https://launchpad.net/ubuntu/+source/gubbins/2.3.4-1/+build/17954886 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-052 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:46:18 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_183 python-lpbuildd_183 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 17 Dec 08:06:59 ntpdate[1921]: adjust time server 10.211.37.1 offset -0.029919 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17954886 --image-type chroot /home/buildd/filecache-default/f005b6164729459c78307140747b338a2f357aa2 Creating target for build PACKAGEBUILD-17954886 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17954886 Starting target for build PACKAGEBUILD-17954886 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17954886 'deb http://ftpmaster.internal/ubuntu focal main universe' Overriding sources.list in build-PACKAGEBUILD-17954886 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17954886 Updating target for build PACKAGEBUILD-17954886 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf Packages [932 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [500 kB] Get:4 http://ftpmaster.internal/ubuntu focal/universe armhf Packages [8390 kB] Get:5 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5175 kB] Fetched 15.3 MB in 6s (2355 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 cpp-9 debianutils fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lsb-base mount ncurses-base ncurses-bin perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 89 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 57.7 MB of archives. After this operation, 41.1 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main armhf libc6-dev armhf 2.30-0ubuntu3 [1943 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main armhf libc-dev-bin armhf 2.30-0ubuntu3 [63.6 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main armhf linux-libc-dev armhf 5.3.0-24.26 [1079 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main armhf libisl22 armhf 0.22-2 [460 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main armhf libcc1-0 armhf 9.2.1-21ubuntu1 [41.8 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main armhf binutils-arm-linux-gnueabihf armhf 2.33.1-6ubuntu1 [2102 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main armhf libbinutils armhf 2.33.1-6ubuntu1 [315 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main armhf binutils-common armhf 2.33.1-6ubuntu1 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main armhf binutils armhf 2.33.1-6ubuntu1 [3352 B] Get:10 http://ftpmaster.internal/ubuntu focal/main armhf gcc-9-base armhf 9.2.1-21ubuntu1 [19.0 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main armhf libgcc1 armhf 1:9.2.1-21ubuntu1 [37.4 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main armhf libgomp1 armhf 9.2.1-21ubuntu1 [77.4 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main armhf libatomic1 armhf 9.2.1-21ubuntu1 [7104 B] Get:14 http://ftpmaster.internal/ubuntu focal/main armhf libasan5 armhf 9.2.1-21ubuntu1 [387 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main armhf libubsan1 armhf 9.2.1-21ubuntu1 [118 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main armhf g++-9 armhf 9.2.1-21ubuntu1 [8541 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++-9-dev armhf 9.2.1-21ubuntu1 [1777 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main armhf libgcc-9-dev armhf 9.2.1-21ubuntu1 [690 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main armhf gcc-9 armhf 9.2.1-21ubuntu1 [8073 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main armhf cpp-9 armhf 9.2.1-21ubuntu1 [7470 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main armhf libstdc++6 armhf 9.2.1-21ubuntu1 [451 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main armhf libc6 armhf 2.30-0ubuntu3 [2144 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main armhf base-files armhf 11ubuntu2 [59.8 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main armhf debianutils armhf 4.9.1 [84.6 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main armhf bash armhf 5.0-5ubuntu1 [576 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main armhf bsdutils armhf 1:2.34-0.1ubuntu4 [58.4 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main armhf gzip armhf 1.10-0ubuntu4 [91.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main armhf hostname armhf 3.23 [10.4 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main armhf ncurses-bin armhf 6.1+20191019-1ubuntu1 [163 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main armhf perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main armhf libperl5.30 armhf 5.30.0-9 [3286 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main armhf perl armhf 5.30.0-9 [224 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main armhf perl-base armhf 5.30.0-9 [1408 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main armhf bzip2 armhf 1.0.8-2 [32.4 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main armhf libbz2-1.0 armhf 1.0.8-2 [31.0 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main armhf libblkid1 armhf 2.34-0.1ubuntu4 [124 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main armhf libuuid1 armhf 2.34-0.1ubuntu4 [19.8 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main armhf libfdisk1 armhf 2.34-0.1ubuntu4 [163 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main armhf libpcre2-8-0 armhf 10.34-7 [172 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main armhf libselinux1 armhf 3.0-1 [60.1 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main armhf libmount1 armhf 2.34-0.1ubuntu4 [135 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main armhf libncurses6 armhf 6.1+20191019-1ubuntu1 [79.7 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main armhf libtinfo6 armhf 6.1+20191019-1ubuntu1 [72.8 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main armhf libncursesw6 armhf 6.1+20191019-1ubuntu1 [106 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main armhf libsmartcols1 armhf 2.34-0.1ubuntu4 [89.1 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main armhf fdisk armhf 2.34-0.1ubuntu4 [109 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main armhf util-linux armhf 2.34-0.1ubuntu4 [959 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main armhf libdebconfclient0 armhf 0.250ubuntu1 [5820 B] Get:49 http://ftpmaster.internal/ubuntu focal/main armhf base-passwd armhf 3.5.47 [46.4 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main armhf libc-bin armhf 2.30-0ubuntu3 [496 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main armhf ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main armhf lsb-base all 11.1.0ubuntu1 [12.2 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main armhf sysvinit-utils armhf 2.96-1ubuntu1 [19.2 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main armhf liblz4-1 armhf 1.9.2-2 [51.7 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main armhf systemd-sysv armhf 243-3ubuntu1 [9364 B] Get:56 http://ftpmaster.internal/ubuntu focal/main armhf libacl1 armhf 2.2.53-5 [15.9 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main armhf libapparmor1 armhf 2.13.3-5ubuntu5 [29.7 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main armhf libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:59 http://ftpmaster.internal/ubuntu focal/main armhf libcap-ng0 armhf 0.7.9-2.1 [9692 B] Get:60 http://ftpmaster.internal/ubuntu focal/main armhf libaudit1 armhf 1:2.8.5-2ubuntu5 [35.9 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main armhf libcap2 armhf 1:2.27-1 [12.7 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main armhf libudev1 armhf 243-3ubuntu1 [71.0 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main armhf libdevmapper1.02.1 armhf 2:1.02.155-2ubuntu7 [118 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main armhf libjson-c4 armhf 0.13.1+dfsg-6 [25.6 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main armhf libcryptsetup12 armhf 2:2.2.2-1ubuntu1 [163 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main armhf libnettle7 armhf 3.5.1+really3.5.1-2 [126 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main armhf libhogweed5 armhf 3.5.1+really3.5.1-2 [127 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main armhf libp11-kit0 armhf 0.23.18.1-2 [166 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main armhf libtasn1-6 armhf 4.15.0-2 [33.0 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main armhf libgnutls30 armhf 3.6.11.1-2 [732 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main armhf libkmod2 armhf 26-3ubuntu1 [37.0 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main armhf libpam0g armhf 1.3.1-5ubuntu3 [50.1 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main armhf mount armhf 2.34-0.1ubuntu4 [108 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main armhf systemd armhf 243-3ubuntu1 [3479 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main armhf libsystemd0 armhf 243-3ubuntu1 [243 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main armhf libzstd1 armhf 1.4.4+dfsg-1 [207 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main armhf libapt-pkg5.90 armhf 1.9.5 [772 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main armhf libgcrypt20 armhf 1.8.5-3ubuntu1 [364 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main armhf gpgv armhf 2.2.17-3ubuntu1 [170 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main armhf apt armhf 1.9.5 [1237 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main armhf libpam-modules-bin armhf 1.3.1-5ubuntu3 [33.8 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main armhf libpam-modules armhf 1.3.1-5ubuntu3 [232 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main armhf libattr1 armhf 1:2.4.48-5 [11.5 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main armhf libpam-runtime all 1.3.1-5ubuntu3 [37.3 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main armhf libsepol1 armhf 3.0-1 [220 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main armhf libsemanage-common all 2.9-3build1 [9736 B] Get:87 http://ftpmaster.internal/ubuntu focal/main armhf libsemanage1 armhf 2.9-3build1 [73.7 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main armhf sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main armhf libsqlite3-0 armhf 3.30.1-1ubuntu1 [460 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main armhf gpg armhf 2.2.17-3ubuntu1 [421 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main armhf gpgconf armhf 2.2.17-3ubuntu1 [107 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main armhf gpg-agent armhf 2.2.17-3ubuntu1 [195 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main armhf liblockfile-bin armhf 1.16-1.1 [10.5 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main armhf liblockfile1 armhf 1.16-1.1 [5620 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 57.7 MB in 2s (28.8 MB/s) (Reading database ... 12487 files and directories currently installed.) 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Setting up gpg (2.2.17-3ubuntu1) ... Setting up libkmod2:armhf (26-3ubuntu1) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up binutils (2.33.1-6ubuntu1) ... Setting up libgcc-9-dev:armhf (9.2.1-21ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-21ubuntu1) ... Setting up libc6-dev:armhf (2.30-0ubuntu3) ... Setting up libcryptsetup12:armhf (2:2.2.2-1ubuntu1) ... Setting up gcc-9 (9.2.1-21ubuntu1) ... Setting up libstdc++-9-dev:armhf (9.2.1-21ubuntu1) ... Setting up systemd (243-3ubuntu1) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-21ubuntu1) ... Setting up systemd-sysv (243-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-17954886 armhf focal -c chroot:build-PACKAGEBUILD-17954886 --arch=armhf --dist=focal --nolog gubbins_2.3.4-1.dsc Initiating build PACKAGEBUILD-17954886 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:46:18 UTC 2019 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-052.buildd +==============================================================================+ | gubbins 2.3.4-1 (armhf) 17 Dec 2019 08:07 | +==============================================================================+ Package: gubbins Version: 2.3.4-1 Source Version: 2.3.4-1 Distribution: focal Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/gubbins-gpgvpA/gubbins-2.3.4' with '<>' I: NOTICE: Log filtering will replace 'build/gubbins-gpgvpA' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-17954886/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- gubbins_2.3.4-1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-jNbfH3/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-jNbfH3/apt_archive ./ InRelease Get:2 copy:/<>/resolver-jNbfH3/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-jNbfH3/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-jNbfH3/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-jNbfH3/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (125 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-jNbfH3/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14420 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged 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 Filtered 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 dpkg-deb: building package 'sbuild-build-depends-gubbins-dummy' in '/<>/resolver-xSKADQ/apt_archive/sbuild-build-depends-gubbins-dummy.deb'. Ign:1 copy:/<>/resolver-xSKADQ/apt_archive ./ InRelease Get:2 copy:/<>/resolver-xSKADQ/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-xSKADQ/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-xSKADQ/apt_archive ./ Sources [289 B] Get:5 copy:/<>/resolver-xSKADQ/apt_archive ./ Packages [614 B] Fetched 3022 B in 0s (128 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install gubbins build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils check debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz fasttree file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran5 libglib2.0-0 libicu63 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libsubunit-dev libsubunit0 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-biopython python3-dendropy python3-distutils python3-lib2to3 python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-reportlab-accel python3-setuptools python3.7 python3.7-minimal python3.8 python3.8-minimal raxml zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff liblcms2-utils libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv clustalo clustalw dialign dssp emboss mafft muscle phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-rdflib python3-renderpm python3-psycopg2 python3-scipy samtools t-coffee wise w3-dtd-mathml python-nose-doc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pil-doc python3-pil-dbg pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-setuptools-doc python3.7-venv python3.7-doc binfmt-support python3.8-venv python3.8-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-olefile python3-renderpm The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils check debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz fasttree file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libblas3 libbsd0 libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libfreetype6 libgfortran5 libglib2.0-0 libicu63 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 liblapack3 liblcms2-2 libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libsubunit-dev libsubunit0 libtiff5 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-biopython python3-dendropy python3-distutils python3-lib2to3 python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources python3-reportlab python3-reportlab-accel python3-setuptools python3.7 python3.7-minimal python3.8 python3.8-minimal raxml sbuild-build-depends-gubbins-dummy zlib1g-dev 0 upgraded, 80 newly installed, 0 to remove and 0 not upgraded. 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Setting up libpython3.8-minimal:armhf (3.8.0-5) ... Setting up mime-support (3.64ubuntu1) ... Setting up libmagic-mgc (1:5.37-6) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:armhf (2.63.1-2ubuntu1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.7.1ubuntu1) ... Setting up libmagic1:armhf (1:5.37-6) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.37-6) ... Setting up libsubunit0:armhf (1.3.0-5) ... Setting up libjbig0:armhf (2.1-3.1build1) ... Setting up libicu63:armhf (63.2-2) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:armhf (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libfreetype6:armhf (2.10.1-2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libimagequant0:armhf (2.12.2-1.1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libwebp6:armhf (0.6.1-2) ... Setting up pkg-config (0.29.1-0ubuntu3) ... Setting up libjpeg-turbo8:armhf (2.0.3-0ubuntu1) ... Setting up libgfortran5:armhf (9.2.1-21ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1ubuntu3) ... Setting up python3.8-minimal (3.8.0-5) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up fasttree (2.1.11-1) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libpython3.8-stdlib:armhf (3.8.0-5) ... Setting up python3.8 (3.8.0-5) ... Setting up libwebpmux3:armhf (0.6.1-2) ... Setting up libbsd0:armhf (0.10.0-1) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up libxml2:armhf (2.9.4+dfsg1-8ubuntu1) ... Setting up raxml (8.2.12+dfsg-2) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.6.3-1) ... Setting up libpython3.7-stdlib:armhf (3.7.5-2) ... Setting up liblapack3:armhf (3.9.0-1) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up libtool (2.4.6-11) ... Setting up libwebpdemux2:armhf (0.6.1-2) ... Setting up libsubunit-dev:armhf (1.3.0-5) ... Setting up m4 (1.4.18-4) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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:armhf (0.10.0-3build2) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up autoconf (2.69-11ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-3) ... Setting up libtiff5:armhf (4.1.0+git191117-1) ... Setting up libpython3-stdlib:armhf (3.7.5-1ubuntu1) ... Setting up automake (1:1.16.1-4ubuntu3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.5-2) ... Setting up gettext (0.19.8.1-10) ... Setting up python3 (3.7.5-1ubuntu1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:armhf (6.2.1-2) ... Setting up python3-reportlab-accel:armhf (3.5.31-1) ... Setting up python3-reportlab (3.5.31-1) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up python3-pkg-resources (41.4.0-1) ... Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu1) ... Setting up python3-setuptools (41.4.0-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-nose (1.3.7-4) ... Setting up python3-numpy (1:1.17.4-3ubuntu2) ... Setting up python3-biopython (1.73+dfsg-1ubuntu4) ... /usr/lib/python3/dist-packages/Bio/KEGG/__init__.py:82: SyntaxWarning: "is not" with a literal. Did you mean "!="? if item is not "": # ensure item is only written on first line /usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py:939: SyntaxWarning: "is" with a literal. Did you mean "=="? elif state is ',': Setting up python3-dendropy (4.4.0-2) ... Setting up debhelper (12.7.1ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-gubbins-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic arm64 (armv7l) Toolchain package versions: binutils_2.33.1-6ubuntu1 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-21ubuntu1 gcc-9_9.2.1-21ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 linux-libc-dev_5.3.0-24.26 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.5 autoconf_2.69-11ubuntu1 automake_1:1.16.1-4ubuntu3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.1-6ubuntu1 binutils-arm-linux-gnueabihf_2.33.1-6ubuntu1 binutils-common_2.33.1-6ubuntu1 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 check_0.10.0-3build2 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-21ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.1ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017ubuntu1 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu2 fakeroot_1.24-1 fasttree_2.1.11-1 fdisk_2.34-0.1ubuntu4 file_1:5.37-6 findutils_4.6.0+git+20190209-2ubuntu1 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-21ubuntu1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-21ubuntu1 gcc-9-base_9.2.1-21ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.3-1build1 groff-base_1.22.4-3 gzip_1.10-0ubuntu4 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5 libapparmor1_2.13.3-5ubuntu5 libapt-pkg5.90_1.9.5 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-21ubuntu1 libassuan0_2.5.3-7ubuntu1 libatomic1_9.2.1-21ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.33.1-6ubuntu1 libblas3_3.9.0-1 libblkid1_2.34-0.1ubuntu4 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcc1-0_9.2.1-21ubuntu1 libcom-err2_1.45.3-4ubuntu2 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu1 libdebhelper-perl_12.7.1ubuntu1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.3-4ubuntu2 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu4 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-21ubuntu1 libgcc1_1:9.2.1-21ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-21ubuntu1 libglib2.0-0_2.63.1-2ubuntu1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-21ubuntu1 libgpg-error0_1.36-7 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libimagequant0_2.12.2-1.1 libip4tc2_1.8.3-2ubuntu5 libisl21_0.21-2 libisl22_0.22-2 libjbig0_2.1-3.1build1 libjpeg-turbo8_2.0.3-0ubuntu1 libjpeg8_8c-2ubuntu8 libjson-c4_0.13.1+dfsg-6 libkmod2_26-3ubuntu1 liblapack3_3.9.0-1 liblcms2-2_2.9-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1ubuntu4 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20191019-1ubuntu1 libncursesw6_6.1+20191019-1ubuntu1 libnettle6_3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-modules_1.3.1-5ubuntu3 libpam-modules-bin_1.3.1-5ubuntu3 libpam-runtime_1.3.1-5ubuntu3 libpam0g_1.3.1-5ubuntu3 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.1-3 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpython3-stdlib_3.7.5-1ubuntu1 libpython3.7-minimal_3.7.5-2 libpython3.7-stdlib_3.7.5-2 libpython3.8-minimal_3.8.0-5 libpython3.8-stdlib_3.8.0-5 libreadline8_8.0-3 libseccomp2_2.4.1-0ubuntu0.19.10.3 libselinux1_3.0-1 libsemanage-common_2.9-3build1 libsemanage1_2.9-3build1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu4 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu2 libssl1.1_1.1.1c-1ubuntu4 libstdc++-9-dev_9.2.1-21ubuntu1 libstdc++6_9.2.1-21ubuntu1 libsub-override-perl_0.09-2 libsubunit-dev_1.3.0-5 libsubunit0_1.3.0-5 libsystemd0_243-3ubuntu1 libtasn1-6_4.15.0-2 libtiff5_4.1.0+git191117-1 libtinfo6_6.1+20191019-1ubuntu1 libtool_2.4.6-11 libubsan1_9.2.1-21ubuntu1 libuchardet0_0.0.6-3 libudev1_243-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu4 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libxml2_2.9.4+dfsg1-8ubuntu1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.3.0-24.26 lockfile-progs_0.1.18 login_1:4.5-1.1ubuntu4 logsave_1.45.3-4ubuntu2 lsb-base_11.1.0ubuntu1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1c-1ubuntu4 optipng_0.7.7-1 passwd_1:4.5-1.1ubuntu4 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkg-config_0.29.1-0ubuntu3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python3_3.7.5-1ubuntu1 python3-biopython_1.73+dfsg-1ubuntu4 python3-dendropy_4.4.0-2 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-1ubuntu1 python3-nose_1.3.7-4 python3-numpy_1:1.17.4-3ubuntu2 python3-pil_6.2.1-2 python3-pkg-resources_41.4.0-1 python3-reportlab_3.5.31-1 python3-reportlab-accel_3.5.31-1 python3-setuptools_41.4.0-1 python3.7_3.7.5-2 python3.7-minimal_3.7.5-2 python3.8_3.8.0-5 python3.8-minimal_3.8.0-5 raxml_8.2.12+dfsg-2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gubbins-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_243-3ubuntu1 systemd-sysv_243-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 util-linux_2.34-0.1ubuntu4 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Wed Sep 26 14:51:33 2018 UTC 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 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-17954886 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-17954886 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-17954886 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package gubbins dpkg-buildpackage: info: source version 2.3.4-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -rf python/*.egg-info python/build python/Makefile find . -name "*.pyc" -delete make[1]: Leaving directory '/<>' debian/rules build-arch dh build-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a 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 -a ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --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... 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PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for zlib... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for a Python interpreter with version >= 3.0... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.7 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.7/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.7/site-packages 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 release/Makefile config.status: creating python/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build -a make -j4 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in src make[3]: Entering directory '/<>/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o main.o main.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o Newickform.lo Newickform.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o alignment_file.lo alignment_file.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o block_tab_file.lo block_tab_file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c Newickform.c -fPIC -DPIC -o .libs/Newickform.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c alignment_file.c -fPIC -DPIC -o .libs/alignment_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c block_tab_file.c -fPIC -DPIC -o .libs/block_tab_file.o /bin/bash ../libtool --tag=CC --mode=compile gcc 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fasta_of_snp_sites.c /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gff_file.lo gff_file.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -fPIC -DPIC -o .libs/fasta_of_snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c gff_file.c -fPIC -DPIC -o .libs/gff_file.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c fasta_of_snp_sites.c -o fasta_of_snp_sites.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time 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.libs/snp_searching.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c seqUtil.c -o seqUtil.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o snp_sites.lo snp_sites.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_sites.c -fPIC -DPIC -o .libs/snp_sites.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c snp_searching.c -o snp_searching.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time 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-Wformat -Werror=format-security -c -o vcf.lo vcf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_scaling.c -fPIC -DPIC -o .libs/tree_scaling.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c tree_statistics.c -o tree_statistics.o >/dev/null 2>&1 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -fPIC -DPIC -o .libs/vcf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c vcf.c -o vcf.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 0:1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o libgubbins.la -rpath /usr/lib/arm-linux-gnueabihf 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,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,-soname -Wl,libgubbins.so.0 -o .libs/libgubbins.so.0.0.1 libtool: link: (cd ".libs" && rm -f "libgubbins.so.0" && ln -s "libgubbins.so.0.0.1" "libgubbins.so.0") libtool: link: (cd ".libs" && rm -f "libgubbins.so" && ln -s "libgubbins.so.0.0.1" "libgubbins.so") libtool: link: ar cru .libs/libgubbins.a Newickform.o alignment_file.o block_tab_file.o branch_sequences.o string_cat.o fasta_of_snp_sites.o gff_file.o gubbins.o parse_phylip.o parse_vcf.o phylip_of_snp_sites.o seqUtil.o snp_searching.o snp_sites.o tree_statistics.o tree_scaling.o vcf.o ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libgubbins.a libtool: link: ( cd ".libs" && rm -f "libgubbins.la" && ln -s "../libgubbins.la" "libgubbins.la" ) /bin/bash ../libtool --tag=CC --mode=link gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o gubbins main.o libgubbins.la -lz -lm libtool: link: gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/gubbins main.o ./.libs/libgubbins.so -lz -lm make[3]: Leaving directory '/<>/src' Making all in release make[3]: Entering directory '/<>/release' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/release' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' dh_auto_test make -j4 check VERBOSE=1 make[2]: Entering directory '/<>' Making check in src make[3]: Entering directory '/<>/src' make run_all_tests make[4]: Entering directory '/<>/src' gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 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_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] 67 | output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | copy_and_concat_integer_arrays ../tests/check_gubbins.c:21:15: warning: implicit declaration of function ‘number_of_recombinations_in_file’ [-Wimplicit-function-declaration] 21 | fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 -fdebug-prefix-map=/<>=. -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 ../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] 27 | 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] 34 | fread(actual_buffer, sizeof(char), numbytes, actual_output_fh); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -pthread -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -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 '/<>/src' make check-TESTS make[4]: Entering directory '/<>/src' make[5]: Entering directory '/<>/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 '/<>/src' make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' Making check in release make[3]: Entering directory '/<>/release' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/<>/release' make[3]: Entering directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' 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 /<>/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)+'\.') /<>/python/gubbins/common.py:550: DeprecationWarning: invalid escape sequence \. regex_for_file_deletions.append("^"+starting_base_filename+".iteration_"+str(file_iteration)+'[$|\.]') /<>/python/gubbins/common.py:711: DeprecationWarning: invalid escape sequence \d elif re.match('^\d', vcf_line) != None : /<>/python/gubbins/common.py:823: DeprecationWarning: invalid escape sequence \d searchObj = re.search('misc_feature ([\d]+)..([\d]+)$', line) /<>/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 since Python 3.3,and in 3.9 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 0.912s OK make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install make -j1 install DESTDIR=/<>/debian/gubbins AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' Making install in src make[3]: Entering directory '/<>/src' make[4]: Entering directory '/<>/src' /bin/mkdir -p '/<>/debian/gubbins/usr/lib/arm-linux-gnueabihf' /bin/bash ../libtool --mode=install /usr/bin/install -c libgubbins.la '/<>/debian/gubbins/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/libgubbins.so.0.0.1 /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 libtool: install: (cd /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf && { 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 /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf && { 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 /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.la libtool: install: /usr/bin/install -c .libs/libgubbins.a /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.a libtool: install: chmod 644 /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.a libtool: install: ranlib /<>/debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.a libtool: warning: remember to run 'libtool --finish /usr/lib/arm-linux-gnueabihf' /bin/mkdir -p '/<>/debian/gubbins/usr/bin' /bin/bash ../libtool --mode=install /usr/bin/install -c gubbins '/<>/debian/gubbins/usr/bin' libtool: warning: 'libgubbins.la' has not been installed in '/usr/lib/arm-linux-gnueabihf' libtool: install: /usr/bin/install -c .libs/gubbins /<>/debian/gubbins/usr/bin/gubbins make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>/src' make[3]: Leaving directory '/<>/src' Making install in release make[3]: Entering directory '/<>/release' make[4]: Entering directory '/<>/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 '/<>/release' make[3]: Leaving directory '/<>/release' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' # 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/ValidateFastaAlignment.py -> build/lib/gubbins copying gubbins/RAxMLExecutable.py -> build/lib/gubbins copying gubbins/PreProcessFasta.py -> build/lib/gubbins copying gubbins/RAxMLSequenceReconstruction.py -> build/lib/gubbins copying gubbins/__init__.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 664 to 775 changing mode of build/scripts-3.7/gubbins_drawer.py from 664 to 775 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/ValidateFastaAlignment.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/RAxMLSequenceReconstruction.py -> ../debian/gubbins/usr/share/gubbins/gubbins copying build/lib/gubbins/__init__.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/ValidateFastaAlignment.py to ValidateFastaAlignment.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/RAxMLSequenceReconstruction.py to RAxMLSequenceReconstruction.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/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/run_gubbins.py -> ../debian/gubbins/usr/share/gubbins copying build/scripts-3.7/gubbins_drawer.py -> ../debian/gubbins/usr/share/gubbins changing mode of ../debian/gubbins/usr/share/gubbins/run_gubbins.py to 775 changing mode of ../debian/gubbins/usr/share/gubbins/gubbins_drawer.py to 775 make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' 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 '/<>' dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_python3 -a 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 -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: symbol gzclose used by debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzread used by debian/gubbins/usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 found in none of the libraries dpkg-shlibdeps: warning: symbol gzopen used by debian/gubbins/usr/lib/arm-linux-gnueabihf/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 -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing gubbins (in debian/gubbins); do_strip: , oemstrip: pkgstriptranslations: processing gubbins-dbgsym (in debian/.debhelper/gubbins/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/gubbins/DEBIAN/control, package gubbins, directory debian/gubbins pkgstripfiles: Truncating usr/share/doc/gubbins/changelog.Debian.gz to topmost ten records pkgstripfiles: processing control file: debian/.debhelper/gubbins/dbgsym-root/DEBIAN/control, package gubbins-dbgsym, directory debian/.debhelper/gubbins/dbgsym-root dpkg-deb: building package 'gubbins-dbgsym' in 'debian/.debhelper/scratch-space/build-gubbins/gubbins-dbgsym_2.3.4-1_armhf.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package gubbins ... pkgstripfiles: No PNG files. dpkg-deb: building package 'gubbins' in '../gubbins_2.3.4-1_armhf.deb'. Renaming gubbins-dbgsym_2.3.4-1_armhf.deb to gubbins-dbgsym_2.3.4-1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../gubbins_2.3.4-1_armhf.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20191217-0809 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ gubbins_2.3.4-1_armhf.changes: ------------------------------ Format: 1.8 Date: Wed, 26 Sep 2018 16:48:49 +0200 Source: gubbins Binary: gubbins Architecture: armhf Version: 2.3.4-1 Distribution: focal Urgency: medium Maintainer: Launchpad Build Daemon 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: 2be92a35298af00efdb0769e2f5c34775676e60f 74872 gubbins-dbgsym_2.3.4-1_armhf.ddeb dc72cea1d3c8ea18367ee3bd9ea6f72cf1896bf3 6387 gubbins_2.3.4-1_armhf.buildinfo 9b1fae8a347576888f2344174206efa2a446290c 39776 gubbins_2.3.4-1_armhf.deb Checksums-Sha256: 13c39298c8d9d2c4af1b062b53355357825f74f014bf51fc596cb65eccb9dcab 74872 gubbins-dbgsym_2.3.4-1_armhf.ddeb ff9a9359bbe5655a5e8571d0c9465691df394b6989cbf75c40c098eefcb9a8fc 6387 gubbins_2.3.4-1_armhf.buildinfo 76d26a6d2a80a5bfd04526198a916f26bc381bbcec90908bf6c8b7c0484873b0 39776 gubbins_2.3.4-1_armhf.deb Files: f8addd9d878c230026b1d071e3858d33 74872 debug optional gubbins-dbgsym_2.3.4-1_armhf.ddeb a6b2f8f7ac938bc235d15cabfcf1f749 6387 science optional gubbins_2.3.4-1_armhf.buildinfo f195e23066263458254160a333f73b78 39776 science optional gubbins_2.3.4-1_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ gubbins_2.3.4-1_armhf.deb ------------------------- new debian package, version 2.0. size 39776 bytes: control archive=2044 bytes. 1181 bytes, 22 lines control 1545 bytes, 20 lines md5sums 276 bytes, 12 lines * postinst #!/bin/sh 389 bytes, 12 lines * prerm #!/bin/sh 21 bytes, 1 lines shlibs 74 bytes, 2 lines triggers Package: gubbins Version: 2.3.4-1 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 151 Depends: libc6 (>= 2.29), zlib1g (>= 1:1.1.4), python3-biopython, python3-dendropy, python3-nose, python3-reportlab, python3:any, python3, fasttree, raxml (>= 8) Section: science Priority: optional Homepage: https://sanger-pathogens.github.io/gubbins/ Description: phylogenetic analysis of genome sequences Gubbins supports rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. . Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. drwxr-xr-x root/root 0 2018-09-26 14:48 ./ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/bin/ lrwxrwxrwx root/root 0 2018-09-26 14:48 ./usr/bin/gubbins_drawer -> ../share/gubbins/gubbins_drawer.py lrwxrwxrwx root/root 0 2018-09-26 14:48 ./usr/bin/run_gubbins -> ../share/gubbins/run_gubbins.py drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/lib/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/lib/arm-linux-gnueabihf/ lrwxrwxrwx root/root 0 2018-09-26 14:48 ./usr/lib/arm-linux-gnueabihf/libgubbins.so -> libgubbins.so.0.0.1 lrwxrwxrwx root/root 0 2018-09-26 14:48 ./usr/lib/arm-linux-gnueabihf/libgubbins.so.0 -> libgubbins.so.0.0.1 -rw-r--r-- root/root 34056 2018-09-26 14:48 ./usr/lib/arm-linux-gnueabihf/libgubbins.so.0.0.1 drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/lib/gubbins/ -rwxr-xr-x root/root 9780 2018-09-26 14:48 ./usr/lib/gubbins/gubbins drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/doc/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/doc/gubbins/ -rw-r--r-- root/root 795 2018-09-26 14:48 ./usr/share/doc/gubbins/changelog.Debian.gz -rw-r--r-- root/root 1277 2018-09-26 14:48 ./usr/share/doc/gubbins/copyright drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/gubbins/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/gubbins/gubbins-2.3.4.egg-info/ -rw-r--r-- root/root 760 2018-09-26 14:48 ./usr/share/gubbins/gubbins-2.3.4.egg-info/PKG-INFO -rw-r--r-- root/root 1 2018-09-26 14:48 ./usr/share/gubbins/gubbins-2.3.4.egg-info/dependency_links.txt -rw-r--r-- root/root 57 2018-09-26 14:48 ./usr/share/gubbins/gubbins-2.3.4.egg-info/requires.txt -rw-r--r-- root/root 8 2018-09-26 14:48 ./usr/share/gubbins/gubbins-2.3.4.egg-info/top_level.txt drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/gubbins/gubbins/ -rw-r--r-- root/root 4560 2018-07-30 15:30 ./usr/share/gubbins/gubbins/PreProcessFasta.py -rw-r--r-- root/root 4262 2018-07-30 15:30 ./usr/share/gubbins/gubbins/RAxMLExecutable.py -rw-r--r-- root/root 7054 2018-07-30 15:30 ./usr/share/gubbins/gubbins/RAxMLSequenceReconstruction.py -rw-r--r-- root/root 3343 2018-07-30 15:30 ./usr/share/gubbins/gubbins/ValidateFastaAlignment.py -rw-r--r-- root/root 1941 2018-07-30 15:30 ./usr/share/gubbins/gubbins/__init__.py -rw-r--r-- root/root 40716 2018-09-26 14:48 ./usr/share/gubbins/gubbins/common.py -rwxr-xr-x root/root 574 2018-09-26 14:48 ./usr/share/gubbins/gubbins_drawer.py -rwxr-xr-x root/root 3660 2018-09-26 14:48 ./usr/share/gubbins/run_gubbins.py drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/lintian/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 252 2018-09-26 14:48 ./usr/share/lintian/overrides/gubbins drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/man/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/man/man1/ -rw-r--r-- root/root 456 2018-09-26 14:48 ./usr/share/man/man1/gubbins_drawer.1.gz -rw-r--r-- root/root 1634 2018-09-26 14:48 ./usr/share/man/man1/run_gubbins.1.gz drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/python3/ drwxr-xr-x root/root 0 2018-09-26 14:48 ./usr/share/python3/runtime.d/ -rwxr-xr-x root/root 133 2018-09-26 14:48 ./usr/share/python3/runtime.d/gubbins.rtupdate +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 13212 Build-Time: 51 Distribution: focal Host Architecture: armhf Install-Time: 47 Job: gubbins_2.3.4-1.dsc Machine Architecture: arm64 Package: gubbins Package-Time: 100 Source-Version: 2.3.4-1 Space: 13212 Status: successful Version: 2.3.4-1 -------------------------------------------------------------------------------- Finished at 20191217-0809 Build needed 00:01:40, 13212k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=armhf PACKAGEBUILD-17954886 Scanning for processes to kill in build PACKAGEBUILD-17954886