I: pbuilder: network access will be disabled during build
I: Current time: Fri May 5 20:04:10 -12 2023
I: pbuilder-time-stamp: 1683360250
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/27559/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='armhf'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='armhf'
IFS='
'
INVOCATION_ID='96429e51415846619f313e9e90e64d19'
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='27559'
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.37SYfVzy/pbuilderrc_lbJe --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.37SYfVzy/b1 --logfile b1/build.log clonalorigin_1.0-6.dsc'
SUDO_GID='113'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://10.0.0.15:3142/'
I: uname -a
Linux virt64c 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux
I: ls -l /bin
total 5072
-rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 67632 Sep 20 2022 cat
-rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 67684 Sep 20 2022 chown
-rwxr-xr-x 1 root root 133532 Sep 20 2022 cp
-rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash
-rwxr-xr-x 1 root root 133220 Sep 20 2022 date
-rwxr-xr-x 1 root root 67732 Sep 20 2022 dd
-rwxr-xr-x 1 root root 68104 Sep 20 2022 df
-rwxr-xr-x 1 root root 133632 Sep 20 2022 dir
-rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname
-rwxr-xr-x 1 root root 67560 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep
-rwxr-xr-x 1 root root 67548 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep
-rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt
-rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount
-rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname
-rwxr-xr-x 1 root root 67720 Sep 20 2022 ln
-rwxr-xr-x 1 root root 35132 Mar 22 21:51 login
-rwxr-xr-x 1 root root 133632 Sep 20 2022 ls
-rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk
-rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 38504 Mar 22 21:02 more
-rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount
-rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint
-rwxr-xr-x 1 root root 133532 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash
-rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 67672 Sep 20 2022 rm
-rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed
lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 67644 Sep 20 2022 stty
-rwsr-xr-x 1 root root 50800 Mar 22 21:02 su
-rwxr-xr-x 1 root root 67584 Sep 20 2022 sync
-rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar
-rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 133224 Sep 20 2022 touch
-rwxr-xr-x 1 root root 67548 Sep 20 2022 true
-rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount
-rwxr-xr-x 1 root root 67572 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/27559/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <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 ... 19329 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 19.9 MB of archives. After unpacking 75.1 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB]
Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB]
Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB]
Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB]
Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB]
Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB]
Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB]
Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB]
Get: 24 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB]
Get: 25 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB]
Get: 26 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB]
Get: 27 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB]
Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main armhf libgslcblas0 armhf 2.7.1+dfsg-3+b1 [87.7 kB]
Get: 32 http://deb.debian.org/debian bookworm/main armhf libgsl27 armhf 2.7.1+dfsg-3+b1 [773 kB]
Get: 33 http://deb.debian.org/debian bookworm/main armhf libgsl-dev armhf 2.7.1+dfsg-3+b1 [975 kB]
Get: 34 http://deb.debian.org/debian bookworm/main armhf rename all 2.01-1 [21.0 kB]
Fetched 19.9 MB in 1s (38.4 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 ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19329 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_armhf.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_armhf.deb ...
Unpacking file (1:5.44-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../04-gettext-base_0.21-12_armhf.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../05-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../06-groff-base_1.22.4-10_armhf.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_armhf.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../08-libpipeline1_1.5.7-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.7-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../09-man-db_2.11.2-2_armhf.deb ...
Unpacking man-db (2.11.2-2) ...
Selecting previously unselected package m4.
Preparing to unpack .../10-m4_1.4.19-3_armhf.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:armhf.
Preparing to unpack .../22-libelf1_0.188-2.1_armhf.deb ...
Unpacking libelf1:armhf (0.188-2.1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../23-dwz_0.15-1_armhf.deb ...
Unpacking dwz (0.15-1) ...
Selecting previously unselected package libicu72:armhf.
Preparing to unpack .../24-libicu72_72.1-3_armhf.deb ...
Unpacking libicu72:armhf (72.1-3) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.2_armhf.deb ...
Unpacking libxml2:armhf (2.9.14+dfsg-1.2) ...
Selecting previously unselected package gettext.
Preparing to unpack .../26-gettext_0.21-12_armhf.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 libgslcblas0:armhf.
Preparing to unpack .../30-libgslcblas0_2.7.1+dfsg-3+b1_armhf.deb ...
Unpacking libgslcblas0:armhf (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package libgsl27:armhf.
Preparing to unpack .../31-libgsl27_2.7.1+dfsg-3+b1_armhf.deb ...
Unpacking libgsl27:armhf (2.7.1+dfsg-3+b1) ...
Selecting previously unselected package libgsl-dev.
Preparing to unpack .../32-libgsl-dev_2.7.1+dfsg-3+b1_armhf.deb ...
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:armhf (1.5.7-1) ...
Setting up libicu72:armhf (72.1-3) ...
Setting up bsdextrautils (2.38.1-5+b1) ...
Setting up libgslcblas0:armhf (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:armhf (1:5.44-3) ...
Setting up gettext-base (0.21-12) ...
Setting up libgsl27:armhf (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:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:armhf (0.188-2.1) ...
Setting up libxml2:armhf (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 armhf
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=arm-linux-gnueabihf --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/arm-linux-gnueabihf --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... /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 -j3
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
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;
| ^~~~~~~~
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 '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 '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::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-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
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
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-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
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
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);
| ^~~~~~~
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
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
In file included from /usr/include/c++/12/vector:70,
from data.h:3,
from param.h:3,
from move.h:4,
from movesitechange.h:4,
from movesitechange.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)' at movesitechange.cpp:139:19:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)' at movesitechange.cpp:145:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)' at movesitechange.cpp:149:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)' at movesitechange.cpp:154:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)' at movesitechange.cpp:158:30:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'std::vector<double> weakarg::MoveSiteChange::calcPost(std::vector<double>*, std::vector<double>*, int, int, int, int, bool)' at movesitechange.cpp:162:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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;
| ^~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from node.h:4,
from tree.h:3,
from tree.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void weakarg::Tree::makeFromNewick(std::string, bool)' at tree.cpp:60:28:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void weakarg::Tree::makeFromNewick(std::string, bool)' at tree.cpp:62:28:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void weakarg::Tree::makeFromNewick(std::string, bool)' at tree.cpp:72:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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__);
| ^~~~~~~~
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]);
| ^
In file included from /usr/include/c++/12/vector:70,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from weakarg.cpp:6:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'weakarg::ProgramOptions::ProgramOptions()' at weakarg.h:40:16,
inlined from 'weakarg::ProgramOptions& weakarg::opt()' at weakarg.cpp:25:24:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from node.h:4,
from tree.h:3,
from rectree.h:3,
from rectree.cpp:1:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void weakarg::RecTree::chooseNodePath(int, double, std::vector<int>*, std::vector<int>*)' at rectree.cpp:1064:53:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/arm-linux-gnueabihf -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 -j3 check "TESTSUITEFLAGS=-j3 --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 -j3 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'
/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'
/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
dpkg-shlibdeps: warning: debian/clonalorigin/usr/bin/warg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
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' in '../clonalorigin_1.0-6_armhf.deb'.
dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-6_armhf.deb'.
dpkg-genbuildinfo --build=binary -O../clonalorigin_1.0-6_armhf.buildinfo
dpkg-genchanges --build=binary -O../clonalorigin_1.0-6_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
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/27559 and its subdirectories
I: Current time: Fri May 5 20:29:25 -12 2023
I: pbuilder-time-stamp: 1683361765