Sat May 6 08:04:04 UTC 2023 I: starting to build clonalorigin/bookworm/armhf on jenkins on '2023-05-06 08:03' Sat May 6 08:04:04 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_19/91/console.log Sat May 6 08:04:04 UTC 2023 I: Downloading source for bookworm/clonalorigin=1.0-6 --2023-05-06 08:04:04-- 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% 92.2M=0s 2023-05-06 08:04:04 (92.2 MB/s) - ‘clonalorigin_1.0-6.dsc’ saved [1997/1997] Sat May 6 08:04:05 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 Uploaders: Andreas Tille 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 -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmFxutYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFtiw/9EBRlZ/3NJman6hly6jTHekj3KjtXYyr1 pc5kTjncOVa9sb9mf90vK11OLKZ8cZSKkca2Ldn6A3MQW++ntGoYj5k9eEF6uLoH OW/psJVdE2DerN7kkHPnDAxeXBwLARak3R7TaoSSWvrWseNhderi+Tlat7rXORNx RazAzCSdN1F1tZoQ50rwsFg5kS5FuwZv7RQ8iPXJFEftpAFZjd/BHbnwqz/L9eI/ JYM+zFDcgLW419W/8ehI+pfnZi2jk51ViPl5ltlBDIYys8+HahpvGzc2Omj12fQG utv7F2pGWb4F4+BdaWjlik0mYu/5hNrGrUhEXQqRxzTGTWwWVDVUav54ZosgW40u i/zF6N7PlqXhkC/wrw4txXLDMH3/cx3EjvOB1cKMhJZF19HXVzUq9PWJTYMq3nfK wIvF9DV2LR2Efx45zQKRz7KWj5guhX2XNl44HLZ5cnCxAdjYN/9Q9sCJCsQ1wFAt 1fE28hDBPcOY1RgcLtdJNpkewu73DVGJtBpt9N/IbEOpkSJP/79MhZ6Bd2zHVAaU flzmwQmxpN7SWUBzIzWysTulGGxCamWnqTZeGOCGkBklInr6FIyArISmsT4FmQx5 b4FdMPTuWNiOkK32BhObp2KFC7VMSXLn4AJKqHD4IWLfQ2dODwQobStPYO+Su9vy UsVZ/RzDptc= =G/p/ -----END PGP SIGNATURE----- Sat May 6 08:04:05 UTC 2023 I: Checking whether the package is not for us Sat May 6 08:04:05 UTC 2023 I: Starting 1st build on remote node virt64c-armhf-rb.debian.net. Sat May 6 08:04:05 UTC 2023 I: Preparing to do remote build '1' on virt64c-armhf-rb.debian.net. Sat May 6 08:29:32 UTC 2023 I: Deleting $TMPDIR on virt64c-armhf-rb.debian.net. 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 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 ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 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 ... 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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 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)': 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::size_type' {aka 'unsigned int'} [-Wsign-compare] 177 | for(int i=0;i=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<, int>::value_type' {aka 'int'} and 'std::vector::size_type' {aka 'unsigned int'} [-Wsign-compare] 177 | for(int i=0;i=0) {if(!tried[numv[i]]) {regions.push_back(numv[i]);tried[numv[i]]=true;}else{cerr<<"Warning: Duplicate blocks of "<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)': 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]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector weakarg::MoveSiteChange::calcPost(std::vector*, std::vector*, 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector weakarg::MoveSiteChange::calcPost(std::vector*, std::vector*, 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector weakarg::MoveSiteChange::calcPost(std::vector*, std::vector*, 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector weakarg::MoveSiteChange::calcPost(std::vector*, std::vector*, 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector weakarg::MoveSiteChange::calcPost(std::vector*, std::vector*, 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'std::vector weakarg::MoveSiteChange::calcPost(std::vector*, std::vector*, 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 >' 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*, std::vector*)': 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]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' 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 >' 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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' 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 >' 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 weakarg::readInputFiles(Data*&, RecTree*&, std::vector&, std::vector&, std::vector&, std::vector >, 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::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]': /usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector::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]', 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 >' 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]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::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]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void weakarg::RecTree::chooseNodePath(int, double, std::vector*, std::vector*)' 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 >' 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 Sat May 6 08:29:34 UTC 2023 I: 1st build successful. Starting 2nd build on remote node cbxi4a-armhf-rb.debian.net. Sat May 6 08:29:34 UTC 2023 I: Preparing to do remote build '2' on cbxi4a-armhf-rb.debian.net. Sat May 6 13:37:18 UTC 2023 I: Deleting $TMPDIR on cbxi4a-armhf-rb.debian.net. Sat May 6 13:37:22 UTC 2023 I: clonalorigin_1.0-6_armhf.changes: Format: 1.8 Date: Thu, 21 Oct 2021 20:59:46 +0200 Source: clonalorigin Binary: clonalorigin clonalorigin-dbgsym Architecture: armhf Version: 1.0-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille 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: 1c0f776423ea21042e149bfe3fc2dfbade061c12 1685860 clonalorigin-dbgsym_1.0-6_armhf.deb f51741a81c22a86f49a6442488ce55d19849826e 5116 clonalorigin_1.0-6_armhf.buildinfo ccec236e6a6a0a9d56d74e37ef7d9cc74cf9ebf5 139332 clonalorigin_1.0-6_armhf.deb Checksums-Sha256: ecaf8a52437fbc091f35d258e67738c16f307d3046320e6d9167fe0ee139097a 1685860 clonalorigin-dbgsym_1.0-6_armhf.deb 7f76bdb5c66d7443b64d74d6f3122424ef7e9a0323c76aa66bc651d43da14dc3 5116 clonalorigin_1.0-6_armhf.buildinfo c8c0c1e61315fabaffe9b5e0d4ce061bc5bdfbc6394b5d2682520077aad7fecc 139332 clonalorigin_1.0-6_armhf.deb Files: 305a1bd3cbf1426e8a79f6db3d629cf4 1685860 debug optional clonalorigin-dbgsym_1.0-6_armhf.deb 5e49c7f31e273f4a18314299e6fd0f51 5116 science optional clonalorigin_1.0-6_armhf.buildinfo db88e8160251215d469356de0395cace 139332 science optional clonalorigin_1.0-6_armhf.deb Sat May 6 13:37:23 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.37SYfVzy/clonalorigin_1.0-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.37SYfVzy/clonalorigin_1.0-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.37SYfVzy/clonalorigin_1.0-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.37SYfVzy/b1/clonalorigin_1.0-6_armhf.changes /srv/reproducible-results/rbuild-debian/r-b-build.37SYfVzy/b2/clonalorigin_1.0-6_armhf.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: 0.394s) 0.394s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.070s) 0.069s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Sat May 6 13:37:25 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Sat May 6 13:37:25 UTC 2023 I: clonalorigin from bookworm built successfully and reproducibly on armhf. Sat May 6 13:37:26 UTC 2023 I: Submitting .buildinfo files to external archives: Sat May 6 13:37:26 UTC 2023 I: Submitting 8.0K b1/clonalorigin_1.0-6_armhf.buildinfo.asc Sat May 6 13:37:26 UTC 2023 I: Submitting 8.0K b2/clonalorigin_1.0-6_armhf.buildinfo.asc Sat May 6 13:37:28 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat May 6 13:37:28 UTC 2023 I: Done submitting .buildinfo files. Sat May 6 13:37:28 UTC 2023 I: Removing signed clonalorigin_1.0-6_armhf.buildinfo.asc files: removed './b1/clonalorigin_1.0-6_armhf.buildinfo.asc' removed './b2/clonalorigin_1.0-6_armhf.buildinfo.asc'