Wed Jul 15 08:32:02 UTC 2020 I: starting to build snp-sites/buster/i386 on jenkins on '2020-07-15 08:31' Wed Jul 15 08:32:02 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_13/3653/console.log Wed Jul 15 08:32:02 UTC 2020 I: Downloading source for buster/snp-sites=2.4.1-1 --2020-07-15 08:32:02-- http://deb.debian.org/debian/pool/main/s/snp-sites/snp-sites_2.4.1-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2266 (2.2K) Saving to: ‘snp-sites_2.4.1-1.dsc’ 0K .. 100% 15.2M=0s 2020-07-15 08:32:02 (15.2 MB/s) - ‘snp-sites_2.4.1-1.dsc’ saved [2266/2266] Wed Jul 15 08:32:02 UTC 2020 I: snp-sites_2.4.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: snp-sites Binary: snp-sites, libsnp-sites1, libsnp-sites1-dev Architecture: any Version: 2.4.1-1 Maintainer: Debian Med Packaging Team Uploaders: Jorge Soares , Andreas Tille , Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/snp-sites Standards-Version: 4.1.4 Vcs-Browser: https://salsa.debian.org/med-team/snp-sites Vcs-Git: https://salsa.debian.org/med-team/snp-sites.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, zlib1g, zlib1g-dev Build-Depends: debhelper (>= 11), zlib1g-dev, check, pkg-config, d-shlibs, asciidoctor Package-List: libsnp-sites1 deb libs optional arch=any libsnp-sites1-dev deb libdevel optional arch=any snp-sites deb science optional arch=any Checksums-Sha1: d2527b196de1e428ed719daf7198ddb3272cdc58 15574755 snp-sites_2.4.1.orig.tar.gz 739e68505ed90fea5def77e4025611b8a7c4accc 7908 snp-sites_2.4.1-1.debian.tar.xz Checksums-Sha256: 9f37bf30bcbdb52b6c8b201410a9e232b33a105f3197765f51b1b434ae851de3 15574755 snp-sites_2.4.1.orig.tar.gz df96831404dfb899a249be01b35da4ff6dccbf4a8c9803aafbd9acec5b0e9c77 7908 snp-sites_2.4.1-1.debian.tar.xz Files: 628a9f5f056bbc0ac3cb97cb340f697d 15574755 snp-sites_2.4.1.orig.tar.gz bc8537809b629282d5246ea96c6f28db 7908 snp-sites_2.4.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAlu42ywACgkQ6NN64vCf SHJmIBAAhgXSj2rMnvVcMdjjVKlsSSV/wuyLCkKfFcYpsQOSY1JBVCaLUSLR1bMr lZMHqejAYaoO0/GwKk7K9MnBwukTl4VpG7QcO7k2LxfoDw96cw4YezXVep0oBHCp kC5APcYTnBiwZlOWpa4WFopyDkExLyM+0/TdiXafSHUdisqDPX8SPR5QwAl6INfg AduIXalcnHQXtuoqyXct+bH9v20nr6KrPRQuF6CPAYLhCfet5Sx7TfDvCP9j49Uu +x1QDj7QQlAzMDpf3qcmrVFJGxNkj5gbcjX1XCMjHECNI02Po/5fcs4z1+ODDHuJ BjeL0dvOSuBWPGBhmSlw2hk5m48/xq8t5OFn9Dip0otuaMYc1LFno7SxA7gtpp1z 8mrEiiGCgOk/KsBNk41xA/KrpnR+HYHdcwhpya7qbGP49yPV7NOYjbcEwZEnW1Yr dOqJLKvkseUvmfs09YMlvTNU1x3jP/dAShCjea9M9a55mTBVjRMsOQ1TVP9oICpi x4iOlE1YnBFDgaJ++zBunz+Ipob200OgItcZZcKoXcG1Pqj6neEge7PO0VeQV11m I7mxqH9Aiy4+vinlLB0wPJKYUQUWj9X+tU7TrfDCEadtiDU3JnfCYRkJ0bI9mchg zQeLIyxEn8EWQJ7vnp8n2sYgIvGGyi0ZR6z0XBg9pCI0isAGqs4= =TSLH -----END PGP SIGNATURE----- Wed Jul 15 08:32:02 UTC 2020 I: Checking whether the package is not for us Wed Jul 15 08:32:02 UTC 2020 I: Starting 1st build on remote node profitbricks-build12-i386.debian.net. Wed Jul 15 08:32:02 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build12-i386.debian.net. Wed Jul 15 08:36:19 UTC 2020 I: Deleting $TMPDIR on profitbricks-build12-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jul 14 20:32:09 -12 2020 I: pbuilder-time-stamp: 1594801929 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-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_2.4.1-1.dsc] I: copying [./snp-sites_2.4.1.orig.tar.gz] I: copying [./snp-sites_2.4.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Oct 6 03:56:28 2018 -12 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./snp-sites_2.4.1-1.dsc dpkg-source: info: extracting snp-sites in snp-sites-2.4.1 dpkg-source: info: unpacking snp-sites_2.4.1.orig.tar.gz dpkg-source: info: unpacking snp-sites_2.4.1-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/12381/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10' DISTRIBUTION='' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='85ac6ac1643f47ea85a7f2aea81fede4' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='12381' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/pbuilderrc_MLjG --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/b1 --logfile b1/build.log snp-sites_2.4.1-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux profitbricks-build12-i386 4.19.0-9-686-pae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) i686 GNU/Linux I: ls -l /bin total 5484 -rwxr-xr-x 1 root root 1302248 Apr 17 2019 bash -rwxr-xr-x 3 root root 38280 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 38280 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 17768 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 38692 Feb 28 2019 cat -rwxr-xr-x 1 root root 75588 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 63268 Feb 28 2019 chmod -rwxr-xr-x 1 root root 75588 Feb 28 2019 chown -rwxr-xr-x 1 root root 153732 Feb 28 2019 cp -rwxr-xr-x 1 root root 132820 Jan 17 2019 dash -rwxr-xr-x 1 root root 120676 Feb 28 2019 date -rwxr-xr-x 1 root root 92040 Feb 28 2019 dd -rwxr-xr-x 1 root root 100620 Feb 28 2019 df -rwxr-xr-x 1 root root 149736 Feb 28 2019 dir -rwxr-xr-x 1 root root 79412 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 34532 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 34532 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 67700 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 30112 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 206392 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 100952 Jan 5 2019 gzip -rwxr-xr-x 1 root root 21916 Sep 26 2018 hostname -rwxr-xr-x 1 root root 79752 Feb 28 2019 ln -rwxr-xr-x 1 root root 55400 Jul 26 2018 login -rwxr-xr-x 1 root root 149736 Feb 28 2019 ls -rwxr-xr-x 1 root root 112032 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 87972 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 79748 Feb 28 2019 mknod -rwxr-xr-x 1 root root 46916 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 42348 Jan 9 2019 more -rwsr-xr-x 1 root root 50592 Jan 9 2019 mount -rwxr-xr-x 1 root root 13724 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 157832 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38660 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 46852 Feb 28 2019 readlink -rwxr-xr-x 1 root root 75588 Feb 28 2019 rm -rwxr-xr-x 1 root root 42756 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 22276 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 13 20:25 sh -> dash -rwxr-xr-x 1 root root 34532 Feb 28 2019 sleep -rwxr-xr-x 1 root root 79652 Feb 28 2019 stty -rwsr-xr-x 1 root root 71072 Jan 9 2019 su -rwxr-xr-x 1 root root 34564 Feb 28 2019 sync -rwxr-xr-x 1 root root 504024 Apr 23 2019 tar -rwxr-xr-x 1 root root 13860 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 104292 Feb 28 2019 touch -rwxr-xr-x 1 root root 34532 Feb 28 2019 true -rwxr-xr-x 1 root root 17768 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30108 Jan 9 2019 umount -rwxr-xr-x 1 root root 34532 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 149736 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34208 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/12381/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 ... 19234 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} bsdmainutils{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} libcroco3{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libreadline7{a} libruby2.5{a} libsigsegv2{a} libssl1.1{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} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-did-you-mean{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.5{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 libgpm2 libjs-jquery libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 58 newly installed, 0 to remove and 0 not upgraded. Need to get 27.2 MB of archives. After unpacking 96.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 11 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 12 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 14 http://deb.debian.org/debian buster/main i386 openssl i386 1.1.1d-0+deb10u3 [853 kB] Get: 15 http://deb.debian.org/debian buster/main i386 ca-certificates all 20190110 [157 kB] Get: 16 http://deb.debian.org/debian buster/main i386 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 17 http://deb.debian.org/debian buster/main i386 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 18 http://deb.debian.org/debian buster/main i386 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 19 http://deb.debian.org/debian buster/main i386 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 20 http://deb.debian.org/debian buster/main i386 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 21 http://deb.debian.org/debian buster/main i386 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 22 http://deb.debian.org/debian buster/main i386 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 23 http://deb.debian.org/debian buster/main i386 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 24 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libyaml-0-2 i386 0.2.1-1 [49.7 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libruby2.5 i386 2.5.5-3+deb10u1 [3546 kB] Get: 28 http://deb.debian.org/debian buster/main i386 ruby2.5 i386 2.5.5-3+deb10u1 [400 kB] Get: 29 http://deb.debian.org/debian buster/main i386 ruby i386 1:2.5.1 [11.3 kB] Get: 30 http://deb.debian.org/debian buster/main i386 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 31 http://deb.debian.org/debian buster/main i386 asciidoctor all 1.5.8-1 [75.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 33 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 34 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 35 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 36 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 37 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libsubunit0 i386 1.3.0-1 [9312 B] Get: 39 http://deb.debian.org/debian buster/main i386 libsubunit-dev i386 1.3.0-1 [10.3 kB] Get: 40 http://deb.debian.org/debian buster/main i386 check i386 0.10.0-3+b3 [180 kB] Get: 41 http://deb.debian.org/debian buster/main i386 d-shlibs all 0.84 [17.2 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 43 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 46 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 47 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 48 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 49 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 50 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 51 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 52 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 53 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 54 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 55 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 56 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 57 http://deb.debian.org/debian buster/main i386 pkg-config i386 0.29-6 [64.7 kB] Get: 58 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Fetched 27.2 MB in 6s (4202 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../02-libuchardet0_0.0.6-3_i386.deb ... 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Setting up ruby-did-you-mean (1.2.1-1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:i386 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libsubunit-dev:i386 (1.3.0-1) ... Setting up m4 (1.4.18-2) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up check:i386 (0.10.0-3+b3) ... Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up rubygems-integration (1.11+deb10u1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up po-debconf (1.0.21) ... Setting up rake (12.3.1-3+deb10u1) ... Setting up libruby2.5:i386 (2.5.5-3+deb10u1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up ruby2.5 (2.5.5-3+deb10u1) ... Setting up ruby (1:2.5.1) ... Setting up ruby-asciidoctor (1.5.8-1) ... Setting up asciidoctor (1.5.8-1) ... Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20190110) ... 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 (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/snp-sites-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package snp-sites dpkg-buildpackage: info: source version 2.4.1-1 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:13: 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-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode 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... 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... 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... /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 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... /bin/sed checking for fgrep... /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... /bin/dd checking how to truncate binary pipes... /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 configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build make -j10 make[1]: Entering directory '/build/snp-sites-2.4.1' make all-recursive make[2]: Entering directory '/build/snp-sites-2.4.1' Making all in src make[3]: Entering directory '/build/snp-sites-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include --std=c99 -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites-main.o `test -f 'main.c' || echo './'`main.c /bin/bash ../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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment-file.lo alignment-file.c /bin/bash ../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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vcf.lo vcf.c /bin/bash ../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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o phylib-of-snp-sites.lo phylib-of-snp-sites.c /bin/bash ../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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp-sites.lo snp-sites.c /bin/bash ../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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment-file.c -o alignment-file.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 cru .libs/libsnp-sites.a alignment-file.o vcf.o phylib-of-snp-sites.o snp-sites.o fasta-of-snp-sites.o ar: `u' modifier ignored since `D' is the default (see `U') 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/bash ../libtool --tag=CC --mode=link gcc --std=c99 -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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-2.4.1/src' make[3]: Entering directory '/build/snp-sites-2.4.1' make[3]: Leaving directory '/build/snp-sites-2.4.1' make[2]: Leaving directory '/build/snp-sites-2.4.1' make[1]: Leaving directory '/build/snp-sites-2.4.1' dh_auto_test make -j10 check VERBOSE=1 make[1]: Entering directory '/build/snp-sites-2.4.1' Making check in src make[2]: Entering directory '/build/snp-sites-2.4.1/src' make run-all-tests make[3]: Entering directory '/build/snp-sites-2.4.1/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include -pthread -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 /bin/bash ../libtool --tag=CC --mode=link gcc -pthread -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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 -ffile-prefix-map=/build/snp-sites-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/build/snp-sites-2.4.1=. -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-2.4.1/src' make check-TESTS make[3]: Entering directory '/build/snp-sites-2.4.1/src' make[4]: Entering directory '/build/snp-sites-2.4.1/src' PASS: run-all-tests ============================================================================ Testsuite summary for snp-sites 2.4.1 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/snp-sites-2.4.1/src' make[3]: Leaving directory '/build/snp-sites-2.4.1/src' make[2]: Leaving directory '/build/snp-sites-2.4.1/src' make[2]: Entering directory '/build/snp-sites-2.4.1' make[2]: Leaving directory '/build/snp-sites-2.4.1' make[1]: Leaving directory '/build/snp-sites-2.4.1' 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-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/snp-sites-2.4.1' Making install in src make[2]: Entering directory '/build/snp-sites-2.4.1/src' make[3]: Entering directory '/build/snp-sites-2.4.1/src' /bin/mkdir -p '/build/snp-sites-2.4.1/debian/tmp/usr/lib/i386-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libsnp-sites.la '/build/snp-sites-2.4.1/debian/tmp/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libsnp-sites.so.1.0.0 /build/snp-sites-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.so.1.0.0 libtool: install: (cd /build/snp-sites-2.4.1/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-2.4.1/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-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.la libtool: install: /usr/bin/install -c .libs/libsnp-sites.a /build/snp-sites-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a libtool: install: chmod 644 /build/snp-sites-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a libtool: install: ranlib /build/snp-sites-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/build/snp-sites-2.4.1/debian/tmp/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c snp-sites '/build/snp-sites-2.4.1/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-2.4.1/debian/tmp/usr/bin/snp-sites /bin/mkdir -p '/build/snp-sites-2.4.1/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-2.4.1/debian/tmp/usr/include/snp-sites' make[3]: Leaving directory '/build/snp-sites-2.4.1/src' make[2]: Leaving directory '/build/snp-sites-2.4.1/src' make[2]: Entering directory '/build/snp-sites-2.4.1' make[3]: Entering directory '/build/snp-sites-2.4.1' 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-2.4.1' make[2]: Leaving directory '/build/snp-sites-2.4.1' make[1]: Leaving directory '/build/snp-sites-2.4.1' debian/rules override_dh_install make[1]: Entering directory '/build/snp-sites-2.4.1' 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-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/libsnp-sites.so.1 debian/libsnp-sites1/usr/lib/i386-linux-gnu mv /build/snp-sites-2.4.1/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-2.4.1' dh_installdocs dh_installchangelogs debian/rules override_dh_installman make[1]: Entering directory '/build/snp-sites-2.4.1' mkdir -p /build/snp-sites-2.4.1/debian/man asciidoctor -a docdate='' -b manpage /build/snp-sites-2.4.1/snp-sites.txt mv /build/snp-sites-2.4.1/snp-sites.1 /build/snp-sites-2.4.1/debian/man dh_installman -- make[1]: Leaving directory '/build/snp-sites-2.4.1' 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/libsnp-sites1/usr/lib/i386-linux-gnu/libsnp-sites.so.1.0.0 was not linked against libm.so.6 (it uses none of the library's symbols) 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) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libm.so.6 (it uses none of the library's symbols) dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/snp-sites/usr/bin/snp-sites was not linked against libz.so.1 (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 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.4.1-1_i386.deb'. dpkg-deb: building package 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.4.1-1_i386.deb'. dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.4.1-1_i386.deb'. dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.4.1-1_i386.deb'. dpkg-deb: building package 'snp-sites' in '../snp-sites_2.4.1-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snp-sites_2.4.1-1_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: 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/12381 and its subdirectories I: Current time: Tue Jul 14 20:36:18 -12 2020 I: pbuilder-time-stamp: 1594802178 Wed Jul 15 08:36:19 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build6-i386.debian.net. Wed Jul 15 08:36:19 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build6-i386.debian.net. Wed Jul 15 08:36:56 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. Wed Jul 15 08:36:56 UTC 2020 I: snp-sites_2.4.1-1_i386.changes: Format: 1.8 Date: Sat, 06 Oct 2018 17:54:44 +0200 Source: snp-sites Binary: libsnp-sites1 libsnp-sites1-dbgsym libsnp-sites1-dev snp-sites snp-sites-dbgsym Architecture: i386 Version: 2.4.1-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Sascha Steinbiss Description: libsnp-sites1 - Shared libraries of the package snp-sites libsnp-sites1-dev - Static libraries and header files for the package snp-sites snp-sites - Binary code for the package snp-sites Changes: snp-sites (2.4.1-1) unstable; urgency=medium . * New upstream release. Checksums-Sha1: 59aa34ac55698a219bd65e9f3e28774f141a164a 18532 libsnp-sites1-dbgsym_2.4.1-1_i386.deb 375935f348c36e45bf8fbf4bb65dbc41c7272609 15704 libsnp-sites1-dev_2.4.1-1_i386.deb 165ee3ab2321cdffaf1ec927d7b23cbe0c13992c 12144 libsnp-sites1_2.4.1-1_i386.deb d6d17a5b0103252222259653b8ddfd59d1eadde9 6156 snp-sites-dbgsym_2.4.1-1_i386.deb 852f1f04ea873f8bd3e974defaf961f1f6a9b5d8 6551 snp-sites_2.4.1-1_i386.buildinfo 24a0ea82f1aea60d8b67064581011719703eb7db 11200 snp-sites_2.4.1-1_i386.deb Checksums-Sha256: 6a4e189e0b07bd154ba1d9ee41ee2f699e8c9801417ef1a130607cbba765b4e3 18532 libsnp-sites1-dbgsym_2.4.1-1_i386.deb 8ac470e9a547fb3fc0be3acbb6bf1d2fe10276b4748adef37e4a6c26b3db3e6e 15704 libsnp-sites1-dev_2.4.1-1_i386.deb 33b31b73939cb45c9111fb1051f808f7cc5cad9373613f2e8915a09ee9b81279 12144 libsnp-sites1_2.4.1-1_i386.deb 54e9ee42c42aa6405fe4a1f7e3b3d628a59b327eac96625dddfcb463ea758003 6156 snp-sites-dbgsym_2.4.1-1_i386.deb 3cc9d89f36697e31823a651c8cdb626410a2ae86cc704559f0eb37767dbbd2fb 6551 snp-sites_2.4.1-1_i386.buildinfo 4791a538c91e2b7a9edd09b259cababd8e7f02a290f739bfa4e3354f4c5bf278 11200 snp-sites_2.4.1-1_i386.deb Files: 2add55587ff885f9756b29ea1e8b1196 18532 debug optional libsnp-sites1-dbgsym_2.4.1-1_i386.deb 1a7306a0b0ba1f99ba0491f64e0f602c 15704 libdevel optional libsnp-sites1-dev_2.4.1-1_i386.deb 0f256055dfbf7a8ad5cb6451d11d72d0 12144 libs optional libsnp-sites1_2.4.1-1_i386.deb 7200d9b390ae4e5d540c888235a99cf8 6156 debug optional snp-sites-dbgsym_2.4.1-1_i386.deb 3c145c43595877ee85164328e8cb0b6a 6551 science optional snp-sites_2.4.1-1_i386.buildinfo 1cf1bd0cfabb7c13f3cdbb5d06c1f23b 11200 science optional snp-sites_2.4.1-1_i386.deb Wed Jul 15 08:37:06 UTC 2020 I: diffoscope 151 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/snp-sites_2.4.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/snp-sites_2.4.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/snp-sites_2.4.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/b1/snp-sites_2.4.1-1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.sfHN3WCziN/b2/snp-sites_2.4.1-1_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.254s) 0.254s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.030s) 0.029s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Wed Jul 15 08:37:27 UTC 2020 I: diffoscope 151 found no differences in the changes files, and a .buildinfo file also exists. Wed Jul 15 08:37:27 UTC 2020 I: snp-sites from buster built successfully and reproducibly on i386. Wed Jul 15 08:37:29 UTC 2020 I: Submitting .buildinfo files to external archives: Wed Jul 15 08:37:29 UTC 2020 I: Submitting 8.0K b1/snp-sites_2.4.1-1_i386.buildinfo.asc Wed Jul 15 08:37:30 UTC 2020 I: Submitting 8.0K b2/snp-sites_2.4.1-1_i386.buildinfo.asc Wed Jul 15 08:37:31 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Jul 15 08:37:31 UTC 2020 I: Done submitting .buildinfo files. Wed Jul 15 08:37:31 UTC 2020 I: Removing signed snp-sites_2.4.1-1_i386.buildinfo.asc files: removed './b1/snp-sites_2.4.1-1_i386.buildinfo.asc' removed './b2/snp-sites_2.4.1-1_i386.buildinfo.asc'