Diff of the two buildlogs: -- --- b1/build.log 2023-04-13 11:23:40.695980479 +0000 +++ b2/build.log 2023-04-13 11:24:14.134496431 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Apr 12 23:22:35 -12 2023 -I: pbuilder-time-stamp: 1681384955 +I: Current time: Thu May 16 07:46:42 +14 2024 +I: pbuilder-time-stamp: 1715795202 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ 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 @@ -27,137 +27,146 @@ 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/28466/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/49429/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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/49429/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/49429/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' + 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=8' + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' - INVOCATION_ID='c96ea8da3d7e4bd5b9c89d92d78007f2' + INVOCATION_ID='c49d1ef5108e402d8459e64f5bf1fe23' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='de_CH:de' 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' + 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' - PPID='28466' + PPID='49429' PS1='# ' PS2='> ' 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.0A6yFn7c/pbuilderrc_vPKj --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.0A6yFn7c/b1 --logfile b1/build.log mafft_7.505-1.dsc' + 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.0A6yFn7c/pbuilderrc_0YmJ --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.0A6yFn7c/b2 --logfile b2/build.log --extrapackages usrmerge mafft_7.505-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + http_proxy='http://85.184.249.68:3128' I: uname -a - Linux ionos12-i386 5.10.0-21-686-pae #1 SMP Debian 5.10.162-1 (2023-01-21) i686 GNU/Linux + Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 6040 - -rwxr-xr-x 1 root root 1408088 Feb 12 08:21 bash - -rwxr-xr-x 3 root root 38404 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 38404 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 38404 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 17892 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 42920 Sep 20 2022 cat - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown - -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp - -rwxr-xr-x 1 root root 136916 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 137160 Sep 20 2022 date - -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd - -rwxr-xr-x 1 root root 108940 Sep 20 2022 df - -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir - -rwxr-xr-x 1 root root 87760 Mar 22 22:20 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 38760 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 34664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 84272 Mar 22 22:20 findmnt - -rwsr-xr-x 1 root root 30240 Mar 22 20:38 fusermount - -rwxr-xr-x 1 root root 218680 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 100952 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 21916 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln - -rwxr-xr-x 1 root root 55600 Mar 22 23:43 login - -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls - -rwxr-xr-x 1 root root 214568 Mar 22 22:20 lsblk - -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 63016 Mar 22 22:20 more - -rwsr-xr-x 1 root root 58912 Mar 22 22:20 mount - -rwxr-xr-x 1 root root 13856 Mar 22 22:20 mountpoint - -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Dec 18 05:00 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Feb 12 08:21 rbash -> bash - -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm - -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Nov 2 04:31 run-parts - -rwxr-xr-x 1 root root 133224 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty - -rwsr-xr-x 1 root root 83492 Mar 22 22:20 su - -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync - -rwxr-xr-x 1 root root 602584 Feb 16 2021 tar - -rwxr-xr-x 1 root root 13860 Nov 2 04:31 tempfile - -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch - -rwxr-xr-x 1 root root 34664 Sep 20 2022 true - -rwxr-xr-x 1 root root 17892 Mar 22 20:38 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Mar 22 22:20 umount - -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 71216 Mar 22 22:20 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/28466/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1408088 Feb 13 2023 bash + -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 38404 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 38404 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 17892 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 42920 Sep 21 2022 cat + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 79816 Sep 21 2022 chown + -rwxr-xr-x 1 root root 162024 Sep 21 2022 cp + -rwxr-xr-x 1 root root 136916 Jan 6 2023 dash + -rwxr-xr-x 1 root root 137160 Sep 21 2022 date + -rwxr-xr-x 1 root root 100364 Sep 21 2022 dd + -rwxr-xr-x 1 root root 108940 Sep 21 2022 df + -rwxr-xr-x 1 root root 162152 Sep 21 2022 dir + -rwxr-xr-x 1 root root 87760 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 38760 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 34664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 218680 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 100952 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 75756 Sep 21 2022 ln + -rwxr-xr-x 1 root root 55600 Mar 24 2023 login + -rwxr-xr-x 1 root root 162152 Sep 21 2022 ls + -rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 63016 Mar 24 2023 more + -rwsr-xr-x 1 root root 58912 Mar 24 2023 mount + -rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 157932 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Dec 19 2022 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Feb 13 2023 rbash -> bash + -rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 75720 Sep 21 2022 rm + -rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133224 Jan 6 2023 sed + lrwxrwxrwx 1 root root 4 Jan 6 2023 sh -> dash + -rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 87976 Sep 21 2022 stty + -rwsr-xr-x 1 root root 83492 Mar 24 2023 su + -rwxr-xr-x 1 root root 38792 Sep 21 2022 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 120776 Sep 21 2022 touch + -rwxr-xr-x 1 root root 34664 Sep 21 2022 true + -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Mar 24 2023 umount + -rwxr-xr-x 1 root root 38760 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 71216 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/49429/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -223,7 +232,7 @@ Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] -Fetched 19.0 MB in 0s (49.5 MB/s) +Fetched 19.0 MB in 0s (90.0 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 ... 19604 files and directories currently installed.) @@ -357,8 +366,19 @@ 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/49429/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/49429/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 @@ -368,7 +388,7 @@ debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core - cd core && make -j8 clean + cd core && make -j15 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' @@ -391,7 +411,7 @@ 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 -j8 "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 -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" make[2]: Entering directory '/build/mafft-7.505/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl @@ -403,6 +423,28 @@ 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 nj.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 partSalignmm.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 Lalignmm.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 rna.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 Salignmm.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 Dalignmm.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 Falign.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 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 ); + | ^~~~~~~~~~~~~~~~~~~~~ +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 ); + | ^~~~~~~~~~~~~ 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 ); @@ -638,11 +680,6 @@ io.c:6340:17: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 6340 | fgets( buf, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ -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 ); @@ -673,67 +710,26 @@ /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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.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 ); - | ^~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~ -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 Salignmm.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 Dalignmm.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 Falign.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 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 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 '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) - | ^~~~~~ -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/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/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/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 +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 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 -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 -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 -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 -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-distance.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 ); + | ^~~~~~~~~~~~~ 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 ); @@ -741,74 +737,14 @@ 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': -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 sextet5.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-distance.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 MSalign11.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 suboptalign11.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 pairlocalalignmain.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 pairlocalalign.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 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 -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 ); - | ^~~~~~~~~~~~~~~~~ -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 ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 ); @@ -901,6 +837,65 @@ 3473 | system( fn ); | ^~~~~~~~~~~~ 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 +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 ); + | ^~~~~~~~~~~~~~~~~ +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 ); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 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 ); @@ -930,8 +925,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -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 -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 +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 '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 ); @@ -958,33 +955,51 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ -maffttext2hex.c: In function 'main': -maffttext2hex.c:55:25: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] - 55 | fgets( (char *)buf, 999, fp ); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -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 -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 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 ); | ^~~~~~~~~~~~~ -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/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 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 nodepair.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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.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/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 +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 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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c +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); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 @@ -1006,14 +1021,15 @@ 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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/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/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 +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 getlag.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 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 ); @@ -1025,27 +1041,31 @@ 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/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/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/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/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/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/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 +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': +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/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/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/mafft-7.505=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread @@ -1090,7 +1110,7 @@ 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 -j8 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 -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 make[2]: Entering directory '/build/mafft-7.505/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* @@ -1196,12 +1216,14 @@ 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/49429/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/49429/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/28466 and its subdirectories -I: Current time: Wed Apr 12 23:23:40 -12 2023 -I: pbuilder-time-stamp: 1681385020 +I: removing directory /srv/workspace/pbuilder/49429 and its subdirectories +I: Current time: Thu May 16 07:47:13 +14 2024 +I: pbuilder-time-stamp: 1715795233