https://launchpad.net/ubuntu/+source/freebayes/1.3.2-3/+build/19389662 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-068 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... 1 Jun 11:12:20 ntpdate[1864]: adjust time server 10.211.37.1 offset -0.085770 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19389662 --image-type chroot /home/buildd/filecache-default/bb4dbf4bd068f4f4da4a9ba56413a8aa8579df72 Creating target for build PACKAGEBUILD-19389662 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19389662 Starting target for build PACKAGEBUILD-19389662 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19389662 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19389662 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19389662 Updating target for build PACKAGEBUILD-19389662 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main arm64 Packages [942 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe arm64 Packages [8564 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5180 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 Packages [43.5 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [25.6 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 Packages [459 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [285 kB] Fetched 16.6 MB in 5s (3214 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-aarch64-linux-gnu binutils-common bsdutils bzip2 cpp-9 dash debconf debianutils e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libbinutils libblkid1 libbz2-1.0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libitm1 libkmod2 liblsan0 libmount1 libncurses6 libncursesw6 libperl5.30 libprocps8 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 83 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 48.9 MB of archives. After this operation, 515 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main arm64 libcrypt-dev arm64 1:4.4.15-1ubuntu1 [111 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main arm64 libcrypt1 arm64 1:4.4.15-1ubuntu1 [82.5 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main arm64 base-files arm64 11ubuntu7 [60.0 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 bsdutils arm64 1:2.35.1-5ubuntu2 [82.5 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main arm64 debianutils arm64 4.11 [85.3 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main arm64 perl-modules-5.30 all 5.30.2-1 [2740 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main arm64 libperl5.30 arm64 5.30.2-1 [3759 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main arm64 perl arm64 5.30.2-1 [224 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main arm64 perl-base arm64 5.30.2-1 [1391 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 bzip2 arm64 1.0.8-3 [32.4 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libbz2-1.0 arm64 1.0.8-3 [33.0 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main arm64 debconf all 1.5.74 [121 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main arm64 dash arm64 0.5.10.2-7 [84.2 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 gzip arm64 1.10-2ubuntu1 [92.8 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 login arm64 1:4.8.1-1ubuntu6 [218 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main arm64 ncurses-bin arm64 6.2-1 [167 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libblkid1 arm64 2.35.1-5ubuntu2 [125 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libuuid1 arm64 2.35.1-5ubuntu2 [21.6 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libfdisk1 arm64 2.35.1-5ubuntu2 [156 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libmount1 arm64 2.35.1-5ubuntu2 [137 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main arm64 libncurses6 arm64 6.2-1 [91.8 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main arm64 libncursesw6 arm64 6.2-1 [120 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main arm64 libtinfo6 arm64 6.2-1 [81.2 kB] Get:24 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libsmartcols1 arm64 2.35.1-5ubuntu2 [89.9 kB] Get:25 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 fdisk arm64 2.35.1-5ubuntu2 [117 kB] Get:26 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 util-linux arm64 2.35.1-5ubuntu2 [1009 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main arm64 ncurses-base all 6.2-1 [18.7 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main arm64 sysvinit-utils arm64 2.96-3ubuntu1 [20.4 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main arm64 libatomic1 arm64 10.1.0-3ubuntu1 [9868 B] Get:30 http://ftpmaster.internal/ubuntu groovy/main arm64 libubsan1 arm64 10.1.0-3ubuntu1 [127 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main arm64 libtsan0 arm64 10.1.0-3ubuntu1 [302 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main arm64 liblsan0 arm64 10.1.0-3ubuntu1 [130 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main arm64 libitm1 arm64 10.1.0-3ubuntu1 [24.2 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main arm64 libgomp1 arm64 10.1.0-3ubuntu1 [93.2 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc-10-base arm64 10.1.0-3ubuntu1 [20.1 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main arm64 libgcc-s1 arm64 10.1.0-3ubuntu1 [34.7 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main arm64 libcc1-0 arm64 10.1.0-3ubuntu1 [37.1 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main arm64 libstdc++6 arm64 10.1.0-3ubuntu1 [463 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd-sysv arm64 245.5-3ubuntu1 [10.3 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd-timesyncd arm64 245.5-3ubuntu1 [26.2 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main arm64 libacl1 arm64 2.2.53-8 [17.9 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main arm64 libapparmor1 arm64 2.13.3-7ubuntu6 [33.1 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main arm64 libcap2 arm64 1:2.34-2 [16.7 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main arm64 libudev1 arm64 245.5-3ubuntu1 [68.4 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main arm64 libdevmapper1.02.1 arm64 2:1.02.167-1ubuntu3 [110 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main arm64 libcryptsetup12 arm64 2:2.3.1-1ubuntu1 [176 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main arm64 libidn2-0 arm64 2.3.0-1 [51.9 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main arm64 libkmod2 arm64 27+20200310-2ubuntu1 [40.7 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main arm64 libseccomp2 arm64 2.4.3-1ubuntu2 [39.9 kB] Get:50 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 mount arm64 2.35.1-5ubuntu2 [115 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main arm64 systemd arm64 245.5-3ubuntu1 [3487 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main arm64 libsystemd0 arm64 245.5-3ubuntu1 [245 kB] Get:53 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libapt-pkg6.0 arm64 2.1.5 [765 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main arm64 gpgv arm64 2.2.20-1ubuntu1 [184 kB] Get:55 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 apt arm64 2.1.5 [1238 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main arm64 logsave arm64 1.45.6-1ubuntu1 [10.2 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main arm64 libext2fs2 arm64 1.45.6-1ubuntu1 [177 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main arm64 e2fsprogs arm64 1.45.6-1ubuntu1 [504 kB] Get:59 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 passwd arm64 1:4.8.1-1ubuntu6 [770 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main arm64 libcom-err2 arm64 1.45.6-1ubuntu1 [9336 B] Get:61 http://ftpmaster.internal/ubuntu groovy/main arm64 libprocps8 arm64 2:3.3.16-4ubuntu1 [31.6 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main arm64 libss2 arm64 1.45.6-1ubuntu1 [10.7 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main arm64 procps arm64 2:3.3.16-4ubuntu1 [229 kB] Get:64 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libsqlite3-0 arm64 3.32.1-1 [508 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main arm64 tzdata all 2020a-0ubuntu1 [293 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main arm64 libctf0 arm64 2.34-7ubuntu1 [43.0 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils-aarch64-linux-gnu arm64 2.34-7ubuntu1 [1988 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main arm64 libbinutils arm64 2.34-7ubuntu1 [473 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils arm64 2.34-7ubuntu1 [3348 B] Get:70 http://ftpmaster.internal/ubuntu groovy/main arm64 binutils-common arm64 2.34-7ubuntu1 [207 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main arm64 libctf-nobfd0 arm64 2.34-7ubuntu1 [43.8 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main arm64 libasan5 arm64 9.3.0-13ubuntu1 [365 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main arm64 g++-9 arm64 9.3.0-13ubuntu1 [6820 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc-9 arm64 9.3.0-13ubuntu1 [6691 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main arm64 libstdc++-9-dev arm64 9.3.0-13ubuntu1 [1679 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main arm64 libgcc-9-dev arm64 9.3.0-13ubuntu1 [920 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main arm64 cpp-9 arm64 9.3.0-13ubuntu1 [5965 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main arm64 gcc-9-base arm64 9.3.0-13ubuntu1 [19.6 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main arm64 gpg arm64 2.2.20-1ubuntu1 [443 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main arm64 gpgconf arm64 2.2.20-1ubuntu1 [117 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main arm64 gpg-agent arm64 2.2.20-1ubuntu1 [216 kB] Get:82 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 linux-libc-dev arm64 5.4.0-33.37 [1077 kB] Get:83 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 make arm64 4.3-1 [160 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 48.9 MB in 2s (26.2 MB/s) (Reading database ... 12809 files and directories currently installed.) 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Setting up systemd-sysv (245.5-3ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19389662 arm64 groovy-proposed -c chroot:build-PACKAGEBUILD-19389662 --arch=arm64 --dist=groovy-proposed --nolog freebayes_1.3.2-3.dsc Initiating build PACKAGEBUILD-19389662 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 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-068.buildd +==============================================================================+ | freebayes 1.3.2-3 (arm64) 01 Jun 2020 11:13 | +==============================================================================+ Package: freebayes Version: 1.3.2-3 Source Version: 1.3.2-3 Distribution: groovy-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/freebayes-3eKrLz/freebayes-1.3.2' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-3eKrLz' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19389662/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- freebayes_1.3.2-3.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-5VyWqg/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-5VyWqg/apt_archive ./ InRelease Get:2 copy:/<>/resolver-5VyWqg/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-5VyWqg/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-5VyWqg/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-5VyWqg/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (104 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 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-5VyWqg/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (69.4 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12817 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.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 (= 13), 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 (= 13), 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-35aB62/apt_archive/sbuild-build-depends-freebayes-dummy.deb'. Ign:1 copy:/<>/resolver-35aB62/apt_archive ./ InRelease Get:2 copy:/<>/resolver-35aB62/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-35aB62/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-35aB62/apt_archive ./ Sources [331 B] Get:5 copy:/<>/resolver-35aB62/apt_archive ./ Packages [639 B] Fetched 3089 B in 0s (101 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 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 libhts3 libhx509-5-heimdal libice6 libicu66 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 libpython3.8-minimal libpython3.8-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 python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle 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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr 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 python3.8-venv python3.8-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode 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-viridis r-cran-unitizer 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-stringr r-cran-magick r-cran-getopt r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-curl r-cran-inline r-cran-mockr r-cran-dichromat r-cran-devtools r-cran-usethis r-cran-bit64 r-cran-blob r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot 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-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-xml2 r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-generics 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 libhts3 libhx509-5-heimdal libice6 libicu66 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 libpython3.8-minimal libpython3.8-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 python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle 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-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samtools sbuild-build-depends-freebayes-dummy sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 207 newly installed, 0 to remove and 0 not upgraded. Need to get 97.5 MB of archives. After this operation, 266 MB of additional disk space will be used. Get:1 copy:/<>/resolver-35aB62/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [968 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3.8-minimal arm64 3.8.3-1 [711 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main arm64 libexpat1 arm64 2.2.9-1build1 [61.3 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main arm64 python3.8-minimal arm64 3.8.3-1 [1829 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main arm64 python3-minimal arm64 3.8.2-0ubuntu2 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main arm64 mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main arm64 libmpdec2 arm64 2.4.2-3 [79.6 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3.8-stdlib arm64 3.8.3-1 [1642 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main arm64 python3.8 arm64 3.8.3-1 [369 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main arm64 libpython3-stdlib arm64 3.8.2-0ubuntu2 [7068 B] Get:11 http://ftpmaster.internal/ubuntu groovy/main arm64 python3 arm64 3.8.2-0ubuntu2 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main arm64 libbsd0 arm64 0.10.0-1 [43.7 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main arm64 bsdmainutils arm64 11.1.2ubuntu3 [179 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libuchardet0 arm64 0.0.7-1 [68.0 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main arm64 groff-base arm64 1.22.4-5 [797 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main arm64 libpipeline1 arm64 1.5.2-2build1 [26.1 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main arm64 man-db arm64 2.9.1-1 [1095 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main arm64 libmagic-mgc arm64 1:5.38-5 [218 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main arm64 libmagic1 arm64 1:5.38-5 [71.6 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main arm64 file arm64 1:5.38-5 [23.3 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main arm64 libelf1 arm64 0.176-1.1build1 [44.2 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main arm64 libfribidi0 arm64 1.0.8-2 [23.7 kB] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libglib2.0-0 arm64 2.64.3-1 [1199 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main arm64 libicu66 arm64 66.1-2ubuntu2 [8357 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main arm64 libxml2 arm64 2.9.10+dfsg-5 [572 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main arm64 ucf all 3.0042 [56.0 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main arm64 gettext-base arm64 0.19.8.1-10build1 [48.2 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5support0 arm64 1.17-6ubuntu4 [30.4 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main arm64 libk5crypto3 arm64 1.17-6ubuntu4 [80.5 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main arm64 libkeyutils1 arm64 1.6.1-2ubuntu1 [9932 B] Get:31 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5-3 arm64 1.17-6ubuntu4 [312 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main arm64 libgssapi-krb5-2 arm64 1.17-6ubuntu4 [113 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main arm64 libpsl5 arm64 0.21.0-1ubuntu1 [51.3 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main arm64 libuv1 arm64 1.35.0-2ubuntu1 [74.8 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main arm64 libxau6 arm64 1:1.0.9-0ubuntu1 [7356 B] Get:36 http://ftpmaster.internal/ubuntu groovy/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu1 [10.3 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main arm64 libxcb1 arm64 1.14-2 [43.0 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main arm64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main arm64 libx11-6 arm64 2:1.6.9-2ubuntu1 [553 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main arm64 libxext6 arm64 2:1.3.4-0ubuntu1 [27.7 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main arm64 libsigsegv2 arm64 2.12-2 [13.3 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main arm64 m4 arm64 1.4.18-4 [194 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main arm64 autoconf all 2.69-11.1 [321 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main arm64 automake all 1:1.16.2-1ubuntu1 [521 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main arm64 autopoint all 0.19.8.1-10build1 [412 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main arm64 bc arm64 1.07.1-2build1 [84.1 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main arm64 cmake-data all 3.16.3-3ubuntu1 [1612 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main arm64 libarchive13 arm64 3.4.2-1 [305 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main arm64 libbrotli1 arm64 1.0.7-6.1 [260 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-2 [39.4 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-2 [150 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-2 [27.9 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-2 [84.8 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-2 [47.2 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-2 [98.6 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-2 [192 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-2 [14.8 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-2 [88.4 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [15.1 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [48.4 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main arm64 libldap-common all 2.4.49+dfsg-2ubuntu2 [17.4 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main arm64 libldap-2.4-2 arm64 2.4.49+dfsg-2ubuntu2 [146 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main arm64 libnghttp2-14 arm64 1.40.0-1build1 [74.7 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build1 [53.3 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main arm64 libssh-4 arm64 0.9.4-1ubuntu1 [159 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main arm64 libcurl4 arm64 7.68.0-1ubuntu2 [213 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main arm64 libjsoncpp1 arm64 1.7.4-3.1ubuntu2 [69.8 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main arm64 librhash0 arm64 1.3.9-1 [111 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main arm64 cmake arm64 3.16.3-3ubuntu1 [3121 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main arm64 libtool all 2.4.6-14 [161 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main arm64 dh-autoreconf all 19 [16.1 kB] Get:73 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 libdebhelper-perl all 13.1ubuntu1 [64.0 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main arm64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:76 http://ftpmaster.internal/ubuntu groovy/main arm64 libfile-stripnondeterminism-perl all 1.8.1-1 [17.1 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main arm64 dh-strip-nondeterminism all 1.8.1-1 [5232 B] Get:78 http://ftpmaster.internal/ubuntu groovy/main arm64 dwz arm64 0.13-5 [134 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main arm64 gettext arm64 0.19.8.1-10build1 [850 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main arm64 po-debconf all 1.0.21 [233 kB] Get:83 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 debhelper all 13.1ubuntu1 [885 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main arm64 libfreetype6 arm64 2.10.1-2 [316 kB] Get:85 http://ftpmaster.internal/ubuntu groovy-proposed/main arm64 fonts-dejavu-core all 2.37-2 [1041 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main arm64 fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main arm64 libfontconfig1 arm64 2.13.1-2ubuntu3 [111 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main arm64 fontconfig arm64 2.13.1-2ubuntu3 [170 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/universe arm64 libbamtools2.5.1 arm64 2.5.1+dfsg-7 [140 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/universe arm64 libbamtools-dev arm64 2.5.1+dfsg-7 [197 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main arm64 libblas3 arm64 3.9.0-2 [89.1 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/universe arm64 libbwa-dev arm64 0.7.17-5 [125 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main arm64 libpixman-1-0 arm64 0.38.4-0ubuntu1 [130 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main arm64 libxcb-render0 arm64 1.14-2 [14.7 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main arm64 libxcb-shm0 arm64 1.14-2 [5560 B] Get:96 http://ftpmaster.internal/ubuntu groovy/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main arm64 libcairo2 arm64 1.16.0-4ubuntu1 [538 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main arm64 libcurl3-gnutls arm64 7.68.0-1ubuntu2 [211 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main arm64 libdatrie1 arm64 0.2.12-3 [17.9 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/universe arm64 libdeflate0 arm64 1.6-1 [51.1 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/universe arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-1 [4056 B] Get:102 http://ftpmaster.internal/ubuntu groovy/universe arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-1 [3680 B] Get:103 http://ftpmaster.internal/ubuntu groovy/universe arm64 libfastahack0 arm64 1.0.0+dfsg-5build1 [22.1 kB] Get:104 http://ftpmaster.internal/ubuntu groovy/universe arm64 libfastahack-dev arm64 1.0.0+dfsg-5build1 [23.6 kB] Get:105 http://ftpmaster.internal/ubuntu groovy/universe arm64 libfml0 arm64 0.1-13 [65.1 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2ubuntu1 [154 kB] Get:107 http://ftpmaster.internal/ubuntu groovy/universe arm64 libfml-dev arm64 0.1-13 [77.9 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/main arm64 libgfortran5 arm64 10.1.0-3ubuntu1 [345 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/main arm64 libgraphite2-3 arm64 1.3.14-1 [67.8 kB] Get:110 http://ftpmaster.internal/ubuntu groovy/main arm64 libharfbuzz0b arm64 2.6.4-1ubuntu4 [353 kB] Get:111 http://ftpmaster.internal/ubuntu groovy/universe arm64 libhts3 arm64 1.10.2-3 [316 kB] Get:112 http://ftpmaster.internal/ubuntu groovy/main arm64 liblzma-dev arm64 5.2.4-1 [144 kB] Get:113 http://ftpmaster.internal/ubuntu groovy/universe arm64 libhts-dev arm64 1.10.2-3 [92.1 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/main arm64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:115 http://ftpmaster.internal/ubuntu groovy/main arm64 libice6 arm64 2:1.0.10-0ubuntu1 [37.7 kB] Get:116 http://ftpmaster.internal/ubuntu groovy/main arm64 libjpeg-turbo8 arm64 2.0.3-0ubuntu1 [101 kB] Get:117 http://ftpmaster.internal/ubuntu groovy/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:118 http://ftpmaster.internal/ubuntu groovy/main arm64 liblapack3 arm64 3.9.0-2 [1529 kB] Get:119 http://ftpmaster.internal/ubuntu groovy/main arm64 libthai-data all 0.1.28-3 [134 kB] Get:120 http://ftpmaster.internal/ubuntu groovy/main arm64 libthai0 arm64 0.1.28-3 [16.8 kB] Get:121 http://ftpmaster.internal/ubuntu groovy/main arm64 libpango-1.0-0 arm64 1.44.7-2ubuntu4 [153 kB] Get:122 http://ftpmaster.internal/ubuntu groovy/main arm64 libpangoft2-1.0-0 arm64 1.44.7-2ubuntu4 [32.0 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main arm64 libpangocairo-1.0-0 arm64 1.44.7-2ubuntu4 [22.5 kB] Get:124 http://ftpmaster.internal/ubuntu groovy/main arm64 libpaper1 arm64 1.1.28 [12.7 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main arm64 libpaper-utils arm64 1.1.28 [8328 B] Get:126 http://ftpmaster.internal/ubuntu groovy/main arm64 libsensors-config all 1:3.6.0-2ubuntu1 [6092 B] Get:127 http://ftpmaster.internal/ubuntu groovy/main arm64 libsensors5 arm64 1:3.6.0-2ubuntu1 [26.1 kB] Get:128 http://ftpmaster.internal/ubuntu groovy/universe arm64 libssw0 arm64 1.1-9 [17.9 kB] Get:129 http://ftpmaster.internal/ubuntu groovy/universe arm64 libseqlib1 arm64 1.1.2+dfsg-6 [110 kB] Get:130 http://ftpmaster.internal/ubuntu groovy/main arm64 libjsoncpp-dev arm64 1.7.4-3.1ubuntu2 [85.5 kB] Get:131 http://ftpmaster.internal/ubuntu groovy/universe arm64 libssw-dev arm64 1.1-9 [20.2 kB] Get:132 http://ftpmaster.internal/ubuntu groovy/universe arm64 libseqlib-dev arm64 1.1.2+dfsg-6 [163 kB] Get:133 http://ftpmaster.internal/ubuntu groovy/main arm64 libsm6 arm64 2:1.2.3-1 [15.1 kB] Get:134 http://ftpmaster.internal/ubuntu groovy/universe arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-8 [33.4 kB] Get:135 http://ftpmaster.internal/ubuntu groovy/universe arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-8 [37.1 kB] Get:136 http://ftpmaster.internal/ubuntu groovy/universe arm64 libtabixpp0 arm64 1.1.0-3 [8456 B] Get:137 http://ftpmaster.internal/ubuntu groovy/universe arm64 libtabixpp-dev arm64 1.1.0-3 [6920 B] Get:138 http://ftpmaster.internal/ubuntu groovy/main arm64 libtcl8.6 arm64 8.6.10+dfsg-1 [849 kB] Get:139 http://ftpmaster.internal/ubuntu groovy/main arm64 libjbig0 arm64 2.1-3.1build1 [24.0 kB] Get:140 http://ftpmaster.internal/ubuntu groovy/main arm64 libwebp6 arm64 0.6.1-2 [155 kB] Get:141 http://ftpmaster.internal/ubuntu groovy/main arm64 libtiff5 arm64 4.1.0+git191117-2build1 [151 kB] Get:142 http://ftpmaster.internal/ubuntu groovy/main arm64 libxft2 arm64 2.3.3-0ubuntu1 [35.9 kB] Get:143 http://ftpmaster.internal/ubuntu groovy/main arm64 libxss1 arm64 1:1.2.3-1 [8080 B] Get:144 http://ftpmaster.internal/ubuntu groovy/main arm64 libtk8.6 arm64 8.6.10-1 [674 kB] Get:145 http://ftpmaster.internal/ubuntu groovy/universe arm64 libvcflib1 arm64 1.0.1+dfsg-3 [133 kB] Get:146 http://ftpmaster.internal/ubuntu groovy/universe arm64 libvcflib-dev arm64 1.0.1+dfsg-3 [27.0 kB] Get:147 http://ftpmaster.internal/ubuntu groovy/main arm64 zip arm64 3.0-11build1 [146 kB] Get:148 http://ftpmaster.internal/ubuntu groovy/main arm64 unzip arm64 6.0-25ubuntu1 [163 kB] Get:149 http://ftpmaster.internal/ubuntu groovy/main arm64 xdg-utils all 1.1.3-2ubuntu1 [61.6 kB] Get:150 http://ftpmaster.internal/ubuntu groovy/main arm64 libxt6 arm64 1:1.1.5-1 [128 kB] Get:151 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-base-core arm64 4.0.0.20200528-1 [24.7 MB] Get:152 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-littler arm64 0.3.9-1build1 [298 kB] Get:153 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 littler all 0.3.9-1build1 [2496 B] Get:154 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-pkgkitten all 0.1.5-2 [22.6 kB] Get:155 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-rcpp arm64 1.0.4.6-1build1 [1850 kB] Get:156 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-plyr arm64 1.8.6-2build1 [830 kB] Get:157 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-digest arm64 0.6.25-1build1 [164 kB] Get:158 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-glue 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groovy-proposed/universe arm64 r-cran-magrittr all 1.5-6build1 [154 kB] Get:168 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-r6 all 2.4.1-2build1 [79.2 kB] Get:169 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-backports arm64 1.1.7-1build1 [71.8 kB] Get:170 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-rprojroot all 1.3-2-3build1 [98.1 kB] Get:171 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-desc all 1.2.0-3build1 [299 kB] Get:172 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-ps arm64 1.3.3-1build1 [220 kB] Get:173 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-processx arm64 3.4.2-1build1 [268 kB] Get:174 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-callr all 3.4.3-2build1 [385 kB] Get:175 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-prettyunits all 1.1.1-2build1 [39.6 kB] Get:176 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0.20-41-1build1 [1120 kB] Get:185 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-nlme arm64 3.1.148-1build1 [2214 kB] Get:186 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-matrix arm64 1.2-18-1build1 [3408 kB] Get:187 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-mgcv arm64 1.8-31-1build1 [2683 kB] Get:188 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-farver arm64 2.0.3-1build2 [1323 kB] Get:189 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-labeling all 0.3-4build1 [62.3 kB] Get:190 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-lifecycle all 0.2.0-2build1 [93.3 kB] Get:191 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-colorspace arm64 1.4-1+dfsg-1build1 [1490 kB] Get:192 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-munsell all 0.5.0-2build1 [208 kB] Get:193 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-rcolorbrewer all 1.1-2-3 [54.6 kB] Get:194 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-viridislite all 0.3.0-4 [58.9 kB] Get:195 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-scales all 1.1.1-1build1 [486 kB] Get:196 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-utf8 arm64 1.1.4-1build2 [129 kB] Get:197 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-vctrs arm64 0.3.0-2build1 [920 kB] Get:198 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-pillar all 1.4.4-2build1 [229 kB] Get:199 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] Get:200 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-tibble arm64 3.0.1-1build1 [418 kB] Get:201 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-ggplot2 all 3.3.0+dfsg-2build1 [3069 kB] Get:202 http://ftpmaster.internal/ubuntu groovy-proposed/universe arm64 r-cran-gridbase all 0.4-7-5build1 [163 kB] Get:203 http://ftpmaster.internal/ubuntu groovy/universe arm64 libvcflib-tools arm64 1.0.1+dfsg-3 [559 kB] Get:204 http://ftpmaster.internal/ubuntu groovy/main arm64 pkg-config arm64 0.29.2-1ubuntu1 [44.5 kB] Get:205 http://ftpmaster.internal/ubuntu groovy/universe arm64 samtools arm64 1.10-3 [474 kB] Get:206 http://ftpmaster.internal/ubuntu groovy/main arm64 sysstat arm64 12.3.2-1 [430 kB] Get:207 http://ftpmaster.internal/ubuntu groovy/universe arm64 parallel all 20161222-1.1 [260 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 97.5 MB in 6s (16.4 MB/s) Selecting previously unselected package libpython3.8-minimal:arm64. (Reading database ... 12817 files and directories currently installed.) Preparing to unpack .../libpython3.8-minimal_3.8.3-1_arm64.deb ... Unpacking libpython3.8-minimal:arm64 (3.8.3-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.9-1build1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.3-1_arm64.deb ... Unpacking python3.8-minimal (3.8.3-1) ... Setting up libpython3.8-minimal:arm64 (3.8.3-1) ... Setting up libexpat1:arm64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13108 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.8.2-0ubuntu2_arm64.deb ... Unpacking python3-minimal (3.8.2-0ubuntu2) ... Selecting previously unselected package mime-support. 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WARNING: tempfile is deprecated; consider using mktemp instead. Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /lib/systemd/system/sysstat.service. Setting up xdg-utils (1.1.3-2ubuntu1) ... Setting up libjsoncpp1:arm64 (1.7.4-3.1ubuntu2) ... Setting up libpython3-stdlib:arm64 (3.8.2-0ubuntu2) ... Setting up libheimbase1-heimdal:arm64 (7.7.0+dfsg-2) ... Setting up libjpeg8:arm64 (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libpaper1:arm64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:arm64 (2:1.0.10-0ubuntu1) ... Setting up libjsoncpp-dev:arm64 (1.7.4-3.1ubuntu2) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu1) ... 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Processing triggers for systemd (245.5-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (aarch64) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-3ubuntu1 linux-libc-dev_5.4.0-33.37 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.5 autoconf_2.69-11.1 automake_1:1.16.2-1ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 bc_1.07.1-2build1 binutils_2.34-7ubuntu1 binutils-aarch64-linux-gnu_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-3 ca-certificates_20190110ubuntu1 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python3.8-minimal_3.8.3-1 r-base-core_4.0.0.20200528-1 r-cran-assertthat_0.2.1-2build1 r-cran-backports_1.1.7-1build1 r-cran-callr_3.4.3-2build1 r-cran-cli_2.0.2-2build1 r-cran-colorspace_1.4-1+dfsg-1build1 r-cran-crayon_1.3.4-4ubuntu2 r-cran-desc_1.2.0-3build1 r-cran-digest_0.6.25-1build1 r-cran-ellipsis_0.3.1-1build1 r-cran-evaluate_0.14-2build1 r-cran-fansi_0.4.1-1build1 r-cran-farver_2.0.3-1build2 r-cran-ggplot2_3.3.0+dfsg-2build1 r-cran-glue_1.4.1-1build1 r-cran-gridbase_0.4-7-5build1 r-cran-gtable_0.3.0+dfsg-2build1 r-cran-isoband_0.2.1-1build1 r-cran-labeling_0.3-4build1 r-cran-lattice_0.20-41-1build1 r-cran-lifecycle_0.2.0-2build1 r-cran-littler_0.3.9-1build1 r-cran-magrittr_1.5-6build1 r-cran-mass_7.3-51.6-1build1 r-cran-matrix_1.2-18-1build1 r-cran-mgcv_1.8-31-1build1 r-cran-munsell_0.5.0-2build1 r-cran-nlme_3.1.148-1build1 r-cran-pillar_1.4.4-2build1 r-cran-pkgbuild_1.0.8-2build1 r-cran-pkgconfig_2.0.3-2build1 r-cran-pkgkitten_0.1.5-2 r-cran-pkgload_1.0.2-2build1 r-cran-plyr_1.8.6-2build1 r-cran-praise_1.0.0-4build1 r-cran-prettyunits_1.1.1-2build1 r-cran-processx_3.4.2-1build1 r-cran-ps_1.3.3-1build1 r-cran-r6_2.4.1-2build1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.4.6-1build1 r-cran-rlang_0.4.6-1build1 r-cran-rprojroot_1.3-2-3build1 r-cran-rstudioapi_0.11-2 r-cran-scales_1.1.1-1build1 r-cran-testthat_2.3.2-2build1 r-cran-tibble_3.0.1-1build1 r-cran-utf8_1.1.4-1build2 r-cran-vctrs_0.3.0-2build1 r-cran-viridislite_0.3.0-4 r-cran-withr_2.2.0-2 readline-common_8.0-4 samtools_1.10-3 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_12.3.2-1 systemd_245.5-3ubuntu1 systemd-sysv_245.5-3ubuntu1 systemd-timesyncd_245.5-3ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 ucf_3.0042 unzip_6.0-25ubuntu1 util-linux_2.35.1-5ubuntu2 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-2ubuntu1 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Jun 1 07:31:39 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./freebayes_1.3.2-3.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_1.3.2-3.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 dpkg-source: info: applying hardening dpkg-source: info: applying version_bump Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19389662 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19389662 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19389662 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 1.3.2-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 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 binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -O--no-parallel dh_auto_configure -a -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make -j1 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make[2]: Entering directory '/<>' cd src && make make[3]: Entering directory '/<>/src' DETECTED_VERSION = v1.3.2 CURRENT_VERSION = Updating version file. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c freebayes.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c BedReader.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c CNV.cpp gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c fastlz.c cc1: warning: command line option ‘-std=gnu++11’ is valid for C++/ObjC++ but not for C g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Utility.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Fasta.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Parameters.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/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++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Sample.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Result.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c AlleleParser.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Genotype.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c DataLikelihood.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Multinomial.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Ewens.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c ResultData.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Dirichlet.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Marginals.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c split.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c LeftAlign.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c IndelAllele.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Bias.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o Contamination.o Contamination.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c NonCall.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c SegfaultHandler.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/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 -lz -pthread -lbamtools -ltabixpp -lz -lm -lpthread -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -lseqlib -lbwa -ljsoncpp -lz -pthread g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c bamleftalign.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp bamleftalign.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/bamleftalign -lz -pthread -lbamtools -ltabixpp -lz -lm -lpthread -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -lseqlib -lbwa -ljsoncpp -lz -pthread make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir -p /<>/test/bash-tap/ for bt in /<>/debian/bash-tap/* ; do ln -s ${bt} /<>/test/bash-tap/`basename ${bt}` ; done ln -s /<>/debian/test-simple-bash/lib test/test-simple-bash chmod +x vcflib/scripts/vcffirstheader # export PATH=/usr/lib/vcflib/binaries/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test && echo "Tests were running successfully" Tests should be run make -j1 test make[2]: Entering directory '/<>' cd test && make test make[3]: Entering directory '/<>/test' prove -v t t/00_region_and_target_handling.t .. 1..11 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty ok 3 - ref:5-6 ref:7-8 ok 4 - ref:5 ref:7 ok 5 - ref:5- ok 6 - full output ok 7 - --targets t/../00_region_and_target_handling.t.bed ok 8 - --region ref ok 9 - ref:1,0- ok 10 - ref:1,0-1,1 ok 11 - region outside of bounds error ok [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 t/01_call_variants.t ............... 1..23 ok 1 - variant calling recovers most of the GiAB variants in a test region ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference ok 5 - freebayes processes all alignments in input ok 6 - freebayes correctly handles variant input ok 7 - freebayes puts required variants in output ok 8 - freebayes limits calls to input variants correctly ok 9 - freebayes reports all input variants even when there is no input data ok 10 - freebayes handles region and variant input ok 11 - freebayes limits to variant input correctly when region is given ok 12 - freebayes handles variant input and reading from stdin ok 13 - freebayes limits to variant input when reading from stdin ok 14 - freebayes handles region, stdin, and variant input ok 15 - freebayes bails out when given a gzipped or corrupted reference ok 16 - running in parallel makes no difference ok 17 - freebayes handles region and variant input even with : in contig names ok 18 - freebayes can handle spliced reads ok 19 - freebayes produces the expected number of lines of gVCF output ok 20 - freebayes produces the expected number of lines of gVCF output ok 21 - freebayes produces the expected number of lines of gVCF output ok 22 - the CNV map may be used to specify per-sample copy numbers ok 23 - freebayes makes the expected number of calls when capping coverage ok t/02_multi_bam.t ................... 1..7 ok 1 - freebayes calls from two identical BAMs ok 2 - freebayes calls from two BAMs with different samples for different read groups ok 3 - freebayes calls from two BAMs with different technologies for different read groups ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups ok 6 - freebayes calls multiple alts from two different BAMs ok 7 - freebayes rejects two BAMs with the same name ok t/03_reference_bases.t ............. 1..3 ok 1 - freebayes rejects invalid reference ok 2 - freebayes does not put uppercase IUPAC bases in VCFs ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. Files=4, Tests=44, 30 wallclock secs ( 0.09 usr 0.01 sys + 21.96 cusr 13.66 csys = 35.72 CPU) Result: PASS make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>' Tests were running successfully rm -rf /<>/test/bash-tap rm test/test-simple-bash/lib make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--no-parallel dh_prep -a -O--no-parallel debian/rules override_dh_auto_install make[1]: Entering directory '/<>' echo "Skip autoinstall process - files are moved around by dh_install" Skip autoinstall process - files are moved around by dh_install make[1]: Leaving directory '/<>' dh_install -a -O--no-parallel dh_installdocs -a -O--no-parallel dh_installchangelogs -a -O--no-parallel dh_installexamples -a -O--no-parallel dh_installsystemduser -a -O--no-parallel dh_perl -a -O--no-parallel dh_link -a -O--no-parallel dh_strip_nondeterminism -a -O--no-parallel dh_compress -a -O--no-parallel dh_fixperms -a -O--no-parallel dh_missing -a -O--no-parallel dh_dwz -a -a -O--no-parallel dh_strip -a -a -O--no-parallel dh_makeshlibs -a -a -O--no-parallel dh_shlibdeps -a -a -O--no-parallel dh_installdeb -a -O--no-parallel dh_gencontrol -a -O--no-parallel dh_md5sums -a -O--no-parallel dh_builddeb -a -O--no-parallel INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing freebayes (in debian/freebayes); do_strip: , oemstrip: pkgstriptranslations: processing freebayes-dbgsym (in debian/.debhelper/freebayes/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/freebayes/DEBIAN/control, package freebayes, directory debian/freebayes pkgstripfiles: Running PNG optimization (using 4 cpus) for package freebayes ... pkgstripfiles: No PNG files. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.2-3_arm64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/freebayes/dbgsym-root/DEBIAN/control, package freebayes-dbgsym, directory debian/.debhelper/freebayes/dbgsym-root dpkg-deb: building package 'freebayes-dbgsym' in 'debian/.debhelper/scratch-space/build-freebayes/freebayes-dbgsym_1.3.2-3_arm64.deb'. Renaming freebayes-dbgsym_1.3.2-3_arm64.deb to freebayes-dbgsym_1.3.2-3_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../freebayes_1.3.2-3_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200601-1120 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ freebayes_1.3.2-3_arm64.changes: -------------------------------- Format: 1.8 Date: Mon, 01 Jun 2020 02:50:39 +0530 Source: freebayes Binary: freebayes Architecture: arm64 Version: 1.3.2-3 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Pranav Ballaney Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.2-3) unstable; urgency=medium . * Team upload . [ Pranav Ballaney ] * Install test data * Add autopkgtests * Install docs and binaries . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * Add missing files to debian/source/include-binaries Checksums-Sha1: 16831c47d95e9ac00c0bb5b423d65b75fe312514 10005220 freebayes-dbgsym_1.3.2-3_arm64.ddeb beca5cb5af08391020d2abf09e82fef3b47524be 11248 freebayes_1.3.2-3_arm64.buildinfo a552e63e0eafd077bc36a6dd73c87960dffaa233 1309304 freebayes_1.3.2-3_arm64.deb Checksums-Sha256: 9362cf9cefb9183067ab2b19d3c74ca92c3a9f7c243bed945e4da886f9c3e832 10005220 freebayes-dbgsym_1.3.2-3_arm64.ddeb 26ed3b840a84f404f9478820d20edccf9b9c3a7d3393aca6b27b530c6432bbd6 11248 freebayes_1.3.2-3_arm64.buildinfo fa4056510eca8c1f073b446c23e69d9aa118628b569bb6a4199aa34e7b07cb15 1309304 freebayes_1.3.2-3_arm64.deb Files: f4587625e6d388b49ac610839f38ad63 10005220 debug optional freebayes-dbgsym_1.3.2-3_arm64.ddeb 722028ce37c13bca9937833c5a86a269 11248 science optional freebayes_1.3.2-3_arm64.buildinfo 2d1c5c1616487ff6a835e7ddf221b116 1309304 science optional freebayes_1.3.2-3_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ freebayes_1.3.2-3_arm64.deb --------------------------- new debian package, version 2.0. size 1309304 bytes: control archive=2048 bytes. 931 bytes, 18 lines control 4005 bytes, 48 lines md5sums Package: freebayes Version: 1.3.2-3 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 4225 Depends: libc6 (>= 2.29), libgcc-s1 (>= 4.5), libseqlib1 (>= 1.1.2+dfsg-5), libstdc++6 (>= 9), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.1+dfsg), zlib1g (>= 1:1.1.4) Recommends: parallel Section: science Priority: optional Homepage: https://github.com/ekg/freebayes Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. drwxr-xr-x root/root 0 2020-05-31 21:20 ./ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/bin/ -rwxr-xr-x root/root 1780216 2020-05-31 21:20 ./usr/bin/bamleftalign -rwxr-xr-x root/root 1800472 2020-05-31 21:20 ./usr/bin/freebayes drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/share/ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/share/doc/freebayes/ -rw-r--r-- root/root 9516 2019-10-06 08:14 ./usr/share/doc/freebayes/README.md.gz -rw-r--r-- root/root 278 2020-05-31 21:20 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+------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: arm64 Build-Space: 170196 Build-Time: 390 Distribution: groovy-proposed Host Architecture: arm64 Install-Time: 52 Job: freebayes_1.3.2-3.dsc Machine Architecture: arm64 Package: freebayes Package-Time: 444 Source-Version: 1.3.2-3 Space: 170196 Status: successful Version: 1.3.2-3 -------------------------------------------------------------------------------- Finished at 20200601-1120 Build needed 00:07:24, 170196k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=arm64 PACKAGEBUILD-19389662 Scanning for processes to kill in build PACKAGEBUILD-19389662