Tue Jul 7 17:11:27 UTC 2020 I: starting to build libbio-tools-phylo-paml-perl/buster/i386 on jenkins on '2020-07-07 17:11' Tue Jul 7 17:11:27 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_9/8703/console.log Tue Jul 7 17:11:27 UTC 2020 I: Downloading source for buster/libbio-tools-phylo-paml-perl=1.7.3-2 --2020-07-07 17:11:27-- http://deb.debian.org/debian/pool/main/libb/libbio-tools-phylo-paml-perl/libbio-tools-phylo-paml-perl_1.7.3-2.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2465 (2.4K) Saving to: ‘libbio-tools-phylo-paml-perl_1.7.3-2.dsc’ 0K .. 100% 176M=0s 2020-07-07 17:11:27 (176 MB/s) - ‘libbio-tools-phylo-paml-perl_1.7.3-2.dsc’ saved [2465/2465] Tue Jul 7 17:11:27 UTC 2020 I: libbio-tools-phylo-paml-perl_1.7.3-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbio-tools-phylo-paml-perl Binary: libbio-tools-phylo-paml-perl Architecture: all Version: 1.7.3-2 Maintainer: Debian Perl Group Uploaders: David Miguel Susano Pinto Homepage: https://metacpan.org/release/Bio-Tools-Phylo-PAML Standards-Version: 4.1.5 Vcs-Browser: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl Vcs-Git: https://salsa.debian.org/perl-team/modules/packages/libbio-tools-phylo-paml-perl.git Testsuite: autopkgtest-pkg-perl Build-Depends: debhelper (>= 10) Build-Depends-Indep: libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl Package-List: libbio-tools-phylo-paml-perl deb science optional arch=all Checksums-Sha1: 4ced4b0905ad258cb119656f84b442bca950487a 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz ce85d06455016d3669df5b36c61bf99a4c11f7d5 2436 libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz Checksums-Sha256: 424dccca82b61e3daf62f52e33de35efdbe1b69644d07015e987671fa7130cb4 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz 9312c2b696ee512dce8495ea1a0a8da5d7c04b74af4a088c7ac7c36b17b361d6 2436 libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz Files: 0030a118c958b93967a470b8bc3e21a0 137819 libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz e4886bb10e001031d8c2fe6545e1ac99 2436 libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQKTBAEBCgB9FiEE0eExbpOnYKgQTYX6uzpoAYZJqgYFAltExEhfFIAAAAAALgAo aXNzdWVyLWZwckBub3RhdGlvbnMub3BlbnBncC5maWZ0aGhvcnNlbWFuLm5ldEQx RTEzMTZFOTNBNzYwQTgxMDREODVGQUJCM0E2ODAxODY0OUFBMDYACgkQuzpoAYZJ qgaE2g//dgOhBxABDTCG3dV4bz54xLcOAfKYoBEJEvm+J8uQd0BnNQmk8nUjcBBA vhJhkns55htH8tVPj+gthGgtFAm1DF1WKNPQKVB/1nuKRZxzhE30F3Q79e8uN1n4 P2plDenG3f/3K5dsmlga9Egmg8EaTr62MOQdwvfhI51vBR08bX4IbxtvTN7LQg3O c+ErbqhDo+cPKM4KKCNYA8dq8jtxaXf7L59nRdNIuEPaIDMfFqNP/U9GmI3Ra3E5 TOMM607z8xLiSXv5oDt6LyGYKMSFP1wcQg0uGIbdGN1upT222aHZ+8fh4ptbfBN5 10yjZWzCPQV7jrGXek2OV0PnrLAU6Qaic0l7TUu6Fad6Fy3wbrG3z/3SSn4e0ddF HxWJgEmn2atSGPIK//jJ/CX2LWaENyKLpTkXn9qPwkP9+hpGdoR6v3S8IeYSFY64 m16aeEd/0muAmdBI54EFx0HR4cJMC5oJK3WRntg6KxvwSE+LfOyp0At0KVOBgF5B oGuuHpzMzuU3uTZ+8eLoM6xf+OcAo5NnU+IwJPgSW++N6GUec3rm4Unm88bJWhtn I3AU9nO+aenn5SvcuXMYmOVLLT/isaxQdRBSGILxH3N2lV9nRDsIuB8Z+rlodvNl I/mbr6CshyYfiY72IrcTO2qzvRV4XJOXG8r81sxiAV1jbXwqlsE= =K3wS -----END PGP SIGNATURE----- Tue Jul 7 17:11:27 UTC 2020 I: Checking whether the package is not for us Tue Jul 7 17:11:27 UTC 2020 I: Starting 1st build on remote node profitbricks-build2-i386.debian.net. Tue Jul 7 17:11:27 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build2-i386.debian.net. Tue Jul 7 17:15:28 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. W: cgroups are not available on the host, not using them. unshare: unshare failed: Cannot allocate memory W: pbuilder: unshare CLONE_NEWNET not available I: pbuilder: network access is available during build! I: Current time: Tue Jul 7 05:11:29 -12 2020 I: pbuilder-time-stamp: 1594141889 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 [libbio-tools-phylo-paml-perl_1.7.3-2.dsc] I: copying [./libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz] I: copying [./libbio-tools-phylo-paml-perl_1.7.3-2.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 Tue Jul 10 02:35:52 2018 -12 gpgv: using RSA key D1E1316E93A760A8104D85FABB3A68018649AA06 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./libbio-tools-phylo-paml-perl_1.7.3-2.dsc dpkg-source: info: extracting libbio-tools-phylo-paml-perl in libbio-tools-phylo-paml-perl-1.7.3 dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz dpkg-source: info: unpacking libbio-tools-phylo-paml-perl_1.7.3-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying evolver-program-name.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/30699/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=' ' 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='30699' 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.mkFIwMqMe9/pbuilderrc_XYW0 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.mkFIwMqMe9/b1 --logfile b1/build.log libbio-tools-phylo-paml-perl_1.7.3-2.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/sbin/chroot' http_proxy='http://78.137.99.97:3128' I: uname -a Linux profitbricks-build2-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 5476 -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 6 20:26 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/30699/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 (>= 10), libbio-perl-perl, libbio-perl-run-perl, libdevel-checkbin-perl, libio-string-perl, paml, perl 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 (>= 10); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-perl; however: Package libbio-perl-perl is not installed. pbuilder-satisfydepends-dummy depends on libbio-perl-run-perl; however: Package libbio-perl-run-perl is not installed. pbuilder-satisfydepends-dummy depends on libdevel-checkbin-perl; however: Package libdevel-checkbin-perl is not installed. pbuilder-satisfydepends-dummy depends on libio-string-perl; however: Package libio-string-perl is not installed. pbuilder-satisfydepends-dummy depends on paml; however: Package paml 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} libbio-perl-perl{a} libbio-perl-run-perl{a} libbsd0{a} libcroco3{a} libdata-stag-perl{a} libdevel-checkbin-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} libio-string-perl{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libpipeline1{a} libsigsegv2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} paml{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libace-perl libalgorithm-diff-perl libalgorithm-munkres-perl libarchive-cpio-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libgd-perl libglib2.0-data libgpm2 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl libipc-run-perl liblist-moreutils-perl libltdl-dev libmail-sendmail-perl libmldbm-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-graph-perl libsvg-perl liburi-perl libwww-perl libxml-dom-xpath-perl libxml-libxml-perl libxml-libxslt-perl libxml-parser-perl libxml-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl lynx perl-tk shared-mime-info wget xdg-user-dirs 0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded. Need to get 25.8 MB of archives. After unpacking 91.6 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 sensible-utils all 0.0.12 [15.8 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 10 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 11 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 12 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 14 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 15 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 16 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 17 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 19 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 20 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 22 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 23 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 24 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 26 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 27 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 28 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 29 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 30 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 31 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 32 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 33 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libio-string-perl all 1.08-3 [12.3 kB] Get: 35 http://deb.debian.org/debian buster/main i386 libdata-stag-perl all 0.14-2 [448 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libbio-perl-perl all 1.7.2-3 [4553 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libbio-perl-run-perl all 1.7.2-4 [748 kB] Get: 38 http://deb.debian.org/debian buster/main i386 libdevel-checkbin-perl all 0.04-1 [5418 B] Get: 39 http://deb.debian.org/debian buster/main i386 paml i386 4.9h+dfsg-1 [661 kB] Fetched 25.8 MB in 24s (1095 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 ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../04-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../06-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../07-libmagic-mgc_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic-mgc (1:5.35-4+deb10u1) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../08-libmagic1_1%3a5.35-4+deb10u1_i386.deb ... Unpacking libmagic1:i386 (1:5.35-4+deb10u1) ... 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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: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 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 debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... 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/libbio-tools-phylo-paml-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl dpkg-buildpackage: info: source version 1.7.3-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by David Miguel Susano Pinto dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure perl -I. Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/libbio-tools-phylo-paml-perl-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/libbio-tools-phylo-paml-perl-1.7.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro" Warning: prerequisite Bio::Tools::Run::Alignment::Clustalw 0 not found. Warning: prerequisite Bio::Tools::Run::Alignment::TCoffee 0 not found. Locating bin:basemlg... found at /usr/bin/basemlg. Locating bin:codeml... found at /usr/bin/codeml. Locating bin:paml-evolver... found at /usr/bin/paml-evolver. Locating bin:yn00... found at /usr/bin/yn00. Checking if your kit is complete... Looks good Generating a Unix-style Makefile Writing Makefile for Bio::Tools::Phylo::PAML Writing MYMETA.yml and MYMETA.json dh_auto_build make -j10 make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3' cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Phylo/PAML.pm blib/lib/Bio/Tools/Phylo/PAML.pm cp lib/Bio/Tools/Phylo/PAML/ModelResult.pm blib/lib/Bio/Tools/Phylo/PAML/ModelResult.pm cp lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Codeml.pm cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm cp bin/bp_pairwise_kaks blib/script/bp_pairwise_kaks "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/bp_pairwise_kaks Manifying 1 pod document Manifying 8 pod documents make[1]: Leaving directory '/build/libbio-tools-phylo-paml-perl-1.7.3' dh_auto_test make -j10 test TEST_VERBOSE=1 make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3' PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t t/00-compile.t ........... 1..9 ok 1 - Bio/Tools/Phylo/PAML.pm loaded ok ok 2 - Bio/Tools/Phylo/PAML/Codeml.pm loaded ok ok 3 - Bio/Tools/Phylo/PAML/ModelResult.pm loaded ok ok 4 - Bio/Tools/Phylo/PAML/Result.pm loaded ok ok 5 - Bio/Tools/Run/Phylo/PAML/Baseml.pm loaded ok ok 6 - Bio/Tools/Run/Phylo/PAML/Codeml.pm loaded ok ok 7 - Bio/Tools/Run/Phylo/PAML/Evolver.pm loaded ok ok 8 - Bio/Tools/Run/Phylo/PAML/Yn00.pm loaded ok ok 9 # skip bin/bp_pairwise_kaks isn't perl ok t/author-eol.t ........... skipped: these tests are for testing by the author t/author-mojibake.t ...... skipped: these tests are for testing by the author t/author-no-tabs.t ....... skipped: these tests are for testing by the author t/author-pod-coverage.t .. skipped: these tests are for testing by the author t/author-pod-syntax.t .... skipped: these tests are for testing by the author t/PAML-parser.t .......... ok 1 ok 2 ok 3 ok 4 ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 ok 15 ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 ok 29 ok 30 ok 31 ok 32 ok 33 ok 34 ok 35 ok 36 ok 37 ok 38 ok 39 ok 40 ok 41 ok 42 ok 43 ok 44 ok 45 ok 46 ok 47 ok 48 ok 49 ok 50 ok 51 ok 52 ok 53 ok 54 ok 55 ok 56 ok 57 ok 58 ok 59 ok 60 ok 61 ok 62 ok 63 ok 64 ok 65 ok 66 ok 67 ok 68 ok 69 ok 70 ok 71 ok 72 ok 73 ok 74 ok 75 ok 76 ok 77 ok 78 ok 79 ok 80 ok 81 ok 82 ok 83 ok 84 ok 85 ok 86 ok 87 ok 88 ok 89 ok 90 ok 91 ok 92 ok 93 ok 94 ok 95 ok 96 ok 97 ok 98 ok 99 ok 100 ok 101 ok 102 ok 103 ok 104 ok 105 ok 106 ok 107 ok 108 ok 109 ok 110 ok 111 ok 112 ok 113 ok 114 ok 115 ok 116 ok 117 ok 118 ok 119 ok 120 ok 121 ok 122 ok 123 ok 124 ok 125 ok 126 ok 127 ok 128 ok 129 ok 130 ok 131 ok 132 ok 133 ok 134 ok 135 ok 136 ok 137 ok 138 ok 139 ok 140 ok 141 ok 142 ok 143 ok 144 ok 145 ok 146 ok 147 ok 148 ok 149 ok 150 ok 151 ok 152 ok 153 ok 154 ok 155 ok 156 ok 157 ok 158 ok 159 ok 160 ok 161 ok 162 - node\#8 reconstructed seq ok 163 - ancestral AA ok 164 - ancestral AA ok 165 - derived AA ok 166 - ancestral AA ok 167 - ancestral AA ok 168 - derived AA ok 169 - derived AA ok 170 ok 171 ok 172 ok 173 ok 174 ok 175 ok 176 ok 177 ok 178 ok 179 ok 180 ok 181 ok 182 ok 183 ok 184 ok 185 ok 186 ok 187 ok 188 ok 189 ok 190 ok 191 ok 192 ok 193 ok 194 ok 195 ok 196 ok 197 ok 198 ok 199 ok 200 ok 201 ok 202 ok 203 - codeml 4.3 runmode=-2 ok 204 ok 205 ok 206 ok 207 ok 208 ok 209 ok 210 ok 211 ok 212 ok 213 ok 214 - codeml 4.3 two NSSites models ok 215 ok 216 ok 217 ok 218 ok 219 ok 220 ok 221 ok 222 ok 223 ok 224 ok 225 ok 226 ok 227 ok 228 ok 229 ok 230 ok 231 ok 232 ok 233 ok 234 ok 235 ok 236 ok 237 ok 238 - NEB positively selected sites ok 239 ok 240 ok 241 ok 242 ok 243 ok 244 ok 245 ok 246 ok 247 ok 248 ok 249 ok 250 - bug 3040 ok 251 - bug 3365 ok 252 - bug 3366 ok 253 - bug 3367 ok 254 - bug 3332 ok 255 - bug 3331 1..255 ok t/PAML-run.t ............. ok 1 ok 2 ok 3 - got results ok 4 - got a result ok 5 ok 6 ok 7 ok 8 ok 9 ok 10 ok 11 ok 12 ok 13 ok 14 - got results ok 15 - got a result ok 16 ok 17 ok 18 ok 19 ok 20 ok 21 ok 22 ok 23 ok 24 ok 25 ok 26 ok 27 ok 28 - got results ok 29 1..29 ok All tests successful. Files=8, Tests=293, 5 wallclock secs ( 0.08 usr 0.02 sys + 3.42 cusr 0.30 csys = 3.82 CPU) Result: PASS make[1]: Leaving directory '/build/libbio-tools-phylo-paml-perl-1.7.3' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install make -j10 install DESTDIR=/build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl AM_UPDATE_INFO_DIR=no PREFIX=/usr make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3' Manifying 1 pod document Manifying 8 pod documents Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Baseml.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Yn00.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Codeml.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Run/Phylo/PAML/Evolver.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Result.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/ModelResult.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/perl5/Bio/Tools/Phylo/PAML/Codeml.pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man1/bp_pairwise_kaks.1p Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Baseml.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Evolver.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Yn00.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Codeml.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::Result.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML::ModelResult.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Phylo::PAML.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/share/man/man3/Bio::Tools::Run::Phylo::PAML::Codeml.3pm Installing /build/libbio-tools-phylo-paml-perl-1.7.3/debian/libbio-tools-phylo-paml-perl/usr/bin/bp_pairwise_kaks make[1]: Leaving directory '/build/libbio-tools-phylo-paml-perl-1.7.3' dh_installdocs dh_installchangelogs dh_installman dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbio-tools-phylo-paml-perl' in '../libbio-tools-phylo-paml-perl_1.7.3-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../libbio-tools-phylo-paml-perl_1.7.3-2_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: 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/30699 and its subdirectories I: Current time: Tue Jul 7 05:15:27 -12 2020 I: pbuilder-time-stamp: 1594142127 Tue Jul 7 17:15:28 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build6-i386.debian.net. Tue Jul 7 17:15:28 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build6-i386.debian.net. Tue Jul 7 17:15:53 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. Tue Jul 7 17:15:53 UTC 2020 I: libbio-tools-phylo-paml-perl_1.7.3-2_i386.changes: Format: 1.8 Date: Tue, 10 Jul 2018 13:02:50 +0100 Source: libbio-tools-phylo-paml-perl Binary: libbio-tools-phylo-paml-perl Architecture: all Version: 1.7.3-2 Distribution: unstable Urgency: medium Maintainer: Debian Perl Group Changed-By: David Miguel Susano Pinto Description: libbio-tools-phylo-paml-perl - Bioperl interface to the PAML suite Closes: 903456 Changes: libbio-tools-phylo-paml-perl (1.7.3-2) unstable; urgency=medium . * This package also breaks/replaces bioperl << 1.7.2 Closes: #903456 * Bump Standards-Version to 4.1.5 (no changes needed) Checksums-Sha1: c08884606190ccbc1cb072282bcea74a587e83bc 80560 libbio-tools-phylo-paml-perl_1.7.3-2_all.deb 32dfdccc9b919d699eba4164226d534d17edbe5e 4626 libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo Checksums-Sha256: 588d553a182a7e7647c0b73107c57db337f636884f10e8f29a197e8360cf83d3 80560 libbio-tools-phylo-paml-perl_1.7.3-2_all.deb 5bcdf93f1c61c9b0b40dff91ca553ef78757b5b453564b1f6b16a62d662042c1 4626 libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo Files: 0efe9d63b2332cf01692c0e534050ca5 80560 science optional libbio-tools-phylo-paml-perl_1.7.3-2_all.deb 525cb9bbf4db23b995fe41766233332c 4626 science optional libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo Tue Jul 7 17:16:06 UTC 2020 I: diffoscope 150 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.mkFIwMqMe9/libbio-tools-phylo-paml-perl_1.7.3-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.mkFIwMqMe9/libbio-tools-phylo-paml-perl_1.7.3-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.mkFIwMqMe9/libbio-tools-phylo-paml-perl_1.7.3-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.mkFIwMqMe9/b1/libbio-tools-phylo-paml-perl_1.7.3-2_i386.changes /srv/reproducible-results/rbuild-debian/tmp.mkFIwMqMe9/b2/libbio-tools-phylo-paml-perl_1.7.3-2_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: 0.292s) 0.292s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.035s) 0.034s 10 calls diffoscope.comparators.binary.FilesystemFile 0.000s 8 calls abc.DotChangesFile Tue Jul 7 17:16:28 UTC 2020 I: diffoscope 150 found no differences in the changes files, and a .buildinfo file also exists. Tue Jul 7 17:16:28 UTC 2020 I: libbio-tools-phylo-paml-perl from buster built successfully and reproducibly on i386. Tue Jul 7 17:16:29 UTC 2020 I: Submitting .buildinfo files to external archives: Tue Jul 7 17:16:29 UTC 2020 I: Submitting 8.0K b1/libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo.asc Tue Jul 7 17:16:29 UTC 2020 I: Submitting 8.0K b2/libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo.asc Tue Jul 7 17:16:32 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Jul 7 17:16:32 UTC 2020 I: Done submitting .buildinfo files. Tue Jul 7 17:16:32 UTC 2020 I: Removing signed libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo.asc files: removed './b1/libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo.asc' removed './b2/libbio-tools-phylo-paml-perl_1.7.3-2_i386.buildinfo.asc'