetreefile' at mltaln9.c:2850:2: +/usr/include/x86_64-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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ); | ^~~~~~~~~~~~~~~~~~~~~~~ -mltaln9.c: In function 'createchain': -mltaln9.c:2113:31: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-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 [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-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/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c @@ -1018,22 +1066,17 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c -In function 'fgets', - inlined from 'check_guidetreefile' at mltaln9.c:2850:2: -/usr/include/x86_64-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); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 +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:_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': @@ -1087,7 +1130,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/mafft-7.505' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft - cd core && make -j15 install DESTDIR=/build/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 -j16 install DESTDIR=/build/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/mafft-7.505/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* @@ -1193,12 +1236,14 @@ 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/1213750/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1213750/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/2085893 and its subdirectories -I: Current time: Tue Apr 18 23:15:02 -12 2023 -I: pbuilder-time-stamp: 1681902902 +I: removing directory /srv/workspace/pbuilder/1213750 and its subdirectories +I: Current time: Wed May 22 07:38:49 +14 2024 +I: pbuilder-time-stamp: 1716313129