Diff of the two buildlogs: -- --- b1/build.log 2021-08-16 19:23:55.329866590 +0000 +++ b2/build.log 2021-08-16 19:26:10.200862967 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Aug 16 07:23:07 -12 2021 -I: pbuilder-time-stamp: 1629141787 +I: Current time: Mon Sep 19 15:46:59 +14 2022 +I: pbuilder-time-stamp: 1663552019 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Sat Dec 1 22:43:32 2018 -12 +gpgv: Signature made Mon Dec 3 00:43:32 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,136 +29,170 @@ dpkg-source: info: applying fix_bashism.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22041/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/44345/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/44345/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/44345/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='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(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= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9f586393e01e40f496fd4dbda0aa3da9' - 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='22041' - PS1='# ' - PS2='> ' + INVOCATION_ID=4acb33901fc74ab085bf0de75d21bee1 + 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=44345 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/tmp.tTMzD4SKty/pbuilderrc_GNRs --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tTMzD4SKty/b1 --logfile b1/build.log mafft_7.407-2.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/tmp.tTMzD4SKty/pbuilderrc_zJNn --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tTMzD4SKty/b2 --logfile b2/build.log mafft_7.407-2.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-0.bpo.8-amd64 #1 SMP Debian 5.10.46-2~bpo10+1 (2021-07-22) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 6 20:24 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/22041/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 19 15:47 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 10 04:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/44345/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -227,7 +261,7 @@ Get: 31 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] -Fetched 19.0 MB in 0s (62.1 MB/s) +Fetched 19.0 MB in 1s (29.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (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 ... 19195 files and directories currently installed.) @@ -382,7 +416,7 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/mafft-7.407/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/mafft-7.407/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.407-2 dpkg-buildpackage: info: source distribution unstable @@ -392,7 +426,7 @@ fakeroot 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-7.407/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 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-7.407/core' @@ -415,7 +449,7 @@ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -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-7.407=. -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-7.407/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl @@ -424,20 +458,10 @@ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from partSalignmm.c:1: + from io.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ @@ -448,69 +472,80 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from Lalignmm.c:1: + from tddis.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from io.c:1: + from constants.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from tddis.c:1: + from nj.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from Falign.c:1: + from partSalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from constants.c:1: + from Lalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from nj.c:1: + from rna.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from Dalignmm.c:1: + from Salignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from Falign_localhom.c:1: + from Dalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from Lalign11.c:1: + from Falign.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -521,14 +556,26 @@ In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from rna.c:1: + from Falign_localhom.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from Salignmm.c:1: + from Lalign11.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ +In file included from constants.c:7: +blosum.c: In function 'overridematrix': +blosum.c:342:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( buf, 499, fp ); + ^~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from genalign11.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ @@ -542,11 +589,6 @@ rna.c:285:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( cmd ); ^~~~~~~~~~~~~ -In file included from constants.c:7: -blosum.c: In function 'overridematrix': -blosum.c:342:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( buf, 499, fp ); - ^~~~~~~~~~~~~~~~~~~~~ io.c: In function 'PreRead': io.c:1065:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( b, B-1, fp ); *locnjob = atoi( b ); @@ -795,23 +837,16 @@ mltaln9.c:15192:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread( &c, sizeof( char ), 1, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from genalign11.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, from MSalignmm.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -819,7 +854,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -828,7 +862,6 @@ # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -836,6 +869,7 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -844,10 +878,6 @@ # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c -dvtditr.c: In function 'main': -dvtditr.c:1020:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] - system( "cp infile.tree GuideTree" ); // tekitou - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -855,6 +885,10 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +dvtditr.c: In function 'main': +dvtditr.c:1020:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] + system( "cp infile.tree GuideTree" ); // tekitou + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, @@ -865,7 +899,6 @@ ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -880,6 +913,7 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -892,6 +926,8 @@ system( com ); ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -899,14 +935,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -dndblast.c: In function 'main': -dndblast.c:203:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] - system( com ); - ^~~~~~~~~~~~~ -dndblast.c:384:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] - system( com ); - ^~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -914,7 +942,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -930,6 +957,13 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +dndblast.c: In function 'main': +dndblast.c:203:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] + system( com ); + ^~~~~~~~~~~~~ +dndblast.c:384:2: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] + system( com ); + ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, @@ -939,6 +973,7 @@ # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -946,7 +981,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -962,23 +996,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, - from pairash.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, - from addsingle.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ pairlocalalign.c: In function 'calllast_once': pairlocalalign.c:1055:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); @@ -986,10 +1003,6 @@ pairlocalalign.c:1091:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ -maffttext2hex.c: In function 'main': -maffttext2hex.c:55:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( (char *)buf, 999, fp ); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx': pairlocalalign.c:607:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 9999, fp ); @@ -1074,6 +1087,24 @@ pairlocalalign.c:3444:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( fn ); ^~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from pairash.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from addsingle.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ +maffttext2hex.c: In function 'main': pairash.c: In function 'prepareash': pairash.c:639:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); @@ -1081,6 +1112,7 @@ pairash.c:681:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ +gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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': pairash.c:485:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( com ); @@ -1108,6 +1140,9 @@ pairash.c:587:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( command ); ^~~~~~~~~~~~~~~~~ +maffttext2hex.c:55:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( (char *)buf, 999, fp ); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'checkcbeta': pairash.c:321:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( linec, 999, fp ); @@ -1132,7 +1167,26 @@ pairash.c:238:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( line, nlenmax*2, fp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from splittbfast.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c +splittbfast.c: In function 'main': +splittbfast.c:3218:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] + system( com ); + ^~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from disttbfast.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ pairash.c: In function 'callrash.isra.1': pairash.c:428:29: warning: '.' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); @@ -1156,6 +1210,26 @@ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from tbfast.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from nodepair.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ +disttbfast.c: In function 'disttbfast': +disttbfast.c:3638:6: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] + system( "cp infile.tree GuideTree" ); // tekitou + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'calltmalign.isra.2': pairash.c:346:27: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] sprintf( com, "mkdir -p %s", cachedir ); @@ -1179,23 +1253,19 @@ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, - from splittbfast.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from disttbfast.c:1: + from mafft-profile.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c +tbfast.c: In function 'main': +tbfast.c:3181:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] + system( "cp infile.tree GuideTree" ); // tekitou + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c pairash.c: In function 'preparetmalign.constprop': pairash.c:586:29: warning: '%s' directive writing up to 999 bytes into a region of size 996 [-Wformat-overflow=] sprintf( command, "cp %s %s.pdb", sline, fname ); @@ -1222,50 +1292,6 @@ In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from tbfast.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -splittbfast.c: In function 'main': -splittbfast.c:3218:3: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] - system( com ); - ^~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, - from nodepair.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, - from mafft-profile.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -disttbfast.c: In function 'disttbfast': -disttbfast.c:3638:6: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] - system( "cp infile.tree GuideTree" ); // tekitou - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/stdio.h:873, - from mltaln.h:13, - from mltaln9.c:1: -In function 'fgets', - inlined from 'check_guidetreefile' at mltaln9.c:2802:2: -/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer - return __fgets_chk_warn (__s, __bos (__s), __n, __stream); - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tbfast.c: In function 'main': -tbfast.c:3181:5: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] - system( "cp infile.tree GuideTree" ); // tekitou - ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, from f2cl.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" @@ -1278,10 +1304,18 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c f2cl.c: In function 'main': f2cl.c:283:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, B-1, orderfp ); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, + from /usr/include/stdio.h:27, + from mltaln.h:13, + from contrafoldwrap.c:1: +/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] + # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + ^~~~~~~ mccaskillwrap.c: In function 'main': mccaskillwrap.c:372:4: warning: ignoring return value of 'system', declared with attribute warn_unused_result [-Wunused-result] system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran @@ -1303,23 +1337,29 @@ mccaskillwrap.c:46:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets( gett, 999, fp ); ^~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, - from contrafoldwrap.c:1: -/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] - # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" - ^~~~~~~ -In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, - from /usr/include/stdio.h:27, - from mltaln.h:13, from countlen.c:1: /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +contrafoldwrap.c: In function 'readcontrafold': +contrafoldwrap.c:57:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( gett, 9999, fp ); + ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c +In file included from /usr/include/stdio.h:873, + from mltaln.h:13, + from mltaln9.c:1: +In function 'fgets', + inlined from 'check_guidetreefile' at mltaln9.c:2802:2: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:263:9: warning: call to '__fgets_chk_warn' declared with attribute warning: fgets called with bigger size than length of destination buffer + return __fgets_chk_warn (__s, __bos (__s), __n, __stream); + ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1327,11 +1367,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -contrafoldwrap.c: In function 'readcontrafold': -contrafoldwrap.c:57:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( gett, 9999, fp ); - ^~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1339,18 +1374,7 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -regtable2seq.c: In function 'readereg': -regtable2seq.c:69:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( gett, 999, regfp ); - ^~~~~~~~~~~~~~~~~~~~~~~~~ -regtable2seq.c:97:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( gett, 999, regfp ); - ^~~~~~~~~~~~~~~~~~~~~~~~~ -regtable2seq.c: In function 'readreg': -regtable2seq.c:120:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( gett, 999, regfp ); - ^~~~~~~~~~~~~~~~~~~~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1358,7 +1382,7 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1366,8 +1390,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1375,6 +1397,7 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1382,6 +1405,17 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +regtable2seq.c: In function 'readereg': +regtable2seq.c:69:2: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( gett, 999, regfp ); + ^~~~~~~~~~~~~~~~~~~~~~~~~ +regtable2seq.c:97:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( gett, 999, regfp ); + ^~~~~~~~~~~~~~~~~~~~~~~~~ +regtable2seq.c: In function 'readreg': +regtable2seq.c:120:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( gett, 999, regfp ); + ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, @@ -1392,6 +1426,7 @@ ^~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c +gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1406,11 +1441,6 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -gcc -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c -restoreu.c: In function 'main': -restoreu.c:177:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( gett, 999, dlfp ); - ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1418,12 +1448,7 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ -setdirection.c: In function 'main': -setdirection.c:132:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] - fgets( line, 99, difp ); - ^~~~~~~~~~~~~~~~~~~~~~~ gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -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 In file included from /usr/include/x86_64-linux-gnu/bits/libc-header-start.h:33, from /usr/include/stdio.h:27, from mltaln.h:13, @@ -1431,6 +1456,15 @@ /usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" ^~~~~~~ +restoreu.c: In function 'main': +sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft +restoreu.c:177:4: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + fgets( gett, 999, dlfp ); + ^~~~~~~~~~~~~~~~~~~~~~~~ +setdirection.c: In function 'main': +setdirection.c:132:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] + 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 gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -ffile-prefix-map=/build/mafft-7.407=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread @@ -1478,7 +1512,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/mafft-7.407' 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-7.407/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-7.407/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-7.407/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* @@ -1537,20 +1571,22 @@ dh_gencontrol -O--sourcedirectory=core dh_md5sums -O--sourcedirectory=core dh_builddeb -O--sourcedirectory=core -dpkg-deb: building package 'mafft' in '../mafft_7.407-2_amd64.deb'. dpkg-deb: building package 'mafft-dbgsym' in '../mafft-dbgsym_7.407-2_amd64.deb'. +dpkg-deb: building package 'mafft' in '../mafft_7.407-2_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mafft_7.407-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/44345/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/44345/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/22041 and its subdirectories -I: Current time: Mon Aug 16 07:23:54 -12 2021 -I: pbuilder-time-stamp: 1629141834 +I: removing directory /srv/workspace/pbuilder/44345 and its subdirectories +I: Current time: Mon Sep 19 15:49:11 +14 2022 +I: pbuilder-time-stamp: 1663552151