Fri Aug 14 13:49:51 UTC 2020 I: starting to build proteinortho/buster/armhf on jenkins on '2020-08-14 13:49' Fri Aug 14 13:49:51 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_47/3006/console.log Fri Aug 14 13:49:51 UTC 2020 I: Downloading source for buster/proteinortho=5.16.b+dfsg-1 --2020-08-14 13:49:51-- http://deb.debian.org/debian/pool/main/p/proteinortho/proteinortho_5.16.b+dfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2074 (2.0K) Saving to: ‘proteinortho_5.16.b+dfsg-1.dsc’ 0K .. 100% 232M=0s 2020-08-14 13:49:51 (232 MB/s) - ‘proteinortho_5.16.b+dfsg-1.dsc’ saved [2074/2074] Fri Aug 14 13:49:51 UTC 2020 I: proteinortho_5.16.b+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: proteinortho Binary: proteinortho Architecture: any Version: 5.16.b+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://www.bioinf.uni-leipzig.de/Software/proteinortho/ Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/proteinortho Vcs-Git: https://salsa.debian.org/med-team/proteinortho.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), ncbi-blast+ Package-List: proteinortho deb science optional arch=any Checksums-Sha1: ccf2b31efd50de32cf67f78d8215d4c1c46f0d11 102540 proteinortho_5.16.b+dfsg.orig.tar.xz 1cc1059ef64e383c819a280a29ae9419bf9a031a 4192 proteinortho_5.16.b+dfsg-1.debian.tar.xz Checksums-Sha256: 8e43a3d3f7d4dbeaff924228661f614c815474c3bf8b4a946e6f950c4a2983a5 102540 proteinortho_5.16.b+dfsg.orig.tar.xz 627bbd52a57bf34c76866dfc865578b881343ed0fbdcc972867e3cb3627ea48c 4192 proteinortho_5.16.b+dfsg-1.debian.tar.xz Files: a268e8a99e98202728de8745c0715b36 102540 proteinortho_5.16.b+dfsg.orig.tar.xz 21f9c5dae5877a86d1c944e0f33f3af4 4192 proteinortho_5.16.b+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlw0YRQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGi3xAAmWhau7Xu1BCa4+w/SV8KfvhhNATOyat5 g7m506kv8a3yPME/EJIUugZ9yOML6e8Zf6qzMwz1Qe2HD2gf4Wf9GNj3A2FeuWq1 mFHHY8AAFXqnAnGgEmCzRImn9iX/utkGtqunWqupl5ho82Xn647j8TFU8si2v4Bg RxbH87fs5qQUcGUxKHAKY58FALXnte8sL1/eywiOVysLN1ZZ+XvxhEBjE2CMpVBm kKccOY8JOvH2NpYRe4ruwVuO2ynnt28cOag848cNGp0tMz7NHVlen5t9Tlu1EpwJ Pa2ltrLCIEerIIJGWMyCudVa8ELm0N4pI+bl/tsHmBPhMHivRnClukQwo4wBF5te mgQYWObfXWt/vtoFVJVwVf825fJaaw3mXzDjfGusMqfgP94ghp9Ya9Eeuwzjfqjl 6j8PfQGEuuCTvwd6Ki829RFzXIP8sB8ZyOT7z0R/9MX0kobPF25Y7o6awCJ7ZOaQ 18J9jn42lKojV2OHiXGX7SolpuIFZSrFdpDiuTmsI8IxdW9nd1+KJwegTwURowzG MplydY3Cdo3v6MoURIonvidLypN37Sws5YDjCbVHIL98QDYd1jTm1URmEv70GKYZ JQagvGP4yTswb5OmApf0nh620jnzMYH6K16fWzWTQAaghzQwnplklVKfK2wHDDnk Ba9DQJJC2zE= =ShK5 -----END PGP SIGNATURE----- Fri Aug 14 13:49:51 UTC 2020 I: Checking whether the package is not for us Fri Aug 14 13:49:51 UTC 2020 I: Starting 1st build on remote node jtx1a-armhf-rb.debian.net. Fri Aug 14 13:49:51 UTC 2020 I: Preparing to do remote build '1' on jtx1a-armhf-rb.debian.net. Fri Aug 14 13:52:56 UTC 2020 I: Deleting $TMPDIR on jtx1a-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Fri Aug 14 01:50:05 -12 2020 I: pbuilder-time-stamp: 1597413005 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 [proteinortho_5.16.b+dfsg-1.dsc] I: copying [./proteinortho_5.16.b+dfsg.orig.tar.xz] I: copying [./proteinortho_5.16.b+dfsg-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 Mon Jan 7 20:36:36 2019 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./proteinortho_5.16.b+dfsg-1.dsc dpkg-source: info: extracting proteinortho in proteinortho-5.16.b+dfsg dpkg-source: info: unpacking proteinortho_5.16.b+dfsg.orig.tar.xz dpkg-source: info: unpacking proteinortho_5.16.b+dfsg-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11831/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='93b29281ab804121942578c1a647879f' 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='11831' 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.mpSI37k7gy/pbuilderrc_YQeF --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.mpSI37k7gy/b1 --logfile b1/build.log proteinortho_5.16.b+dfsg-1.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux jtx1a 4.19.0-10-arm64 #1 SMP Debian 4.19.132-1 (2020-07-24) aarch64 GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 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 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 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 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 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 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 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 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 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 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Aug 12 20:27 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 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/11831/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: armhf 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~), ncbi-blast+ dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 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 ncbi-blast+; however: Package ncbi-blast+ is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{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} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} ncbi-blast+{a} ncbi-data{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 54 newly installed, 0 to remove and 0 not upgraded. Need to get 36.8 MB of archives. After unpacking 139 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 25 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 26 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 27 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 28 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 29 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 34 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 35 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 36 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 37 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 38 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 39 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 40 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 41 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 42 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 44 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 45 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 46 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 47 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 48 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 49 http://deb.debian.org/debian buster/main armhf liblmdb0 armhf 0.9.22-1 [38.2 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libmbedcrypto3 armhf 2.16.0-1 [191 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libmbedx509-0 armhf 2.16.0-1 [87.4 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libmbedtls12 armhf 2.16.0-1 [123 kB] Get: 53 http://deb.debian.org/debian buster/main armhf ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 54 http://deb.debian.org/debian buster/main armhf ncbi-blast+ armhf 2.8.1-1+deb10u1 [9115 kB] Fetched 36.8 MB in 16s (2312 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... Unpacking libuchardet0:armhf (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_armhf.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../04-libpipeline1_1.5.1-2_armhf.deb ... Unpacking libpipeline1:armhf (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_armhf.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:armhf. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking libpython2.7-minimal:armhf (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_armhf.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. 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Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libmbedcrypto3:armhf (2.16.0-1) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libtool (2.4.6-9) ... Setting up libmbedx509-0:armhf (2.16.0-1) ... Setting up libmbedtls12:armhf (2.16.0-1) ... Setting up m4 (1.4.18-2) ... Setting up libpython2.7-stdlib:armhf (2.7.16-2+deb10u1) ... 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 libcroco3:armhf (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 python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:armhf (2.7.16-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python2 (2.7.16-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython-stdlib:armhf (2.7.16-1) ... Setting up python (2.7.16-1) ... Setting up po-debconf (1.0.21) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Setting up debhelper (12.1.1) ... Processing triggers for libc-bin (2.28-10) ... 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/proteinortho-5.16.b+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package proteinortho dpkg-buildpackage: info: source version 5.16.b+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean dh_auto_clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j3 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/proteinortho-5.16.b+dfsg' g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -std=gnu++11 -Wno-unused-result -Wl,-z,relro -Wl,-z,now -o proteinortho5_clustering proteinortho5_clustering.cpp g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -std=gnu++11 -Wno-unused-result -Wl,-z,relro -Wl,-z,now -o proteinortho5_tree po_tree.c make[1]: Leaving directory '/build/proteinortho-5.16.b+dfsg' dh_auto_test make -j3 test make[1]: Entering directory '/build/proteinortho-5.16.b+dfsg' ./proteinortho5.pl -project=test -synteny -singles test/*.faa ***************************************************************** Proteinortho with PoFF version 5.16b - An orthology detection tool ***************************************************************** Detected 4 available CPU threads, Detected NCBI BLAST version 2.8.1+ Checking input files Checking test/C.faa... test/C.faa 109 genes ok Checking test/E.faa... test/E.faa 72 genes ok Checking test/L.faa... test/L.faa 40 genes ok Checking test/M.faa... test/M.faa 40 genes ok **Step 1** Generating indices Building database for 'test/C.faa' (109 sequences) Building database for 'test/E.faa' (72 sequences) Building database for 'test/L.faa' (40 sequences) Building database for 'test/M.faa' (40 sequences) **Step 2** Running blast analysis: 0% (0/6) Running blast analysis: 16.66% (1/6) Running blast analysis: 33.33% (2/6) Running blast analysis: 100% (6/6) Running blast analysis: 83.33% (5/6) Running blast analysis: 50% (3/6) Running blast analysis: 66.66% (4/6) Running blast analysis: 100% (6/6) [OUTPUT] -> written to test.blast-graph **Step 3** Clustering by similarity (Proteinortho mode) Reading test.blast-graph 4 species 112 paired proteins 144 bidirectional edges Clustering: 1.79% Clustering: 3.57% Clustering: 5.36% Clustering: 7.14% Clustering: 8.93% Clustering: 10.71% Clustering: 12.50% Clustering: 14.29% Clustering: 18.75% Clustering: 20.54% Clustering: 23.21% Clustering: 25.89% Clustering: 28.57% Clustering: 42.86% Clustering: 58.04% Clustering: 58.93% Clustering: 62.50% Clustering: 64.29% Clustering: 66.07% Clustering: 67.86% Clustering: 69.64% Clustering: 71.43% Clustering: 73.21% Clustering: 75.00% Clustering: 76.79% Clustering: 78.57% Clustering: 85.71% Clustering: 89.29% Clustering: 93.75% Clustering: 95.54% Clustering: 100.00% Done Adding singles... [OUTPUT] -> written to test.proteinortho Writing graph... Cleaning edge list... Removed 20 / 144 edges Done. [OUTPUT] -> written to test.proteinortho-graph Clustering by gene-order (POFF mode) Reading test.ffadj-graph 4 species 105 paired proteins 104 bidirectional edges Clustering: 1.90% Clustering: 3.81% Clustering: 5.71% Clustering: 7.62% Clustering: 9.52% Clustering: 11.43% Clustering: 13.33% Clustering: 15.24% Clustering: 17.14% Clustering: 19.05% Clustering: 20.95% Clustering: 21.90% Clustering: 22.86% Clustering: 35.24% Clustering: 37.14% Clustering: 50.48% Clustering: 54.29% Clustering: 56.19% Clustering: 58.10% Clustering: 60.00% Clustering: 61.90% Clustering: 64.76% Clustering: 66.67% Clustering: 68.57% Clustering: 70.48% Clustering: 72.38% Clustering: 74.29% Clustering: 76.19% Clustering: 78.10% Clustering: 79.05% Clustering: 80.95% Clustering: 82.86% Clustering: 84.76% Clustering: 86.67% Clustering: 88.57% Clustering: 90.48% Clustering: 92.38% Clustering: 100.00% Done Adding singles... [OUTPUT] -> written to test.poff Writing graph... Cleaning edge list... Removed 0 / 104 edges Done. [OUTPUT] -> written to test.poff-graph All finished. rm test.* Test okay make[1]: Leaving directory '/build/proteinortho-5.16.b+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_installdirs debian/rules override_dh_auto_install make[1]: Entering directory '/build/proteinortho-5.16.b+dfsg' dh_auto_install --buildsystem=makefile -- install INSTALLDIR=/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho make -j3 install DESTDIR=/build/proteinortho-5.16.b\+dfsg/debian/proteinortho AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" install INSTALLDIR=/build/proteinortho-5.16.b\+dfsg/debian/proteinortho/usr/lib/proteinortho make[2]: Entering directory '/build/proteinortho-5.16.b+dfsg' install -v proteinortho5.pl proteinortho5_clustering proteinortho5_singletons.pl proteinortho5_clean_edges2.pl ffadj_mcs.py po2tree.pl proteinortho5_tree /build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho 'proteinortho5.pl' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5.pl' 'proteinortho5_clustering' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_clustering' 'proteinortho5_singletons.pl' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_singletons.pl' 'proteinortho5_clean_edges2.pl' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_clean_edges2.pl' 'ffadj_mcs.py' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/ffadj_mcs.py' 'po2tree.pl' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/po2tree.pl' 'proteinortho5_tree' -> '/build/proteinortho-5.16.b+dfsg/debian/proteinortho/usr/lib/proteinortho/proteinortho5_tree' make[2]: 'install' is up to date. make[2]: Leaving directory '/build/proteinortho-5.16.b+dfsg' make[1]: Leaving directory '/build/proteinortho-5.16.b+dfsg' dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: debian/proteinortho/usr/lib/proteinortho/proteinortho5_clustering contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dpkg-gencontrol: warning: package proteinortho: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package proteinortho: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'proteinortho-dbgsym' in '../proteinortho-dbgsym_5.16.b+dfsg-1_armhf.deb'. dpkg-deb: building package 'proteinortho' in '../proteinortho_5.16.b+dfsg-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../proteinortho_5.16.b+dfsg-1_armhf.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/11831 and its subdirectories I: Current time: Fri Aug 14 01:52:45 -12 2020 I: pbuilder-time-stamp: 1597413165 Fri Aug 14 13:53:00 UTC 2020 I: 1st build successful. Starting 2nd build on remote node cbxi4b-armhf-rb.debian.net. Fri Aug 14 13:53:00 UTC 2020 I: Preparing to do remote build '2' on cbxi4b-armhf-rb.debian.net. Fri Aug 14 13:58:26 UTC 2020 I: Deleting $TMPDIR on cbxi4b-armhf-rb.debian.net. Fri Aug 14 13:58:29 UTC 2020 I: proteinortho_5.16.b+dfsg-1_armhf.changes: Format: 1.8 Date: Tue, 08 Jan 2019 09:29:46 +0100 Source: proteinortho Binary: proteinortho proteinortho-dbgsym Architecture: armhf Version: 5.16.b+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: proteinortho - Detection of (Co-)orthologs in large-scale protein analysis Changes: proteinortho (5.16.b+dfsg-1) unstable; urgency=medium . * d/watch: Also catch letters in version number * New upstream version Checksums-Sha1: 1005307b062b30a8c99a21fcbf3447d5636b0b8b 6800 proteinortho-dbgsym_5.16.b+dfsg-1_armhf.deb f0590e435f93472652c7d77d6830fdb159dc7f94 5281 proteinortho_5.16.b+dfsg-1_armhf.buildinfo df026a07f000a40da74b1ee0ec6b11e9bb19929a 138176 proteinortho_5.16.b+dfsg-1_armhf.deb Checksums-Sha256: 13824b41045c418aa43e96f45f198ba9d25f17e500c68f401425b1c993f1e04a 6800 proteinortho-dbgsym_5.16.b+dfsg-1_armhf.deb f98faafd5905e59a0cd99daf2fa61ff250036fd6c24b1ee5bdae09f3d6bcdf12 5281 proteinortho_5.16.b+dfsg-1_armhf.buildinfo a0ef58193ec07cccbe04697854406fc46a20e1b939b429a0b72af5d7b8d8628f 138176 proteinortho_5.16.b+dfsg-1_armhf.deb Files: eab97ace2db6d9943378c1fc5363c6a6 6800 debug optional proteinortho-dbgsym_5.16.b+dfsg-1_armhf.deb 1926fd02884245be72b0db689d052deb 5281 science optional proteinortho_5.16.b+dfsg-1_armhf.buildinfo cfea07811e5e4df847574251650fb061 138176 science optional proteinortho_5.16.b+dfsg-1_armhf.deb Fri Aug 14 13:58:30 UTC 2020 I: diffoscope 155 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.mpSI37k7gy/proteinortho_5.16.b+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.mpSI37k7gy/proteinortho_5.16.b+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.mpSI37k7gy/proteinortho_5.16.b+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.mpSI37k7gy/b1/proteinortho_5.16.b+dfsg-1_armhf.changes /srv/reproducible-results/rbuild-debian/tmp.mpSI37k7gy/b2/proteinortho_5.16.b+dfsg-1_armhf.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: 0.219s) 0.219s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.025s) 0.025s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Fri Aug 14 13:58:31 UTC 2020 I: diffoscope 155 found no differences in the changes files, and a .buildinfo file also exists. Fri Aug 14 13:58:31 UTC 2020 I: proteinortho from buster built successfully and reproducibly on armhf. Fri Aug 14 13:58:32 UTC 2020 I: Submitting .buildinfo files to external archives: Fri Aug 14 13:58:32 UTC 2020 I: Submitting 8.0K b1/proteinortho_5.16.b+dfsg-1_armhf.buildinfo.asc Fri Aug 14 13:58:34 UTC 2020 I: Submitting 8.0K b2/proteinortho_5.16.b+dfsg-1_armhf.buildinfo.asc Fri Aug 14 13:58:35 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Aug 14 13:58:35 UTC 2020 I: Done submitting .buildinfo files. Fri Aug 14 13:58:35 UTC 2020 I: Removing signed proteinortho_5.16.b+dfsg-1_armhf.buildinfo.asc files: removed './b1/proteinortho_5.16.b+dfsg-1_armhf.buildinfo.asc' removed './b2/proteinortho_5.16.b+dfsg-1_armhf.buildinfo.asc'