https://launchpad.net/ubuntu/+archive/test-rebuild-20200728-groovy/+build/19681498 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-012 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 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... 2 Aug 21:03:40 ntpdate[1913]: adjust time server 10.211.37.1 offset 0.039067 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681498 --image-type chroot /home/buildd/filecache-default/6f3c84eb9e6a781060c5439a51cfc1d7c8c4fc5d Creating target for build PACKAGEBUILD-19681498 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681498 Starting target for build PACKAGEBUILD-19681498 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681498 'deb http://ftpmaster.internal/ubuntu groovy main universe' Overriding sources.list in build-PACKAGEBUILD-19681498 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681498 Updating target for build PACKAGEBUILD-19681498 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf Packages [938 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main Translation-en [510 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/universe armhf Packages [8518 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5251 kB] Fetched 15.5 MB in 5s (2923 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files bsdutils build-essential ca-certificates libblkid1 libmount1 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libuuid1 mount util-linux 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1889 kB of archives. After this operation, 2048 B of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main armhf base-files armhf 11ubuntu10 [59.9 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf bsdutils armhf 1:2.35.2-9ubuntu1 [78.8 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf libselinux1 armhf 3.1-2 [60.4 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf util-linux armhf 2.35.2-9ubuntu1 [984 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf mount armhf 2.35.2-9ubuntu1 [111 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf libblkid1 armhf 2.35.2-9ubuntu1 [120 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libmount1 armhf 2.35.2-9ubuntu1 [132 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libsemanage-common all 3.1-1 [10.2 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf libsemanage1 armhf 3.1-1 [75.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf libsmartcols1 armhf 2.35.2-9ubuntu1 [84.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf libuuid1 armhf 2.35.2-9ubuntu1 [21.3 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf ca-certificates all 20200601 [147 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf build-essential armhf 12.8ubuntu3 [4636 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 1889 kB in 1s (3714 kB/s) (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu10_armhf.deb ... Unpacking base-files (11ubuntu10) over (11ubuntu9) ... Setting up base-files (11ubuntu10) ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.35.2-9ubuntu1_armhf.deb ... Unpacking bsdutils (1:2.35.2-9ubuntu1) over (1:2.35.2-7ubuntu3) ... Setting up bsdutils (1:2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libselinux1_3.1-2_armhf.deb ... Unpacking libselinux1:armhf (3.1-2) over (3.0-1build2) ... Setting up libselinux1:armhf (3.1-2) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../util-linux_2.35.2-9ubuntu1_armhf.deb ... Unpacking util-linux (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up util-linux (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../mount_2.35.2-9ubuntu1_armhf.deb ... Unpacking mount (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Preparing to unpack .../libblkid1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libblkid1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libblkid1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libmount1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libmount1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libmount1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.1-1_all.deb ... Unpacking libsemanage-common (3.1-1) over (3.0-1build2) ... Setting up libsemanage-common (3.1-1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libsemanage1_3.1-1_armhf.deb ... Unpacking libsemanage1:armhf (3.1-1) over (3.0-1build2) ... Setting up libsemanage1:armhf (3.1-1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libsmartcols1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libsmartcols1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../libuuid1_2.35.2-9ubuntu1_armhf.deb ... Unpacking libuuid1:armhf (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libuuid1:armhf (2.35.2-9ubuntu1) ... (Reading database ... 12533 files and directories currently installed.) Preparing to unpack .../ca-certificates_20200601_all.deb ... Unpacking ca-certificates (20200601) over (20190110ubuntu2) ... Preparing to unpack .../build-essential_12.8ubuntu3_armhf.deb ... Unpacking build-essential (12.8ubuntu3) over (12.8ubuntu1) ... Setting up ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 13 added, 14 removed; done. Setting up mount (2.35.2-9ubuntu1) ... Setting up build-essential (12.8ubuntu3) ... Processing triggers for systemd (245.6-3ubuntu3) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19681498 armhf groovy -c chroot:build-PACKAGEBUILD-19681498 --arch=armhf --dist=groovy --nolog jellyfish_2.3.0-6.dsc Initiating build PACKAGEBUILD-19681498 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-012.buildd +==============================================================================+ | jellyfish 2.3.0-6 (armhf) 02 Aug 2020 21:04 | +==============================================================================+ Package: jellyfish Version: 2.3.0-6 Source Version: 2.3.0-6 Distribution: groovy Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/jellyfish-uRNSn6/jellyfish-2.3.0' with '<>' I: NOTICE: Log filtering will replace 'build/jellyfish-uRNSn6' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19681498/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- jellyfish_2.3.0-6.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-lD15qC/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-lD15qC/apt_archive ./ InRelease Get:2 copy:/<>/resolver-lD15qC/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-lD15qC/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-lD15qC/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-lD15qC/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (96.5 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 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-lD15qC/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 (79.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12532 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-compat (= 12), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools Filtered Build-Depends: debhelper-compat (= 12), d-shlibs, yaggo, pkg-config, bc, time, procps, swig, python3-all-dev, dh-python, perl, chrpath, libhts-dev, dos2unix, samtools dpkg-deb: building package 'sbuild-build-depends-jellyfish-dummy' in '/<>/resolver-pCC7bp/apt_archive/sbuild-build-depends-jellyfish-dummy.deb'. Ign:1 copy:/<>/resolver-pCC7bp/apt_archive ./ InRelease Get:2 copy:/<>/resolver-pCC7bp/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-pCC7bp/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-pCC7bp/apt_archive ./ Sources [291 B] Get:5 copy:/<>/resolver-pCC7bp/apt_archive ./ Packages [613 B] Fetched 3023 B in 0s (103 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install jellyfish build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 libyaml-0-2 m4 man-db mime-support pkg-config po-debconf python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-dev python3.8-minimal rake ruby ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools swig swig4.0 time yaggo zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support ri ruby-dev bundler cwltool swig-doc swig-examples swig4.0-examples swig4.0-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdextrautils chrpath d-shlibs debhelper dh-autoreconf dh-python dh-strip-nondeterminism dos2unix dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasn1-8-heimdal libbrotli1 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libicu66 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtool libuchardet0 libwind0-heimdal libxml2 libyaml-0-2 m4 man-db mime-support pkg-config po-debconf python3 python3-all python3-all-dev python3-dev python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-dev python3.8-minimal rake ruby ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools sbuild-build-depends-jellyfish-dummy swig swig4.0 time yaggo zlib1g-dev 0 upgraded, 105 newly installed, 0 to remove and 0 not upgraded. Need to get 39.6 MB of archives. After this operation, 135 MB of additional disk space will be used. Get:1 copy:/<>/resolver-pCC7bp/apt_archive ./ sbuild-build-depends-jellyfish-dummy 0.invalid.0 [944 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3.8-minimal armhf 3.8.5-1 [705 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf libexpat1 armhf 2.2.9-1build1 [53.3 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf python3.8-minimal armhf 3.8.5-1 [1582 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf python3-minimal armhf 3.8.2-0ubuntu2 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libmpdec2 armhf 2.4.2-3 [66.8 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3.8-stdlib armhf 3.8.5-1 [1597 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf python3.8 armhf 3.8.5-1 [373 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3-stdlib armhf 3.8.2-0ubuntu2 [7068 B] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf python3 armhf 3.8.2-0ubuntu2 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf bsdextrautils armhf 2.35.2-9ubuntu1 [70.2 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main armhf groff-base armhf 1.22.4-5 [759 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main armhf libpipeline1 armhf 1.5.2-2build1 [23.5 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf man-db armhf 2.9.3-2 [1082 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic-mgc armhf 1:5.38-5 [218 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic1 armhf 1:5.38-5 [68.4 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main armhf file armhf 1:5.38-5 [22.4 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main armhf libelf1 armhf 0.180-0ubuntu1 [41.1 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf libglib2.0-0 armhf 2.64.4-1 [1125 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf libicu66 armhf 66.1-2ubuntu3 [8225 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main armhf libxml2 armhf 2.9.10+dfsg-5 [546 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf libyaml-0-2 armhf 0.2.2-1 [41.3 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf gettext-base armhf 0.19.8.1-10build1 [46.0 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5support0 armhf 1.17-10 [27.9 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf libk5crypto3 armhf 1.17-10 [79.5 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf libkeyutils1 armhf 1.6.1-2ubuntu1 [9028 B] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5-3 armhf 1.17-10 [287 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libgssapi-krb5-2 armhf 1.17-10 [101 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf libpsl5 armhf 0.21.0-1.1 [50.3 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main armhf time armhf 1.7-25.1build2 [26.2 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf libsigsegv2 armhf 2.12-2build1 [13.0 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf m4 armhf 1.4.18-4 [187 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main armhf autoconf all 2.69-11.1 [321 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main armhf automake all 1:1.16.2-3ubuntu1 [548 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main armhf autopoint all 0.19.8.1-10build1 [412 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main armhf bc armhf 1.07.1-2build2 [80.4 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/universe armhf chrpath armhf 0.16-2 [11.9 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/universe armhf d-shlibs all 0.93 [9712 B] Get:42 http://ftpmaster.internal/ubuntu groovy/main armhf libtool all 2.4.6-14 [161 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main armhf dh-autoreconf all 19 [16.1 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf libdebhelper-perl all 13.2ubuntu1 [64.2 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:47 http://ftpmaster.internal/ubuntu groovy/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main armhf dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:49 http://ftpmaster.internal/ubuntu groovy/main armhf dwz armhf 0.13-5 [153 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main armhf gettext armhf 0.19.8.1-10build1 [835 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main armhf po-debconf all 1.0.21 [233 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main armhf debhelper all 13.2ubuntu1 [878 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main armhf python3-lib2to3 all 3.8.5-1 [75.6 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main armhf python3-distutils all 3.8.5-1 [141 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/universe armhf dh-python all 4.20200315ubuntu1 [85.8 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main armhf libroken18-heimdal armhf 7.7.0+dfsg-2 [34.5 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main armhf libasn1-8-heimdal armhf 7.7.0+dfsg-2 [140 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main armhf libbrotli1 armhf 1.0.7-7 [259 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main armhf libheimbase1-heimdal armhf 7.7.0+dfsg-2 [24.3 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main armhf libhcrypto4-heimdal armhf 7.7.0+dfsg-2 [78.5 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main armhf libwind0-heimdal armhf 7.7.0+dfsg-2 [47.2 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main armhf libhx509-5-heimdal armhf 7.7.0+dfsg-2 [88.8 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5-26-heimdal armhf 7.7.0+dfsg-2 [170 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main armhf libheimntlm0-heimdal armhf 7.7.0+dfsg-2 [13.2 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main armhf libgssapi3-heimdal armhf 7.7.0+dfsg-2 [79.9 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2 [13.4 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main armhf libsasl2-2 armhf 2.1.27+dfsg-2 [42.7 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main armhf libldap-common all 2.4.50+dfsg-1ubuntu3 [16.9 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main armhf libldap-2.4-2 armhf 2.4.50+dfsg-1ubuntu3 [133 kB] Get:72 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Get:82 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3.8 armhf 3.8.5-1 [1394 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3.8-dev armhf 3.8.5-1 [3135 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3-dev armhf 3.8.2-0ubuntu2 [7236 B] Get:85 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3-all-dev armhf 3.8.2-0ubuntu2 [1116 B] Get:86 http://ftpmaster.internal/ubuntu groovy/main armhf rubygems-integration all 1.17.2 [5284 B] Get:87 http://ftpmaster.internal/ubuntu groovy/main armhf ruby2.7 armhf 2.7.1-3 [95.4 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main armhf ruby armhf 1:2.7+1 [5412 B] Get:89 http://ftpmaster.internal/ubuntu groovy/main armhf rake all 13.0.1-4 [61.6 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main armhf ruby-minitest all 5.13.0-1 [40.9 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main armhf ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main armhf ruby-power-assert all 1.1.7-1 [11.4 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main armhf ruby-test-unit all 3.3.5-1 [73.2 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main armhf ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main armhf libruby2.7 armhf 2.7.1-3 [3285 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main armhf pkg-config armhf 0.29.2-1ubuntu1 [43.4 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main armhf python3-all armhf 3.8.2-0ubuntu2 [1100 B] Get:98 http://ftpmaster.internal/ubuntu groovy/main armhf python3.8-dev armhf 3.8.5-1 [515 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main armhf python3-dev armhf 3.8.2-0ubuntu2 [1212 B] Get:100 http://ftpmaster.internal/ubuntu groovy/main armhf python3-all-dev armhf 3.8.2-0ubuntu2 [1112 B] Get:101 http://ftpmaster.internal/ubuntu groovy/universe armhf samtools armhf 1.10-4 [468 kB] Get:102 http://ftpmaster.internal/ubuntu groovy/universe armhf swig4.0 armhf 4.0.1-5build1 [1030 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/universe armhf swig all 4.0.1-5build1 [5528 B] Get:104 http://ftpmaster.internal/ubuntu groovy/universe armhf yaggo all 1.5.10-2 [19.0 kB] Get:105 http://ftpmaster.internal/ubuntu groovy/universe armhf dos2unix armhf 7.4.1-1 [370 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 39.6 MB in 2s (22.2 MB/s) Selecting previously unselected package libpython3.8-minimal:armhf. (Reading database ... 12532 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.5-1_armhf.deb ... Unpacking libpython3.8-minimal:armhf (3.8.5-1) ... Selecting previously unselected package libexpat1:armhf. Preparing to unpack .../libexpat1_2.2.9-1build1_armhf.deb ... Unpacking libexpat1:armhf (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.5-1_armhf.deb ... Unpacking python3.8-minimal (3.8.5-1) ... Setting up libpython3.8-minimal:armhf (3.8.5-1) ... Setting up libexpat1:armhf (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.5-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 12823 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_armhf.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... Selecting previously unselected package mime-support. 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Setting up libglib2.0-0:armhf (2.64.4-1) ... No schema files found: doing nothing. Setting up libicu66:armhf (66.1-2ubuntu3) ... Setting up libdebhelper-perl (13.2ubuntu1) ... Setting up libbrotli1:armhf (1.0.7-7) ... Setting up libnghttp2-14:armhf (1.41.0-2) ... Setting up libmagic1:armhf (1:5.38-5) ... Setting up libdeflate0:armhf (1.6-1) ... Setting up bc (1.07.1-2build2) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up rubygems-integration (1.17.2) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.50+dfsg-1ubuntu3) ... Setting up libkrb5support0:armhf (1.17-10) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:armhf (2.2.9-1build1) ... Setting up ruby-test-unit (3.3.5-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:armhf (2.12-2build1) ... Setting up autopoint (0.19.8.1-10build1) ... Setting up pkg-config (0.29.2-1ubuntu1) ... Setting up d-shlibs (0.93) ... Setting up libk5crypto3:armhf (1.17-10) ... Setting up libsasl2-2:armhf (2.1.27+dfsg-2) ... Setting up libroken18-heimdal:armhf (7.7.0+dfsg-2) ... Setting up liblzma-dev:armhf (5.2.4-1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:armhf (1.17-10) ... Setting up dos2unix (7.4.1-1) ... Setting up libmpdec2:armhf (2.4.2-3) ... Setting up swig4.0 (4.0.1-5build1) ... Setting up libpython3.8-stdlib:armhf (3.8.5-1) ... Setting up python3.8 (3.8.5-1) ... Setting up libelf1:armhf (0.180-0ubuntu1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:armhf (2.9.10+dfsg-5) ... Setting up chrpath (0.16-2) ... Setting up libpython3-stdlib:armhf (3.8.2-0ubuntu2) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libfile-stripnondeterminism-perl (1.9.0-1) ... Setting up swig (4.0.1-5build1) ... Setting up libtool (2.4.6-14) ... Setting up libasn1-8-heimdal:armhf (7.7.0+dfsg-2) ... Setting up m4 (1.4.18-4) ... Setting up python3 (3.8.2-0ubuntu2) ... Setting up libhcrypto4-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libwind0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libpython3.8:armhf (3.8.5-1) ... Setting up libgssapi-krb5-2:armhf (1.17-10) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up libssh-4:armhf (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.9.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up python3-lib2to3 (3.8.5-1) ... Setting up automake (1:1.16.2-3ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3-distutils (3.8.5-1) ... Setting up dh-python (4.20200315ubuntu1) ... Setting up gettext (0.19.8.1-10build1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up python3-all (3.8.2-0ubuntu2) ... Setting up man-db (2.9.3-2) ... 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 libpython3.8-dev:armhf (3.8.5-1) ... Setting up python3.8-dev (3.8.5-1) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libpython3-dev:armhf (3.8.2-0ubuntu2) ... Setting up po-debconf (1.0.21) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libpython3-all-dev:armhf (3.8.2-0ubuntu2) ... Setting up python3-dev (3.8.2-0ubuntu2) ... Setting up python3-all-dev (3.8.2-0ubuntu2) ... Setting up libldap-2.4-2:armhf (2.4.50+dfsg-1ubuntu3) ... Setting up libcurl3-gnutls:armhf (7.68.0-1ubuntu4) ... Setting up libhts3:armhf (1.10.2-4) ... Setting up libhts-dev:armhf (1.10.2-4) ... Setting up samtools (1.10-4) ... Setting up libruby2.7:armhf (2.7.1-3) ... Setting up dh-autoreconf (19) ... Setting up ruby2.7 (2.7.1-3) ... Setting up debhelper (13.2ubuntu1) ... Setting up ruby (1:2.7+1) ... Setting up rake (13.0.1-4) ... Setting up yaggo (1.5.10-2) ... Setting up sbuild-build-depends-jellyfish-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.35-1ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-10_10.2.0-3ubuntu1 gcc-10_10.2.0-3ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 linux-libc-dev_5.4.0-42.46 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu10 base-passwd_3.5.47 bash_5.0-6ubuntu2 bc_1.07.1-2build2 binutils_2.35-1ubuntu1 binutils-arm-linux-gnueabihf_2.35-1ubuntu1 binutils-common_2.35-1ubuntu1 bsdextrautils_2.35.2-9ubuntu1 bsdutils_1:2.35.2-9ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 chrpath_0.16-2 coreutils_8.30-3ubuntu3 cpp_4:10.1.0-1ubuntu1 cpp-10_10.2.0-3ubuntu1 d-shlibs_0.93 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-python_4.20200315ubuntu1 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3build1 dos2unix_7.4.1-1 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:10.1.0-1ubuntu1 g++-10_10.2.0-3ubuntu1 gcc_4:10.1.0-1ubuntu1 gcc-10_10.2.0-3ubuntu1 gcc-10-base_10.2.0-3ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.0-3ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7.1 libatomic1_10.2.0-3ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.35-1ubuntu1 libblkid1_2.35.2-9ubuntu1 libbrotli1_1.0.7-7 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcc1-0_10.2.0-3ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu3 libctf-nobfd0_2.35-1ubuntu1 libctf0_2.35-1ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu4 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.2ubuntu1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.19.7ubuntu4 libelf1_0.180-0ubuntu1 libexpat1_2.2.9-1build1 libexpat1-dev_2.2.9-1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-3ubuntu1 libgcc-s1_10.2.0-3ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu4 libgomp1_10.2.0-3ubuntu1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10 libgssapi3-heimdal_7.7.0+dfsg-2 libhcrypto4-heimdal_7.7.0+dfsg-2 libheimbase1-heimdal_7.7.0+dfsg-2 libheimntlm0-heimdal_7.7.0+dfsg-2 libhogweed6_3.6-2 libhts-dev_1.10.2-4 libhts3_1.10.2-4 libhx509-5-heimdal_7.7.0+dfsg-2 libicu66_66.1-2ubuntu3 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libjson-c4_0.13.1+dfsg-9 libk5crypto3_1.17-10 libkeyutils1_1.6.1-2ubuntu1 libkmod2_27+20200310-2ubuntu1 libkrb5-26-heimdal_7.7.0+dfsg-2 libkrb5-3_1.17-10 libkrb5support0_1.17-10 libldap-2.4-2_2.4.50+dfsg-1ubuntu3 libldap-common_2.4.50+dfsg-1ubuntu3 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-9ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1build1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu5 libpam-modules-bin_1.3.1-5ubuntu5 libpam-runtime_1.3.1-5ubuntu5 libpam0g_1.3.1-5ubuntu5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libpsl5_0.21.0-1.1 libpython3-all-dev_3.8.2-0ubuntu2 libpython3-dev_3.8.2-0ubuntu2 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8_3.8.5-1 libpython3.8-dev_3.8.5-1 libpython3.8-minimal_3.8.5-1 libpython3.8-stdlib_3.8.5-1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build2 libruby2.7_2.7.1-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu4 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.35.2-9ubuntu1 libsqlite3-0_3.32.3-1 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu1 libssl1.1_1.1.1f-1ubuntu3 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-3ubuntu3 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-3ubuntu1 libuchardet0_0.0.7-1 libudev1_245.6-3ubuntu3 libunistring2_0.9.10-4 libuuid1_2.35.2-9ubuntu1 libwind0-heimdal_7.7.0+dfsg-2 libxml2_2.9.10+dfsg-5 libyaml-0-2_0.2.2-1 libzstd1_1.4.5+dfsg-3 linux-libc-dev_5.4.0-42.46 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.35.2-9ubuntu1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu1 python3_3.8.2-0ubuntu2 python3-all_3.8.2-0ubuntu2 python3-all-dev_3.8.2-0ubuntu2 python3-dev_3.8.2-0ubuntu2 python3-distutils_3.8.5-1 python3-lib2to3_3.8.5-1 python3-minimal_3.8.2-0ubuntu2 python3.8_3.8.5-1 python3.8-dev_3.8.5-1 python3.8-minimal_3.8.5-1 rake_13.0.1-4 readline-common_8.0-4 ruby_1:2.7+1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-test-unit_3.3.5-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.1-3 rubygems-integration_1.17.2 samtools_1.10-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-jellyfish-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 swig_4.0.1-5build1 swig4.0_4.0.1-5build1 systemd_245.6-3ubuntu3 systemd-sysv_245.6-3ubuntu3 systemd-timesyncd_245.6-3ubuntu3 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 time_1.7-25.1build2 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.2-9ubuntu1 xz-utils_5.2.4-1 yaggo_1.5.10-2 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Jun 4 14:28:12 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./jellyfish_2.3.0-6.dsc dpkg-source: info: extracting jellyfish in jellyfish-2.3.0 dpkg-source: info: unpacking jellyfish_2.3.0.orig.tar.gz dpkg-source: info: unpacking jellyfish_2.3.0-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying manpage_whatis_entry.patch dpkg-source: info: applying reproducible.patch dpkg-source: info: applying portability.patch dpkg-source: info: applying fix_replacement_of_-L_option.patch dpkg-source: info: applying test_needs_bash dpkg-source: info: applying python3 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym 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-19681498 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19681498 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19681498 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package jellyfish dpkg-buildpackage: info: source version 2.3.0-6 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --with python3 debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean if [ -d debian/tmp_save_tests ] ; then \ mv debian/tmp_save_tests/* tests ; \ rmdir debian/tmp_save_tests ; \ fi rm -f tests/compat.sh rm -f swig/python/jellyfish* # swig/python/dna_jellyfish.py rm -f swig/perl5/blib/arch/auto/jellyfish/jellyfish.so rm -f swig/perl5/blib/bin/.exists rm -f swig/perl5/blib/lib/.exists rm -f swig/perl5/blib/lib/auto/jellyfish/.exists rm -f swig/perl5/blib/man1/.exists rm -f swig/perl5/blib/man3/.exists rm -f swig/perl5/blib/script/.exists rm -f swig/perl5/jellyfish.bs rm -f swig/perl5/pm_to_blib rm -rf swig/perl5/MYMETA.json swig/perl5/MYMETA.yml swig/perl5/Makefile swig/perl5/blib/ make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-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:8: installing './compile' configure.ac:2: installing './config.guess' configure.ac:2: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' Makefile.am: installing './depcomp' parallel-tests: installing './test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 ./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --enable-swig --enable-perl-binding --enable-htslib --enable-python-binding PYTHON=/usr/bin/python3 checking build system type... arm-unknown-linux-gnueabihf checking host system type... arm-unknown-linux-gnueabihf 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 whether make supports nested variables... (cached) yes 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 arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop checking how to convert arm-unknown-linux-gnueabihf 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 ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for shared library run path origin... done checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes 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 for htslib... yes checking for samtools... /usr/bin/samtools checking for unix2dos... /usr/bin/unix2dos checking for md5sum... md5sum checking for yaggo... /usr/bin/yaggo checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for __int128... no checking for std::numeric_limits<__int128>... no checking for _NSGetExecutablePath... no checking for execinfo.h... yes checking for ext/stdio_filebuf.h... yes checking for sys/syscall.h... yes checking for siginfo_t.si_int... yes checking for swig... /usr/bin/swig checking SWIG version... 4.0.1 checking for SWIG library... /usr/share/swig4.0 checking for python... /usr/bin/python3 checking for a version of Python >= '2.1.0'... yes checking for the distutils Python package... yes checking for Python include path... -I/usr/include/python3.8 checking for Python library path... -L/usr/lib -lpython3.8 checking for Python site-packages path... /usr/lib/python3/dist-packages checking python extra libraries... -lcrypt -lpthread -ldl -lutil -lm -lm checking python extra linking flags... -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions checking consistency of all components of python development environment... yes checking for perl... /usr/bin/perl checking for Perl prefix... /usr checking for Perl extension include path... /usr/lib/arm-linux-gnueabihf/perl/5.30/CORE checking for Perl extension target directory... /usr/lib/perl/5.30.0 checking for Perl extensions C preprocessor flags... -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing -pipe -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib -fstack-protector-strong checking for posix_memalign... yes checking for aligned_alloc... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating compat.sh config.status: creating jellyfish-2.0.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_configure --sourcedirectory=swig/perl5 cd swig/perl5 && perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=arm-linux-gnueabihf-gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -lpthread" -I/<>/debian/tmp//usr/include/jellyfish-2.3.0 -L/<>/debian/tmp//usr/lib/arm-linux-gnueabihf -ljellyfish-2.0 -lpthread -L/<>/debian/tmp//usr/lib/arm-linux-gnueabihf Warning (mostly harmless): No library found for -ljellyfish-2.0 Generating a Unix-style Makefile Writing Makefile for jellyfish Writing MYMETA.yml and MYMETA.json dh_auto_configure --sourcedirectory=swig/python --buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config running config make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' mkdir -p debian/tmp_save_tests cp -a tests/* debian/tmp_save_tests dh_auto_build --no-parallel -- all bin/generate_sequence bin/test_all bin/fastq2sam make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam make[2]: Entering directory '/<>' /usr/bin/yaggo --license ./header-license -o sub_commands/count_main_cmdline.hpp sub_commands/count_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/info_main_cmdline.hpp sub_commands/info_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/dump_main_cmdline.hpp sub_commands/dump_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/histo_main_cmdline.hpp sub_commands/histo_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/stats_main_cmdline.hpp sub_commands/stats_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/merge_main_cmdline.hpp sub_commands/merge_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/bc_main_cmdline.hpp sub_commands/bc_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/query_main_cmdline.hpp sub_commands/query_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/cite_main_cmdline.hpp sub_commands/cite_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o sub_commands/mem_main_cmdline.hpp sub_commands/mem_main_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/generate_sequence_cmdline.hpp jellyfish/generate_sequence_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o jellyfish/fastq2sam_cmdline.hpp jellyfish/fastq2sam_cmdline.yaggo /usr/bin/yaggo --license ./header-license -o unit_tests/test_main_cmdline.hpp unit_tests/test_main_cmdline.yaggo /usr/bin/swig -c++ -python -I./../include -o swig/python/swig_wrap.cpp swig/jellyfish.i /usr/bin/swig -c++ -perl5 -I./../include -o swig/perl5/swig_wrap.cpp swig/jellyfish.i make all-am make[3]: Entering directory '/<>' g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/jellyfish.o sub_commands/jellyfish.cc g++ -DHAVE_CONFIG_H -I. -Wall -Wnon-virtual-dtor -I. -I./include -Wdate-time -D_FORTIFY_SOURCE=2 -Werror -std=c++11 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sub_commands/count_main.o sub_commands/count_main.cc In file included from ./include/jellyfish/large_hash_array.hpp:19, from ./include/jellyfish/hash_counter.hpp:14, from sub_commands/count_main.cc:38: ./include/jellyfish/rectangular_binary_matrix.hpp: In member function ‘bool jellyfish::RectangularBinaryMatrix::is_zero() const’: ./include/jellyfish/rectangular_binary_matrix.hpp:121:29: error: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Werror=sign-compare] 121 | return (p - _columns) == _c; | ~~~~~~~~~~~~~~~^~~~~ cc1plus: all warnings being treated as errors make[3]: *** [Makefile:1710: sub_commands/count_main.o] Error 1 make[3]: Leaving directory '/<>' make[2]: *** [Makefile:1025: all] Error 2 make[2]: Leaving directory '/<>' dh_auto_build: error: make -j1 all bin/generate_sequence bin/test_all bin/fastq2sam returned exit code 2 make[1]: *** [debian/rules:78: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:21: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200802-2105 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 9192 Build-Time: 62 Distribution: groovy Fail-Stage: build Host Architecture: armhf Install-Time: 31 Job: jellyfish_2.3.0-6.dsc Machine Architecture: arm64 Package: jellyfish Package-Time: 95 Source-Version: 2.3.0-6 Space: 9192 Status: attempted Version: 2.3.0-6 -------------------------------------------------------------------------------- Finished at 20200802-2105 Build needed 00:01:35, 9192k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19681498 Scanning for processes to kill in build PACKAGEBUILD-19681498