https://launchpad.net/ubuntu/+archive/test-rebuild-20191220-focal/+build/18295119 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-030 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 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... 5 Jan 12:25:32 ntpdate[1888]: adjust time server 10.211.37.1 offset 0.014664 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18295119 --image-type chroot /home/buildd/filecache-default/e96c25c651525abc9f0cabeb95ea71010abf4ecb Creating target for build PACKAGEBUILD-18295119 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18295119 Starting target for build PACKAGEBUILD-18295119 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18295119 'deb http://ftpmaster.internal/ubuntu focal main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-18295119 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18295119 Updating target for build PACKAGEBUILD-18295119 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 Packages [966 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main Translation-en [499 kB] Get:4 http://ftpmaster.internal/ubuntu focal/restricted amd64 Packages [18.4 kB] Get:5 http://ftpmaster.internal/ubuntu focal/restricted Translation-en [5768 B] Get:6 http://ftpmaster.internal/ubuntu focal/universe amd64 Packages [8671 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5195 kB] Get:8 http://ftpmaster.internal/ubuntu focal/multiverse amd64 Packages [152 kB] Get:9 http://ftpmaster.internal/ubuntu focal/multiverse Translation-en [110 kB] Fetched 15.9 MB in 4s (4472 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-common binutils-x86-64-linux-gnu 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 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 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 94 upgraded, 5 newly installed, 0 to remove and 0 not upgraded. Need to get 70.2 MB of archives. After this operation, 51.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main amd64 libc6-dev amd64 2.30-0ubuntu3 [2549 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 libc-dev-bin amd64 2.30-0ubuntu3 [71.8 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 linux-libc-dev amd64 5.3.0-24.26 [1096 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 libisl22 amd64 0.22-2 [592 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 libcc1-0 amd64 9.2.1-21ubuntu1 [49.0 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-x86-64-linux-gnu amd64 2.33.1-6ubuntu3 [1639 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libbinutils amd64 2.33.1-6ubuntu3 [474 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 binutils-common amd64 2.33.1-6ubuntu3 [203 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 binutils amd64 2.33.1-6ubuntu3 [3400 B] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9-base amd64 9.2.1-21ubuntu1 [19.1 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc1 amd64 1:9.2.1-21ubuntu1 [40.8 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 libgomp1 amd64 9.2.1-21ubuntu1 [89.3 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 libitm1 amd64 9.2.1-21ubuntu1 [28.1 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 libatomic1 amd64 9.2.1-21ubuntu1 [9236 B] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 libasan5 amd64 9.2.1-21ubuntu1 [395 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 liblsan0 amd64 9.2.1-21ubuntu1 [139 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 libtsan0 amd64 9.2.1-21ubuntu1 [301 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 libubsan1 amd64 9.2.1-21ubuntu1 [130 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main amd64 libquadmath0 amd64 9.2.1-21ubuntu1 [146 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 g++-9 amd64 9.2.1-21ubuntu1 [11.0 MB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++-9-dev amd64 9.2.1-21ubuntu1 [1709 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 libgcc-9-dev amd64 9.2.1-21ubuntu1 [2362 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main amd64 gcc-9 amd64 9.2.1-21ubuntu1 [10.4 MB] Get:24 http://ftpmaster.internal/ubuntu focal/main amd64 cpp-9 amd64 9.2.1-21ubuntu1 [9729 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main amd64 libstdc++6 amd64 9.2.1-21ubuntu1 [512 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 libc6 amd64 2.30-0ubuntu3 [2725 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 base-files amd64 11ubuntu2 [60.1 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 debianutils amd64 4.9.1 [85.8 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 bash amd64 5.0-5ubuntu1 [639 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 bsdutils amd64 1:2.34-0.1ubuntu4 [63.8 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 gzip amd64 1.10-0ubuntu4 [95.3 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 hostname amd64 3.23 [11.4 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-bin amd64 6.1+20191019-1ubuntu1 [172 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libperl5.30 amd64 5.30.0-9 [3950 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 perl amd64 5.30.0-9 [224 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 perl-base amd64 5.30.0-9 [1511 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 bzip2 amd64 1.0.8-2 [34.1 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 libbz2-1.0 amd64 1.0.8-2 [32.3 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 libblkid1 amd64 2.34-0.1ubuntu4 [137 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 libuuid1 amd64 2.34-0.1ubuntu4 [20.5 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 libfdisk1 amd64 2.34-0.1ubuntu4 [175 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 libpcre2-8-0 amd64 10.34-7 [197 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 libselinux1 amd64 3.0-1 [68.7 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 libmount1 amd64 2.34-0.1ubuntu4 [149 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 libncurses6 amd64 6.1+20191019-1ubuntu1 [101 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 libtinfo6 amd64 6.1+20191019-1ubuntu1 [85.9 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libncursesw6 amd64 6.1+20191019-1ubuntu1 [132 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libsmartcols1 amd64 2.34-0.1ubuntu4 [101 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 fdisk amd64 2.34-0.1ubuntu4 [120 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 util-linux amd64 2.34-0.1ubuntu4 [1022 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libdebconfclient0 amd64 0.250ubuntu2 [6336 B] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 base-passwd amd64 3.5.47 [47.7 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libc-bin amd64 2.30-0ubuntu3 [625 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 sysvinit-utils amd64 2.96-1ubuntu1 [20.8 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 liblz4-1 amd64 1.9.2-2 [55.9 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 systemd-sysv amd64 244-3ubuntu1 [9368 B] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libacl1 amd64 2.2.53-5ubuntu1 [18.7 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libapparmor1 amd64 2.13.3-7ubuntu1 [34.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libcap-ng0 amd64 0.7.9-2.1 [11.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 libaudit1 amd64 1:2.8.5-2ubuntu5 [39.1 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libcap2 amd64 1:2.27-1 [14.1 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 libudev1 amd64 244-3ubuntu1 [76.3 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-2ubuntu7 [127 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 libjson-c4 amd64 0.13.1+dfsg-6 [29.2 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libcryptsetup12 amd64 2:2.2.2-1ubuntu1 [182 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 libnettle7 amd64 3.5.1+really3.5.1-2 [114 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libhogweed5 amd64 3.5.1+really3.5.1-2 [138 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 libp11-kit0 amd64 0.23.18.1-2 [189 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libtasn1-6 amd64 4.15.0-2 [37.7 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 libgnutls30 amd64 3.6.11.1-2 [793 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libkmod2 amd64 26-3ubuntu1 [42.9 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libpam0g amd64 1.3.1-5ubuntu4 [55.4 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 libseccomp2 amd64 2.4.2-2ubuntu1 [39.4 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 mount amd64 2.34-0.1ubuntu4 [115 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 systemd amd64 244-3ubuntu1 [3677 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 libsystemd0 amd64 244-3ubuntu1 [260 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 libzstd1 amd64 1.4.4+dfsg-1 [237 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 libapt-pkg5.90 amd64 1.9.5 [851 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 libgcrypt20 amd64 1.8.5-3ubuntu1 [419 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 gpgv amd64 2.2.17-3ubuntu1 [200 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 apt amd64 1.9.5 [1281 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules-bin amd64 1.3.1-5ubuntu4 [37.7 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-modules amd64 1.3.1-5ubuntu4 [250 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 libattr1 amd64 1:2.4.48-5 [12.7 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main amd64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main amd64 libsepol1 amd64 3.0-1 [252 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage-common all 3.0-1 [9880 B] Get:92 http://ftpmaster.internal/ubuntu focal/main amd64 libsemanage1 amd64 3.0-1 [85.3 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libsqlite3-0 amd64 3.30.1-1ubuntu1 [540 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 gpg amd64 2.2.17-3ubuntu1 [479 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 gpgconf amd64 2.2.17-3ubuntu1 [124 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 gpg-agent amd64 2.2.17-3ubuntu1 [232 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile-bin amd64 1.16-1.1 [11.7 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 liblockfile1 amd64 1.16-1.1 [6680 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.2 MB in 1s (51.6 MB/s) (Reading database ... 12741 files and directories currently installed.) 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Setting up libstdc++-9-dev:amd64 (9.2.1-21ubuntu1) ... Setting up systemd (244-3ubuntu1) ... 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 (244-3ubuntu1) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18295119 amd64 focal -c chroot:build-PACKAGEBUILD-18295119 --arch=amd64 --dist=focal --nolog -A freebayes_1.3.2-1.dsc Initiating build PACKAGEBUILD-18295119 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-170-generic #199-Ubuntu SMP Thu Nov 14 01:45:04 UTC 2019 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-030.buildd +==============================================================================+ | freebayes 1.3.2-1 (amd64) 05 Jan 2020 12:26 | +==============================================================================+ Package: freebayes Version: 1.3.2-1 Source Version: 1.3.2-1 Distribution: focal Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/freebayes-53gfPF/freebayes-1.3.2' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-53gfPF' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18295119/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- freebayes_1.3.2-1.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-qPeEm1/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-qPeEm1/apt_archive ./ InRelease Get:2 copy:/<>/resolver-qPeEm1/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-qPeEm1/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-qPeEm1/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-qPeEm1/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (220 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-qPeEm1/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 ... 14652 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.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), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) Filtered Build-Depends: debhelper-compat (= 12), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) dpkg-deb: building package 'sbuild-build-depends-freebayes-dummy' in '/<>/resolver-tIgIeu/apt_archive/sbuild-build-depends-freebayes-dummy.deb'. Ign:1 copy:/<>/resolver-tIgIeu/apt_archive ./ InRelease Get:2 copy:/<>/resolver-tIgIeu/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-tIgIeu/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-tIgIeu/apt_archive ./ Sources [320 B] Get:5 copy:/<>/resolver-tIgIeu/apt_archive ./ Packages [639 B] Fetched 3078 B in 0s (231 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install freebayes 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 bc bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libice6 libicu63 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db mime-support parallel pkg-config po-debconf python3 python3-minimal python3.7 python3.7-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-zeallot samtools sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc krb5-doc krb5-user liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.7-venv python3.7-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-webshot r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-knitr r-cran-rmarkdown r-cran-viridis r-cran-rstudioapi r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-getopt r-cran-testthat r-cran-foreach r-cran-doparallel libgdal-dev r-cran-iterators r-cran-inline r-cran-dichromat r-cran-htmltools r-cran-bit64 r-cran-generics r-cran-purrr isag 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 r-recommended r-base-dev r-doc-html r-cran-testthat r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-lubridate r-cran-domc r-cran-abind r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-dbi cwltool cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts2 libhx509-5-heimdal libice6 libicu63 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db mime-support parallel pkg-config po-debconf python3 python3-minimal python3.7 python3.7-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-cli r-cran-colorspace r-cran-crayon r-cran-digest r-cran-ellipsis r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr r-cran-zeallot samtools sbuild-build-depends-freebayes-dummy sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 197 newly installed, 0 to remove and 0 not upgraded. Need to get 93.3 MB of archives. After this operation, 266 MB of additional disk space will be used. Get:1 copy:/<>/resolver-tIgIeu/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [968 B] Get:2 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3.7-minimal amd64 3.7.5-2 [545 kB] Get:3 http://ftpmaster.internal/ubuntu focal/main amd64 libexpat1 amd64 2.2.9-1 [73.3 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main amd64 python3.7-minimal amd64 3.7.5-2 [1766 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main amd64 python3-minimal amd64 3.7.5-1ubuntu1 [23.3 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main amd64 libmpdec2 amd64 2.4.2-2 [84.1 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3.7-stdlib amd64 3.7.5-2 [1732 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main amd64 python3.7 amd64 3.7.5-2 [301 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main amd64 libpython3-stdlib amd64 3.7.5-1ubuntu1 [6844 B] Get:11 http://ftpmaster.internal/ubuntu focal/main amd64 python3 amd64 3.7.5-1ubuntu1 [47.2 kB] Get:12 http://ftpmaster.internal/ubuntu focal/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main amd64 bsdmainutils amd64 11.1.2ubuntu2 [181 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main amd64 groff-base amd64 1.22.4-4 [865 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main amd64 libpipeline1 amd64 1.5.1-3 [27.4 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main amd64 man-db amd64 2.9.0-2 [1114 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main amd64 libmagic-mgc amd64 1:5.37-6 [209 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main amd64 libmagic1 amd64 1:5.37-6 [75.3 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main amd64 file amd64 1:5.37-6 [23.2 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main amd64 libelf1 amd64 0.176-1.1 [44.1 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main amd64 libfribidi0 amd64 1.0.7-1.1 [23.6 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main amd64 libglib2.0-0 amd64 2.63.3-1 [1279 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main amd64 libicu63 amd64 63.2-2 [8294 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main amd64 libxml2 amd64 2.9.4+dfsg1-8ubuntu1 [648 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main amd64 ucf all 3.0038+nmu1 [51.6 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main amd64 gettext-base amd64 0.19.8.1-10 [50.2 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5support0 amd64 1.17-6 [31.4 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main amd64 libk5crypto3 amd64 1.17-6 [80.2 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main amd64 libkeyutils1 amd64 1.6-6ubuntu1 [10.2 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-3 amd64 1.17-6 [330 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi-krb5-2 amd64 1.17-6 [121 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main amd64 libpsl5 amd64 0.20.2-2 [50.0 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:35 http://ftpmaster.internal/ubuntu focal/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb1 amd64 1.13.1-2 [45.2 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-data all 2:1.6.8-1 [113 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main amd64 libx11-6 amd64 2:1.6.8-1 [573 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main amd64 autoconf all 2.69-11ubuntu1 [321 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main amd64 automake all 1:1.16.1-4ubuntu3 [522 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main amd64 autopoint all 0.19.8.1-10 [412 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main amd64 bc amd64 1.07.1-2build1 [86.3 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main amd64 cmake-data all 3.15.4-1ubuntu2 [1562 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main amd64 libarchive13 amd64 3.4.0-1build1 [327 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main amd64 libbrotli1 amd64 1.0.7-5 [265 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-1 [41.9 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-1 [181 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-1 [29.7 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-1 [87.8 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-1 [47.9 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-1 [107 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-1 [207 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-1 [15.1 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-1 [96.6 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:60 http://ftpmaster.internal/ubuntu focal/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main amd64 libldap-common all 2.4.48+dfsg-1ubuntu3 [17.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main amd64 libldap-2.4-2 amd64 2.4.48+dfsg-1ubuntu3 [155 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main amd64 libnghttp2-14 amd64 1.40.0-1 [78.1 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main amd64 libssh-4 amd64 0.9.0-1ubuntu5 [196 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl4 amd64 7.66.0-1ubuntu1 [232 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main amd64 libjsoncpp1 amd64 1.7.4-3 [73.6 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main amd64 librhash0 amd64 1.3.9-1 [113 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main amd64 libuv1 amd64 1.33.1-2 [80.1 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main amd64 cmake amd64 3.15.4-1ubuntu2 [3607 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main amd64 libtool all 2.4.6-11 [194 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main amd64 dh-autoreconf all 19 [16.1 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main amd64 libdebhelper-perl all 12.7.1ubuntu1 [52.0 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main amd64 libarchive-zip-perl all 1.67-1 [90.4 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:76 http://ftpmaster.internal/ubuntu focal/main amd64 libfile-stripnondeterminism-perl all 1.6.3-1 [16.0 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main amd64 dh-strip-nondeterminism all 1.6.3-1 [5224 B] Get:78 http://ftpmaster.internal/ubuntu focal/main amd64 dwz amd64 0.13-5 [151 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main amd64 gettext amd64 0.19.8.1-10 [897 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main amd64 po-debconf all 1.0.21 [233 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main amd64 debhelper all 12.7.1ubuntu1 [875 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main amd64 libfreetype6 amd64 2.10.1-2 [341 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main amd64 fonts-dejavu-core all 2.37-1 [1041 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main amd64 fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main amd64 libfontconfig1 amd64 2.13.1-2ubuntu2 [114 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main amd64 fontconfig amd64 2.13.1-2ubuntu2 [171 kB] Get:89 http://ftpmaster.internal/ubuntu focal/universe amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-5 [158 kB] Get:90 http://ftpmaster.internal/ubuntu focal/universe amd64 libbamtools-dev amd64 2.5.1+dfsg-5 [19.8 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main amd64 libblas3 amd64 3.9.0-1 [142 kB] Get:92 http://ftpmaster.internal/ubuntu focal/universe amd64 libbwa-dev amd64 0.7.17-4 [130 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main amd64 libpixman-1-0 amd64 0.38.4-0ubuntu1 [227 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-render0 amd64 1.13.1-2 [14.8 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main amd64 libxcb-shm0 amd64 1.13.1-2 [5548 B] Get:96 http://ftpmaster.internal/ubuntu focal/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main amd64 libcairo2 amd64 1.16.0-4ubuntu1 [583 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main amd64 libcurl3-gnutls amd64 7.66.0-1ubuntu1 [231 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main amd64 libdatrie1 amd64 0.2.12-3 [18.7 kB] Get:100 http://ftpmaster.internal/ubuntu focal/universe amd64 libdeflate0 amd64 1.5-1 [87.2 kB] Get:101 http://ftpmaster.internal/ubuntu focal/universe amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-1 [4308 B] Get:102 http://ftpmaster.internal/ubuntu focal/universe amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-1 [3840 B] Get:103 http://ftpmaster.internal/ubuntu focal/universe amd64 libfastahack0 amd64 0.0+git20160702.bbc645f+dfsg-6 [24.1 kB] Get:104 http://ftpmaster.internal/ubuntu focal/universe amd64 libfastahack-dev amd64 0.0+git20160702.bbc645f+dfsg-6 [23.5 kB] Get:105 http://ftpmaster.internal/ubuntu focal/universe amd64 libfml0 amd64 0.1-7 [70.0 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1ubuntu3 [172 kB] Get:107 http://ftpmaster.internal/ubuntu focal/universe amd64 libfml-dev amd64 0.1-7 [81.1 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main amd64 libgfortran5 amd64 9.2.1-21ubuntu1 [642 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main amd64 libgraphite2-3 amd64 1.3.13-11 [73.7 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main amd64 libharfbuzz0b amd64 2.6.4-1ubuntu1 [391 kB] Get:111 http://ftpmaster.internal/ubuntu focal/universe amd64 libhts2 amd64 1.9-12 [313 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main amd64 liblzma-dev amd64 5.2.4-1 [145 kB] Get:113 http://ftpmaster.internal/ubuntu focal/universe amd64 libhts-dev amd64 1.9-12 [71.8 kB] Get:114 http://ftpmaster.internal/ubuntu focal/main amd64 x11-common all 1:7.7+19ubuntu12 [22.4 kB] Get:115 http://ftpmaster.internal/ubuntu focal/main amd64 libice6 amd64 2:1.0.10-0ubuntu1 [41.0 kB] Get:116 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg-turbo8 amd64 2.0.3-0ubuntu1 [118 kB] Get:117 http://ftpmaster.internal/ubuntu focal/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:118 http://ftpmaster.internal/ubuntu focal/main amd64 liblapack3 amd64 3.9.0-1 [2155 kB] Get:119 http://ftpmaster.internal/ubuntu focal/main amd64 libthai-data all 0.1.28-3 [134 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main amd64 libthai0 amd64 0.1.28-3 [18.1 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main amd64 libpango-1.0-0 amd64 1.44.7-1 [161 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main amd64 libpangoft2-1.0-0 amd64 1.44.7-1 [34.7 kB] Get:123 http://ftpmaster.internal/ubuntu focal/main amd64 libpangocairo-1.0-0 amd64 1.44.7-1 [24.8 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main amd64 libpaper1 amd64 1.1.28 [13.0 kB] Get:125 http://ftpmaster.internal/ubuntu focal/main amd64 libpaper-utils amd64 1.1.28 [8400 B] Get:126 http://ftpmaster.internal/ubuntu focal/main amd64 libsensors-config all 1:3.6.0-2ubuntu1 [6092 B] Get:127 http://ftpmaster.internal/ubuntu focal/main amd64 libsensors5 amd64 1:3.6.0-2ubuntu1 [27.4 kB] Get:128 http://ftpmaster.internal/ubuntu focal/universe amd64 libseqlib1 amd64 1.1.2+dfsg-5 [121 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main amd64 libjsoncpp-dev amd64 1.7.4-3 [85.3 kB] Get:130 http://ftpmaster.internal/ubuntu focal/universe amd64 libssw0 amd64 1.1-7 [18.9 kB] Get:131 http://ftpmaster.internal/ubuntu focal/universe amd64 libssw-dev amd64 1.1-7 [20.7 kB] Get:132 http://ftpmaster.internal/ubuntu focal/universe amd64 libseqlib-dev amd64 1.1.2+dfsg-5 [169 kB] Get:133 http://ftpmaster.internal/ubuntu focal/main amd64 libsm6 amd64 2:1.2.3-1 [16.1 kB] Get:134 http://ftpmaster.internal/ubuntu focal/universe amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-7 [35.8 kB] Get:135 http://ftpmaster.internal/ubuntu focal/universe amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-7 [37.9 kB] Get:136 http://ftpmaster.internal/ubuntu focal/universe amd64 libtabixpp0 amd64 1.0.0-4 [7880 B] Get:137 http://ftpmaster.internal/ubuntu focal/universe amd64 libtabixpp-dev amd64 1.0.0-4 [6668 B] Get:138 http://ftpmaster.internal/ubuntu focal/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [902 kB] Get:139 http://ftpmaster.internal/ubuntu focal/main amd64 libjbig0 amd64 2.1-3.1build1 [26.7 kB] Get:140 http://ftpmaster.internal/ubuntu focal/main amd64 libwebp6 amd64 0.6.1-2 [185 kB] Get:141 http://ftpmaster.internal/ubuntu focal/main amd64 libtiff5 amd64 4.1.0+git191117-1 [162 kB] Get:142 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amd64 r-cran-utf8 amd64 1.1.4-1build1 [130 kB] Get:183 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-backports amd64 1.1.5-1 [58.2 kB] Get:184 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-ellipsis amd64 0.3.0-1 [30.6 kB] Get:185 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-zeallot all 0.1.0-2 [60.0 kB] Get:186 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-vctrs amd64 0.2.0-1 [695 kB] Get:187 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-pillar all 1.4.2-1 [225 kB] Get:188 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-pkgconfig all 2.0.3-1 [19.7 kB] Get:189 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-tibble amd64 2.1.3-1 [324 kB] Get:190 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-withr all 2.1.2-3 [153 kB] Get:191 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-ggplot2 all 3.2.1+dfsg-1 [2834 kB] Get:192 http://ftpmaster.internal/ubuntu focal/universe amd64 r-cran-gridbase all 0.4-7-4 [170 kB] Get:193 http://ftpmaster.internal/ubuntu focal/universe amd64 libvcflib-tools amd64 1.0.1+dfsg-1 [635 kB] Get:194 http://ftpmaster.internal/ubuntu focal/main amd64 pkg-config amd64 0.29.1-0ubuntu3 [45.2 kB] Get:195 http://ftpmaster.internal/ubuntu focal/universe amd64 samtools amd64 1.9-7 [423 kB] Get:196 http://ftpmaster.internal/ubuntu focal/main amd64 sysstat amd64 12.2.0-2 [453 kB] Get:197 http://ftpmaster.internal/ubuntu focal/universe amd64 parallel all 20161222-1.1 [260 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 93.3 MB in 2s (49.8 MB/s) Selecting previously unselected package libpython3.7-minimal:amd64. 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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 fontconfig (2.13.1-2ubuntu2) ... Regenerating fonts cache... done. Setting up gettext (0.19.8.1-10) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-1) ... Setting up libpango-1.0-0:amd64 (1.44.7-1) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... 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 libcairo2:amd64 (1.16.0-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.44.7-1) ... 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Processing triggers for systemd (244-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-170-generic amd64 (x86_64) Toolchain package versions: binutils_2.33.1-6ubuntu3 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 bc_1.07.1-2build1 binutils_2.33.1-6ubuntu3 binutils-common_2.33.1-6ubuntu3 binutils-x86-64-linux-gnu_2.33.1-6ubuntu3 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu4 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 cmake_3.15.4-1ubuntu2 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r-cran-colorspace_1.4-1+dfsg-1 r-cran-crayon_1.3.4-4ubuntu1 r-cran-digest_0.6.23-1 r-cran-ellipsis_0.3.0-1 r-cran-fansi_0.4.0-1 r-cran-ggplot2_3.2.1+dfsg-1 r-cran-glue_1.3.1-1 r-cran-gridbase_0.4-7-4 r-cran-gtable_0.3.0+dfsg-1 r-cran-labeling_0.3-3 r-cran-lattice_0.20-38-1 r-cran-lazyeval_0.2.2-1 r-cran-littler_0.3.9-1 r-cran-magrittr_1.5-5 r-cran-mass_7.3-51.4-2 r-cran-matrix_1.2-18-1 r-cran-mgcv_1.8-31-1 r-cran-munsell_0.5.0-1 r-cran-nlme_3.1.142-1 r-cran-pillar_1.4.2-1 r-cran-pkgconfig_2.0.3-1 r-cran-pkgkitten_0.1.5-1 r-cran-plyr_1.8.4-2 r-cran-r6_2.4.1-1 r-cran-rcolorbrewer_1.1-2-2 r-cran-rcpp_1.0.3-1 r-cran-reshape2_1.4.3-2 r-cran-rlang_0.4.0-1 r-cran-scales_1.0.0-2 r-cran-stringi_1.4.3-1 r-cran-stringr_1.4.0-1 r-cran-tibble_2.1.3-1 r-cran-utf8_1.1.4-1build1 r-cran-vctrs_0.2.0-1 r-cran-viridislite_0.3.0-3 r-cran-withr_2.1.2-3 r-cran-zeallot_0.1.0-2 readline-common_8.0-3 samtools_1.9-7 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-freebayes-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysstat_12.2.0-2 systemd_244-3ubuntu1 systemd-sysv_244-3ubuntu1 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 ucf_3.0038+nmu1 unzip_6.0-25ubuntu1 util-linux_2.34-0.1ubuntu4 x11-common_1:7.7+19ubuntu12 xdg-utils_1.1.3-1ubuntu2 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Thu Dec 19 13:39:42 2019 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./freebayes_1.3.2-1.dsc dpkg-source: info: extracting freebayes in freebayes-1.3.2 dpkg-source: info: unpacking freebayes_1.3.2.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.2-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_libs.patch dpkg-source: info: applying fix_all_target.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying vcffirstheader.patch dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch 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-18295119 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18295119 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18295119 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.2-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/<>' cd src && make clean make[2]: Entering directory '/<>/src' rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp make[2]: Leaving directory '/<>/src' rm -fr bin/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules build dh build --no-parallel dh_update_autotools_config -O--no-parallel dh_autoreconf -O--no-parallel dh_auto_configure -O--no-parallel dh_auto_build -O--no-parallel make -j1 "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' cd src && make make[2]: Entering directory '/<>/src' DETECTED_VERSION = v1.0.0 CURRENT_VERSION = Updating version file. g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c freebayes.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c BedReader.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c CNV.cpp gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c fastlz.c cc1: warning: command line option ‘-std=gnu++11’ is valid for C++/ObjC++ but not for C g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Utility.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Fasta.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Parameters.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Allele.cpp Allele.cpp: In member function ‘const string Allele::base() const’: Allele.cpp:297:1: warning: control reaches end of non-void function [-Wreturn-type] 297 | } | ^ g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Sample.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Result.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c AlleleParser.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Genotype.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c DataLikelihood.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Multinomial.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Ewens.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c ResultData.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Dirichlet.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Marginals.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c split.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c LeftAlign.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c IndelAllele.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c Bias.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -Wdate-time -D_FORTIFY_SOURCE=2 -c -o Contamination.o Contamination.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c NonCall.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` -c SegfaultHandler.cpp g++ -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -O3 -D_FILE_OFFSET_BITS=64 -g -ggdb -I../ttmath -I/usr/include/bamtools `pkg-config --cflags libvcflib` `pkg-config --cflags libseqlib` `pkg-config --cflags htslib` `pkg-config --cflags jsoncpp` freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/freebayes -lbamtools -ltabixpp -lz -lm -lpthread `pkg-config --libs libvcflib` `pkg-config --libs htslib` `pkg-config --libs libseqlib` `pkg-config --libs jsoncpp` /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libseqlib.so: undefined reference to `sam_hdr_init' /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/libseqlib.so: undefined reference to `sam_hdr_destroy' collect2: error: ld returned 1 exit status make[2]: *** [Makefile:73: ../bin/freebayes] Error 1 make[2]: Leaving directory '/<>/src' make[1]: *** [Makefile:5: all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: make -j1 "INSTALL=install --strip-program=true" returned exit code 2 make: *** [debian/rules:7: build] Error 255 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200105-1229 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build-Space: 93424 Build-Time: 144 Distribution: focal Fail-Stage: build Host Architecture: amd64 Install-Time: 32 Job: freebayes_1.3.2-1.dsc Machine Architecture: amd64 Package: freebayes Package-Time: 178 Source-Version: 1.3.2-1 Space: 93424 Status: attempted Version: 1.3.2-1 -------------------------------------------------------------------------------- Finished at 20200105-1229 Build needed 00:02:58, 93424k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=amd64 PACKAGEBUILD-18295119 Scanning for processes to kill in build PACKAGEBUILD-18295119