Wed May 29 07:57:12 UTC 2024 I: starting to build clonalorigin/unstable/amd64 on jenkins on '2024-05-29 07:56' Wed May 29 07:57:12 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_27/22543/console.log Wed May 29 07:57:12 UTC 2024 I: Downloading source for unstable/clonalorigin=1.0-8 --2024-05-29 07:57:12-- http://deb.debian.org/debian/pool/main/c/clonalorigin/clonalorigin_1.0-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2183 (2.1K) [text/prs.lines.tag] Saving to: ‘clonalorigin_1.0-8.dsc’ 0K .. 100% 300M=0s 2024-05-29 07:57:12 (300 MB/s) - ‘clonalorigin_1.0-8.dsc’ saved [2183/2183] Wed May 29 07:57:12 UTC 2024 I: clonalorigin_1.0-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: clonalorigin Binary: clonalorigin Architecture: any Version: 1.0-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/xavierdidelot/clonalorigin Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/clonalorigin Vcs-Git: https://salsa.debian.org/med-team/clonalorigin.git Testsuite: autopkgtest 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 8b84785b3d7ffb55e62b2b9932c4c62ec9900f03 10608 clonalorigin_1.0-8.debian.tar.xz Checksums-Sha256: 73962415160b8b496c81d3e9cbbf68f76c02caf4dd6b41860f01d493b71c6e3a 185865 clonalorigin_1.0.orig.tar.gz 192e0da0642eea3f9e86d40b535ac89c900be9cfe557d163ca29a54e7f479882 10608 clonalorigin_1.0-8.debian.tar.xz Files: 310a0c5714e7629c052ab4da50c90f44 185865 clonalorigin_1.0.orig.tar.gz 905b8b38da217ad00e12e9f849ec267d 10608 clonalorigin_1.0-8.debian.tar.xz Dgit: b3fc1b67fb518bb450b668e97a3abd1aad93e880 debian archive/debian/1.0-8 https://git.dgit.debian.org/clonalorigin -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmWOuYIUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdqpLRAAlNK1ErVhpNbWQg9JbH8pUmb/hafe 4sqdQYUZfy+tcsLF6Z/Cg4ZNUVTOXnZqkio9j+w9Jnkwso6uEwtsnrYuZpkgyq6b bo9Zw72KXMObXOkYNXFyOC8eDJ2GW0ja60v7uCWDeews4/uUEuHVvUa+WMHtpwP5 d5L4LzhMfOpt4ph7rwWewJygNSMfS3x7TIWa+iJbdKxppxgvWFDHbVv42405HpFu c7aYVdJIErhIpBEl19i+xt+REkCHbnxF/UPjWzThMd+H9+H7F8xEdqi9gSDbmRWY NYxxit/A9HWIds1sWCho4MsMCdDTWpaxUF/rskxLI6HmqreIuFFlE2J4WJYfnT4a qe3JH/FblMoQQdEFHifif0ST0kyb5h4HyoL2syQ7oDidEP2UmpQ+C6G0Tbnd3DA3 Hlq+cjYEUAZPTDNtoWJi0IBjOIu6rPCkUggW61KnlD/HvKwl9FOatdVOGuQj63Iv allzBEyfG/EC56TyDMZgZfKOMv0ri6Uzb8RAaQci8qEWPyg7VXXYMZNEciK1xrIC sxGgwziuEQVF8ZeiLgGNKom/u6GYBHZYiiaQp8KDIHCexcXz9VabN1sN9/7bxMVK n/5mk6Re+mqku5JhnOMekh/QxstEALo+Td53zjLbVItWBfMy39LYnUBhKnAVOnw3 TGWTkPv8gXLFCSg= =dgh7 -----END PGP SIGNATURE----- Wed May 29 07:57:12 UTC 2024 I: Checking whether the package is not for us Wed May 29 07:57:13 UTC 2024 I: Starting 1st build on remote node ionos11-amd64.debian.net. Wed May 29 07:57:13 UTC 2024 I: Preparing to do remote build '1' on ionos11-amd64.debian.net. Wed May 29 08:03:27 UTC 2024 I: Deleting $TMPDIR on ionos11-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue May 28 19:57:15 -12 2024 I: pbuilder-time-stamp: 1716969435 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [clonalorigin_1.0-8.dsc] I: copying [./clonalorigin_1.0.orig.tar.gz] I: copying [./clonalorigin_1.0-8.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 29 12:20:18 2023 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./clonalorigin_1.0-8.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_1.0-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying portability.patch dpkg-source: info: applying gcc-11.patch dpkg-source: info: applying shorten-test.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2382349/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='906beb6ed8234e18b2f5517865230fe5' 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='2382349' 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.pcjd4bwv/pbuilderrc_ufGN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pcjd4bwv/b1 --logfile b1/build.log clonalorigin_1.0-8.dsc' SUDO_GID='111' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos11-amd64 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 May 27 07:42 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2382349/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team 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 ... 19716 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on libgsl-dev; however: Package libgsl-dev is not installed. pbuilder-satisfydepends-dummy depends on rename; however: Package rename is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libgsl-dev{a} libgsl27{a} libgslcblas0{a} libicu72{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{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, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After unpacking 84.3 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.1-2 [94.2 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 22 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-2 [670 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.7.1+dfsg-6+b1 [107 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libgsl27 amd64 2.7.1+dfsg-6+b1 [934 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.7.1+dfsg-6+b1 [1146 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 rename all 2.02-1 [21.8 kB] Fetched 21.2 MB in 0s (44.7 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 ... 19716 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_amd64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.1-2_amd64.deb ... Unpacking bsdextrautils (2.40.1-2) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.7-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_amd64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_amd64.deb ... Unpacking m4 (1.4.19-4) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.191-1+b1_amd64.deb ... Unpacking libelf1t64:amd64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_amd64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../23-libicu72_72.1-4+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-4+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../24-libxml2_2.12.7+dfsg-2_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg-2) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../29-libgslcblas0_2.7.1+dfsg-6+b1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libgsl27:amd64. Preparing to unpack .../30-libgsl27_2.7.1+dfsg-6+b1_amd64.deb ... Unpacking libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Selecting previously unselected package libgsl-dev. Preparing to unpack .../31-libgsl-dev_2.7.1+dfsg-6+b1_amd64.deb ... Unpacking libgsl-dev (2.7.1+dfsg-6+b1) ... Selecting previously unselected package rename. Preparing to unpack .../32-rename_2.02-1_all.deb ... Unpacking rename (2.02-1) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-2) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-6+b1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-6+b1) ... Setting up m4 (1.4.19-4) ... Setting up rename (2.02-1) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up file (1:5.45-3) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-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 (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libgsl-dev (2.7.1+dfsg-6+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-11) ... 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/reproducible-path/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_1.0-8_source.changes dpkg-buildpackage: info: source package clonalorigin dpkg-buildpackage: info: source version 1.0-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=warg dh_auto_clean -O--sourcedirectory=warg debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0' test ! -e warg/src/truth.xml.preserve \ || mv -v warg/src/truth.xml.preserve warg/src/truth.xml make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0' dh_autoreconf_clean -O--sourcedirectory=warg dh_clean -O--sourcedirectory=warg debian/rules binary dh binary --sourcedirectory=warg dh_update_autotools_config -O--sourcedirectory=warg dh_autoreconf -O--sourcedirectory=warg configure.ac:58: warning: The macro `AC_TRY_RUN' is obsolete. configure.ac:58: You should run autoupdate. ./lib/autoconf/general.m4:2997: 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' debian/rules execute_before_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0' cp -v warg/src/truth.xml warg/src/truth.xml.preserve 'warg/src/truth.xml' -> 'warg/src/truth.xml.preserve' make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0' dh_auto_configure -O--sourcedirectory=warg cd warg && ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for gsl-config... /usr/bin/gsl-config checking for GSL - version >= 0.2.5... yes checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for inline... inline checking for floor... no checking for pow... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating scripts/Makefile config.status: creating src/config.h config.status: executing depfiles commands dh_auto_build -O--sourcedirectory=warg cd warg && make -j20 make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' Making all in src make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make all-am make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-data.o `test -f 'data.cpp' || echo './'`data.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-rng.o `test -f 'rng.cpp' || echo './'`rng.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-wargxml.o `test -f 'wargxml.cpp' || echo './'`wargxml.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-move.o `test -f 'move.cpp' || echo './'`move.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-metropolis.o `test -f 'metropolis.cpp' || echo './'`metropolis.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveaddedge.o `test -f 'moveaddedge.cpp' || echo './'`moveaddedge.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveageclonal.o `test -f 'moveageclonal.cpp' || echo './'`moveageclonal.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movedelta.o `test -f 'movedelta.cpp' || echo './'`movedelta.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveedgechange.o `test -f 'moveedgechange.cpp' || echo './'`moveedgechange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveregraftclonal.o `test -f 'moveregraftclonal.cpp' || echo './'`moveregraftclonal.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moveremedge.o `test -f 'moveremedge.cpp' || echo './'`moveremedge.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-moverho.o `test -f 'moverho.cpp' || echo './'`moverho.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movescaletree.o `test -f 'movescaletree.cpp' || echo './'`movescaletree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movegreedytree.o `test -f 'movegreedytree.cpp' || echo './'`movegreedytree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movesitechange.o `test -f 'movesitechange.cpp' || echo './'`movesitechange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movetheta.o `test -f 'movetheta.cpp' || echo './'`movetheta.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-movetimechange.o `test -f 'movetimechange.cpp' || echo './'`movetimechange.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-mpiutils.o `test -f 'mpiutils.cpp' || echo './'`mpiutils.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-node.o `test -f 'node.cpp' || echo './'`node.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-param.o `test -f 'param.cpp' || echo './'`param.cpp 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 'long 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 'long 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); | ^~~~~~~ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-recedge.o `test -f 'recedge.cpp' || echo './'`recedge.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-rectree.o `test -f 'rectree.cpp' || echo './'`rectree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-tree.o `test -f 'tree.cpp' || echo './'`tree.cpp g++ -DHAVE_CONFIG_H -I. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o warg-weakarg.o `test -f 'weakarg.cpp' || echo './'`weakarg.cpp weakarg.cpp:40:20: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 40 | ret.append(__DATE__); | ^~~~~~~~ weakarg.cpp:42:20: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 42 | ret.append(__TIME__); | ^~~~~~~~ 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; | ^~~~~~~~~ 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]); | ^ g++ -I/usr/include -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wall -g -O2 -ffile-prefix-map=/build/reproducible-path/clonalorigin-1.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -funroll-loops -fomit-frame-pointer -ftree-vectorize -funsafe-math-optimizations -Wl,-z,relro -Wl,-z,now -o warg warg-data.o warg-rng.o warg-wargxml.o warg-move.o warg-metropolis.o warg-moveaddedge.o warg-moveageclonal.o warg-movedelta.o warg-moveedgechange.o warg-moveregraftclonal.o warg-moveremedge.o warg-moverho.o warg-movescaletree.o warg-movegreedytree.o warg-movesitechange.o warg-movetheta.o warg-movetimechange.o warg-mpiutils.o warg-node.o warg-param.o warg-recedge.o warg-rectree.o warg-tree.o warg-weakarg.o -L/usr/lib/x86_64-linux-gnu -lgsl -lgslcblas -lm make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' Making all in scripts make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' dh_auto_test -O--sourcedirectory=warg cd warg && make -j20 check "TESTSUITEFLAGS=-j20 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' Making check in src make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make profilerun.sh make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[3]: 'profilerun.sh' is up to date. make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make check-TESTS make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[4]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' PASS: profilerun.sh ============================================================================ Testsuite summary for clonalorigin 0.0.1 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[4]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' Making check in scripts make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' make[2]: Nothing to be done for 'check-am'. make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=warg dh_prep -O--sourcedirectory=warg dh_auto_install --destdir=debian/clonalorigin/ -O--sourcedirectory=warg cd warg && make -j20 install DESTDIR=/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' Making install in src make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c warg '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/src' Making install in scripts make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[3]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin' /usr/bin/install -c blocksplit.pl computeMedians.pl makeMauveWargFile.pl '/build/reproducible-path/clonalorigin-1.0/debian/clonalorigin/usr/bin' make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg/scripts' make[2]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' make[3]: Entering directory '/build/reproducible-path/clonalorigin-1.0/warg' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' make[2]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0/warg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/clonalorigin-1.0' dh_install rename 's/\.pl//' debian/clonalorigin/usr/bin/*.pl make[1]: Leaving directory '/build/reproducible-path/clonalorigin-1.0' dh_installdocs -O--sourcedirectory=warg dh_installchangelogs -O--sourcedirectory=warg dh_installman -O--sourcedirectory=warg dh_installsystemduser -O--sourcedirectory=warg dh_lintian -O--sourcedirectory=warg dh_perl -O--sourcedirectory=warg dh_link -O--sourcedirectory=warg dh_strip_nondeterminism -O--sourcedirectory=warg dh_compress -O--sourcedirectory=warg dh_fixperms -O--sourcedirectory=warg dh_missing -O--sourcedirectory=warg dh_dwz -a -O--sourcedirectory=warg dh_strip -a -O--sourcedirectory=warg dh_makeshlibs -a -O--sourcedirectory=warg dh_shlibdeps -a -O--sourcedirectory=warg dh_installdeb -O--sourcedirectory=warg dh_gencontrol -O--sourcedirectory=warg dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package clonalorigin: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=warg dh_builddeb -O--sourcedirectory=warg dpkg-deb: building package 'clonalorigin' in '../clonalorigin_1.0-8_amd64.deb'. dpkg-deb: building package 'clonalorigin-dbgsym' in '../clonalorigin-dbgsym_1.0-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../clonalorigin_1.0-8_amd64.buildinfo dpkg-genchanges --build=binary -O../clonalorigin_1.0-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: 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/2382349 and its subdirectories I: Current time: Tue May 28 20:03:27 -12 2024 I: pbuilder-time-stamp: 1716969807 Wed May 29 08:03:28 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Wed May 29 08:03:28 UTC 2024 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Wed May 29 08:04:55 UTC 2024 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Wed May 29 08:04:55 UTC 2024 I: clonalorigin_1.0-8_amd64.changes: Format: 1.8 Date: Fri, 29 Dec 2023 13:11:47 +0100 Source: clonalorigin Binary: clonalorigin clonalorigin-dbgsym Architecture: amd64 Version: 1.0-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: clonalorigin - inference of homologous recombination in bacteria using whole gen Closes: 884475 Changes: clonalorigin (1.0-8) unstable; urgency=medium . * shorten-test.patch: new: reduce stress on buildds. (Closes: #884475) * d/tests/: new: add autopkgtest. * clonalorigin-gui.1: minor fixups. * d/blocksplit.1: new: document upstream script. * d/computeMedians.1: new: document upstream script. * d/makeMauveWargFile.1: new: document upstream script. * d/clonalorigin-gui.1: minor fixup. * d/warg.1: minor fixup in description. * d/clonalorigin.1: remove: unused. The real manual page in the binary package is a link to warg(1). * d/clonalorigin.manpages: add missing script manuals. * d/control: recommend libxml-parser-perl. This library is needed by computeMedians, although it does not seem critical to typical clonalorigin workloads. * d/*lintian-overrides: new: flag a false positive. Checksums-Sha1: 33c0cd6b884fd214914e3965bf782f46cc6130cd 1687496 clonalorigin-dbgsym_1.0-8_amd64.deb 372df4b75c36b725ba60ab8b6c2b61307b2f0286 5093 clonalorigin_1.0-8_amd64.buildinfo e50130dcb20daca5f66ef6f1149403cf08f73506 171020 clonalorigin_1.0-8_amd64.deb Checksums-Sha256: 8add9c41034469a3d0bb23a5c72e0dc085bf38049234efb3318463b667f6756d 1687496 clonalorigin-dbgsym_1.0-8_amd64.deb 75a07d903eaa3a6ce5ff6d19bdadda9114a3b47c66209ef816552c387d911099 5093 clonalorigin_1.0-8_amd64.buildinfo a87610a966e23e65af4910197300ff6720f85ee33bd082d770abbbd4e3fdf13f 171020 clonalorigin_1.0-8_amd64.deb Files: f6fd9ee2f08de250d4d0e9db0e487c10 1687496 debug optional clonalorigin-dbgsym_1.0-8_amd64.deb cbae4b0d2ad8a3ab94f3237381a15d03 5093 science optional clonalorigin_1.0-8_amd64.buildinfo 4c80242f83bd8095de0d859b75a9d1cc 171020 science optional clonalorigin_1.0-8_amd64.deb Wed May 29 08:04:56 UTC 2024 I: diffoscope 268 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_27-22543.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.pcjd4bwv/clonalorigin_1.0-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.pcjd4bwv/clonalorigin_1.0-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.pcjd4bwv/clonalorigin_1.0-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.pcjd4bwv/b1/clonalorigin_1.0-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.pcjd4bwv/b2/clonalorigin_1.0-8_amd64.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: 0.386s) 0.386s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.038s) 0.038s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 721ms CPU time consumed: 716ms Wed May 29 08:04:57 UTC 2024 I: diffoscope 268 found no differences in the changes files, and a .buildinfo file also exists. Wed May 29 08:04:57 UTC 2024 I: clonalorigin from unstable built successfully and reproducibly on amd64. Wed May 29 08:04:59 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 29 08:04:59 UTC 2024 I: Submitting 8.0K b1/clonalorigin_1.0-8_amd64.buildinfo.asc Wed May 29 08:05:00 UTC 2024 I: Submitting 8.0K b2/clonalorigin_1.0-8_amd64.buildinfo.asc Wed May 29 08:05:00 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 29 08:05:00 UTC 2024 I: Done submitting .buildinfo files. Wed May 29 08:05:00 UTC 2024 I: Removing signed clonalorigin_1.0-8_amd64.buildinfo.asc files: removed './b1/clonalorigin_1.0-8_amd64.buildinfo.asc' removed './b2/clonalorigin_1.0-8_amd64.buildinfo.asc'