I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 12 13:00:11 +14 2021 I: pbuilder-time-stamp: 1626044411 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: using eatmydata during job I: Copying source file I: copying [snp-sites_2.5.1-1.dsc] I: copying [./snp-sites_2.5.1.orig.tar.gz] I: copying [./snp-sites_2.5.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.4P8zzOfq/trustedkeys.kbx': General error gpgv: Signature made Thu Oct 24 07:01:37 2019 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./snp-sites_2.5.1-1.dsc dpkg-source: info: extracting snp-sites in snp-sites-2.5.1 dpkg-source: info: unpacking snp-sites_2.5.1.orig.tar.gz dpkg-source: info: unpacking snp-sites_2.5.1-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/28056/tmp/hooks/D01_modify_environment starting debug: Running on ionos12-i386. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash 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/28056/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/28056/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]="i686-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=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=c9a9a1d11b2a41fcb7dafe44fd831f7c LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=28056 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.5K8Ug7hoiS/pbuilderrc_Vgqx --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.5K8Ug7hoiS/b2 --logfile b2/build.log --extrapackages usrmerge snp-sites_2.5.1-1.dsc' SUDO_GID=112 SUDO_UID=107 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 4.19.0-17-686-pae #1 SMP Debian 4.19.194-2 (2021-06-21) i686 GNU/Linux I: ls -l /bin total 5788 -rwxr-xr-x 1 root root 1367848 Jun 22 16:25 bash -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 38280 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 38280 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 17768 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 38824 Sep 23 2020 cat -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash -rwxr-xr-x 1 root root 124904 Sep 23 2020 date -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd -rwxr-xr-x 1 root root 100752 Sep 23 2020 df -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir -rwxr-xr-x 1 root root 83644 Feb 8 04:38 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 34664 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 34664 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 71928 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 30112 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe -rwxr-xr-x 1 root root 100952 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln -rwxr-xr-x 1 root root 55572 Feb 8 2020 login -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls -rwxr-xr-x 1 root root 153124 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 58920 Feb 8 04:38 more -rwsr-xr-x 1 root root 50720 Feb 8 04:38 mount -rwxr-xr-x 1 root root 13856 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:25 rbash -> bash -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 12 13:03 sh -> bash lrwxrwxrwx 1 root root 4 Jul 9 22:43 sh.distrib -> dash -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty -rwsr-xr-x 1 root root 79396 Feb 8 04:38 su -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync -rwxr-xr-x 1 root root 602584 Feb 17 23:55 tar -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch -rwxr-xr-x 1 root root 34664 Sep 23 2020 true -rwxr-xr-x 1 root root 17768 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30236 Feb 8 04:38 umount -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir -rwxr-xr-x 1 root root 63024 Feb 8 04:38 wdctl lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew I: user script /srv/workspace/pbuilder/28056/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: i386 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 (>= 11), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19675 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 (>= 11); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} check{a} d-shlibs{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} libbsd0{a} libdebhelper-perl{a} libedit2{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu67{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libpipeline1{a} libruby2.7{a} libsigsegv2{a} libsub-override-perl{a} libsubunit-dev{a} libsubunit0{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} openssl{a} pkg-config{a} po-debconf{a} rake{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato libarchive-cpio-perl libglib2.0-data libjs-jquery libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 27.6 MB of archives. After unpacking 98.8 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main i386 bsdextrautils i386 2.36.1-7 [148 kB] Get: 2 http://deb.debian.org/debian bullseye/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main i386 groff-base i386 1.22.4-6 [952 kB] Get: 4 http://deb.debian.org/debian bullseye/main i386 libpipeline1 i386 1.5.3-1 [36.8 kB] Get: 5 http://deb.debian.org/debian bullseye/main i386 man-db i386 2.9.4-2 [1367 kB] Get: 6 http://deb.debian.org/debian bullseye/main i386 sensible-utils all 0.0.14 [14.8 kB] Get: 7 http://deb.debian.org/debian bullseye/main i386 openssl i386 1.1.1k-1 [860 kB] Get: 8 http://deb.debian.org/debian bullseye/main i386 ca-certificates all 20210119 [158 kB] Get: 9 http://deb.debian.org/debian bullseye/main i386 libmagic-mgc i386 1:5.39-3 [273 kB] Get: 10 http://deb.debian.org/debian bullseye/main i386 libmagic1 i386 1:5.39-3 [133 kB] Get: 11 http://deb.debian.org/debian bullseye/main i386 file i386 1:5.39-3 [69.0 kB] Get: 12 http://deb.debian.org/debian bullseye/main i386 gettext-base i386 0.21-4 [176 kB] Get: 13 http://deb.debian.org/debian bullseye/main i386 rubygems-integration all 1.18 [6704 B] Get: 14 http://deb.debian.org/debian bullseye/main i386 rake all 13.0.3-1 [84.7 kB] Get: 15 http://deb.debian.org/debian bullseye/main i386 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 16 http://deb.debian.org/debian bullseye/main i386 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 17 http://deb.debian.org/debian bullseye/main i386 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 18 http://deb.debian.org/debian bullseye/main i386 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 19 http://deb.debian.org/debian bullseye/main i386 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 20 http://deb.debian.org/debian bullseye/main i386 libmd0 i386 1.0.3-3 [28.9 kB] Get: 21 http://deb.debian.org/debian bullseye/main i386 libbsd0 i386 0.11.3-1 [111 kB] Get: 22 http://deb.debian.org/debian bullseye/main i386 libedit2 i386 3.1-20191231-2+b1 [101 kB] Get: 23 http://deb.debian.org/debian bullseye/main i386 libyaml-0-2 i386 0.2.2-1 [51.7 kB] Get: 24 http://deb.debian.org/debian bullseye/main i386 libruby2.7 i386 2.7.3-2 [4305 kB] Get: 25 http://deb.debian.org/debian bullseye/main i386 ruby2.7 i386 2.7.3-2 [744 kB] Get: 26 http://deb.debian.org/debian bullseye/main i386 ruby-rubygems all 3.2.5-2 [281 kB] Get: 27 http://deb.debian.org/debian bullseye/main i386 ruby i386 1:2.7+2 [11.7 kB] Get: 28 http://deb.debian.org/debian bullseye/main i386 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 29 http://deb.debian.org/debian bullseye/main i386 asciidoctor all 2.0.12-2 [83.9 kB] Get: 30 http://deb.debian.org/debian bullseye/main i386 libsigsegv2 i386 2.13-1 [35.1 kB] Get: 31 http://deb.debian.org/debian bullseye/main i386 m4 i386 1.4.18-5 [206 kB] Get: 32 http://deb.debian.org/debian bullseye/main i386 autoconf all 2.69-14 [313 kB] Get: 33 http://deb.debian.org/debian bullseye/main i386 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 34 http://deb.debian.org/debian bullseye/main i386 automake all 1:1.16.3-2 [814 kB] Get: 35 http://deb.debian.org/debian bullseye/main i386 autopoint all 0.21-4 [510 kB] Get: 36 http://deb.debian.org/debian bullseye/main i386 libsubunit0 i386 1.4.0-3 [9884 B] Get: 37 http://deb.debian.org/debian bullseye/main i386 libsubunit-dev i386 1.4.0-3 [10.9 kB] Get: 38 http://deb.debian.org/debian bullseye/main i386 check i386 0.15.2-2 [118 kB] Get: 39 http://deb.debian.org/debian bullseye/main i386 d-shlibs all 0.98 [17.9 kB] Get: 40 http://deb.debian.org/debian bullseye/main i386 libdebhelper-perl all 13.3.4 [189 kB] Get: 41 http://deb.debian.org/debian bullseye/main i386 libtool all 2.4.6-15 [513 kB] Get: 42 http://deb.debian.org/debian bullseye/main i386 dh-autoreconf all 20 [17.1 kB] Get: 43 http://deb.debian.org/debian bullseye/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 44 http://deb.debian.org/debian bullseye/main i386 libsub-override-perl all 0.09-2 [10.2 kB] Get: 45 http://deb.debian.org/debian bullseye/main i386 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 46 http://deb.debian.org/debian bullseye/main i386 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 47 http://deb.debian.org/debian bullseye/main i386 libelf1 i386 0.183-1 [171 kB] Get: 48 http://deb.debian.org/debian bullseye/main i386 dwz i386 0.13+20210201-1 [179 kB] Get: 49 http://deb.debian.org/debian bullseye/main i386 libicu67 i386 67.1-7 [8775 kB] Get: 50 http://deb.debian.org/debian bullseye/main i386 libxml2 i386 2.9.10+dfsg-6.7 [728 kB] Get: 51 http://deb.debian.org/debian bullseye/main i386 gettext i386 0.21-4 [1322 kB] Get: 52 http://deb.debian.org/debian bullseye/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 53 http://deb.debian.org/debian bullseye/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian bullseye/main i386 debhelper all 13.3.4 [1049 kB] Get: 55 http://deb.debian.org/debian bullseye/main i386 libglib2.0-0 i386 2.66.8-1 [1437 kB] Get: 56 http://deb.debian.org/debian bullseye/main i386 pkg-config i386 0.29.2-1 [66.3 kB] Get: 57 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] Fetched 27.6 MB in 3s (9455 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 ... 19675 files and directories currently installed.) Preparing to unpack .../00-bsdextrautils_2.36.1-7_i386.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../01-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../02-groff-base_1.22.4-6_i386.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../03-libpipeline1_1.5.3-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../04-man-db_2.9.4-2_i386.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 openssl. Preparing to unpack .../06-openssl_1.1.1k-1_i386.deb ... Unpacking openssl (1.1.1k-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../07-ca-certificates_20210119_all.deb ... Unpacking ca-certificates (20210119) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../08-libmagic-mgc_1%3a5.39-3_i386.deb ... Unpacking libmagic-mgc (1:5.39-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../09-libmagic1_1%3a5.39-3_i386.deb ... Unpacking libmagic1:i386 (1:5.39-3) ... Selecting previously unselected package file. Preparing to unpack .../10-file_1%3a5.39-3_i386.deb ... Unpacking file (1:5.39-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../11-gettext-base_0.21-4_i386.deb ... Unpacking gettext-base (0.21-4) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../12-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../13-rake_13.0.3-1_all.deb ... Unpacking rake (13.0.3-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../14-ruby-minitest_5.13.0-1_all.deb ... Unpacking ruby-minitest (5.13.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../15-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../16-ruby-power-assert_1.1.7-2_all.deb ... Unpacking ruby-power-assert (1.1.7-2) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../17-ruby-test-unit_3.3.9-1_all.deb ... Unpacking ruby-test-unit (3.3.9-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../18-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libmd0:i386. Preparing to unpack .../19-libmd0_1.0.3-3_i386.deb ... Unpacking libmd0:i386 (1.0.3-3) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../20-libbsd0_0.11.3-1_i386.deb ... Unpacking libbsd0:i386 (0.11.3-1) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../21-libedit2_3.1-20191231-2+b1_i386.deb ... Unpacking libedit2:i386 (3.1-20191231-2+b1) ... Selecting previously unselected package libyaml-0-2:i386. 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Setting up libedit2:i386 (3.1-20191231-2+b1) ... Setting up libsubunit-dev:i386 (1.4.0-3) ... Setting up m4 (1.4.18-5) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up check:i386 (0.15.2-2) ... Setting up autoconf (2.69-14) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... 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 rubygems-integration (1.18) ... 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) ... Setting up rake (13.0.3-1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up libruby2.7:i386 (2.7.3-2) ... Setting up ruby2.7 (2.7.3-2) ... Setting up ruby (1:2.7+2) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up asciidoctor (2.0.12-2) ... Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). The following additional packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl The following NEW packages will be installed: libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 59.5 kB of archives. After this operation, 157 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (667 kB/s) Selecting previously unselected package libnumber-compare-perl. (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 ... 24133 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... Unpacking libnumber-compare-perl (0.03-1.1) ... Selecting previously unselected package libtext-glob-perl. Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... Unpacking libtext-glob-perl (0.11-1) ... Selecting previously unselected package libfile-find-rule-perl. Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... 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I: Building the package I: Running cd /build/snp-sites-2.5.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package snp-sites dpkg-buildpackage: info: source version 2.5.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with autoreconf dh_clean debian/rules build dh build --with autoreconf dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:14: installing './compile' configure.ac:7: installing './config.guess' configure.ac:7: installing './config.sub' configure.ac:2: installing './install-sh' configure.ac:2: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=i686-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/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-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... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for check >= 0.8.2... yes 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 how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/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 zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking getopt.h usability... yes checking getopt.h presence... yes checking for getopt.h... yes checking for floor in -lm... yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /usr/bin/dd checking how to truncate binary pipes... /usr/bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes 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 how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j10 make[1]: Entering directory '/build/snp-sites-2.5.1' make all-recursive make[2]: Entering directory '/build/snp-sites-2.5.1' Making all in src make[3]: Entering directory '/build/snp-sites-2.5.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include --std=c99 -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites-main.o `test -f 'main.c' || echo './'`main.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment-file.lo alignment-file.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylib-of-snp-sites.lo phylib-of-snp-sites.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp-sites.lo snp-sites.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fasta-of-snp-sites.lo fasta-of-snp-sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment-file.c -fPIC -DPIC -o .libs/alignment-file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta-of-snp-sites.c -fPIC -DPIC -o .libs/fasta-of-snp-sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp-sites.c -fPIC -DPIC -o .libs/snp-sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -fPIC -DPIC -o .libs/phylib-of-snp-sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta-of-snp-sites.c -o fasta-of-snp-sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c phylib-of-snp-sites.c -o phylib-of-snp-sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c snp-sites.c -o snp-sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment-file.c -o alignment-file.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 1:0 -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o libsnp-sites.la -rpath /usr/lib/i386-linux-gnu alignment-file.lo vcf.lo phylib-of-snp-sites.lo snp-sites.lo fasta-of-snp-sites.lo -lz -lm libtool: link: gcc -shared -fPIC -DPIC .libs/alignment-file.o .libs/vcf.o .libs/phylib-of-snp-sites.o .libs/snp-sites.o .libs/fasta-of-snp-sites.o -L/usr/lib -lz -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libsnp-sites.so.1 -o .libs/libsnp-sites.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libsnp-sites.so.1" && ln -s "libsnp-sites.so.1.0.0" "libsnp-sites.so.1") libtool: link: (cd ".libs" && rm -f "libsnp-sites.so" && ln -s "libsnp-sites.so.1.0.0" "libsnp-sites.so") libtool: link: ar cr .libs/libsnp-sites.a alignment-file.o vcf.o phylib-of-snp-sites.o snp-sites.o fasta-of-snp-sites.o libtool: link: ranlib .libs/libsnp-sites.a libtool: link: ( cd ".libs" && rm -f "libsnp-sites.la" && ln -s "../libsnp-sites.la" "libsnp-sites.la" ) /bin/sh ../libtool --tag=CC --mode=link gcc --std=c99 -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o snp-sites snp_sites-main.o libsnp-sites.la -lpthread -lz -lm libtool: link: gcc --std=c99 -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/snp-sites snp_sites-main.o -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lz -lm make[3]: Leaving directory '/build/snp-sites-2.5.1/src' make[3]: Entering directory '/build/snp-sites-2.5.1' make[3]: Leaving directory '/build/snp-sites-2.5.1' make[2]: Leaving directory '/build/snp-sites-2.5.1' make[1]: Leaving directory '/build/snp-sites-2.5.1' dh_auto_test make -j10 check VERBOSE=1 make[1]: Entering directory '/build/snp-sites-2.5.1' Making check in src make[2]: Entering directory '/build/snp-sites-2.5.1/src' make run-all-tests make[3]: Entering directory '/build/snp-sites-2.5.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-snp-sites.o `test -f '../tests/check-snp-sites.c' || echo './'`../tests/check-snp-sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check-vcf.o `test -f '../tests/check-vcf.c' || echo './'`../tests/check-vcf.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper-methods.o `test -f '../tests/helper-methods.c' || echo './'`../tests/helper-methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run-all-tests.o `test -f '../tests/run-all-tests.c' || echo './'`../tests/run-all-tests.c In file included from ../tests/check-snp-sites.c:23: ../tests/check-snp-sites.c: In function 'valid_alignment_with_one_line_per_sequence_fn': ../tests/check-snp-sites.c:40:147: warning: too many arguments for format [-Wformat-extra-args] 40 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:41:153: warning: too many arguments for format [-Wformat-extra-args] 41 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:42:167: warning: too many arguments for format [-Wformat-extra-args] 42 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_n_as_gap_fn': ../tests/check-snp-sites.c:53:118: warning: too many arguments for format [-Wformat-extra-args] 53 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.vcf", "alignment_file_with_n.aln.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:54:124: warning: too many arguments for format [-Wformat-extra-args] 54 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.phylip", "alignment_file_with_n.aln.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:55:138: warning: too many arguments for format [-Wformat-extra-args] 55 | fail_unless( compare_files("../tests/data/alignment_file_with_n.aln.snp_sites.aln","alignment_file_with_n.aln.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_one_line_per_sequence_gzipped_fn': ../tests/check-snp-sites.c:67:150: warning: too many arguments for format [-Wformat-extra-args] 67 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_one_line_per_sequence.aln.gz.vcf" ) == 1, "Invalid VCF file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:68:156: warning: too many arguments for format [-Wformat-extra-args] 68 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_one_line_per_sequence.aln.gz.phylip" ) == 1, "Invalid Phylip file for 1 line per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:69:170: warning: too many arguments for format [-Wformat-extra-args] 69 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.gz.snp_sites.aln" ) == 1 , "Invalid ALN file for 1 line per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_multiple_lines_per_sequence_fn': ../tests/check-snp-sites.c:79:155: warning: too many arguments for format [-Wformat-extra-args] 79 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "alignment_file_multiple_lines_per_sequence.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:80:161: warning: too many arguments for format [-Wformat-extra-args] 80 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "alignment_file_multiple_lines_per_sequence.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:81:174: warning: too many arguments for format [-Wformat-extra-args] 81 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_multiple_lines_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_pure_mode_fn': ../tests/check-snp-sites.c:91:115: warning: too many arguments for format [-Wformat-extra-args] 91 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.vcf", "pure_mode_alignment.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:92:121: warning: too many arguments for format [-Wformat-extra-args] 92 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.phylip", "pure_mode_alignment.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:93:134: warning: too many arguments for format [-Wformat-extra-args] 93 | fail_unless( compare_files("../tests/data/pure_mode_alignment.aln.snp_sites.aln","pure_mode_alignment.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_alignment_with_monomorphic_sites_fn': ../tests/check-snp-sites.c:103:139: warning: too many arguments for format [-Wformat-extra-args] 103 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.vcf", "pure_mode_monomorphic_alignment.aln.vcf" ) == 1, "Invalid VCF file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:104:145: warning: too many arguments for format [-Wformat-extra-args] 104 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.phylip", "pure_mode_monomorphic_alignment.aln.phylip" ) == 1, "Invalid Phylip file for multiple lines per seq" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:105:158: warning: too many arguments for format [-Wformat-extra-args] 105 | fail_unless( compare_files("../tests/data/pure_mode_monomorphic_alignment.aln.snp_sites.aln","pure_mode_monomorphic_alignment.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_default_fn': ../tests/check-snp-sites.c:116:169: warning: too many arguments for format [-Wformat-extra-args] 116 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_fn': ../tests/check-snp-sites.c:124:169: warning: too many arguments for format [-Wformat-extra-args] 124 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_only_aln_file_output_with_custom_name_fn': ../tests/check-snp-sites.c:133:131: warning: too many arguments for format [-Wformat-extra-args] 133 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name" ) == 1 ,"Only aln with custom name should be outputted"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_phylip_outputted_with_custom_name_fn': ../tests/check-snp-sites.c:141:122: warning: too many arguments for format [-Wformat-extra-args] 141 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name" ) == 1, "Custom name needs extra extension for phylip" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_with_all_outputted_with_custom_name_fn': ../tests/check-snp-sites.c:157:123: warning: too many arguments for format [-Wformat-extra-args] 157 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.vcf", "some_custom_name.vcf" ) == 1, "Custom name needs extra extension for VCF" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:158:129: warning: too many arguments for format [-Wformat-extra-args] 158 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.phylip", "some_custom_name.phylip" ) == 1, "Custom name needs extra extension for phylip" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c:159:143: warning: too many arguments for format [-Wformat-extra-args] 159 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence.aln.snp_sites.aln","some_custom_name.snp_sites.aln" ) == 1 , "Custom name needs extra extension for ALN"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_aln_plus_reference_fn': ../tests/check-snp-sites.c:170:175: warning: too many arguments for format [-Wformat-extra-args] 170 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence_reference.snp_sites.aln","alignment_file_one_line_per_sequence.aln.snp_sites.aln" ) == 1 ,"Invalid ALN file for multiple lines per seq"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check-snp-sites.c: In function 'valid_phylip_plus_reference_fn': ../tests/check-snp-sites.c:178:163: warning: too many arguments for format [-Wformat-extra-args] 178 | fail_unless( compare_files("../tests/data/alignment_file_one_line_per_sequence_reference.aln.phylip", "alignment_file_one_line_per_sequence.aln.phylip" ) == 1, "invalid phylib with reference" ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/sh ../libtool --tag=CC --mode=link gcc -pthread -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -L/usr/lib -L/usr/lib -o run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o libsnp-sites.la -lpthread -lcheck_pic -pthread -lrt -lm -lsubunit -lz -lm libtool: link: gcc -pthread -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/build/snp-sites-2.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run-all-tests ../tests/run_all_tests-check-snp-sites.o ../tests/run_all_tests-check-vcf.o ../tests/run_all_tests-helper-methods.o ../tests/run_all_tests-run-all-tests.o -pthread -L/usr/lib ./.libs/libsnp-sites.so -lpthread -lcheck_pic -lrt -lsubunit -lz -lm -pthread make[3]: Leaving directory '/build/snp-sites-2.5.1/src' make check-TESTS make[3]: Entering directory '/build/snp-sites-2.5.1/src' make[4]: Entering directory '/build/snp-sites-2.5.1/src' PASS: run-all-tests ============================================================================ Testsuite summary for snp-sites 2.5.1 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/snp-sites-2.5.1/src' make[3]: Leaving directory '/build/snp-sites-2.5.1/src' make[2]: Leaving directory '/build/snp-sites-2.5.1/src' make[2]: Entering directory '/build/snp-sites-2.5.1' make[2]: Leaving directory '/build/snp-sites-2.5.1' make[1]: Leaving directory '/build/snp-sites-2.5.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with autoreconf dh_testroot dh_prep dh_auto_install make -j1 install DESTDIR=/build/snp-sites-2.5.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/snp-sites-2.5.1' Making install in src make[2]: Entering directory '/build/snp-sites-2.5.1/src' make[3]: Entering directory '/build/snp-sites-2.5.1/src' /usr/bin/mkdir -p '/build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu' /bin/sh ../libtool --mode=install /usr/bin/install -c libsnp-sites.la '/build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsnp-sites.so.1.0.0 /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.so.1.0.0 libtool: install: (cd /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so.1 || { rm -f libsnp-sites.so.1 && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so.1; }; }) libtool: install: (cd /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu && { ln -s -f libsnp-sites.so.1.0.0 libsnp-sites.so || { rm -f libsnp-sites.so && ln -s libsnp-sites.so.1.0.0 libsnp-sites.so; }; }) libtool: install: /usr/bin/install -c .libs/libsnp-sites.lai /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.la libtool: install: /usr/bin/install -c .libs/libsnp-sites.a /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a libtool: install: chmod 644 /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a libtool: install: ranlib /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /usr/bin/mkdir -p '/build/snp-sites-2.5.1/debian/tmp/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/install -c snp-sites '/build/snp-sites-2.5.1/debian/tmp/usr/bin' libtool: warning: 'libsnp-sites.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/snp-sites /build/snp-sites-2.5.1/debian/tmp/usr/bin/snp-sites /usr/bin/mkdir -p '/build/snp-sites-2.5.1/debian/tmp/usr/include/snp-sites' /usr/bin/install -c -m 644 alignment-file.h vcf.h phylib-of-snp-sites.h snp-sites.h fasta-of-snp-sites.h kseq.h '/build/snp-sites-2.5.1/debian/tmp/usr/include/snp-sites' make[3]: Leaving directory '/build/snp-sites-2.5.1/src' make[2]: Leaving directory '/build/snp-sites-2.5.1/src' make[2]: Entering directory '/build/snp-sites-2.5.1' make[3]: Entering directory '/build/snp-sites-2.5.1' 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/snp-sites-2.5.1' make[2]: Leaving directory '/build/snp-sites-2.5.1' make[1]: Leaving directory '/build/snp-sites-2.5.1' debian/rules override_dh_install make[1]: Entering directory '/build/snp-sites-2.5.1' dh_install d-shlibmove --commit \ --multiarch \ --exclude-la \ --movedev "debian/tmp/usr/include/snp-sites/*.h" usr/include/snp-sites \ debian/tmp/usr/lib/*/libsnp-sites.so Library package automatic movement utility --> zlib1g-dev package exists. set -e install -d -m 755 debian/libsnp-sites1-dev/usr/lib/i386-linux-gnu install -d -m 755 debian/libsnp-sites1/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a debian/libsnp-sites1-dev/usr/lib/i386-linux-gnu mv debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.so debian/libsnp-sites1-dev/usr/lib/i386-linux-gnu mv /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.so.1 debian/libsnp-sites1/usr/lib/i386-linux-gnu mv /build/snp-sites-2.5.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.so.1.0.0 debian/libsnp-sites1/usr/lib/i386-linux-gnu PKGDEV=libsnp-sites1-dev PKGSHL=libsnp-sites1 install -d -m 755 debian/libsnp-sites1-dev/usr/include/snp-sites mv debian/tmp/usr/include/snp-sites/*.h debian/libsnp-sites1-dev/usr/include/snp-sites make[1]: Leaving directory '/build/snp-sites-2.5.1' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/snp-sites-2.5.1' mkdir -p /build/snp-sites-2.5.1/debian/man asciidoctor -a docdate='' -b manpage /build/snp-sites-2.5.1/snp-sites.txt mv /build/snp-sites-2.5.1/snp-sites.1 /build/snp-sites-2.5.1/debian/man dh_installman -- make[1]: Leaving directory '/build/snp-sites-2.5.1' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libsnp-sites1-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libsnp-sites1-dev: substitution variable ${devlibs:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.5.1-1_i386.deb'. dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.5.1-1_i386.deb'. dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.5.1-1_i386.deb'. dpkg-deb: building package 'snp-sites' in '../snp-sites_2.5.1-1_i386.deb'. dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.5.1-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snp-sites_2.5.1-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/28056/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/28056/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/28056 and its subdirectories I: Current time: Mon Jul 12 13:05:35 +14 2021 I: pbuilder-time-stamp: 1626044735