I: pbuilder: network access will be disabled during build I: Current time: Wed Aug 2 05:15:45 +14 2023 I: pbuilder-time-stamp: 1690902945 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [mafft_7.475-1.dsc] I: copying [./mafft_7.475.orig.tar.gz] I: copying [./mafft_7.475-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.mMI95llu/trustedkeys.kbx': General error gpgv: Signature made Tue Dec 8 07:24:09 2020 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./mafft_7.475-1.dsc dpkg-source: info: extracting mafft in mafft-7.475 dpkg-source: info: unpacking mafft_7.475.orig.tar.gz dpkg-source: info: unpacking mafft_7.475-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc10.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3463282/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Aug 2 05:15 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/3463282/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/3463282/tmp/hooks/D02_print_environment starting I: set 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.1.4(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,-fixfilepath parallel=15 ' DIRSTACK=() DISTRIBUTION=bullseye EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=4bf4ca2426da4d9095693a2373e1bbb3 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=3463282 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.SyeOvAC3/pbuilderrc_Vjjy --distribution bullseye --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.SyeOvAC3/b2 --logfile b2/build.log mafft_7.475-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-10-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.38-2 (2023-07-27) x86_64 GNU/Linux I: ls -l /bin total 5476 -rwxr-xr-x 1 root root 1234376 Mar 28 2022 bash -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash -rwxr-xr-x 1 root root 113664 Sep 24 2020 date -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd -rwxr-xr-x 1 root root 93936 Sep 24 2020 df -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir -rwxr-xr-x 1 root root 84440 Jan 21 2022 dmesg lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo -rwxr-xr-x 1 root root 28 Jan 25 2023 egrep -rwxr-xr-x 1 root root 39680 Sep 24 2020 false -rwxr-xr-x 1 root root 28 Jan 25 2023 fgrep -rwxr-xr-x 1 root root 69032 Jan 21 2022 findmnt -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 203072 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 98048 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln -rwxr-xr-x 1 root root 56952 Feb 8 2020 login -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls -rwxr-xr-x 1 root root 149736 Jan 21 2022 lsblk -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp -rwxr-xr-x 1 root root 59632 Jan 21 2022 more -rwsr-xr-x 1 root root 55528 Jan 21 2022 mount -rwxr-xr-x 1 root root 18664 Jan 21 2022 mountpoint -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Dec 17 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd lrwxrwxrwx 1 root root 4 Mar 28 2022 rbash -> bash -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 9 Aug 2 05:15 sh -> /bin/bash -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty -rwsr-xr-x 1 root root 71912 Jan 21 2022 su -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch -rwxr-xr-x 1 root root 39680 Sep 24 2020 true -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 35040 Jan 21 2022 umount -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir -rwxr-xr-x 1 root root 63744 Jan 21 2022 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 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 5898 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 8049 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/3463282/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13) dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19707 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 18.3 MB of archives. After unpacking 67.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main amd64 bsdextrautils amd64 2.36.1-8+deb11u1 [145 kB] Get: 2 http://deb.debian.org/debian bullseye/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 3 http://deb.debian.org/debian bullseye/main amd64 groff-base amd64 1.22.4-6 [936 kB] Get: 4 http://deb.debian.org/debian bullseye/main amd64 libpipeline1 amd64 1.5.3-1 [34.3 kB] Get: 5 http://deb.debian.org/debian bullseye/main amd64 man-db amd64 2.9.4-2 [1354 kB] Get: 6 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3 [273 kB] Get: 8 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3 [126 kB] Get: 9 http://deb.debian.org/debian bullseye/main amd64 file amd64 1:5.39-3 [69.1 kB] Get: 10 http://deb.debian.org/debian bullseye/main amd64 gettext-base amd64 0.21-4 [175 kB] Get: 11 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main amd64 m4 amd64 1.4.18-5 [204 kB] Get: 13 http://deb.debian.org/debian bullseye/main amd64 autoconf all 2.69-14 [313 kB] Get: 14 http://deb.debian.org/debian bullseye/main amd64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main amd64 automake all 1:1.16.3-2 [814 kB] Get: 16 http://deb.debian.org/debian bullseye/main amd64 autopoint all 0.21-4 [510 kB] Get: 17 http://deb.debian.org/debian bullseye/main amd64 libdebhelper-perl all 13.3.4 [189 kB] Get: 18 http://deb.debian.org/debian bullseye/main amd64 libtool all 2.4.6-15 [513 kB] Get: 19 http://deb.debian.org/debian bullseye/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 20 http://deb.debian.org/debian bullseye/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 21 http://deb.debian.org/debian bullseye/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 22 http://deb.debian.org/debian bullseye/main amd64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 23 http://deb.debian.org/debian bullseye/main amd64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 24 http://deb.debian.org/debian bullseye/main amd64 libelf1 amd64 0.183-1 [165 kB] Get: 25 http://deb.debian.org/debian bullseye/main amd64 dwz amd64 0.13+20210201-1 [175 kB] Get: 26 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get: 27 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get: 28 http://deb.debian.org/debian bullseye/main amd64 gettext amd64 0.21-4 [1311 kB] Get: 29 http://deb.debian.org/debian bullseye/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 30 http://deb.debian.org/debian bullseye/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 31 http://deb.debian.org/debian bullseye/main amd64 debhelper all 13.3.4 [1049 kB] Fetched 18.3 MB in 3s (5241 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19707 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-8+deb11u1_amd64.deb ... Unpacking bsdextrautils (2.36.1-8+deb11u1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../01-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_amd64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../03-libpipeline1_1.5.3-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_amd64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../05-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../06-libmagic-mgc_1%3a5.39-3_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../07-libmagic1_1%3a5.39-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../08-file_1%3a5.39-3_amd64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../09-gettext-base_0.21-4_amd64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../10-libsigsegv2_2.13-1_amd64.deb ... Unpacking libsigsegv2:amd64 (2.13-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.18-5_amd64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../14-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../15-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../16-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../17-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../18-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../19-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../20-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../21-libfile-stripnondeterminism-perl_1.12.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.12.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../22-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../23-libelf1_0.183-1_amd64.deb ... Unpacking libelf1:amd64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../24-dwz_0.13+20210201-1_amd64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../25-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../26-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package gettext. Preparing to unpack .../27-gettext_0.21-4_amd64.deb ... Unpacking gettext (0.21-4) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../28-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../29-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../30-debhelper_13.3.4_all.deb ... Unpacking debhelper (13.3.4) ... Setting up libpipeline1:amd64 (1.5.3-1) ... Setting up bsdextrautils (2.36.1-8+deb11u1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libmagic1:amd64 (1:5.39-3) ... Setting up gettext-base (0.21-4) ... Setting up file (1:5.39-3) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libsigsegv2:amd64 (2.13-1) ... Setting up autopoint (0.21-4) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libelf1:amd64 (0.183-1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libfile-stripnondeterminism-perl (1.12.0-1) ... Setting up gettext (0.21-4) ... Setting up libtool (2.4.6-15) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.12.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up dh-autoreconf (20) ... Setting up debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/3463282/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for bullseye I: user script /srv/workspace/pbuilder/3463282/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/mafft-7.475/ && 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_7.475-1_source.changes dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.475-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core cd core && make -j15 clean make[1]: Entering directory '/build/mafft-7.475/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-7.475/core' dh_autoreconf_clean -O--sourcedirectory=core debian/rules override_dh_clean make[1]: Entering directory '/build/mafft-7.475' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory '/build/mafft-7.475' debian/rules binary dh binary --sourcedirectory=core dh_update_autotools_config -O--sourcedirectory=core dh_autoreconf -O--sourcedirectory=core dh_auto_configure -O--sourcedirectory=core debian/rules override_dh_auto_build make[1]: Entering directory '/build/mafft-7.475' dh_auto_build -- \ PREFIX=/usr/lib/mafft \ ENABLE_MULTITHREAD=-Denablemultithread \ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -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-7.475/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c rna.c: In function 'rnaalifoldcall': rna.c:225:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 225 | system( cmd ); | ^~~~~~~~~~~~~ rna.c:245:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 245 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 285 | system( cmd ); | ^~~~~~~~~~~~~ In file included from constants.c:7: blosum.c: In function 'overridematrix': blosum.c:370:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 370 | fgets( buf, 499, fp ); | ^~~~~~~~~~~~~~~~~~~~~ io.c: In function 'PreRead': io.c:1096:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1096 | fgets( b, B-1, fp ); *locnjob = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c:1101:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1101 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1105:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1105 | fgets( b, B-1, fp ); nleni = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'FRead': io.c:1141:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1141 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1231:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1231 | fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_part_pointer': io.c:2666:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2666 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2668:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2668 | fgets( b, B, fp ); nseq0 = atoi( b ); // 2020/Oct/23 | ^~~~~~~~~~~~~~~~~ io.c:2674:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2674 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf_pointer': io.c:2704:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2704 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2705:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2705 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) | ^~~~~~~~~~~~~~~~~ io.c:2710:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2710 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_doublehalf': io.c:2738:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2738 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2739:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2739 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2740:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2740 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_double': io.c:2768:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2768 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2769:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2769 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2770:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2770 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_int': io.c:2798:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2798 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2799:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2799 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2800:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2800 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2_pointer': io.c:2829:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2829 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2830:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2830 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2831:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2831 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'readhat2': io.c:2859:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2859 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2860:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2860 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2861:5: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2861 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta_sub': io.c:3061:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3061 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3076:13: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3076 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadSsearch': io.c:3095:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3095 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_avscore': io.c:3223:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3223 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3230:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3230 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3231:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3231 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadBlastm7_scoreonly': io.c:3346:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3346 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3353:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3353 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3354:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3354 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'check_guidetreefile': io.c: In function 'ReadBlastm7': io.c:3464:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3464 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3471:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3471 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3472:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3472 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ mltaln9.c:2850:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 2850 | fgets( string, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34noalign': io.c:3496:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3496 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_nuc': io.c:3533:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3533 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3559:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3559 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10': io.c:3672:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3672 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3696:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3696 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nucbk': io.c:3799:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3799 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly_nuc': io.c:3849:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3849 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34m10_scoreonly': io.c:3910:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3910 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta34': io.c:3966:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3966 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3992:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3992 | fgets( b, B-1, fp ); // initn: | ^~~~~~~~~~~~~~~~~~~ io.c:3995:10: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 3995 | fgets( b, B-1, fp ); // Smith-Waterman score | ^~~~~~~~~~~~~~~~~~~ io.c:4007:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4007 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta3': io.c:4029:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4029 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadFasta': io.c:4054:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4054 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt': io.c:4091:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4091 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'ReadOpt2': io.c:4112:9: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4112 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'readOtherOptions': io.c:4208:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 4208 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function 'loadaamtx': io.c:5466:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5466 | fgets( inorder, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5498:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5498 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5521:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5521 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readsubalignmentstable': io.c:5677:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5677 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5698:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5698 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readmccaskill': io.c:5752:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5752 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5762:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5762 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readpairfoldalign': io.c:5821:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5821 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5834:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5834 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5841:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5841 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5855:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5855 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5861:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 5861 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function 'readexternalanchors': io.c:6299:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 6299 | fgets( buf, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function 'readlocalhomtable2_single_bin_noseek': mltaln9.c:15182:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15182 | fread( &size, sizeof( int ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15183:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15183 | fread( &opt, sizeof( double ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15186:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15186 | fread( m, size*sizeof( int ), 3, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15222:2: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 15222 | fread( &c, sizeof( char ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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] 1020 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o defs.c:173:12: warning: 'nadd' initialized and declared 'extern' 173 | extern int nadd = 0; // <- static in tbfast.c, pairlocalalign.c | ^~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndblast.c dndfast7.c: In function 'main': dndfast7.c:326:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 326 | system( com ); | ^~~~~~~~~~~~~ dndblast.c: In function 'main': dndblast.c:201:4: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 201 | system( com ); | ^~~~~~~~~~~~~ dndblast.c:382:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 382 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c pairlocalalign.c: In function 'calllast_once': pairlocalalign.c:1055:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1055 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1091:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1091 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx': pairlocalalign.c:607:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 607 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calllast_fast': pairlocalalign.c:980:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 980 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'lastcallthread': pairlocalalign.c:871:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 871 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readlastresx_singleq': pairlocalalign.c:373:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 373 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'readhat4': pairlocalalign.c:1531:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1531 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1543:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1543 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'recalllara': pairlocalalign.c:1244:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1244 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'callmxscarna_giving_bpp': pairlocalalign.c:1407:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1407 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1409:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1409 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1429:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1429 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1450:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1450 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1464:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1464 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1484:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1484 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1486:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1486 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'calldafs_giving_bpp': pairlocalalign.c:1290:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1290 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1292:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1292 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1312:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1312 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1333:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1333 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1343:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 1343 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1363:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1363 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1365:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1365 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1367:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 1367 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function 'pairalign_node': pairlocalalign.c:3445:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3445 | system( "rm -rf hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3446:2: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3446 | system( "mkdir hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3451:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3451 | system( fn ); | ^~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -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/stdio.h:867, from mltaln.h:12, from mltaln9.c:1: In function 'fgets', inlined from 'check_guidetreefile' at mltaln9.c:2850:2: /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 [-Wattribute-warning] 263 | return __fgets_chk_warn (__s, __bos (__s), __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'prepareash': pairash.c:639:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 639 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:3: 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:485:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 485 | system( com ); | ^~~~~~~~~~~~~ pairash.c: In function 'readrash': pairash.c:277:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 277 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 284 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 289 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:4: 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:530:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 530 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 576 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:4: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 587 | system( command ); | ^~~~~~~~~~~~~~~~~ pairash.c: In function 'checkcbeta': pairash.c:321:3: 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:347:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 347 | system( com ); | ^~~~~~~~~~~~~ pairash.c:356:4: 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:228:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 228 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 232 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 235 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 238 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ maffttext2hex.c: In function 'main': maffttext2hex.c:55:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 55 | fgets( (char *)buf, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function 'callrash.constprop': pairash.c:428:29: 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 ); | ^ In file included from /usr/include/stdio.h:867, from mltaln.h:12, from pairash.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 8 or more bytes (assuming 10007) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:484:22: warning: '%s' directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=] 484 | sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); | ^~ ~~~~~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:12, from pairash.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 16 and 11014 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c pairash.c: In function 'calltmalign.constprop': pairash.c:346:27: warning: '%s' directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] 346 | sprintf( com, "mkdir -p %s", cachedir ); | ^~ ~~~~~~~~ In file included from /usr/include/stdio.h:867, from mltaln.h:12, from pairash.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 10 and 10009 bytes into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:349:31: warning: '-' directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 349 | sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); | ^ In file included from /usr/include/stdio.h:867, from mltaln.h:12, from pairash.c:1: /usr/include/x86_64-linux-gnu/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output 3 or more bytes (assuming 10002) into a destination of size 10000 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c splittbfast.c: In function 'main': splittbfast.c:3218:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3218 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c tbfast.c: In function 'main': tbfast.c:3194:5: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 3194 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ disttbfast.c: In function 'disttbfast': disttbfast.c:4578:6: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 4578 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c f2cl.c: In function 'main': f2cl.c:287:4: 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 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c mccaskillwrap.c: In function 'main': mccaskillwrap.c:372:4: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 372 | system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function 'athread': mccaskillwrap.c:115:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 115 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:117:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 117 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:129:3: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 129 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ mccaskillwrap.c:155:4: warning: ignoring return value of 'system' declared with attribute 'warn_unused_result' [-Wunused-result] 155 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c: In function 'readrawmccaskill': mccaskillwrap.c:46:3: 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 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c contrafoldwrap.c: In function 'readcontrafold': contrafoldwrap.c:57:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 57 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c: In function 'readereg': regtable2seq.c:69:2: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 69 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 97 | 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] 120 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c gcc -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c gcc -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -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:177:4: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 177 | fgets( gett, 999, dlfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb setdirection.c: In function 'main': setdirection.c:132:3: warning: ignoring return value of 'fgets' declared with attribute 'warn_unused_result' [-Wunused-result] 132 | fgets( line, 99, difp ); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -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 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -fdebug-prefix-map=/build/mafft-7.475=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp 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 ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. make[2]: Leaving directory '/build/mafft-7.475/core' make[1]: Leaving directory '/build/mafft-7.475' dh_auto_test -O--sourcedirectory=core create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=core dh_prep -O--sourcedirectory=core debian/rules override_dh_auto_install make[1]: Entering directory '/build/mafft-7.475' 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-7.475/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-7.475/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp 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 ../binaries chmod 755 ../binaries/* cp mafft.1 mafft-homologs.1 ../binaries done. mkdir -p /build/mafft-7.475/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /build/mafft-7.475/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /build/mafft-7.475/debian/mafft/usr/lib/mafft/bin chmod 755 /build/mafft-7.475/debian/mafft/usr/lib/mafft/bin chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb install --strip-program=true mafft mafft-homologs.rb mafft-sparsecore.rb /build/mafft-7.475/debian/mafft/usr/lib/mafft/bin install: WARNING: ignoring --strip-program option as -s option was not specified chmod 755 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 ||: # in MinGW, it's ok if this fails strip 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 ||: # may fail for dash_client on mac. install --strip-program=true 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 /build/mafft-7.475/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /build/mafft-7.475/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/mafft-7.475/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified ( cd /build/mafft-7.475/debian/mafft/usr/lib/mafft/bin; \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-distance . ) mkdir -p /build/mafft-7.475/debian/mafft/usr/share/man/man1 chmod 755 /build/mafft-7.475/debian/mafft/usr/share/man/man1 install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/mafft-7.475/debian/mafft/usr/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/mafft-7.475/core' rm debian/mafft/usr/lib/mafft/lib/mafft/*.1 make[1]: Leaving directory '/build/mafft-7.475' dh_installdocs -O--sourcedirectory=core dh_installchangelogs -O--sourcedirectory=core dh_installman -O--sourcedirectory=core dh_installsystemduser -O--sourcedirectory=core dh_perl -O--sourcedirectory=core dh_link -O--sourcedirectory=core dh_strip_nondeterminism -O--sourcedirectory=core debian/rules override_dh_compress make[1]: Entering directory '/build/mafft-7.475' dh_compress -X test/sample make[1]: Leaving directory '/build/mafft-7.475' dh_fixperms -O--sourcedirectory=core dh_missing -O--sourcedirectory=core dh_dwz -a -O--sourcedirectory=core dwz: debian/mafft/usr/lib/mafft/lib/mafft/addsingle: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/contrafoldwrap: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/countlen: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/disttbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndblast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndfast7: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndpre: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dvtditr: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/f2cl: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/filter: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/getlag: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/hex2maffttext: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/maffttext2hex: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/makedirectionlist: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mccaskillwrap: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/multi2hat3s: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/nodepair: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairash: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairlocalalign: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/regtable2seq: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/replaceu: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/restoreu: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/score: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/seq2regtable: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/setcore: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/setdirection: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/sextet5: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/splittbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/tbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/version: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a -O--sourcedirectory=core dh_makeshlibs -a -O--sourcedirectory=core dh_shlibdeps -a -O--sourcedirectory=core dh_installdeb -O--sourcedirectory=core dh_gencontrol -O--sourcedirectory=core dh_md5sums -O--sourcedirectory=core dh_builddeb -O--sourcedirectory=core dpkg-deb: building package 'mafft' in '../mafft_7.475-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../mafft_7.475-1_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) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/3463282/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/3463282/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/3463282 and its subdirectories I: Current time: Wed Aug 2 05:16:25 +14 2023 I: pbuilder-time-stamp: 1690902985