Thu Apr 27 18:34:42 UTC 2023 I: starting to build clonalorigin/bookworm/arm64 on jenkins on '2023-04-27 18:34'
Thu Apr 27 18:34:42 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_21/22959/console.log
Thu Apr 27 18:34:42 UTC 2023 I: Downloading source for bookworm/clonalorigin=1.0-6
--2023-04-27 18:34:43-- http://cdn-fastly.deb.debian.org/debian/pool/main/c/clonalorigin/clonalorigin_1.0-6.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 1997 (2.0K) [text/prs.lines.tag]
Saving to: ‘clonalorigin_1.0-6.dsc’
0K . 100% 183M=0s
2023-04-27 18:34:43 (183 MB/s) - ‘clonalorigin_1.0-6.dsc’ saved [1997/1997]
Thu Apr 27 18:34:43 UTC 2023 I: clonalorigin_1.0-6.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: clonalorigin
Binary: clonalorigin
Architecture: any
Version: 1.0-6
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/xavierdidelot/clonalorigin
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/clonalorigin
Vcs-Git: https://salsa.debian.org/med-team/clonalorigin.git
Build-Depends: debhelper-compat (= 13), libgsl-dev, rename
Package-List:
clonalorigin deb science optional arch=any
Checksums-Sha1:
a7bc183ea6aea575a5f5fa9217d9112d2ff4884f 185865 clonalorigin_1.0.orig.tar.gz
21c5cad96af167c2712eeb93a794d23917c19a3e 8736 clonalorigin_1.0-6.debian.tar.xz
Checksums-Sha256:
73962415160b8b496c81d3e9cbbf68f76c02caf4dd6b41860f01d493b71c6e3a 185865 clonalorigin_1.0.orig.tar.gz
8d30d10f26b0f3ecc8943e5908a7e7b921ce79a644215ba37653c9db59a1fbeb 8736 clonalorigin_1.0-6.debian.tar.xz
Files:
310a0c5714e7629c052ab4da50c90f44 185865 clonalorigin_1.0.orig.tar.gz
39fc9d35ba9d4f873dac18ea3ff193f6 8736 clonalorigin_1.0-6.debian.tar.xz
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Thu Apr 27 18:34:43 UTC 2023 I: Checking whether the package is not for us
Thu Apr 27 18:34:43 UTC 2023 I: Starting 1st build on remote node codethink14-arm64.debian.net.
Thu Apr 27 18:34:43 UTC 2023 I: Preparing to do remote build '1' on codethink14-arm64.debian.net.
Thu Apr 27 19:02:28 UTC 2023 I: Deleting $TMPDIR on codethink14-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu Apr 27 06:34:46 -12 2023
I: pbuilder-time-stamp: 1682620486
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 [clonalorigin_1.0-6.dsc]
I: copying [./clonalorigin_1.0.orig.tar.gz]
I: copying [./clonalorigin_1.0-6.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Oct 21 07:09:10 2021 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./clonalorigin_1.0-6.dsc: no acceptable signature found
dpkg-source: info: extracting clonalorigin in clonalorigin-1.0
dpkg-source: info: unpacking clonalorigin_1.0.orig.tar.gz
dpkg-source: info: unpacking clonalorigin_1.0-6.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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/21608/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='21608'
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/r-b-build.uWppAzgF/pbuilderrc_KTtf --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.uWppAzgF/b1 --logfile b1/build.log clonalorigin_1.0-6.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink14-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Apr 24 22:27 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/21608/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), 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 ... 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 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} libelf1{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{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 20.3 MB of archives. After unpacking 84.9 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 libgslcblas0 arm64 2.7.1+dfsg-3+b1 [82.3 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 libgsl27 arm64 2.7.1+dfsg-3+b1 [824 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 libgsl-dev arm64 2.7.1+dfsg-3+b1 [1035 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 rename all 2.01-1 [21.0 kB]
Fetched 20.3 MB in 1s (35.0 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
(Reading database ...
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(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) ...
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Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ...
Unpacking man-db (2.11.2-2) ...
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Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ...
Unpacking m4 (1.4.19-3) ...
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Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ...
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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) ...
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Preparing to unpack .../17-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
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Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
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Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ...
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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 ...
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Unpacking dwz (0.15-1) ...
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Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ...
Unpacking libicu72:arm64 (72.1-3) ...
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Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ...
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Unpacking debhelper (13.11.4) ...
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Unpacking libgslcblas0:arm64 (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package libgsl27:arm64.
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Unpacking libgsl-dev (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package rename.
Preparing to unpack .../33-rename_2.01-1_all.deb ...
Unpacking rename (2.01-1) ...
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 libgslcblas0:arm64 (2.7.1+dfsg-3+b1) ...
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 libgsl27:arm64 (2.7.1+dfsg-3+b1) ...
Setting up m4 (1.4.19-3) ...
Setting up rename (2.01-1) ...
update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode
Setting up file (1:5.44-3) ...
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-12) ...
Setting up autoconf (2.71-3) ...
Setting up sensible-utils (0.0.17+nmu1) ...
Setting up libuchardet0:arm64 (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:arm64 (0.188-2.1) ...
Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ...
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 gettext (0.21-12) ...
Setting up libgsl-dev (2.7.1+dfsg-3+b1) ...
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
I: Building the package
I: Running cd /build/clonalorigin-1.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../clonalorigin_1.0-6_source.changes
dpkg-buildpackage: info: source package clonalorigin
dpkg-buildpackage: info: source version 1.0-6
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --sourcedirectory=warg
dh_auto_clean -O--sourcedirectory=warg
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.m4:2997: 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.m4:2920: 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'
dh_auto_configure -O--sourcedirectory=warg
cd warg && ./configure --build=aarch64-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/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
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 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... 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 -j8
make[1]: Entering directory '/build/clonalorigin-1.0/warg'
Making all in src
make[2]: Entering directory '/build/clonalorigin-1.0/warg/src'
make all-am
make[3]: Entering directory '/build/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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movedelta.o `test -f 'movedelta.cpp' || echo './'`movedelta.cpp
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);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-moveremedge.o `test -f 'moveremedge.cpp' || echo './'`moveremedge.cpp
moveageclonal.cpp: In member function 'virtual int weakarg::MoveAgeClonal::move()':
moveageclonal.cpp:126:43: warning: 'movetemp' may be used uninitialized [-Wmaybe-uninitialized]
126 | if(movetemp!=NULL) delete(movetemp);
| ^
moveageclonal.cpp:105:17: note: 'movetemp' was declared here
105 | Metropolis *movetemp;
| ^~~~~~~~
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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -c -o warg-movesitechange.o `test -f 'movesitechange.cpp' || echo './'`movesitechange.cpp
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);
| ^~~~~~~
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;
| ^~~
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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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__);
| ^~~~~~~~
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;
| ^~~~~~~~~
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]);
| ^
g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/clonalorigin-1.0=. -fstack-protector-strong -Wformat -Werror=format-security -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/aarch64-linux-gnu -lgsl -lgslcblas -lm
make[3]: Leaving directory '/build/clonalorigin-1.0/warg/src'
make[2]: Leaving directory '/build/clonalorigin-1.0/warg/src'
Making all in scripts
make[2]: Entering directory '/build/clonalorigin-1.0/warg/scripts'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/build/clonalorigin-1.0/warg/scripts'
make[2]: Entering directory '/build/clonalorigin-1.0/warg'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/build/clonalorigin-1.0/warg'
make[1]: Leaving directory '/build/clonalorigin-1.0/warg'
dh_auto_test -O--sourcedirectory=warg
cd warg && make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1
make[1]: Entering directory '/build/clonalorigin-1.0/warg'
Making check in src
make[2]: Entering directory '/build/clonalorigin-1.0/warg/src'
make profilerun.sh
make[3]: Entering directory '/build/clonalorigin-1.0/warg/src'
make[3]: 'profilerun.sh' is up to date.
make[3]: Leaving directory '/build/clonalorigin-1.0/warg/src'
make check-TESTS
make[3]: Entering directory '/build/clonalorigin-1.0/warg/src'
make[4]: Entering directory '/build/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/clonalorigin-1.0/warg/src'
make[3]: Leaving directory '/build/clonalorigin-1.0/warg/src'
make[2]: Leaving directory '/build/clonalorigin-1.0/warg/src'
Making check in scripts
make[2]: Entering directory '/build/clonalorigin-1.0/warg/scripts'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/clonalorigin-1.0/warg/scripts'
make[2]: Entering directory '/build/clonalorigin-1.0/warg'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/build/clonalorigin-1.0/warg'
make[1]: Leaving directory '/build/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 -j8 install DESTDIR=/build/clonalorigin-1.0/debian/clonalorigin AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/build/clonalorigin-1.0/warg'
Making install in src
make[2]: Entering directory '/build/clonalorigin-1.0/warg/src'
make[3]: Entering directory '/build/clonalorigin-1.0/warg/src'
/usr/bin/mkdir -p '/build/clonalorigin-1.0/debian/clonalorigin/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c warg '/build/clonalorigin-1.0/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/build/clonalorigin-1.0/warg/src'
make[2]: Leaving directory '/build/clonalorigin-1.0/warg/src'
Making install in scripts
make[2]: Entering directory '/build/clonalorigin-1.0/warg/scripts'
make[3]: Entering directory '/build/clonalorigin-1.0/warg/scripts'
/usr/bin/mkdir -p '/build/clonalorigin-1.0/debian/clonalorigin/usr/bin'
make[3]: Nothing to be done for 'install-data-am'.
/usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/build/clonalorigin-1.0/debian/clonalorigin/usr/bin'
make[3]: Leaving directory '/build/clonalorigin-1.0/warg/scripts'
make[2]: Leaving directory '/build/clonalorigin-1.0/warg/scripts'
make[2]: Entering directory '/build/clonalorigin-1.0/warg'
make[3]: Entering directory '/build/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/clonalorigin-1.0/warg'
make[2]: Leaving directory '/build/clonalorigin-1.0/warg'
make[1]: Leaving directory '/build/clonalorigin-1.0/warg'
debian/rules override_dh_install
make[1]: Entering directory '/build/clonalorigin-1.0'
dh_install
rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl
make[1]: Leaving directory '/build/clonalorigin-1.0'
dh_installdocs -O--sourcedirectory=warg
dh_installchangelogs -O--sourcedirectory=warg
dh_installman -O--sourcedirectory=warg
dh_installsystemduser -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_1.0-6_arm64.deb'.
dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-6_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../clonalorigin_1.0-6_arm64.buildinfo
dpkg-genchanges --build=binary -O../clonalorigin_1.0-6_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: 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/21608 and its subdirectories
I: Current time: Thu Apr 27 07:02:26 -12 2023
I: pbuilder-time-stamp: 1682622146
Thu Apr 27 19:02:29 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink9-arm64.debian.net.
Thu Apr 27 19:02:29 UTC 2023 I: Preparing to do remote build '2' on codethink9-arm64.debian.net.
Thu Apr 27 19:23:35 UTC 2023 I: Deleting $TMPDIR on codethink9-arm64.debian.net.
Thu Apr 27 19:23:36 UTC 2023 I: clonalorigin_1.0-6_arm64.changes:
Format: 1.8
Date: Thu, 21 Oct 2021 20:59:46 +0200
Source: clonalorigin
Binary: clonalorigin clonalorigin-dbgsym
Architecture: arm64
Version: 1.0-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
clonalorigin - inference of homologous recombination in bacteria using whole gen
Closes: 984018
Changes:
clonalorigin (1.0-6) unstable; urgency=medium
.
* Fix build issue with gcc-11
Closes: #984018
* Enable uscan fetching a sensible filename
Checksums-Sha1:
88f36211448081ee4a012c7d28481fac2e3aef4f 1651528 clonalorigin-dbgsym_1.0-6_arm64.deb
eb259365526e28615e6f993b2d63a50049c08ab9 5274 clonalorigin_1.0-6_arm64.buildinfo
1f949b70e846314a8ed8639b22472012e6c514b7 147508 clonalorigin_1.0-6_arm64.deb
Checksums-Sha256:
967d49fdd97d958f16dba657574fb0b62895955b9b75d63dd6aabb4539547ad4 1651528 clonalorigin-dbgsym_1.0-6_arm64.deb
fae109c83cef5dd53a3782c773ee3d5625d366b1f88faf96a5372a52272bfc7c 5274 clonalorigin_1.0-6_arm64.buildinfo
ee5ff78f3674bb03ff50b0625e23b1877476e1026b6a672cc81117e6eaf42afa 147508 clonalorigin_1.0-6_arm64.deb
Files:
80e557872cb9ad08f07c4566fdac08e7 1651528 debug optional clonalorigin-dbgsym_1.0-6_arm64.deb
167168cb1a508cb6fbcc03ccfccbf331 5274 science optional clonalorigin_1.0-6_arm64.buildinfo
5c1d22886c9dce088f4089e6c25239f7 147508 science optional clonalorigin_1.0-6_arm64.deb
Thu Apr 27 19:23:37 UTC 2023 I: diffoscope 241 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.uWppAzgF/clonalorigin_1.0-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.uWppAzgF/clonalorigin_1.0-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.uWppAzgF/clonalorigin_1.0-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.uWppAzgF/b1/clonalorigin_1.0-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.uWppAzgF/b2/clonalorigin_1.0-6_arm64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.418s)
0.418s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.128s)
0.128s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Thu Apr 27 19:23:38 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists.
Thu Apr 27 19:23:38 UTC 2023 I: clonalorigin from bookworm built successfully and reproducibly on arm64.
Thu Apr 27 19:23:39 UTC 2023 I: Submitting .buildinfo files to external archives:
Thu Apr 27 19:23:39 UTC 2023 I: Submitting 8.0K b1/clonalorigin_1.0-6_arm64.buildinfo.asc
Thu Apr 27 19:23:41 UTC 2023 I: Submitting 8.0K b2/clonalorigin_1.0-6_arm64.buildinfo.asc
Thu Apr 27 19:23:41 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Thu Apr 27 19:23:41 UTC 2023 I: Done submitting .buildinfo files.
Thu Apr 27 19:23:41 UTC 2023 I: Removing signed clonalorigin_1.0-6_arm64.buildinfo.asc files:
removed './b1/clonalorigin_1.0-6_arm64.buildinfo.asc'
removed './b2/clonalorigin_1.0-6_arm64.buildinfo.asc'