Fri May 29 11:10:41 UTC 2020 I: starting to build gubbins/buster/i386 on jenkins on '2020-05-29 11:10' Fri May 29 11:10:41 UTC 2020 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_2/6396/console.log Fri May 29 11:10:41 UTC 2020 I: Downloading source for buster/gubbins=2.3.4-1 --2020-05-29 11:10:41-- http://deb.debian.org/debian/pool/main/g/gubbins/gubbins_2.3.4-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2161 (2.1K) Saving to: ‘gubbins_2.3.4-1.dsc’ 0K .. 100% 121M=0s 2020-05-29 11:10:41 (121 MB/s) - ‘gubbins_2.3.4-1.dsc’ saved [2161/2161] Fri May 29 11:10:41 UTC 2020 I: gubbins_2.3.4-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: gubbins Binary: gubbins Architecture: any Version: 2.3.4-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Aidan Delaney Homepage: https://sanger-pathogens.github.io/gubbins/ Standards-Version: 4.2.1 Vcs-Browser: https://salsa.debian.org/med-team/gubbins Vcs-Git: https://salsa.debian.org/med-team/gubbins.git Testsuite: autopkgtest Build-Depends: debhelper (>= 11~), dh-python, fasttree, raxml (>= 8), python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-nose, pkg-config Package-List: gubbins deb science optional arch=any Checksums-Sha1: 9aa22acb705d6738c3d8c77dd0bdfc40b5154c7c 687963 gubbins_2.3.4.orig.tar.gz 1e16bbc889987832a9ad33a564653b65bbe9abad 5988 gubbins_2.3.4-1.debian.tar.xz Checksums-Sha256: 1d748857aaa51dfbd54fe3ab6047f86f758968f7cadc0351737909ae0f609d41 687963 gubbins_2.3.4.orig.tar.gz a9846df1c674832379befde6945ed99fb22412a572741ea76c460c4477e2e9ed 5988 gubbins_2.3.4-1.debian.tar.xz Files: b176c3f0e1a0e008eda4bb9beb23432b 687963 gubbins_2.3.4.orig.tar.gz 20d097bd27441b563b08563979681099 5988 gubbins_2.3.4-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlurnPURHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHg2Q//UXAMacCjpyQNcJpoGIVjvENTY8nEC1AJ +YjtzFjoPc9WFBdDUJdLVkTKysYOg6EFGFw1Giw994xSrJfmev7BiH7PeiCJkQ2e z4ruVdmf1IN600jLHnNPRfr8Z70asqhoU1sxTOXM8IG6DqMSlf5YXexLhibmaOWs rpmd5g8tTENibfJYwWug1daXAssNBOeWiLT/fWB6wEH92YiQVwLfFwThlCrU/ZvB wlA36EoU6PNERlXTAHHrK/U/NUnOrNtOAvtChuOQG7YsI0kiBIwRRsiz8yTaZUg6 uSqooBwZ1U4xywDPpviI50AuIVDA5oOL9zUxxKkX035jj4vxpj1Da2nZntMk4sfN RKh7PH7BMio4+bm0k7dYFeBjliaRdh4JK6GSojMWAKIkR1fv4DZBOI0vmIsbQ2DX 1wUMQgNr19g/LmMUeHaKxIjOsl984wANprtqjg4WNd8vhLwPD/Yp9rD+ZeRn1zXQ WVMYmoVYRNaY/GwEoawMORWLBwii5qiTyDTP/l6iHmVjWsZkwMzj0MA4Ru/dHJyG QOUIc3pBOSVIo/PDGzumcJ4B7CXD5aPOZ4fMkFA+v2Xpg8q4YFWEPZYBbbTAdbzK VkFI/8eMU7BEoJ1ixZro0RFG3jd4huzPODUatN/pajX6xumRdmzWCny18RfyXLEk KsHsVWgju+k= =iEKl -----END PGP SIGNATURE----- Fri May 29 11:10:41 UTC 2020 I: Checking whether the package is not for us Fri May 29 11:10:41 UTC 2020 I: Starting 1st build on remote node profitbricks-build6-i386.debian.net. Fri May 29 11:10:41 UTC 2020 I: Preparing to do remote build '1' on profitbricks-build6-i386.debian.net. Fri May 29 11:11:25 UTC 2020 I: Deleting $TMPDIR on profitbricks-build6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jul 1 05:33:42 -12 2021 I: pbuilder-time-stamp: 1625160822 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration 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: using eatmydata during job I: Copying source file I: copying [gubbins_2.3.4-1.dsc] I: copying [./gubbins_2.3.4.orig.tar.gz] I: copying [./gubbins_2.3.4-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Sep 26 02:51:33 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./gubbins_2.3.4-1.dsc dpkg-source: info: extracting gubbins in gubbins-2.3.4 dpkg-source: info: unpacking gubbins_2.3.4.orig.tar.gz dpkg-source: info: unpacking gubbins_2.3.4-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying do_not_handle_python_by_upstream_build_system.patch dpkg-source: info: applying gubbins_exe_in_usr_lib.patch dpkg-source: info: applying disable_test.patch I: using fakeroot in build. I: Installing the build-deps -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 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 (>= 11~), dh-python, fasttree, raxml (>= 8), python3-setuptools, zlib1g-dev, check, python3, python3-biopython, python3-dendropy, python3-reportlab, python3-nose, pkg-config dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19234 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 (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on fasttree; however: Package fasttree is not installed. pbuilder-satisfydepends-dummy depends on raxml (>= 8); however: Package raxml is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on check; however: Package check is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-reportlab; however: Package python3-reportlab is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config 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} bsdmainutils{a} check{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fasttree{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} liblapack3{a} liblcms2-2{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libpipeline1{a} libpng16-16{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libsubunit-dev{a} libsubunit0{a} libtiff5{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libxml2{a} m4{a} man-db{a} mime-support{a} pkg-config{a} po-debconf{a} python3{a} python3-biopython{a} python3-dendropy{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3.7{a} python3.7-minimal{a} raxml{a} readline-common{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx ncbi-blast+ python-biopython-doc python3-olefile python3-renderpm shared-mime-info wget xdg-user-dirs 0 packages upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 37.8 MB of archives. After unpacking 150 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main i386 libbsd0 i386 0.9.1-2 [104 kB] Get: 2 http://deb.debian.org/debian buster/main i386 bsdmainutils i386 11.1.2+b1 [193 kB] Get: 3 http://deb.debian.org/debian buster/main i386 libuchardet0 i386 0.0.6-3 [65.2 kB] Get: 4 http://deb.debian.org/debian buster/main i386 groff-base i386 1.22.4-3 [935 kB] Get: 5 http://deb.debian.org/debian buster/main i386 libpipeline1 i386 1.5.1-2 [33.3 kB] Get: 6 http://deb.debian.org/debian buster/main i386 man-db i386 2.8.5-2 [1284 kB] Get: 7 http://deb.debian.org/debian buster/main i386 libssl1.1 i386 1.1.1d-0+deb10u3 [1537 kB] Get: 8 http://deb.debian.org/debian buster/main i386 libpython3.7-minimal i386 3.7.3-2+deb10u1 [590 kB] Get: 9 http://deb.debian.org/debian buster/main i386 libexpat1 i386 2.2.6-2+deb10u1 [104 kB] Get: 10 http://deb.debian.org/debian buster/main i386 python3.7-minimal i386 3.7.3-2+deb10u1 [1745 kB] Get: 11 http://deb.debian.org/debian buster/main i386 python3-minimal i386 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main i386 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main i386 libmpdec2 i386 2.4.2-2 [83.2 kB] Get: 14 http://deb.debian.org/debian buster/main i386 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main i386 libreadline7 i386 7.0-5 [156 kB] Get: 16 http://deb.debian.org/debian buster/main i386 libpython3.7-stdlib i386 3.7.3-2+deb10u1 [1750 kB] Get: 17 http://deb.debian.org/debian buster/main i386 python3.7 i386 3.7.3-2+deb10u1 [330 kB] Get: 18 http://deb.debian.org/debian buster/main i386 libpython3-stdlib i386 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main i386 python3 i386 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main i386 sensible-utils all 0.0.12 [15.8 kB] Get: 21 http://deb.debian.org/debian buster/main i386 libmagic-mgc i386 1:5.35-4+deb10u1 [242 kB] Get: 22 http://deb.debian.org/debian buster/main i386 libmagic1 i386 1:5.35-4+deb10u1 [124 kB] Get: 23 http://deb.debian.org/debian buster/main i386 file i386 1:5.35-4+deb10u1 [66.3 kB] Get: 24 http://deb.debian.org/debian buster/main i386 gettext-base i386 0.19.8.1-9 [124 kB] Get: 25 http://deb.debian.org/debian buster/main i386 libsigsegv2 i386 2.12-2 [33.2 kB] Get: 26 http://deb.debian.org/debian buster/main i386 m4 i386 1.4.18-2 [205 kB] Get: 27 http://deb.debian.org/debian buster/main i386 autoconf all 2.69-11 [341 kB] Get: 28 http://deb.debian.org/debian buster/main i386 autotools-dev all 20180224.1 [77.0 kB] Get: 29 http://deb.debian.org/debian buster/main i386 automake all 1:1.16.1-4 [771 kB] Get: 30 http://deb.debian.org/debian buster/main i386 autopoint all 0.19.8.1-9 [434 kB] Get: 31 http://deb.debian.org/debian buster/main i386 libsubunit0 i386 1.3.0-1 [9312 B] Get: 32 http://deb.debian.org/debian buster/main i386 libsubunit-dev i386 1.3.0-1 [10.3 kB] Get: 33 http://deb.debian.org/debian buster/main i386 check i386 0.10.0-3+b3 [180 kB] Get: 34 http://deb.debian.org/debian buster/main i386 libtool all 2.4.6-9 [547 kB] Get: 35 http://deb.debian.org/debian buster/main i386 dh-autoreconf all 19 [16.9 kB] Get: 36 http://deb.debian.org/debian buster/main i386 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 37 http://deb.debian.org/debian buster/main i386 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 38 http://deb.debian.org/debian buster/main i386 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 39 http://deb.debian.org/debian buster/main i386 libelf1 i386 0.176-1.1 [166 kB] Get: 40 http://deb.debian.org/debian buster/main i386 dwz i386 0.12-3 [81.4 kB] Get: 41 http://deb.debian.org/debian buster/main i386 libglib2.0-0 i386 2.58.3-2+deb10u2 [1334 kB] Get: 42 http://deb.debian.org/debian buster/main i386 libicu63 i386 63.1-6+deb10u1 [8451 kB] Get: 43 http://deb.debian.org/debian buster/main i386 libxml2 i386 2.9.4+dfsg1-7+b3 [721 kB] Get: 44 http://deb.debian.org/debian buster/main i386 libcroco3 i386 0.6.12-3 [151 kB] Get: 45 http://deb.debian.org/debian buster/main i386 libncurses6 i386 6.1+20181013-2+deb10u2 [109 kB] Get: 46 http://deb.debian.org/debian buster/main i386 gettext i386 0.19.8.1-9 [1314 kB] Get: 47 http://deb.debian.org/debian buster/main i386 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 48 http://deb.debian.org/debian buster/main i386 po-debconf all 1.0.21 [248 kB] Get: 49 http://deb.debian.org/debian buster/main i386 debhelper all 12.1.1 [1016 kB] Get: 50 http://deb.debian.org/debian buster/main i386 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 51 http://deb.debian.org/debian buster/main i386 python3-distutils all 3.7.3-1 [142 kB] Get: 52 http://deb.debian.org/debian buster/main i386 dh-python all 3.20190308 [99.3 kB] Get: 53 http://deb.debian.org/debian buster/main i386 fasttree i386 2.1.10-2 [177 kB] Get: 54 http://deb.debian.org/debian buster/main i386 libgfortran5 i386 8.3.0-6 [549 kB] Get: 55 http://deb.debian.org/debian buster/main i386 libblas3 i386 3.8.0-2 [142 kB] Get: 56 http://deb.debian.org/debian buster/main i386 libpng16-16 i386 1.6.36-6 [301 kB] Get: 57 http://deb.debian.org/debian buster/main i386 libfreetype6 i386 2.9.1-3+deb10u1 [395 kB] Get: 58 http://deb.debian.org/debian buster/main i386 libimagequant0 i386 2.12.2-1.1 [32.4 kB] Get: 59 http://deb.debian.org/debian buster/main i386 libjbig0 i386 2.1-3.1+b2 [31.5 kB] Get: 60 http://deb.debian.org/debian buster/main i386 libjpeg62-turbo i386 1:1.5.2-2+b1 [142 kB] Get: 61 http://deb.debian.org/debian buster/main i386 liblapack3 i386 3.8.0-2 [1974 kB] Get: 62 http://deb.debian.org/debian buster/main i386 liblcms2-2 i386 2.9-3 [156 kB] Get: 63 http://deb.debian.org/debian buster/main i386 libwebp6 i386 0.6.1-2 [275 kB] Get: 64 http://deb.debian.org/debian buster/main i386 libtiff5 i386 4.1.0+git191117-2~deb10u1 [284 kB] Get: 65 http://deb.debian.org/debian buster/main i386 libwebpdemux2 i386 0.6.1-2 [87.8 kB] Get: 66 http://deb.debian.org/debian buster/main i386 libwebpmux3 i386 0.6.1-2 [99.1 kB] Get: 67 http://deb.debian.org/debian buster/main i386 pkg-config i386 0.29-6 [64.7 kB] Get: 68 http://deb.debian.org/debian buster/main i386 python3-pkg-resources all 40.8.0-1 [153 kB] Get: 69 http://deb.debian.org/debian buster/main i386 python3-numpy i386 1:1.16.2-1 [2115 kB] Get: 70 http://deb.debian.org/debian buster/main i386 python3-reportlab-accel i386 3.5.13-1+deb10u1 [36.2 kB] Get: 71 http://deb.debian.org/debian buster/main i386 python3-pil i386 5.4.1-2+deb10u1 [398 kB] Get: 72 http://deb.debian.org/debian buster/main i386 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get: 73 http://deb.debian.org/debian buster/main i386 python3-biopython i386 1.73+dfsg-1 [1288 kB] Get: 74 http://deb.debian.org/debian buster/main i386 python3-dendropy all 4.4.0-1 [265 kB] Get: 75 http://deb.debian.org/debian buster/main i386 python3-nose all 1.3.7-4 [132 kB] Get: 76 http://deb.debian.org/debian buster/main i386 python3-setuptools all 40.8.0-1 [306 kB] Get: 77 http://deb.debian.org/debian buster/main i386 raxml i386 8.2.12+dfsg-1 [1199 kB] Get: 78 http://deb.debian.org/debian buster/main i386 zlib1g-dev i386 1:1.2.11.dfsg-1 [216 kB] Fetched 37.8 MB in 4s (9308 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:i386. (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 ... 19234 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2_i386.deb ... Unpacking libbsd0:i386 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_i386.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../2-libuchardet0_0.0.6-3_i386.deb ... Unpacking libuchardet0:i386 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../3-groff-base_1.22.4-3_i386.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../4-libpipeline1_1.5.1-2_i386.deb ... Unpacking libpipeline1:i386 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../5-man-db_2.8.5-2_i386.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libssl1.1:i386. Preparing to unpack .../6-libssl1.1_1.1.1d-0+deb10u3_i386.deb ... Unpacking libssl1.1:i386 (1.1.1d-0+deb10u3) ... Selecting previously unselected package libpython3.7-minimal:i386. Preparing to unpack .../7-libpython3.7-minimal_3.7.3-2+deb10u1_i386.deb ... Unpacking libpython3.7-minimal:i386 (3.7.3-2+deb10u1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../8-libexpat1_2.2.6-2+deb10u1_i386.deb ... Unpacking libexpat1:i386 (2.2.6-2+deb10u1) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../9-python3.7-minimal_3.7.3-2+deb10u1_i386.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u1) ... Setting up libssl1.1:i386 (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:i386 (3.7.3-2+deb10u1) ... Setting up libexpat1:i386 (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u1) ... Selecting previously unselected package python3-minimal. (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 ... 20129 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.7.3-1_i386.deb ... Unpacking python3-minimal (3.7.3-1) ... Selecting previously unselected package mime-support. Preparing to unpack .../1-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libmpdec2:i386. Preparing to unpack .../2-libmpdec2_2.4.2-2_i386.deb ... Unpacking libmpdec2:i386 (2.4.2-2) ... 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Setting up autotools-dev (20180224.1) ... Setting up libjpeg62-turbo:i386 (1:1.5.2-2+b1) ... Setting up libncurses6:i386 (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:i386 (2.12-2) ... Setting up libimagequant0:i386 (2.12.2-1.1) ... Setting up libpng16-16:i386 (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libwebp6:i386 (0.6.1-2) ... Setting up pkg-config (0.29-6) ... Setting up libgfortran5:i386 (8.3.0-6) ... Setting up zlib1g-dev:i386 (1:1.2.11.dfsg-1) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:i386 (0.0.6-3) ... Setting up fasttree (2.1.10-2) ... Setting up libtiff5:i386 (4.1.0+git191117-2~deb10u1) ... Setting up libmpdec2:i386 (2.4.2-2) ... Setting up libwebpmux3:i386 (0.6.1-2) ... Setting up libbsd0:i386 (0.9.1-2) ... Setting up libelf1:i386 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:i386 (2.9.4+dfsg1-7+b3) ... Setting up libreadline7:i386 (7.0-5) ... Setting up raxml (8.2.12+dfsg-1) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libpython3.7-stdlib:i386 (3.7.3-2+deb10u1) ... Setting up libtool (2.4.6-9) ... Setting up libwebpdemux2:i386 (0.6.1-2) ... Setting up libsubunit-dev:i386 (1.3.0-1) ... Setting up m4 (1.4.18-2) ... Setting up libblas3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libfreetype6:i386 (2.9.1-3+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up check:i386 (0.10.0-3+b3) ... Setting up libcroco3:i386 (0.6.12-3) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libpython3-stdlib:i386 (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u1) ... Setting up liblapack3:i386 (3.8.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:i386 (5.4.1-2+deb10u1) ... Setting up python3-reportlab-accel:i386 (3.5.13-1+deb10u1) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up python3-setuptools (40.8.0-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-nose (1.3.7-4) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-biopython (1.73+dfsg-1) ... Setting up python3-dendropy (4.4.0-1) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... 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 Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/gubbins-2.3.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 2.3.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 fakeroot debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/build/gubbins-2.3.4' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete make[1]: Leaving directory '/build/gubbins-2.3.4' debian/rules build dh build --with python3 dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:20: installing './compile' configure.ac:10: installing './config.guess' configure.ac:10: installing './config.sub' configure.ac:3: installing './install-sh' configure.ac:3: installing './missing' src/Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' dh_auto_configure ./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --libexecdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking configure: WARNING: unrecognized options: --disable-maintainer-mode checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe 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 how to create a pax tar archive... gnutar checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking how to print strings... printf checking whether make supports the include directive... yes (GNU style) checking for gcc... gcc 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 we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for a sed that does not truncate output... /bin/sed checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for fgrep... /bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert i686-pc-linux-gnu file names to i686-pc-linux-gnu format... func_convert_file_noop checking how to convert i686-pc-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC -DPIC checking if gcc PIC flag -fPIC -DPIC works... yes checking if gcc static flag -static works... yes checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking dependency style of gcc... (cached) none checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... none checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... 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-D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c string_cat.c -o string_cat.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -o tree_scaling.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -o gff_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -o block_tab_file.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 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branch_sequences.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/i386-linux-gnu Newickform.lo alignment_file.lo block_tab_file.lo branch_sequences.lo string_cat.lo fasta_of_snp_sites.lo gff_file.lo gubbins.lo parse_phylip.lo parse_vcf.lo phylip_of_snp_sites.lo seqUtil.lo snp_searching.lo snp_sites.lo tree_statistics.lo tree_scaling.lo vcf.lo -lm libtool: link: gcc -shared -fPIC -DPIC .libs/Newickform.o .libs/alignment_file.o .libs/block_tab_file.o .libs/branch_sequences.o .libs/string_cat.o .libs/fasta_of_snp_sites.o .libs/gff_file.o .libs/gubbins.o .libs/parse_phylip.o .libs/parse_vcf.o .libs/phylip_of_snp_sites.o .libs/seqUtil.o .libs/snp_searching.o .libs/snp_sites.o .libs/tree_statistics.o .libs/tree_scaling.o .libs/vcf.o -lm -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now 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-D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c In file included from ../tests/check_gubbins.c:4: ../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations': ../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays': ../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration] fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/check_branch_sequences.c:67:16: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays'; did you mean 'copy_and_concat_integer_arrays'? [-Wimplicit-function-declaration] output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ copy_and_concat_integer_arrays ../tests/helper_methods.c: In function 'compare_files': ../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(expected_buffer, sizeof(char), numbytes, expected_output_fh); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit libtool: link: gcc -I../tests -pthread -g -O2 -ffile-prefix-map=/build/gubbins-2.3.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread make[4]: Leaving directory '/build/gubbins-2.3.4/src' make check-TESTS make[4]: Entering directory '/build/gubbins-2.3.4/src' make[5]: Entering directory '/build/gubbins-2.3.4/src' PASS: run_all_tests ============================================================================ Testsuite summary for gubbins 2.3.4 ============================================================================ # TOTAL: 1 # PASS: 1 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/gubbins-2.3.4/src' make[4]: Leaving directory '/build/gubbins-2.3.4/src' make[3]: Leaving directory '/build/gubbins-2.3.4/src' Making check in release make[3]: Entering directory '/build/gubbins-2.3.4/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/gubbins-2.3.4/release' make[3]: Entering directory '/build/gubbins-2.3.4' make[3]: Leaving directory '/build/gubbins-2.3.4' make[2]: Leaving directory '/build/gubbins-2.3.4' cd python && \ python3 setup.py test running test running egg_info creating gubbins.egg-info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt writing manifest file 'gubbins.egg-info/SOURCES.txt' reading manifest file 'gubbins.egg-info/SOURCES.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' running build_ext /build/gubbins-2.3.4/python/gubbins/common.py:536: DeprecationWarning: invalid escape sequence \. regex_for_file_deletions.append("^RAxML_result."+GubbinsCommon.raxml_base_name(base_filename_without_ext,current_time)+str(file_iteration)+'\.') /build/gubbins-2.3.4/python/gubbins/common.py:550: DeprecationWarning: invalid escape sequence \. regex_for_file_deletions.append("^"+starting_base_filename+".iteration_"+str(file_iteration)+'[$|\.]') /build/gubbins-2.3.4/python/gubbins/common.py:711: DeprecationWarning: invalid escape sequence \d elif re.match('^\d', vcf_line) != None : /build/gubbins-2.3.4/python/gubbins/common.py:823: DeprecationWarning: invalid escape sequence \d searchObj = re.search('misc_feature ([\d]+)..([\d]+)$', line) /build/gubbins-2.3.4/python/gubbins/common.py:830: DeprecationWarning: invalid escape sequence \= searchTaxa = re.search('taxa\=\"([^"]+)\"', line) /usr/lib/python3/dist-packages/dendropy/utility/container.py:357: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working class CaseInsensitiveDict(collections.MutableMapping): test_get_sequence_names_from_alignment (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok test_number_of_sequences_in_alignment (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok test_reconvert_fasta_file (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok test_reinsert_gaps_into_fasta_file (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok test_get_recombination_files (test_converging_recombinations.TestConvergingRecombinations) ... ok test_multiple_files_have_one_match (test_converging_recombinations.TestConvergingRecombinations) ... ok test_reading_embl_file (test_converging_recombinations.TestConvergingRecombinations) ... ok test_two_files_are_different (test_converging_recombinations.TestConvergingRecombinations) ... ok test_two_files_are_same (test_converging_recombinations.TestConvergingRecombinations) ... ok test_dont_filter_input_file_with_multiple_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok test_filter_out_alignments_with_too_much_missing_data (test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_all_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_multiple_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_no_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok test_input_file_with_one_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok test_add_labels_to_tree (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_ancestor_raxml_command_no_verbose (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_ancestor_raxml_command_verbose (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_convert_raw_ancestral_file_to_fasta (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_merging_fasta_files (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_more_complex_tree (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_root_input_tree (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_run_raxml_ancestor_reconstruction (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_transfer_internal_labels (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_working_directory_construction (test_raxml_sequence_reconstruction.TestRAxMLSequenceReconstruction) ... ok test_fasttree_current_tree_name (test_string_construction.TestStringConstruction) ... ok test_fasttree_gubbins_command (test_string_construction.TestStringConstruction) ... ok test_fasttree_previous_tree_name (test_string_construction.TestStringConstruction) ... ok test_fasttree_regex_for_file_deletions (test_string_construction.TestStringConstruction) ... ok test_fasttree_tree_building_command (test_string_construction.TestStringConstruction) ... ok test_raxml_base_name (test_string_construction.TestStringConstruction) ... ok test_raxml_current_tree_name (test_string_construction.TestStringConstruction) ... ok test_raxml_gubbins_command (test_string_construction.TestStringConstruction) ... ok test_raxml_previous_tree (test_string_construction.TestStringConstruction) ... ok test_raxml_previous_tree_name (test_string_construction.TestStringConstruction) ... ok test_raxml_regex_for_file_deletions (test_string_construction.TestStringConstruction) ... ok test_raxml_regex_for_file_deletions_10 (test_string_construction.TestStringConstruction) ... ok test_raxml_tree_building_command (test_string_construction.TestStringConstruction) ... ok test_rename_files (test_string_construction.TestStringConstruction) ... ok test_starting_files_regex (test_string_construction.TestStringConstruction) ... ok test_translation_of_fasttree_filenames_to_final_filenames (test_string_construction.TestStringConstruction) ... ok test_translation_of_raxml_filenames_to_final_filenames (test_string_construction.TestStringConstruction) ... ok test_filter_out_removed_taxa_from_tree_and_return_new_file (test_tree_python_methods.TestTreePythonMethods) ... ok test_has_tree_been_seen_before (test_tree_python_methods.TestTreePythonMethods) ... ok test_internal_node_taxons_removed_when_used_as_starting_tree (test_tree_python_methods.TestTreePythonMethods) ... ok test_remove_internal_node_labels (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_at_midpoint (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_with_outgroup (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_with_outgroups (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_with_outgroups_all_in_different_clade (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_with_outgroups_all_in_one_clade (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_with_outgroups_all_in_one_clade_large (test_tree_python_methods.TestTreePythonMethods) ... ok test_reroot_tree_with_outgroups_with_two_mixed_clades (test_tree_python_methods.TestTreePythonMethods) ... ok test_robinson_foulds_distance (test_tree_python_methods.TestTreePythonMethods) ... ok test_split_all_non_bi_nodes (test_tree_python_methods.TestTreePythonMethods) ... ok test_are_all_sequence_names_unique (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_are_all_sequences_the_same_length (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_are_there_enough_sequences_to_build_a_tree (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_does_each_sequence_have_a_name (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_does_the_sequence_have_sensible_characters (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_input_file_exists (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_valid_fasta_file (test_validate_fasta_input.TestValidateInputFastaFile) ... ok test_are_all_names_unique (test_validate_starting_tree.TestValidationOfStartingTree) ... ok test_do_the_names_match_the_fasta_file (test_validate_starting_tree.TestValidationOfStartingTree) ... ok test_is_it_a_valid_newick_tree (test_validate_starting_tree.TestValidationOfStartingTree) ... ok ---------------------------------------------------------------------- Ran 66 tests in 1.116s OK make[1]: Leaving directory '/build/gubbins-2.3.4' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/gubbins-2.3.4' dh_auto_install make -j1 install DESTDIR=/build/gubbins-2.3.4/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gubbins-2.3.4' Making install in src make[3]: Entering directory '/build/gubbins-2.3.4/src' make[4]: Entering directory '/build/gubbins-2.3.4/src' /bin/mkdir -p '/build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 libtool: install: (cd /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so.0 || { rm -f libgubbins.so.0 && ln -s libgubbins.so.0.0.1 libgubbins.so.0; }; }) libtool: install: (cd /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu && { ln -s -f libgubbins.so.0.0.1 libgubbins.so || { rm -f libgubbins.so && ln -s libgubbins.so.0.0.1 libgubbins.so; }; }) libtool: install: /usr/bin/install -c .libs/libgubbins.lai /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: chmod 644 /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: install: ranlib /build/gubbins-2.3.4/debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/i386-linux-gnu' /bin/mkdir -p '/build/gubbins-2.3.4/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/build/gubbins-2.3.4/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/i386-linux-gnu' libtool: install: /usr/bin/install -c .libs/gubbins /build/gubbins-2.3.4/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gubbins-2.3.4/src' make[3]: Leaving directory '/build/gubbins-2.3.4/src' Making install in release make[3]: Entering directory '/build/gubbins-2.3.4/release' make[4]: Entering directory '/build/gubbins-2.3.4/release' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gubbins-2.3.4/release' make[3]: Leaving directory '/build/gubbins-2.3.4/release' make[3]: Entering directory '/build/gubbins-2.3.4' make[4]: Entering directory '/build/gubbins-2.3.4' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gubbins-2.3.4' make[3]: Leaving directory '/build/gubbins-2.3.4' make[2]: Leaving directory '/build/gubbins-2.3.4' # pybuild --install --system=distutils cd python && \ python3 setup.py install --root=../debian/gubbins --install-layout=deb --install-lib=/usr/share/gubbins --install-scripts=/usr/share/gubbins running install running build running build_py creating build creating build/lib creating build/lib/gubbins copying gubbins/RAxMLSequenceReconstruction.py -> build/lib/gubbins copying gubbins/RAxMLExecutable.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/__init__.py -> build/lib/gubbins copying gubbins/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/common.py -> build/lib/gubbins running build_scripts creating build/scripts-3.7 copying and adjusting scripts/run_gubbins.py -> build/scripts-3.7 copying and adjusting scripts/gubbins_drawer.py -> build/scripts-3.7 changing mode of build/scripts-3.7/run_gubbins.py from 644 to 755 changing mode of build/scripts-3.7/gubbins_drawer.py from 644 to 755 running install_lib creating ../debian/gubbins/usr/share creating ../debian/gubbins/usr/share/gubbins creating ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/RAxMLSequenceReconstruction.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/RAxMLExecutable.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/PreProcessFasta.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/ValidateFastaAlignment.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/common.py -> ../debian/gubbins/usr/share/gubbins/gubbins byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/RAxMLSequenceReconstruction.py to RAxMLSequenceReconstruction.cpython-37.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/RAxMLExecutable.py to RAxMLExecutable.cpython-37.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/PreProcessFasta.py to PreProcessFasta.cpython-37.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/__init__.py to __init__.cpython-37.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/ValidateFastaAlignment.py to ValidateFastaAlignment.cpython-37.pyc byte-compiling ../debian/gubbins/usr/share/gubbins/gubbins/common.py to common.cpython-37.pyc running install_egg_info running egg_info writing gubbins.egg-info/PKG-INFO writing dependency_links to gubbins.egg-info/dependency_links.txt writing requirements to gubbins.egg-info/requires.txt writing top-level names to gubbins.egg-info/top_level.txt reading manifest file 'gubbins.egg-info/SOURCES.txt' writing manifest file 'gubbins.egg-info/SOURCES.txt' Copying gubbins.egg-info to ../debian/gubbins/usr/share/gubbins/gubbins-2.3.4.egg-info Skipping SOURCES.txt running install_scripts copying build/scripts-3.7/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.7/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_drawer.py to 755 changing mode of ../debian/gubbins/usr/share/gubbins/run_gubbins.py to 755 make[1]: Leaving directory '/build/gubbins-2.3.4' debian/rules override_dh_install make[1]: Entering directory '/build/gubbins-2.3.4' dh_install find debian -name "*.la" -delete find debian -name "*.a" -delete mkdir -p debian/gubbins/usr/lib/gubbins mv debian/gubbins/usr/bin/gubbins debian/gubbins/usr/lib/gubbins make[1]: Leaving directory '/build/gubbins-2.3.4' dh_installdocs dh_installchangelogs dh_installman dh_python3 I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/gubbins_drawer.py I: dh_python3 tools:114: replacing shebang in debian/gubbins/usr/share/gubbins/run_gubbins.py dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/i386-linux-gnu/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/gubbins/usr/lib/gubbins/gubbins was not linked against libz.so.1 (it uses none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'gubbins-dbgsym' in '../gubbins-dbgsym_2.3.4-1_i386.deb'. dpkg-deb: building package 'gubbins' in '../gubbins_2.3.4-1_i386.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../gubbins_2.3.4-1_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) 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/39103 and its subdirectories I: Current time: Thu Jul 1 05:34:24 -12 2021 I: pbuilder-time-stamp: 1625160864 Fri May 29 11:11:25 UTC 2020 I: 1st build successful. Starting 2nd build on remote node profitbricks-build2-i386.debian.net. Fri May 29 11:11:25 UTC 2020 I: Preparing to do remote build '2' on profitbricks-build2-i386.debian.net. Fri May 29 11:16:08 UTC 2020 I: Deleting $TMPDIR on profitbricks-build2-i386.debian.net. Fri May 29 11:16:08 UTC 2020 I: gubbins_2.3.4-1_i386.changes: Format: 1.8 Date: Wed, 26 Sep 2018 16:48:49 +0200 Source: gubbins Binary: gubbins gubbins-dbgsym Architecture: i386 Version: 2.3.4-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: gubbins - phylogenetic analysis of genome sequences Changes: gubbins (2.3.4-1) unstable; urgency=medium . * New upstream version * debhelper 11 * Point Vcs fields to salsa.debian.org * Standards-Version: 4.2.1 * debian/rules: - Respect DEB_BUILD_OPTIONS in override_dh_auto_test - Do not parse d/changelog * Remove unneeded Testsuite: autopkgtest Checksums-Sha1: ba4759882f25bec92958976659e93ef23a181608 60916 gubbins-dbgsym_2.3.4-1_i386.deb 1dc78feb36dc449a5d15106269270c5731545ed2 5990 gubbins_2.3.4-1_i386.buildinfo 9c796359b1cb92c06842cba0e839da8724ed6d3a 49496 gubbins_2.3.4-1_i386.deb Checksums-Sha256: e7aa63a0630d16bc623ac9ff2ddb6ab4a334741635f0c04e01cc5a27d8f6b431 60916 gubbins-dbgsym_2.3.4-1_i386.deb 1aad74a977b80c101f066d8e8bcf0c592d2f34f6626ca4e6962f14a0763b8dc3 5990 gubbins_2.3.4-1_i386.buildinfo bb3e4a2df8d78d9457641a0156ad47414651a97629f1b2a2315ced8b48afff0d 49496 gubbins_2.3.4-1_i386.deb Files: 0447298437ad01333e6ddeeb90964056 60916 debug optional gubbins-dbgsym_2.3.4-1_i386.deb 0e636aa06e609b5ed05b38bfae4b8592 5990 science optional gubbins_2.3.4-1_i386.buildinfo 6ed73981cb14a30b3fe29ee376cbb3f5 49496 science optional gubbins_2.3.4-1_i386.deb Fri May 29 11:16:10 UTC 2020 I: diffoscope 145 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/tmp.54mhFtBdK5/gubbins_2.3.4-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/tmp.54mhFtBdK5/gubbins_2.3.4-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/tmp.54mhFtBdK5/gubbins_2.3.4-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/tmp.54mhFtBdK5/b1/gubbins_2.3.4-1_i386.changes /srv/reproducible-results/rbuild-debian/tmp.54mhFtBdK5/b2/gubbins_2.3.4-1_i386.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: 0.333s) 0.333s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.057s) 0.057s 10 calls diffoscope.comparators.binary.FilesystemFile Fri May 29 11:16:12 UTC 2020 I: diffoscope 145 found no differences in the changes files, and a .buildinfo file also exists. Fri May 29 11:16:12 UTC 2020 I: gubbins from buster built successfully and reproducibly on i386. Fri May 29 11:16:14 UTC 2020 I: Submitting .buildinfo files to external archives: Fri May 29 11:16:14 UTC 2020 I: Submitting 8.0K b1/gubbins_2.3.4-1_i386.buildinfo.asc Fri May 29 11:16:15 UTC 2020 I: Submitting 8.0K b2/gubbins_2.3.4-1_i386.buildinfo.asc Fri May 29 11:16:15 UTC 2020 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 29 11:16:15 UTC 2020 I: Done submitting .buildinfo files. Fri May 29 11:16:15 UTC 2020 I: Removing signed gubbins_2.3.4-1_i386.buildinfo.asc files: removed './b1/gubbins_2.3.4-1_i386.buildinfo.asc' removed './b2/gubbins_2.3.4-1_i386.buildinfo.asc'