I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 3 21:54:23 +14 2026
I: pbuilder-time-stamp: 1775202863
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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 [clonalorigin_1.0-8.dsc]
I: copying [./clonalorigin_1.0.orig.tar.gz]
I: copying [./clonalorigin_1.0-8.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./clonalorigin_1.0-8.dsc: unsupported subcommand
dpkg-source: info: extracting clonalorigin in clonalorigin-1.0
dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz
dpkg-source: info: unpacking clonalorigin_1.0-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying portability.patch
dpkg-source: info: applying gcc-11.patch
dpkg-source: info: applying shorten-test.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/245856/tmp/hooks/D01_modify_environment starting
debug: Running on ionos5-amd64.
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 Apr 3 07:54 /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/245856/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/245856/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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
BASH_VERSION='5.2.37(1)-release'
BUILDDIR=/build/reproducible-path
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=amd64
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
DIRSTACK=()
DISTRIBUTION=unstable
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=x86_64
HOST_ARCH=amd64
IFS='
'
INVOCATION_ID=382582656a364af99466d6f94f81f0f0
LANG=C
LANGUAGE=et_EE:et
LC_ALL=C
MACHTYPE=x86_64-pc-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=245856
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.cWfk0Skf/pbuilderrc_v5RA --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cWfk0Skf/b2 --logfile b2/build.log clonalorigin_1.0-8.dsc'
SUDO_GID=110
SUDO_UID=105
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://213.165.73.152:3128
I: uname -a
Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/245856/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: amd64
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), libgsl-dev, rename
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19779 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 libgsl-dev; however:
Package libgsl-dev is not installed.
pbuilder-satisfydepends-dummy depends on rename; however:
Package rename 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} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl28{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} po-debconf{a} rename{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget
0 packages upgraded, 34 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.9 MB of archives. After unpacking 89.5 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.8+dfsg-5 [116 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl28 amd64 2.8+dfsg-5 [994 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.8+dfsg-5 [1222 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-1 [21.8 kB]
Fetched 22.9 MB in 1s (23.5 MB/s)
Preconfiguring packages ...
Selecting previously unselected package sensible-utils.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
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(Reading database ... 50%
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(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 ... 19779 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.24_all.deb ...
Unpacking sensible-utils (0.0.24) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:amd64.
Preparing to unpack .../02-libmagic1t64_1%3a5.45-3+b1_amd64.deb ...
Unpacking libmagic1t64:amd64 (1:5.45-3+b1) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.45-3+b1_amd64.deb ...
Unpacking file (1:5.45-3+b1) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.23.1-1_amd64.deb ...
Unpacking gettext-base (0.23.1-1) ...
Selecting previously unselected package libuchardet0:amd64.
Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_amd64.deb ...
Unpacking libuchardet0:amd64 (0.0.8-1+b2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.23.0-7_amd64.deb ...
Unpacking groff-base (1.23.0-7) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.40.4-5_amd64.deb ...
Unpacking bsdextrautils (2.40.4-5) ...
Selecting previously unselected package libpipeline1:amd64.
Preparing to unpack .../08-libpipeline1_1.5.8-1_amd64.deb ...
Unpacking libpipeline1:amd64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.13.0-1_amd64.deb ...
Unpacking man-db (2.13.0-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-5_amd64.deb ...
Unpacking m4 (1.4.19-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../11-autoconf_2.72-3_all.deb ...
Unpacking autoconf (2.72-3) ...
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%3a1.17-3_all.deb ...
Unpacking automake (1:1.17-3) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../14-autopoint_0.23.1-1_all.deb ...
Unpacking autopoint (0.23.1-1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../15-libdebhelper-perl_13.24.1_all.deb ...
Unpacking libdebhelper-perl (13.24.1) ...
Selecting previously unselected package libtool.
Preparing to unpack .../16-libtool_2.5.4-3_all.deb ...
Unpacking libtool (2.5.4-3) ...
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 libfile-stripnondeterminism-perl.
Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ...
Unpacking dh-strip-nondeterminism (1.14.1-2) ...
Selecting previously unselected package libelf1t64:amd64.
Preparing to unpack .../21-libelf1t64_0.192-4_amd64.deb ...
Unpacking libelf1t64:amd64 (0.192-4) ...
Selecting previously unselected package dwz.
Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ...
Unpacking dwz (0.15-1+b1) ...
Selecting previously unselected package libunistring5:amd64.
Preparing to unpack .../23-libunistring5_1.3-1_amd64.deb ...
Unpacking libunistring5:amd64 (1.3-1) ...
Selecting previously unselected package libicu72:amd64.
Preparing to unpack .../24-libicu72_72.1-6_amd64.deb ...
Unpacking libicu72:amd64 (72.1-6) ...
Selecting previously unselected package libxml2:amd64.
Preparing to unpack .../25-libxml2_2.12.7+dfsg+really2.9.14-0.2+b2_amd64.deb ...
Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.23.1-1_amd64.deb ...
Unpacking gettext (0.23.1-1) ...
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_13.24.1_all.deb ...
Unpacking debhelper (13.24.1) ...
Selecting previously unselected package libgslcblas0:amd64.
Preparing to unpack .../30-libgslcblas0_2.8+dfsg-5_amd64.deb ...
Unpacking libgslcblas0:amd64 (2.8+dfsg-5) ...
Selecting previously unselected package libgsl28:amd64.
Preparing to unpack .../31-libgsl28_2.8+dfsg-5_amd64.deb ...
Unpacking libgsl28:amd64 (2.8+dfsg-5) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../32-libgsl-dev_2.8+dfsg-5_amd64.deb ...
Unpacking libgsl-dev (2.8+dfsg-5) ...
Selecting previously unselected package rename.
Preparing to unpack .../33-rename_2.02-1_all.deb ...
Unpacking rename (2.02-1) ...
Setting up libpipeline1:amd64 (1.5.8-1) ...
Setting up libicu72:amd64 (72.1-6) ...
Setting up bsdextrautils (2.40.4-5) ...
Setting up libgslcblas0:amd64 (2.8+dfsg-5) ...
Setting up libmagic-mgc (1:5.45-3+b1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.24.1) ...
Setting up libmagic1t64:amd64 (1:5.45-3+b1) ...
Setting up gettext-base (0.23.1-1) ...
Setting up m4 (1.4.19-5) ...
Setting up rename (2.02-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.45-3+b1) ...
Setting up libelf1t64:amd64 (0.192-4) ...
Setting up autotools-dev (20220109.1) ...
Setting up libunistring5:amd64 (1.3-1) ...
Setting up autopoint (0.23.1-1) ...
Setting up autoconf (2.72-3) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.24) ...
Setting up libuchardet0:amd64 (0.0.8-1+b2) ...
Setting up libgsl28:amd64 (2.8+dfsg-5) ...
Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b2) ...
Setting up automake (1:1.17-3) ...
update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.14.1-2) ...
Setting up gettext (0.23.1-1) ...
Setting up libgsl-dev (2.8+dfsg-5) ...
Setting up libtool (2.5.4-3) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.1-2) ...
Setting up groff-base (1.23.0-7) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.24.1) ...
Processing triggers for libc-bin (2.40-7) ...
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
I: Building the package
I: user script /srv/workspace/pbuilder/245856/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/245856/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/clonalorigin-1.0/ && 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 > ../clonalorigin_1.0-8_source.changes
dpkg-buildpackage: info: source package clonalorigin
dpkg-buildpackage: info: source version 1.0-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Étienne Mollier <emollier@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --sourcedirectory=warg
dh_auto_clean -O--sourcedirectory=warg
debian/rules execute_after_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0'
test ! -e warg/src/truth.xml.preserve \
|| mv -v warg/src/truth.xml.preserve warg/src/truth.xml
make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0'
dh_autoreconf_clean -O--sourcedirectory=warg
dh_clean -O--sourcedirectory=warg
debian/rules binary
dh binary --sourcedirectory=warg
dh_update_autotools_config -O--sourcedirectory=warg
dh_autoreconf -O--sourcedirectory=warg
configure.ac:58: warning: The macro 'AC_TRY_RUN' is obsolete.
configure.ac:58: You should run autoupdate.
./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from...
m4/gsl.m4:5: AX_PATH_GSL is expanded from...
configure.ac:58: the top level
configure.ac:58: warning: The macro 'AC_TRY_LINK' is obsolete.
configure.ac:58: You should run autoupdate.
./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from...
m4/gsl.m4:5: AX_PATH_GSL is expanded from...
configure.ac:58: the top level
configure.ac:41: installing 'config/compile'
configure.ac:9: installing 'config/install-sh'
configure.ac:9: installing 'config/missing'
Makefile.am: installing './INSTALL'
src/Makefile.am: installing 'config/depcomp'
parallel-tests: installing 'config/test-driver'
debian/rules execute_before_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0'
cp -v warg/src/truth.xml warg/src/truth.xml.preserve
'warg/src/truth.xml' -> 'warg/src/truth.xml.preserve'
make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0'
dh_auto_configure -O--sourcedirectory=warg
cd warg && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether sleep supports fractional seconds... yes
checking filesystem timestamp resolution... 0.01
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking xargs -n works... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for gsl-config... /usr/bin/gsl-config
checking for GSL - version >= 0.2.5... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99 or later... yes
checking for inline... inline
checking for floor... no
checking for pow... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating scripts/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
dh_auto_build -O--sourcedirectory=warg
cd warg && make -j42
make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
Making all in src
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make all-am
make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-data.o `test -f 'data.cpp' || echo './'`data.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-rng.o `test -f 'rng.cpp' || echo './'`rng.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-wargxml.o `test -f 'wargxml.cpp' || echo './'`wargxml.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-move.o `test -f 'move.cpp' || echo './'`move.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-metropolis.o `test -f 'metropolis.cpp' || echo './'`metropolis.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveaddedge.o `test -f 'moveaddedge.cpp' || echo './'`moveaddedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveageclonal.o `test -f 'moveageclonal.cpp' || echo './'`moveageclonal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movedelta.o `test -f 'movedelta.cpp' || echo './'`movedelta.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveedgechange.o `test -f 'moveedgechange.cpp' || echo './'`moveedgechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveregraftclonal.o `test -f 'moveregraftclonal.cpp' || echo './'`moveregraftclonal.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveremedge.o `test -f 'moveremedge.cpp' || echo './'`moveremedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moverho.o `test -f 'moverho.cpp' || echo './'`moverho.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movescaletree.o `test -f 'movescaletree.cpp' || echo './'`movescaletree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movegreedytree.o `test -f 'movegreedytree.cpp' || echo './'`movegreedytree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movesitechange.o `test -f 'movesitechange.cpp' || echo './'`movesitechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movetheta.o `test -f 'movetheta.cpp' || echo './'`movetheta.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movetimechange.o `test -f 'movetimechange.cpp' || echo './'`movetimechange.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-mpiutils.o `test -f 'mpiutils.cpp' || echo './'`mpiutils.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-node.o `test -f 'node.cpp' || echo './'`node.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-param.o `test -f 'param.cpp' || echo './'`param.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-recedge.o `test -f 'recedge.cpp' || echo './'`recedge.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-rectree.o `test -f 'rectree.cpp' || echo './'`rectree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-tree.o `test -f 'tree.cpp' || echo './'`tree.cpp
g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-weakarg.o `test -f 'weakarg.cpp' || echo './'`weakarg.cpp
weakarg.cpp:40:20: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
40 | ret.append(__DATE__);
| ^~~~~~~~
weakarg.cpp:42:20: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
42 | ret.append(__TIME__);
| ^~~~~~~~
data.cpp: In constructor 'weakarg::Data::Data(std::string)':
data.cpp:50:40: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
50 | }else if(getNumber(tmpname)!=which){
| ~~~~~~~~~~~~~~~~~~^~~~~~~
data.cpp: In member function 'void weakarg::Data::subset(std::vector<int>, int)':
data.cpp:169:14: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
169 | if (num<=0 &&seed>=0 || num<0) return;
| ~~~~~~~^~~~~~~~~
data.cpp:177:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
177 | for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
| ~^~~~~~~~~~~~
data.cpp:177:46: warning: comparison of integer expressions of different signedness: '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} and 'std::vector<bool>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
177 | for(int i=0;i<numv.size();i++) if(numv[i]<tried.size()&&numv[i]>=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<<numv[i]<<" were specified and have been removed from the analysis."<<endl;}}else{cerr<<"Warning: Invalid blocks were specified and have been removed from the analysis."<<endl;}
rng.cpp: In function 'long unsigned int weakarg::makerng(bool)':
rng.cpp:17:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
17 | long int rng_seed;
| ^~~~~~~~
rng.cpp: In function 'int weakarg::loadrng(std::string)':
rng.cpp:67:14: warning: variable 'rng_seed' set but not used [-Wunused-but-set-variable]
67 | long int rng_seed;
| ^~~~~~~~
rng.cpp: In function 'long unsigned int weakarg::seedrng(long unsigned int)':
rng.cpp:41:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
41 | fread(&tseed,sizeof(tseed),1,devrandom);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
moveregraftclonal.cpp: In member function 'virtual int weakarg::MoveRegraftClonal::move()':
moveregraftclonal.cpp:43:9: warning: unused variable 'notmovednode' [-Wunused-variable]
43 | int notmovednode=rectree->otherChild(origfather,which);
| ^~~~~~~~~~~~
moveregraftclonal.cpp: In member function 'void weakarg::MoveRegraftClonal::regraft(int, int)':
moveregraftclonal.cpp:157:61: warning: unused variable 'wnode' [-Wunused-variable]
157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
| ^~~~~
moveregraftclonal.cpp:157:93: warning: unused variable 'wtonode' [-Wunused-variable]
157 | Node *fanode=rectree->getNode(which)->getFather(), *wnode=rectree->getNode(which), *wtonode=rectree->getNode(whichto);
| ^~~~~~~
weakarg.cpp: In function 'int main(int, char**)':
weakarg.cpp:127:10: warning: variable 'setregions' set but not used [-Wunused-but-set-variable]
127 | bool setregions=false;
| ^~~~~~~~~~
weakarg.cpp: In function 'std::vector<double> weakarg::readInputFiles(Data*&, RecTree*&, std::vector<double>&, std::vector<int>&, std::vector<int>&, std::vector<std::__cxx11::basic_string<char> >, std::string, int)':
weakarg.cpp:342:14: warning: variable 'setregions' set but not used [-Wunused-but-set-variable]
342 | bool setregions=false;
| ^~~~~~~~~~
weakarg.cpp: In function 'bool weakarg::initializeTree(Data*&, RecTree*&, std::vector<std::__cxx11::basic_string<char> >, std::string)':
weakarg.cpp:404:9: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
404 | if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]);
| ^~
weakarg.cpp:404:45: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
404 | if(readparams) p->setTheta(pars[2]);p->setRho(pars[0]);p->setDelta(pars[2]);
| ^
movegreedytree.cpp: In member function 'void weakarg::MoveGreedyTree::applyChanges(std::vector<double>)':
movegreedytree.cpp:230:26: warning: variable 'tmp' set but not used [-Wunused-but-set-variable]
230 | int whichto=-1,tmp;
| ^~~
rectree.cpp: In member function 'int weakarg::RecTree::moveNodeTime(int, int*, double, int, std::vector<int>*, std::vector<int>*)':
rectree.cpp:1112:14: warning: variable 'newfather' set but not used [-Wunused-but-set-variable]
1112 | int newfather,notnewfather;
| ^~~~~~~~~
g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wl,-z,relro -Wl,-z,now -o warg warg-data.o warg-rng.o warg-wargxml.o warg-move.o warg-metropolis.o warg-moveaddedge.o warg-moveageclonal.o warg-movedelta.o warg-moveedgechange.o warg-moveregraftclonal.o warg-moveremedge.o warg-moverho.o warg-movescaletree.o warg-movegreedytree.o warg-movesitechange.o warg-movetheta.o warg-movetimechange.o warg-mpiutils.o warg-node.o warg-param.o warg-recedge.o warg-rectree.o warg-tree.o warg-weakarg.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm
make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
Making all in scripts
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
dh_auto_test -O--sourcedirectory=warg
cd warg && make -j42 check "TESTSUITEFLAGS=-j42 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
Making check in src
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make profilerun.sh
make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[3]: 'profilerun.sh' is up to date.
make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make check-TESTS
make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[4]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
PASS: profilerun.sh
============================================================================
Testsuite summary for clonalorigin 0.0.1
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
Making check in scripts
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedirectory=warg
dh_prep -O--sourcedirectory=warg
dh_auto_install --destdir=debian/clonalorigin/ -O--sourcedirectory=warg
cd warg && make -j42 install DESTDIR=/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
Making install in src
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin'
/usr/bin/install -c warg '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src'
Making install in scripts
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/mkdir -p '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin'
/usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts'
make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0'
dh_install
rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl
make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0'
dh_installdocs -O--sourcedirectory=warg
dh_installchangelogs -O--sourcedirectory=warg
dh_installman -O--sourcedirectory=warg
dh_installsystemduser -O--sourcedirectory=warg
dh_lintian -O--sourcedirectory=warg
dh_perl -O--sourcedirectory=warg
dh_link -O--sourcedirectory=warg
dh_strip_nondeterminism -O--sourcedirectory=warg
dh_compress -O--sourcedirectory=warg
dh_fixperms -O--sourcedirectory=warg
dh_missing -O--sourcedirectory=warg
dh_dwz -a -O--sourcedirectory=warg
dh_strip -a -O--sourcedirectory=warg
dh_makeshlibs -a -O--sourcedirectory=warg
dh_shlibdeps -a -O--sourcedirectory=warg
dh_installdeb -O--sourcedirectory=warg
dh_gencontrol -O--sourcedirectory=warg
dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -O--sourcedirectory=warg
dh_builddeb -O--sourcedirectory=warg
dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-8_amd64.deb'.
dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-8_amd64.deb'.
dpkg-genbuildinfo --build=binary -O../clonalorigin_1.0-8_amd64.buildinfo
dpkg-genchanges --build=binary -O../clonalorigin_1.0-8_amd64.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/245856/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/245856/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/245856 and its subdirectories
I: Current time: Fri Apr 3 21:56:52 +14 2026
I: pbuilder-time-stamp: 1775203012