I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 27 00:44:01 +14 2022 I: pbuilder-time-stamp: 1664189041 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration 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 [fsa_1.15.9+dfsg-6.dsc] I: copying [./fsa_1.15.9+dfsg.orig.tar.xz] I: copying [./fsa_1.15.9+dfsg-6.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.qk8qdXRV/trustedkeys.kbx': General error gpgv: Signature made Mon Nov 16 07:07:02 2020 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./fsa_1.15.9+dfsg-6.dsc dpkg-source: info: extracting fsa in fsa-1.15.9+dfsg dpkg-source: info: unpacking fsa_1.15.9+dfsg.orig.tar.xz dpkg-source: info: unpacking fsa_1.15.9+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no-display.patch dpkg-source: info: applying removed-pdf-only-docs.patch dpkg-source: info: applying privacy_breach_logo.patch dpkg-source: info: applying fixed-check-for-m64-flag.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/16180/tmp/hooks/D01_modify_environment starting debug: Running on codethink13-arm64. 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/16180/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/16180/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]="aarch64-unknown-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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=16180 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/tmp.6a6WzL84MP/pbuilderrc_5C38 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.6a6WzL84MP/b2 --logfile b2/build.log fsa_1.15.9+dfsg-6.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Aug 5 2021 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 Jul 29 2021 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 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Jul 29 2021 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Jul 29 2021 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Jul 29 2021 more -rwsr-xr-x 1 root root 51360 Jul 29 2021 mount -rwxr-xr-x 1 root root 14496 Jul 29 2021 mountpoint -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Sep 27 00:44 sh -> bash lrwxrwxrwx 1 root root 4 Sep 24 05:47 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Jul 29 2021 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server -rwsr-xr-x 1 root root 30880 Jul 29 2021 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 Jul 29 2021 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew I: user script /srv/workspace/pbuilder/16180/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: arm64 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), mummer, exonerate, help2man dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on exonerate; however: Package exonerate is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man 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} exonerate{a} file{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu67{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libreadline8{a} libsigsegv2{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mummer{a} po-debconf{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 22.3 MB of archives. After unpacking 86.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-8 [142 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 gawk arm64 1:5.1.0-1 [570 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.12.0-1 [15.4 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 32 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 libglib2.0-0 arm64 2.66.8-1 [1286 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 exonerate arm64 2.4.0-5 [1439 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 mummer arm64 3.23+dfsg-7 [640 kB] Fetched 22.3 MB in 0s (49.1 MB/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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-8_arm64.deb ... Unpacking bsdextrautils (2.36.1-8) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../6-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../7-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Setting up readline-common (8.1-1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package gawk. (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 ... 20252 files and directories currently installed.) Preparing to unpack .../00-gawk_1%3a5.1.0-1_arm64.deb ... Unpacking gawk (1:5.1.0-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../01-liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.39-3_arm64.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../04-libmagic1_1%3a5.39-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.39-3_arm64.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.21-4_arm64.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package m4. Preparing to unpack .../07-m4_1.4.18-5_arm64.deb ... Unpacking m4 (1.4.18-5) ... Selecting previously unselected package autoconf. Preparing to unpack .../08-autoconf_2.69-14_all.deb ... Unpacking autoconf (2.69-14) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../09-autotools-dev_20180224.1+nmu1_all.deb ... Unpacking autotools-dev (20180224.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../10-automake_1%3a1.16.3-2_all.deb ... Unpacking automake (1:1.16.3-2) ... Selecting previously unselected package autopoint. Preparing to unpack .../11-autopoint_0.21-4_all.deb ... Unpacking autopoint (0.21-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../12-libdebhelper-perl_13.3.4_all.deb ... Unpacking libdebhelper-perl (13.3.4) ... Selecting previously unselected package libtool. Preparing to unpack .../13-libtool_2.4.6-15_all.deb ... Unpacking libtool (2.4.6-15) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../14-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../15-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 .../16-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 .../17-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 .../18-dh-strip-nondeterminism_1.12.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.12.0-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../19-libelf1_0.183-1_arm64.deb ... Unpacking libelf1:arm64 (0.183-1) ... Selecting previously unselected package dwz. Preparing to unpack .../20-dwz_0.13+20210201-1_arm64.deb ... Unpacking dwz (0.13+20210201-1) ... Selecting previously unselected package libicu67:arm64. 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Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... 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 debhelper (13.3.4) ... Processing triggers for libc-bin (2.31-13) ... 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 hostname: Temporary failure in name resolution I: Running cd /build/fsa-1.15.9+dfsg/ && 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 > ../fsa_1.15.9+dfsg-6_source.changes dpkg-buildpackage: info: source package fsa dpkg-buildpackage: info: source version 1.15.9+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean # found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate debian/rules binary dh binary dh_update_autotools_config dh_autoreconf aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether UID '2222' is supported by ustar format... yes checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ar... ar checking the archiver (ar) interface... ar checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking for gawk... (cached) gawk checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking how to run the C++ preprocessor... g++ -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for unsigned long long int... yes checking for uintmax_t... yes checking for ptrdiff_t... yes checking tr1/unordered_map usability... yes checking tr1/unordered_map presence... yes checking for tr1/unordered_map... yes checking tr1/unordered_set usability... yes checking tr1/unordered_set presence... yes checking for tr1/unordered_set... yes checking vfork.h usability... no checking vfork.h presence... no checking for vfork.h... no checking for fork... yes checking for vfork... yes checking for working fork... yes checking for working vfork... (cached) yes checking for floor... yes checking for memmove... yes checking for pow... yes checking for regcomp... yes checking for sqrt... yes checking for strchr... yes checking for strcspn... yes checking for strspn... yes checking for strstr... yes checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking if gcc accepts -m64... no checking for mummer... /usr/bin/mummer checking for exonerate... /usr/bin/exonerate checking for struct sysinfo.totalram... yes checking for struct sysinfo.mem_unit... yes checking whether sysctl is declared... yes checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking for javac... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/main/Makefile config.status: creating src/manager/Makefile config.status: creating src/fsa/Makefile config.status: creating src/annealing/Makefile config.status: creating src/math/Makefile config.status: creating src/util/Makefile config.status: creating src/seq/Makefile config.status: creating perl/Makefile config.status: creating examples/Makefile config.status: creating html/Makefile config.status: creating tests/Makefile config.status: creating config.h config.status: executing depfiles commands -- FSA 1.15.9 Configuration Results -- C++ compiler: g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG GCC version: gcc (Debian 10.2.1-6) 10.2.1 20210110 Host System type: aarch64-unknown-linux-gnu Install prefix: /usr See config.h for further configuration information. Email with questions and bug reports. dh_auto_build make -j8 make[1]: Entering directory '/build/fsa-1.15.9+dfsg' make all-recursive make[2]: Entering directory '/build/fsa-1.15.9+dfsg' Making all in src/util make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/util' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dexception.o dexception.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o logfile.o logfile.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o memcheck.o memcheck.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o misc.o misc.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o opts_list.o opts_list.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o regexp.o regexp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sstring.o sstring.cc opts_list.cc:99:25: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 99 | SET_VERSION_INFO(*this); | ^ In file included from opts_list.cc:2: ../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; | ^~~~~~~~ opts_list.cc:99:3: note: in expansion of macro 'SET_VERSION_INFO' 99 | SET_VERSION_INFO(*this); | ^~~~~~~~~~~~~~~~ rm -f libutil.a ar cru libutil.a dexception.o logfile.o memcheck.o misc.o opts_list.o regexp.o sstring.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libutil.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/util' Making all in src/math make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/math' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mathematics.o mathematics.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mst.o mst.cc rm -f libmath.a ar cru libmath.a mathematics.o mst.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmath.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/math' Making all in src/seq make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/seq' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alphabet.o alphabet.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alignment.o alignment.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o gff.o gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mercator.o mercator.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence.o sequence.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o similarity_matrix.o similarity_matrix.cc rm -f libseq.a ar cru libseq.a alphabet.o alignment.o gff.o mercator.o sequence.o similarity_matrix.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libseq.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/seq' Making all in src/manager make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/manager' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o manager.o manager.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o mw_adapter.o mw_adapter.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_adapter.o db_adapter.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o db_misc.o db_misc.cc In file included from ../../src/manager/manager.h:12, from manager.cc:6: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71, from db_misc.cc:7: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ rm -f libmanager.a ar cru libmanager.a manager.o mw_adapter.o db_adapter.o db_misc.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libmanager.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/manager' Making all in src/fsa make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/fsa' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o algebras.o algebras.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o aminoacid_indel2dp.o aminoacid_indel2dp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o aminoaciddp.o aminoaciddp.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o anchors.o anchors.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o constraints.o constraints.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o fsa.o fsa.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o model.o model.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotide_indel2dp.o nucleotide_indel2dp.cc fsa.cc:25:125: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); | ^ In file included from ../../src/fsa/fsa.h:66, from fsa.cc:11: ../../src/util/opts_list.h:146:153: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 146 | #define SET_VERSION_INFO(OPTS) (OPTS).version_info.clear(); (OPTS).version_info << PACKAGE_STRING << " (" << DART_DEBUG_MODE_STRING << ") compiled " << __DATE__ << " " << __TIME__ << "\n"; | ^~~~~~~~ ../../src/util/opts_list.h:152:153: note: in expansion of macro 'SET_VERSION_INFO' 152 | #define INIT_CONSTRUCTED_OPTS_LIST(OPTS,ARGS,SYNTAX,SHORTDESC) OPTS.short_description = (SHORTDESC); OPTS.syntax = (SYNTAX); OPTS.expect_args = (ARGS); SET_VERSION_INFO(OPTS); Log_stream::add_opts(OPTS); | ^~~~~~~~~~~~~~~~ fsa.cc:25:3: note: in expansion of macro 'INIT_CONSTRUCTED_OPTS_LIST' 25 | INIT_CONSTRUCTED_OPTS_LIST (opts, -1, "[options] ", "Distance-based alignment of DNA, RNA and proteins."); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra Forward(NucleotideIndel2AlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotide_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra Backward(NucleotideIndel2AlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotide_indel2dp.cc:1256:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1256 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra ForwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotide_indel2dp.cc:1472:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1472 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotide_indel2dp.cc: In function 'Algebra BackwardBanding(NucleotideIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotide_indel2dp.cc:2029:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2029 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nucleotidedp.o nucleotidedp.cc aminoaciddp.cc: In function 'Algebra Forward(AminoAcidAlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra Backward(AminoAcidAlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoaciddp.cc:1230:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1230 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra ForwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:1448:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1448 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoaciddp.cc: In function 'Algebra BackwardBanding(AminoAcidAlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoaciddp.cc:1979:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1979 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra Forward(AminoAcidIndel2AlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra Backward(AminoAcidIndel2AlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': aminoacid_indel2dp.cc:1320:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1320 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra ForwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:1568:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1568 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ aminoacid_indel2dp.cc: In function 'Algebra BackwardBanding(AminoAcidIndel2AlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': aminoacid_indel2dp.cc:2189:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 2189 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ In file included from ../../src/fsa/anchors.h:17, from anchors.cc:16: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71, from fsa.cc:11: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/fsa/model.h:32, from model.cc:8: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ nucleotidedp.cc: In function 'Algebra Forward(NucleotideAlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotidedp.cc:768:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 768 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra Backward(NucleotideAlignDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&)': nucleotidedp.cc:1166:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1166 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra ForwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1352:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1352 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ nucleotidedp.cc: In function 'Algebra BackwardBanding(NucleotideAlignWithBandingDPTable**, const string&, const string&, const std::vector&, const std::vector >&, const std::vector >&, int)': nucleotidedp.cc:1819:9: warning: variable 'iPrevSlowCoord' set but not used [-Wunused-but-set-variable] 1819 | int iPrevSlowCoord; | ^~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wno-deprecated -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o sequence_pair_selector.o sequence_pair_selector.cc anchors.cc: In member function 'fsa::Anchors fsa::Exonerate_adapter::call_exonerate(const string&, const string&, int) const': anchors.cc:863:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 863 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store exonerate results | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc:864:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 864 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc: In member function 'fsa::Anchors fsa::Mummer_adapter::call_mummer(const string&, const string&, size_t) const': anchors.cc:1100:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1100 | freopen (output_file.c_str(), "w", stdout); // capture stdout (send to file output_file) to store mummer results | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ anchors.cc:1101:13: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1101 | freopen ("/dev/null", "a", stderr); // capture stderr (send to trash) so that it doesn't mess up our logging | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ rm -f libfsa.a ar cru libfsa.a algebras.o aminoacid_indel2dp.o aminoaciddp.o anchors.o constraints.o fsa.o model.o nucleotide_indel2dp.o nucleotidedp.o sequence_pair_selector.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libfsa.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/fsa' Making all in src/annealing make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/annealing' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o alignment_DAG.o alignment_DAG.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dotplot.o dotplot.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o tree_weights.o tree_weights.cc In file included from ../../src/annealing/alignment_DAG.h:58, from alignment_DAG.cc:12: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ rm -f libannealing.a ar cru libannealing.a alignment_DAG.o dotplot.o tree_weights.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libannealing.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/annealing' Making all in src/main make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/main' g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o main.o main.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o gapcleaner.o gapcleaner.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o isect_mercator_alignment_gff.o isect_mercator_alignment_gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_coords.o map_coords.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o map_gff_coords.o map_gff_coords.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o percentid.o percentid.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o prot2codon.o prot2codon.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta.o slice_fasta.cc In file included from /usr/include/c++/10/ext/hash_map:60, from ../../src/fsa/dptables.h:43, from ../../src/fsa/mybanding.h:25, from ../../src/fsa/model.h:24, from ../../src/fsa/anchors.h:20, from ../../src/fsa/fsa.h:71, from main.cc:8: /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ In file included from ../../src/fsa/anchors.h:17, from ../../src/fsa/fsa.h:71, from main.cc:8: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ In file included from ../../src/annealing/alignment_DAG.h:58, from gapcleaner.cc:11: ../../src/annealing/SparseMatrix.h: In constructor 'fsa::SparseMatrix::SparseMatrix(size_t, size_t, size_t, size_t, const Post_probs&)': ../../src/annealing/SparseMatrix.h:241:11: warning: variable 'yprev' set but not used [-Wunused-but-set-variable] 241 | int yprev = -1; // the previous y-coordinate | ^~~~~ g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_fasta_gff.o slice_fasta_gff.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o slice_mercator_alignment.o slice_mercator_alignment.cc g++ -DHAVE_CONFIG_H -I. -I../.. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o translate.o translate.cc g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_gff_coords map_gff_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o percentid percentid.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o prot2codon prot2codon.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta slice_fasta.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o isect_mercator_alignment_gff isect_mercator_alignment_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o map_coords map_coords.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o gapcleaner gapcleaner.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o fsa main.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o translate translate.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_fasta_gff slice_fasta_gff.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a g++ -Wall -Wno-tautological-compare -D_FILE_OFFSET_BITS=64 -O3 -ffast-math -g -O2 -fdebug-prefix-map=/build/fsa-1.15.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -Wl,-z,relro -Wl,-z,now -o slice_mercator_alignment slice_mercator_alignment.o ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/fsa/libfsa.a ../../src/annealing/libannealing.a ../../src/manager/libmanager.a ../../src/seq/libseq.a ../../src/util/libutil.a ../../src/math/libmath.a make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main' Making all in perl make[3]: Entering directory '/build/fsa-1.15.9+dfsg/perl' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/perl' Making all in examples make[3]: Entering directory '/build/fsa-1.15.9+dfsg/examples' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/examples' Making all in html make[3]: Entering directory '/build/fsa-1.15.9+dfsg/html' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/html' Making all in tests make[3]: Entering directory '/build/fsa-1.15.9+dfsg/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/tests' make[3]: Entering directory '/build/fsa-1.15.9+dfsg' make[3]: Leaving directory '/build/fsa-1.15.9+dfsg' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg' make[1]: Leaving directory '/build/fsa-1.15.9+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/fsa-1.15.9+dfsg' echo "Tests seem to miss some files:" Tests seem to miss some files: echo "make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop." make[4]: *** No rule to make target 'apps/isect_d.unmappable.bash', needed by 'apps/isect_d.unmappable.bash.log'. Stop. make[1]: Leaving directory '/build/fsa-1.15.9+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j8 install DESTDIR=/build/fsa-1.15.9\+dfsg/debian/fsa AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/fsa-1.15.9+dfsg' Making install in src/util make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/util' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/util' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/util' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/util' Making install in src/math make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/math' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/math' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/math' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/math' Making install in src/seq make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/seq' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/seq' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/seq' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/seq' Making install in src/manager make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/manager' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/manager' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/manager' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/manager' Making install in src/fsa make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/fsa' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/fsa' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/fsa' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/fsa' Making install in src/annealing make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/annealing' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/annealing' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/annealing' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/annealing' Making install in src/main make[2]: Entering directory '/build/fsa-1.15.9+dfsg/src/main' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/src/main' make[3]: Nothing to be done for 'install-data-am'. /bin/mkdir -p '/build/fsa-1.15.9+dfsg/debian/fsa/usr/bin' /usr/bin/install -c fsa gapcleaner isect_mercator_alignment_gff map_coords map_gff_coords percentid prot2codon slice_fasta slice_fasta_gff slice_mercator_alignment translate '/build/fsa-1.15.9+dfsg/debian/fsa/usr/bin' make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/src/main' Making install in perl make[2]: Entering directory '/build/fsa-1.15.9+dfsg/perl' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/perl' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/perl' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/perl' Making install in examples make[2]: Entering directory '/build/fsa-1.15.9+dfsg/examples' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/examples' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/examples' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/examples' Making install in html make[2]: Entering directory '/build/fsa-1.15.9+dfsg/html' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/html' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/html' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/html' Making install in tests make[2]: Entering directory '/build/fsa-1.15.9+dfsg/tests' make[3]: Entering directory '/build/fsa-1.15.9+dfsg/tests' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg/tests' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg/tests' make[2]: Entering directory '/build/fsa-1.15.9+dfsg' make[3]: Entering directory '/build/fsa-1.15.9+dfsg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/fsa-1.15.9+dfsg' make[2]: Leaving directory '/build/fsa-1.15.9+dfsg' make[1]: Leaving directory '/build/fsa-1.15.9+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/fsa-1.15.9+dfsg' dh_install mv /build/fsa-1.15.9+dfsg/debian/fsa/usr/bin/translate /build/fsa-1.15.9+dfsg/debian/fsa/usr/bin/fsa-translate make[1]: Leaving directory '/build/fsa-1.15.9+dfsg' dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'fsa-dbgsym' in '../fsa-dbgsym_1.15.9+dfsg-6_arm64.deb'. dpkg-deb: building package 'fsa' in '../fsa_1.15.9+dfsg-6_arm64.deb'. # found automatically: --with-mummer=/usr/bin/mummer --with-exonerate=/usr/bin/exonerate dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../fsa_1.15.9+dfsg-6_arm64.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: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/16180/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/16180/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/16180 and its subdirectories I: Current time: Tue Sep 27 00:50:35 +14 2022 I: pbuilder-time-stamp: 1664189435