I: pbuilder: network access will be disabled during build
I: Current time: Thu Jun 20 10:05:51 +14 2024
I: pbuilder-time-stamp: 1718827551
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
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 [libbio-tools-phylo-paml-perl_1.7.3-4.dsc]
I: copying [./libbio-tools-phylo-paml-perl_1.7.3.orig.tar.gz]
I: copying [./libbio-tools-phylo-paml-perl_1.7.3-4.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Oct 15 04:47:44 2022 +14
gpgv:                using RSA key B23862C415D6565A4E86CBD7579C160D4C9E23E8
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libbio-tools-phylo-paml-perl_1.7.3-4.dsc: no acceptable signature found
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_1.7.3-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying evolver-program-name.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/D01_modify_environment starting
debug: Running on codethink11-arm64.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
'/bin/sh' -> '/bin/bash'
lrwxrwxrwx 1 root root 9 Jun 20 10:06 /bin/sh -> /bin/bash
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/D02_print_environment starting
I: set
  BASH=/bin/sh
  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
  BASH_ALIASES=()
  BASH_ARGC=()
  BASH_ARGV=()
  BASH_CMDS=()
  BASH_LINENO=([0]="12" [1]="0")
  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
  BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
  BASH_VERSION='5.2.15(1)-release'
  BUILDDIR=/build
  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
  BUILDUSERNAME=pbuilder2
  BUILD_ARCH=arm64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 '
  DIRSTACK=()
  DISTRIBUTION=bookworm
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/var/lib/jenkins
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=aarch64
  HOST_ARCH=arm64
  IFS=' 	
  '
  LANG=C
  LANGUAGE=nl_BE:nl
  LC_ALL=C
  MACHTYPE=aarch64-unknown-linux-gnu
  MAIL=/var/mail/root
  OPTERR=1
  OPTIND=1
  OSTYPE=linux-gnu
  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
  PBCURRENTCOMMANDLINEOPERATION=build
  PBUILDER_OPERATION=build
  PBUILDER_PKGDATADIR=/usr/share/pbuilder
  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
  PBUILDER_SYSCONFDIR=/etc
  PIPESTATUS=([0]="0")
  POSIXLY_CORRECT=y
  PPID=6108
  PS4='+ '
  PWD=/
  SHELL=/bin/bash
  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
  SHLVL=3
  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/pbuilderrc_Q1Gf --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.RcEMNAnO/b2 --logfile b2/build.log --extrapackages usrmerge libbio-tools-phylo-paml-perl_1.7.3-4.dsc'
  SUDO_GID=117
  SUDO_UID=110
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  USERNAME=root
  _='I: set'
  http_proxy=http://192.168.101.16:3128
I: uname -a
  Linux i-capture-the-hostname 4.15.0-211-generic #222-Ubuntu SMP Tue Apr 18 18:58:27 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
  lrwxrwxrwx 1 root root 7 Jun 18 06:47 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/6108/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 <pbuilder-maint@lists.alioth.debian.org>
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-compat (= 13), 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 ... 19616 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-compat (= 13); however:
  Package debhelper-compat 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} bsdextrautils{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} libdata-stag-perl{a} libdebhelper-perl{a} libdevel-checkbin-perl{a} libelf1{a} libfile-sort-perl{a} libfile-stripnondeterminism-perl{a} libicu72{a} libio-pty-perl{a} libio-string-perl{a} libipc-run-perl{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{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 libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-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 wget 
0 packages upgraded, 39 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.8 MB of archives. After unpacking 89.3 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 libio-string-perl all 1.08-4 [12.1 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 libdata-stag-perl all 0.14-3 [448 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 libbio-perl-perl all 1.7.8-1 [2603 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 libio-pty-perl arm64 1:1.17-1 [34.5 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 libipc-run-perl all 20220807.0-1 [104 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libfile-sort-perl all 1.01-3 [21.3 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libbio-perl-run-perl all 1.7.3-9 [605 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 libdevel-checkbin-perl all 0.04-3 [5228 B]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 paml arm64 4.9j+dfsg-4 [632 kB]
Fetched 22.8 MB in 1s (39.4 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
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(Reading database ... 80%
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(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:arm64.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ...
Unpacking libmagic1:arm64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ...
Unpacking m4 (1.4.19-3) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.21-12_all.deb ...
Unpacking autopoint (0.21-12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ...
Unpacking libdebhelper-perl (13.11.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.4.7-5_all.deb ...
Unpacking libtool (2.4.7-5) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ...
Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.13.1-1) ...
Selecting previously unselected package libelf1:arm64.
Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ...
Unpacking libelf1:arm64 (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_arm64.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:arm64.
Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ...
Unpacking libicu72:arm64 (72.1-3) ...
Selecting previously unselected package libxml2:arm64.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_arm64.deb ...
Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_arm64.deb ...
Unpacking gettext (0.21-12) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.6) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../29-debhelper_13.11.4_all.deb ...
Unpacking debhelper (13.11.4) ...
Selecting previously unselected package libio-string-perl.
Preparing to unpack .../30-libio-string-perl_1.08-4_all.deb ...
Unpacking libio-string-perl (1.08-4) ...
Selecting previously unselected package libdata-stag-perl.
Preparing to unpack .../31-libdata-stag-perl_0.14-3_all.deb ...
Unpacking libdata-stag-perl (0.14-3) ...
Selecting previously unselected package libbio-perl-perl.
Preparing to unpack .../32-libbio-perl-perl_1.7.8-1_all.deb ...
Unpacking libbio-perl-perl (1.7.8-1) ...
Selecting previously unselected package libio-pty-perl.
Preparing to unpack .../33-libio-pty-perl_1%3a1.17-1_arm64.deb ...
Unpacking libio-pty-perl (1:1.17-1) ...
Selecting previously unselected package libipc-run-perl.
Preparing to unpack .../34-libipc-run-perl_20220807.0-1_all.deb ...
Unpacking libipc-run-perl (20220807.0-1) ...
Selecting previously unselected package libfile-sort-perl.
Preparing to unpack .../35-libfile-sort-perl_1.01-3_all.deb ...
Unpacking libfile-sort-perl (1.01-3) ...
Selecting previously unselected package libbio-perl-run-perl.
Preparing to unpack .../36-libbio-perl-run-perl_1.7.3-9_all.deb ...
Unpacking libbio-perl-run-perl (1.7.3-9) ...
Selecting previously unselected package libdevel-checkbin-perl.
Preparing to unpack .../37-libdevel-checkbin-perl_0.04-3_all.deb ...
Unpacking libdevel-checkbin-perl (0.04-3) ...
Selecting previously unselected package paml.
Preparing to unpack .../38-paml_4.9j+dfsg-4_arm64.deb ...
Unpacking paml (4.9j+dfsg-4) ...
Setting up libpipeline1:arm64 (1.5.7-1) ...
Setting up libicu72:arm64 (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libdevel-checkbin-perl (0.04-3) ...
Setting up libio-pty-perl (1:1.17-1) ...
Setting up libmagic-mgc (1:5.44-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.4) ...
Setting up libmagic1:arm64 (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up m4 (1.4.19-3) ...
Setting up file (1:5.44-3) ...
Setting up libio-string-perl (1.08-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up libipc-run-perl (20220807.0-1) ...
Setting up autoconf (2.71-3) ...
Setting up libdata-stag-perl (0.14-3) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up paml (4.9j+dfsg-4) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libbio-perl-perl (1.7.8-1) ...
Setting up libelf1:arm64 (0.188-2.1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ...
Setting up libfile-sort-perl (1.01-3) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up libbio-perl-run-perl (1.7.3-9) ...
Setting up gettext (0.21-12) ...
Setting up libtool (2.4.7-5) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.4) ...
Processing triggers for libc-bin (2.36-9) ...
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...
usrmerge is already the newest version (35).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/A99_set_merged_usr starting
Re-configuring usrmerge...
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/A99_set_merged_usr finished
hostname: Temporary failure in name resolution
I: Running cd /build/libbio-tools-phylo-paml-perl-1.7.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../libbio-tools-phylo-paml-perl_1.7.3-4_source.changes
dpkg-buildpackage: info: source package libbio-tools-phylo-paml-perl
dpkg-buildpackage: info: source version 1.7.3-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Jelmer Vernooij <jelmer@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
	/usr/bin/perl 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=aarch64-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 -j8
make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3'
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.pm blib/lib/Bio/Tools/Phylo/PAML.pm
cp lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Yn00.pm
cp lib/Bio/Tools/Phylo/PAML/Result.pm blib/lib/Bio/Tools/Phylo/PAML/Result.pm
cp lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
cp lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm blib/lib/Bio/Tools/Run/Phylo/PAML/Evolver.pm
cp lib/Bio/Tools/Phylo/PAML/Codeml.pm blib/lib/Bio/Tools/Phylo/PAML/Codeml.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 -j8 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
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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
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ok 214 - codeml 4.3 two NSSites models
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ok 238 - NEB positively selected sites
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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
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ok 14 - got results
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ok 28 - got results
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1..29
ok
All tests successful.
Files=8, Tests=293,  7 wallclock secs ( 0.16 usr  0.03 sys +  6.19 cusr  0.59 csys =  6.97 CPU)
Result: PASS
make[1]: Leaving directory '/build/libbio-tools-phylo-paml-perl-1.7.3'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install --destdir=debian/libbio-tools-phylo-paml-perl/
	make -j8 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/Evolver.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/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/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/Codeml.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/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::Yn00.3pm
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::Codeml.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::Baseml.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::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.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'
   debian/rules override_dh_install
make[1]: Entering directory '/build/libbio-tools-phylo-paml-perl-1.7.3'
dh_install
sed -i '1s|^#!/usr/bin/env perl|#!/usr/bin/perl|' /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_1.7.3-4_all.deb'.
 dpkg-genbuildinfo --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_arm64.buildinfo
 dpkg-genchanges --build=binary -O../libbio-tools-phylo-paml-perl_1.7.3-4_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)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/6108/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env 
I: removing directory /srv/workspace/pbuilder/6108 and its subdirectories
I: Current time: Thu Jun 20 10:06:49 +14 2024
I: pbuilder-time-stamp: 1718827609