Sat Oct 17 03:02:29 UTC 2020 I: starting to build snp-sites/buster/arm64 on jenkins on '2020-10-17 03:02' Sat Oct 17 03:02:29 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_27/15187/console.log Sat Oct 17 03:02:29 UTC 2020 I: Downloading source for buster/snp-sites=2.4.1-1 --2020-10-17 03:02:29-- 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% 180M=0s 2020-10-17 03:02:29 (180 MB/s) - ‘snp-sites_2.4.1-1.dsc’ saved [2266/2266] Sat Oct 17 03:02:30 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----- Sat Oct 17 03:02:30 UTC 2020 I: Checking whether the package is not for us Sat Oct 17 03:02:30 UTC 2020 I: Starting 1st build on remote node codethink-sled15-arm64.debian.net. Sat Oct 17 03:02:30 UTC 2020 I: Preparing to do remote build '1' on codethink-sled15-arm64.debian.net. Sat Oct 17 03:04:10 UTC 2020 I: Deleting $TMPDIR on codethink-sled15-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Nov 18 21:25:47 -12 2021 I: pbuilder-time-stamp: 1637313947 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: 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 '/var/lib/jenkins/.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/7098/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='7098' 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.09VB2CC0r9/pbuilderrc_tQc1 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.09VB2CC0r9/b1 --logfile b1/build.log snp-sites_2.4.1-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled15-arm64 4.4.0-190-generic #220-Ubuntu SMP Fri Aug 28 23:03:33 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 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 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 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 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 2020 fusermount -rwxr-xr-x 1 root root 174304 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 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 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 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Nov 9 02:49 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 2020 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 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/7098/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 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 ... 19168 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 25.9 MB of archives. After unpacking 93.9 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 openssl arm64 1.1.1d-0+deb10u3 [823 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 ca-certificates all 20190110 [157 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 rubygems-integration all 1.11+deb10u1 [5212 B] Get: 17 http://deb.debian.org/debian buster/main arm64 rake all 12.3.1-3+deb10u1 [67.1 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 ruby-minitest all 5.11.3-1 [54.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 libyaml-0-2 arm64 0.2.1-1 [41.4 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libruby2.5 arm64 2.5.5-3+deb10u2 [3303 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 ruby2.5 arm64 2.5.5-3+deb10u2 [400 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 ruby arm64 1:2.5.1 [11.3 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 ruby-asciidoctor all 1.5.8-1 [188 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 asciidoctor all 1.5.8-1 [75.8 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 libsubunit0 arm64 1.3.0-1 [9040 B] Get: 39 http://deb.debian.org/debian buster/main arm64 libsubunit-dev arm64 1.3.0-1 [9964 B] Get: 40 http://deb.debian.org/debian buster/main arm64 check arm64 0.10.0-3+b3 [174 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 d-shlibs all 0.84 [17.2 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 pkg-config arm64 0.29-6 [62.2 kB] Get: 58 http://deb.debian.org/debian buster/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1 [210 kB] Fetched 25.9 MB in 2s (14.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... 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Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libyaml-0-2:arm64 (0.2.1-1) ... Setting up libglib2.0-0:arm64 (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Setting up libmagic1:arm64 (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libsubunit0:arm64 (1.3.0-1) ... Setting up libicu63:arm64 (63.1-6+deb10u1) ... Setting up ruby-minitest (5.11.3-1) ... Setting up autotools-dev (20180224.1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up libncurses6:arm64 (6.1+20181013-2+deb10u2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:arm64 (2.12-2) ... Setting up autopoint (0.19.8.1-9) ... Setting up pkg-config (0.29-6) ... Setting up d-shlibs (0.84) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up openssl (1.1.1d-0+deb10u3) ... Setting up libbsd0:arm64 (0.9.1-2) ... Setting up libelf1:arm64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:arm64 (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libsubunit-dev:arm64 (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:arm64 (0.10.0-3+b3) ... Setting up libcroco3:arm64 (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:arm64 (2.5.5-3+deb10u2) ... 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+deb10u2) ... 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 arm64 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=aarch64-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/aarch64-linux-gnu --libexecdir=\${prefix}/lib/aarch64-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... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-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 aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-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 -j8 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 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 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 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 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 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 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 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 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/aarch64-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 -j8 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/aarch64-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libsnp-sites.la '/build/snp-sites-2.4.1/debian/tmp/usr/lib/aarch64-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/aarch64-linux-gnu/libsnp-sites.so.1.0.0 libtool: install: (cd /build/snp-sites-2.4.1/debian/tmp/usr/lib/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/libsnp-sites.a libtool: install: chmod 644 /build/snp-sites-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libsnp-sites.a libtool: install: ranlib /build/snp-sites-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libsnp-sites.a libtool: warning: remember to run 'libtool --finish /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu install -d -m 755 debian/libsnp-sites1/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsnp-sites.a debian/libsnp-sites1-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libsnp-sites.so debian/libsnp-sites1-dev/usr/lib/aarch64-linux-gnu mv /build/snp-sites-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libsnp-sites.so.1 debian/libsnp-sites1/usr/lib/aarch64-linux-gnu mv /build/snp-sites-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libsnp-sites.so.1.0.0 debian/libsnp-sites1/usr/lib/aarch64-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/aarch64-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 'libsnp-sites1-dbgsym' in '../libsnp-sites1-dbgsym_2.4.1-1_arm64.deb'. dpkg-deb: building package 'snp-sites-dbgsym' in '../snp-sites-dbgsym_2.4.1-1_arm64.deb'. dpkg-deb: building package 'libsnp-sites1' in '../libsnp-sites1_2.4.1-1_arm64.deb'. dpkg-deb: building package 'libsnp-sites1-dev' in '../libsnp-sites1-dev_2.4.1-1_arm64.deb'. dpkg-deb: building package 'snp-sites' in '../snp-sites_2.4.1-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../snp-sites_2.4.1-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/7098 and its subdirectories I: Current time: Thu Nov 18 21:27:07 -12 2021 I: pbuilder-time-stamp: 1637314027 Sat Oct 17 03:04:11 UTC 2020 I: 1st build successful. Starting 2nd build on remote node codethink-sled14-arm64.debian.net. Sat Oct 17 03:04:11 UTC 2020 I: Preparing to do remote build '2' on codethink-sled14-arm64.debian.net. Sat Oct 17 03:06:22 UTC 2020 I: Deleting $TMPDIR on codethink-sled14-arm64.debian.net. Sat Oct 17 03:06:23 UTC 2020 I: snp-sites_2.4.1-1_arm64.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: arm64 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: 4eefffee2c44abf364cb0c252953197819698f95 21040 libsnp-sites1-dbgsym_2.4.1-1_arm64.deb a7b8d1d3740e971687f9a8ab42ede3ceb5d4d8ea 14784 libsnp-sites1-dev_2.4.1-1_arm64.deb d507e3cbee5ff82f18adb41091d90a259685626f 11224 libsnp-sites1_2.4.1-1_arm64.deb 8eedf23b7aa0cd90741318e140071816f87e19bd 6552 snp-sites-dbgsym_2.4.1-1_arm64.deb 3c9f26fd5519d9eabb827dfdb1dab3375c0cba75 6562 snp-sites_2.4.1-1_arm64.buildinfo 4d10151a890f736140e713fcc70ceb49d7523cd8 11284 snp-sites_2.4.1-1_arm64.deb Checksums-Sha256: 72462316d6f6b8973e3b80488ddc713b5ac77e40bd426b124f097919fa4f41b1 21040 libsnp-sites1-dbgsym_2.4.1-1_arm64.deb a6e8a1cec7c14f6f320cf2a6f6cef204439044c91741359e0c543e7b3ed6a20e 14784 libsnp-sites1-dev_2.4.1-1_arm64.deb c4c27c05354aa116d8b089fe4f454b33323a77be44538a2c0bee5fb9ce212dc1 11224 libsnp-sites1_2.4.1-1_arm64.deb 342b8e71a46af492974629a5bfcf12ad12ff6d4b69a033ffd275c1bab7a21ee5 6552 snp-sites-dbgsym_2.4.1-1_arm64.deb f3c7d674c64d7856feefeba5b6f965c37c60b3124448e44e52662ae206a5c33c 6562 snp-sites_2.4.1-1_arm64.buildinfo a06f089a4e79fb7ac5eeccff7385292ba07b48db291bcdbaab261634a33a1fce 11284 snp-sites_2.4.1-1_arm64.deb Files: 46305a4a0d72f262cd568becc83473d0 21040 debug optional libsnp-sites1-dbgsym_2.4.1-1_arm64.deb b47bb5a46bc2f32ff4e20874c89397c9 14784 libdevel optional libsnp-sites1-dev_2.4.1-1_arm64.deb a59777a65ecbd52220ecf6ba0ecbd6ab 11224 libs optional libsnp-sites1_2.4.1-1_arm64.deb 9b83eafe1b3c8d67147aa785b0f11de4 6552 debug optional snp-sites-dbgsym_2.4.1-1_arm64.deb 13d6737d6a46f67050a0e742f7d81a2b 6562 science optional snp-sites_2.4.1-1_arm64.buildinfo de57e27374e5ae0b290cfd9a94cf0e5c 11284 science optional snp-sites_2.4.1-1_arm64.deb Sat Oct 17 03:06:24 UTC 2020 I: diffoscope 160 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.09VB2CC0r9/snp-sites_2.4.1-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.09VB2CC0r9/snp-sites_2.4.1-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.09VB2CC0r9/snp-sites_2.4.1-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.09VB2CC0r9/b1/snp-sites_2.4.1-1_arm64.changes /srv/reproducible-results/rbuild-debian/tmp.09VB2CC0r9/b2/snp-sites_2.4.1-1_arm64.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: 0.208s) 0.208s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.023s) 0.023s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Sat Oct 17 03:06:26 UTC 2020 I: diffoscope 160 found no differences in the changes files, and a .buildinfo file also exists. Sat Oct 17 03:06:26 UTC 2020 I: snp-sites from buster built successfully and reproducibly on arm64. Sat Oct 17 03:06:27 UTC 2020 I: Submitting .buildinfo files to external archives: Sat Oct 17 03:06:27 UTC 2020 I: Submitting 8.0K b1/snp-sites_2.4.1-1_arm64.buildinfo.asc Sat Oct 17 03:06:28 UTC 2020 I: Submitting 8.0K b2/snp-sites_2.4.1-1_arm64.buildinfo.asc Sat Oct 17 03:06:29 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Oct 17 03:06:29 UTC 2020 I: Done submitting .buildinfo files. Sat Oct 17 03:06:29 UTC 2020 I: Removing signed snp-sites_2.4.1-1_arm64.buildinfo.asc files: removed './b1/snp-sites_2.4.1-1_arm64.buildinfo.asc' removed './b2/snp-sites_2.4.1-1_arm64.buildinfo.asc'