autopkgtest [14:08:30]: version 5.8 autopkgtest [14:08:30]: host ci-worker05; command line: /usr/bin/autopkgtest --no-built-binaries --user debci --apt-upgrade --output-dir /tmp/tmp.lEFkk5otvi/autopkgtest-incoming/unstable/amd64/p/paleomix/1713700 paleomix -- lxc --sudo --name ci-1547647710 autopkgtest-unstable-amd64 autopkgtest [14:08:44]: @@@@@@@@@@@@@@@@@@@@ test bed setup Get:1 http://deb.debian.org/debian unstable InRelease [238 kB] Get:2 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [55.3 kB] Get:3 http://deb.debian.org/debian-debug unstable-debug InRelease [63.7 kB] Get:4 http://deb.debian.org/debian unstable/main Sources.diff/Index [27.9 kB] Get:5 http://deb.debian.org/debian unstable/non-free Sources.diff/Index [27.8 kB] Get:6 http://deb.debian.org/debian unstable/contrib Sources.diff/Index [27.8 kB] Get:7 http://deb.debian.org/debian unstable/non-free amd64 Packages.diff/Index [27.8 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:9 http://deb.debian.org/debian unstable/main Sources 2019-01-16-0810.52.pdiff [2,246 B] Get:9 http://deb.debian.org/debian unstable/main Sources 2019-01-16-0810.52.pdiff [2,246 B] Get:10 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [3,508 B] Get:11 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [145 kB] Get:12 http://deb.debian.org/debian unstable/non-free Sources 2019-01-16-0810.52.pdiff [42 B] Get:12 http://deb.debian.org/debian unstable/non-free Sources 2019-01-16-0810.52.pdiff [42 B] Get:13 http://incoming.debian.org/debian-buildd buildd-unstable/contrib amd64 Packages [5,004 B] Get:14 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [170 kB] Get:15 http://deb.debian.org/debian unstable/contrib Sources 2019-01-16-0810.52.pdiff [29 B] Get:15 http://deb.debian.org/debian unstable/contrib Sources 2019-01-16-0810.52.pdiff [29 B] Get:16 http://deb.debian.org/debian unstable/non-free amd64 Packages 2019-01-16-0810.52.pdiff [3,222 B] Get:17 http://deb.debian.org/debian-debug unstable-debug/contrib Sources.diff/Index [27.8 kB] Get:18 http://deb.debian.org/debian-debug unstable-debug/main Sources.diff/Index [27.9 kB] Get:19 http://deb.debian.org/debian-debug unstable-debug/main amd64 Packages.diff/Index [27.9 kB] Get:16 http://deb.debian.org/debian unstable/non-free amd64 Packages 2019-01-16-0810.52.pdiff [3,222 B] Get:20 http://deb.debian.org/debian unstable/main amd64 Packages 2019-01-16-0810.52.pdiff [4,593 B] Get:20 http://deb.debian.org/debian unstable/main amd64 Packages 2019-01-16-0810.52.pdiff [4,593 B] Get:21 http://deb.debian.org/debian-debug unstable-debug/contrib Sources 2019-01-16-0810.52.pdiff [29 B] Get:21 http://deb.debian.org/debian-debug unstable-debug/contrib Sources 2019-01-16-0810.52.pdiff [29 B] Get:22 http://deb.debian.org/debian-debug unstable-debug/main Sources 2019-01-16-0810.52.pdiff [4,246 B] Get:22 http://deb.debian.org/debian-debug unstable-debug/main Sources 2019-01-16-0810.52.pdiff [4,246 B] Get:23 http://deb.debian.org/debian-debug unstable-debug/main amd64 Packages 2019-01-16-0810.52.pdiff [18.4 kB] Get:23 http://deb.debian.org/debian-debug unstable-debug/main amd64 Packages 2019-01-16-0810.52.pdiff [18.4 kB] Fetched 936 kB in 3s (302 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debconf 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 145 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 debconf all 1.5.70 [145 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 145 kB in 1s (183 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12153 files and directories currently installed.) Preparing to unpack .../debconf_1.5.70_all.deb ... Unpacking debconf (1.5.70) over (1.5.69) ... Setting up debconf (1.5.70) ... autopkgtest [14:08:49]: testbed dpkg architecture: amd64 autopkgtest [14:08:50]: testbed running kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.110-3+deb9u5 (2018-09-30) autopkgtest [14:08:50]: @@@@@@@@@@@@@@@@@@@@ apt-source paleomix Get:1 http://deb.debian.org/debian unstable/main paleomix 1.2.13.3-1 (dsc) [2,151 B] Get:2 http://deb.debian.org/debian unstable/main paleomix 1.2.13.3-1 (tar) [5,149 kB] Get:3 http://deb.debian.org/debian unstable/main paleomix 1.2.13.3-1 (diff) [11.2 kB] gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/home/debci/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon 17 Dec 2018 12:47:04 PM 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 ./paleomix_1.2.13.3-1.dsc autopkgtest [14:08:51]: testing package paleomix version 1.2.13.3-1 autopkgtest [14:08:51]: build not needed autopkgtest [14:08:51]: test run-unit-test: preparing testbed Reading package lists... Building dependency tree... Reading state information... Correcting dependencies...Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done Done Starting pkgProblemResolver with broken count: 0 Starting 2 pkgProblemResolver with broken count: 0 Done The following additional packages will be installed: adapterremoval adwaita-icon-theme ant ant-optional bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core glib-networking glib-networking-common glib-networking-services gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme java-common libactivation-java libaopalliance-java libapache-pom-java libargs4j-java libasound2 libasound2-data libatinject-jsr330-api-java libatk-bridge2.0-0 libatk1.0-0 libatk1.0-data libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libcairo-gobject2 libcairo2 libcdi-api-java libcodemodel-java libcolord2 libcommons-cli-java libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcroco3 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdconf1 libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdtd-parser-java libepoxy0 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libfabric1 libfastinfoset-java libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgkl-java libgkl-jni libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl23 libgslcblas0 libgtk-3-0 libgtk-3-common libguava-java libguice-java libharfbuzz0b libhts2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu63 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjson-glib-1.0-0 libjson-glib-1.0-common libjsoup-java libjsr305-java liblapack3 liblcms2-2 liblightcouch-java libllvm7 liblog4j2-java libltdl7 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libnghttp2-14 libngs-java libngs-sdk-dev libngs-sdk2 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-base libopenblas-dev libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libpicard-java libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpmix2 libpng16-16 libproxy1v5 libpsl5 libpsm-infinipath1 libpsm2-2 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 librelaxng-datatype-java librest-0.7-0 librngom-java librsvg2-2 librsvg2-common librtmp1 libsisu-guice-java libsisu-inject-java libsisu-ioc-java libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsoup-gnome2.4-1 libsoup2.4-1 libssh2-1 libstax-ex-java libstreambuffer-java libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtxw2-java libwagon-http-java libwagon-provider-api-java libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6 libxtst6 libxxf86vm1 libxz-java littler mafft mapdamage mime-support ocl-icd-libopencl1 openjdk-11-jre openjdk-11-jre-headless openmpi-bin openmpi-common openssl paleomix phylip picard-tools python python-coverage python-flexmock python-minimal python-pkg-resources python-pysam python-setproctitle python2 python2-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-iterators 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-rcppgsl r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr radiant raxml samtools seqtk shared-mime-info unzip x11-common xdg-utils xkb-data zip Suggested packages: ant-doc default-jdk | java-compiler | java-sdk antlr javacc junit junit4 jython libbcel-java libbsf-java libcommons-net-java libmail-java libjaxp1.3-java libjdepend-java libjsch-java liblog4j1.2-java liboro-java libregexp-java libxalan2-java python-numpy python-matplotlib texlive-latex-recommended bowtie2-examples libaopalliance-java-doc libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc libservlet3.1-java colord libcommons-io-java-doc libcommons-jexl2-java-doc libcommons-lang3-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java cups-common libdom4j-java-doc libmsv-java libxpp2-java libxpp3-java libdtd-parser-java-doc libjdom1-java librhino-java libgoogle-gson-java-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html gvfs libasm-java libcglib-java python3 libhwloc-contrib-plugins libxom-java libjoptsimple-java-doc libjsoup-java-doc libjsr305-java-doc liblcms2-utils liblog4j2-java-doc libmaven-file-management-java-doc libmaven-shared-io-java-doc libmaven-shared-utils-java-doc liblogback-java pciutils pcscd libplexus-cipher-java-doc libplexus-classworlds-java-doc libplexus-interpolation-java-doc libplexus-sec-dispatcher-java-doc libplexus-utils2-java-doc librsvg2-bin testng libosgi-compendium-java libosgi-core-java tcl8.6 tk8.6 libxml-commons-resolver1.1-java-doc opencl-icd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic gfortran phylip-doc python-doc python-tk python-coverage-doc python-setuptools python2-doc python2.7-doc binfmt-support 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-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 libgdal-dev r-cran-getopt r-cran-testthat r-cran-doparallel r-cran-dichromat r-cran-htmltools Recommended packages: at-spi2-core libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgtk-3-bin ibverbs-providers libjansi-java publicsuffix libasm-java libcglib-java blast2 libwww-perl lynx ruby file libatk-wrapper-java-jni fonts-dejavu-extra libopenmpi-dev libjs-jquery-isonscreen libjs-jquery-tablesorter libjs-jquery-throttle-debounce libjs-jquery 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-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 libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: adapterremoval adwaita-icon-theme ant ant-optional bcftools bedtools bowtie2 bwa ca-certificates ca-certificates-java dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless examl fontconfig fontconfig-config fonts-dejavu-core glib-networking glib-networking-common glib-networking-services gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme java-common libactivation-java libaopalliance-java libapache-pom-java libargs4j-java libasound2 libasound2-data libatinject-jsr330-api-java libatk-bridge2.0-0 libatk1.0-0 libatk1.0-data libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbarclay-java libblas3 libcairo-gobject2 libcairo2 libcdi-api-java libcodemodel-java libcolord2 libcommons-cli-java libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-math3-java libcommons-parent-java libcroco3 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdconf1 libdom4j-java libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libdtd-parser-java libepoxy0 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6 libfabric1 libfastinfoset-java libfontconfig1 libfreemarker-java libfreetype6 libfribidi0 libgatk-native-bindings-java libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgeronimo-annotation-1.3-spec-java libgeronimo-interceptor-3.0-spec-java libgfortran5 libgif7 libgkl-java libgkl-jni libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgoogle-gson-java libgraphite2-3 libgsl-dev libgsl23 libgslcblas0 libgtk-3-0 libgtk-3-common libguava-java libguice-java libharfbuzz0b libhts2 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu63 libistack-commons-java libjaxb-api-java libjaxb-java libjaxen-java libjbig0 libjoptsimple-java libjpeg62-turbo libjson-glib-1.0-0 libjson-glib-1.0-common libjsoup-java libjsr305-java liblapack3 liblcms2-2 liblightcouch-java libllvm7 liblog4j2-java libltdl7 libmaven-file-management-java libmaven-parent-java libmaven-resolver-java libmaven-shared-io-java libmaven-shared-utils-java libmaven3-core-java libnghttp2-14 libngs-java libngs-sdk-dev libngs-sdk2 libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenblas-base libopenblas-dev libopenmpi3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libpicard-java libpixman-1-0 libplexus-archiver-java libplexus-cipher-java libplexus-classworlds-java libplexus-component-annotations-java libplexus-interpolation-java libplexus-io-java libplexus-sec-dispatcher-java libplexus-utils2-java libpmix2 libpng16-16 libproxy1v5 libpsl5 libpsm-infinipath1 libpsm2-2 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 librelaxng-datatype-java librest-0.7-0 librngom-java librsvg2-2 librsvg2-common librtmp1 libsisu-guice-java libsisu-inject-java libsisu-ioc-java libsisu-plexus-java libslf4j-java libsm6 libsnappy-java libsnappy-jni libsnappy1v5 libsoup-gnome2.4-1 libsoup2.4-1 libssh2-1 libstax-ex-java libstreambuffer-java libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtxw2-java libwagon-http-java libwagon-provider-api-java libwayland-client0 libwayland-cursor0 libwayland-egl1 libwebp6 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml-commons-resolver1.1-java libxml2 libxrandr2 libxrender1 libxshmfence1 libxsom-java libxss1 libxt6 libxtst6 libxxf86vm1 libxz-java littler mafft mapdamage mime-support ocl-icd-libopencl1 openjdk-11-jre openjdk-11-jre-headless openmpi-bin openmpi-common openssl paleomix phylip picard-tools python python-coverage python-flexmock python-minimal python-pkg-resources python-pysam python-setproctitle python2 python2-minimal python2.7 python2.7-minimal r-base-core r-cran-assertthat r-cran-cli r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-foreach r-cran-gam r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-inline r-cran-iterators 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-rcppgsl r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr radiant raxml samtools seqtk shared-mime-info unzip x11-common xdg-utils xkb-data zip 0 upgraded, 325 newly installed, 0 to remove and 0 not upgraded. 1 not fully installed or removed. Need to get 235 MB of archives. After this operation, 921 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.35.1-1+b1 [82.4 kB] Get:2 http://deb.debian.org/debian unstable/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libssh2-1 amd64 1.8.0-2 [138 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libcurl3-gnutls amd64 7.62.0-1 [321 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 libhts2 amd64 1.9-9 [306 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.15-5 [394 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 python2.7-minimal amd64 2.7.15-5 [1,365 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 python2-minimal amd64 2.7.15-3 [41.3 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 python-minimal amd64 2.7.15-3 [20.9 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 mime-support all 3.61 [37.1 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 libpython2.7-stdlib amd64 2.7.15-5 [1,909 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 python2.7 amd64 2.7.15-5 [299 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 libpython2-stdlib amd64 2.7.15-3 [20.7 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 libpython-stdlib amd64 2.7.15-3 [20.7 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 python2 amd64 2.7.15-3 [41.5 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 python amd64 2.7.15-3 [22.7 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 python-pysam amd64 0.15.1+ds-1 [1,660 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 python-setproctitle amd64 1.1.10-1+b2 [15.4 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 adapterremoval amd64 2.2.2-2 [198 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 bedtools amd64 2.27.1+dfsg-2 [587 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libatomic1 amd64 8.2.0-14 [8,884 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 bowtie2 amd64 2.3.4.3-1 [1,188 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 bwa amd64 0.7.17-2 [194 kB] Get:26 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 libfabric1 amd64 1.6.2-2 [396 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.9-1 [527 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 8.2.0-14 [75.7 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 21.0-1 [50.8 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get:36 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get:37 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.68-4 [177 kB] Get:38 http://deb.debian.org/debian unstable/main amd64 librdmacm1 amd64 21.0-1 [65.0 kB] Get:39 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 8.2.0-14 [133 kB] Get:40 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 8.2.0-14 [581 kB] Get:41 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.6-8 [390 kB] Get:42 http://deb.debian.org/debian unstable/main amd64 libhwloc5 amd64 1.11.12-1 [111 kB] Get:43 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get:44 http://deb.debian.org/debian unstable/main amd64 libicu63 amd64 63.1-5 [8,293 kB] Get:45 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b3 [687 kB] Get:46 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get:47 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 1.11.12-1 [17.3 kB] Get:48 http://deb.debian.org/debian unstable/main amd64 libpmix2 amd64 3.1.0~rc4-1 [497 kB] Get:49 http://deb.debian.org/debian unstable/main amd64 libopenmpi3 amd64 3.1.3-9 [2,174 kB] Get:50 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 3.1.3-9 [165 kB] Get:51 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 3.1.3-9 [200 kB] Get:52 http://deb.debian.org/debian unstable/main amd64 examl amd64 3.0.21-2 [922 kB] Get:53 http://deb.debian.org/debian unstable/main amd64 mafft amd64 7.407-2 [999 kB] Get:54 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:55 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-21 [170 kB] Get:56 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.26 [20.8 kB] Get:57 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.26 [17.9 kB] Get:58 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-1 [73.3 kB] Get:59 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:60 http://deb.debian.org/debian unstable/main amd64 libopenblas-base amd64 0.3.5+ds-1 [4,308 kB] Get:61 http://deb.debian.org/debian unstable/main amd64 libpng16-16 amd64 1.6.36-3 [292 kB] Get:62 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.9.1-3 [379 kB] Get:63 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1,068 kB] Get:64 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 r-cran-colorspace amd64 1.4-0+dfsg-1 [1,580 kB] Get:65 http://deb.debian.org/debian unstable/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:66 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:67 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:68 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:69 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:70 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:71 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.6.7-1 [298 kB] Get:72 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB] Get:73 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:74 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:75 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:76 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:77 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.16.0-2 [690 kB] Get:78 http://deb.debian.org/debian unstable/main amd64 libcurl4 amd64 7.62.0-1 [324 kB] Get:79 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0 amd64 2.58.2-3 [1,257 kB] Get:80 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB] Get:81 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:82 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB] Get:83 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.8.0-2 [2,110 kB] Get:84 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:85 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.5-3.1 [63.5 kB] Get:86 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.28-1 [170 kB] Get:87 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.12-1 [39.1 kB] Get:88 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.28-1 [53.9 kB] Get:89 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.42.4-6 [185 kB] Get:90 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:91 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 2.3.0-1 [1,176 kB] Get:92 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.42.4-6 [67.9 kB] Get:93 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.42.4-6 [55.5 kB] Get:94 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:95 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.9+dfsg-1 [1,004 kB] Get:96 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:97 http://deb.debian.org/debian unstable/main amd64 libwebp6 amd64 0.6.1-2 [263 kB] Get:98 http://deb.debian.org/debian unstable/main amd64 libtiff5 amd64 4.0.10-3 [257 kB] Get:99 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:100 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:101 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.9-1 [768 kB] Get:102 http://deb.debian.org/debian unstable/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:103 http://deb.debian.org/debian unstable/main amd64 openssl amd64 1.1.1a-1 [836 kB] Get:104 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20180409 [161 kB] Get:105 http://deb.debian.org/debian unstable/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get:106 http://deb.debian.org/debian unstable/main amd64 r-cran-codetools all 0.2-16-1 [90.1 kB] Get:107 http://deb.debian.org/debian unstable/main amd64 r-cran-iterators all 1.0.10-1 [330 kB] Get:108 http://deb.debian.org/debian unstable/main amd64 r-cran-foreach all 1.4.4-2 [401 kB] Get:109 http://deb.debian.org/debian unstable/main amd64 r-cran-gam amd64 1.16-1 [303 kB] Get:110 http://deb.debian.org/debian unstable/main amd64 r-cran-digest amd64 0.6.18-1 [136 kB] Get:111 http://deb.debian.org/debian unstable/main amd64 r-cran-gtable all 0.2.0-3 [93.6 kB] Get:112 http://deb.debian.org/debian unstable/main amd64 r-cran-lazyeval amd64 0.2.1-3 [138 kB] Get:113 http://deb.debian.org/debian unstable/main amd64 r-cran-mass amd64 7.3-51.1-1 [1,100 kB] Get:114 http://deb.debian.org/debian unstable/main amd64 r-cran-lattice amd64 0.20-38-1 [1,121 kB] Get:115 http://deb.debian.org/debian unstable/main amd64 r-cran-nlme amd64 3.1.137-1+b3 [2,223 kB] Get:116 http://deb.debian.org/debian unstable/main amd64 r-cran-matrix amd64 1.2-15-1 [3,421 kB] Get:117 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.8-26-1 [2,590 kB] Get:118 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.5-1+b1 [305 kB] Get:119 http://deb.debian.org/debian unstable/main amd64 littler all 0.3.5-1 [13.4 kB] Get:120 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgkitten all 0.1.4-2 [22.4 kB] Get:121 http://deb.debian.org/debian unstable/main amd64 r-cran-rcpp amd64 1.0.0-1 [3,381 kB] Get:122 http://deb.debian.org/debian unstable/main amd64 r-cran-plyr amd64 1.8.4-2 [813 kB] Get:123 http://deb.debian.org/debian unstable/main amd64 r-cran-glue amd64 1.3.0-1 [92.0 kB] Get:124 http://deb.debian.org/debian unstable/main amd64 r-cran-magrittr all 1.5-5 [152 kB] Get:125 http://deb.debian.org/debian unstable/main amd64 r-cran-stringi amd64 1.2.4-2 [8,702 kB] Get:126 http://deb.debian.org/debian unstable/main amd64 r-cran-stringr all 1.3.1-2 [179 kB] Get:127 http://deb.debian.org/debian unstable/main amd64 r-cran-reshape2 amd64 1.4.3-2 [114 kB] Get:128 http://deb.debian.org/debian unstable/main amd64 r-cran-rlang amd64 0.3.1-1 [1,082 kB] Get:129 http://deb.debian.org/debian unstable/main amd64 r-cran-labeling all 0.3-3 [61.4 kB] Get:130 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.0-1 [235 kB] Get:131 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.3.0-1 [73.5 kB] Get:132 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB] Get:133 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB] Get:134 http://deb.debian.org/debian unstable/main amd64 r-cran-scales amd64 1.0.0-2 [546 kB] Get:135 http://deb.debian.org/debian unstable/main amd64 r-cran-assertthat all 0.2.0-2 [54.4 kB] Get:136 http://deb.debian.org/debian unstable/main amd64 r-cran-crayon all 1.3.4-4 [750 kB] Get:137 http://deb.debian.org/debian unstable/main amd64 r-cran-cli all 1.0.1-1 [519 kB] Get:138 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 0.4.0-1 [339 kB] Get:139 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB] Get:140 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.3.1-1 [203 kB] Get:141 http://deb.debian.org/debian unstable/main amd64 r-cran-pkgconfig all 2.0.2-1 [19.4 kB] Get:142 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 2.0.0-1 [322 kB] Get:143 http://deb.debian.org/debian unstable/main amd64 r-cran-withr all 2.1.2-3 [152 kB] Get:144 http://deb.debian.org/debian unstable/main amd64 r-cran-ggplot2 all 3.1.0-1 [3,740 kB] Get:145 http://deb.debian.org/debian unstable/main amd64 r-cran-inline all 0.3.15-2 [123 kB] Get:146 http://deb.debian.org/debian unstable/main amd64 seqtk amd64 1.3-1 [30.8 kB] Get:147 http://deb.debian.org/debian unstable/main amd64 libgslcblas0 amd64 2.5+dfsg-6 [101 kB] Get:148 http://deb.debian.org/debian unstable/main amd64 libgsl23 amd64 2.5+dfsg-6 [880 kB] Get:149 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.5+dfsg-6 [1,063 kB] Get:150 http://deb.debian.org/debian unstable/main amd64 r-cran-rcppgsl amd64 0.3.6-1 [416 kB] Get:151 http://deb.debian.org/debian unstable/main amd64 libopenblas-dev amd64 0.3.5+ds-1 [4,392 kB] Get:152 http://deb.debian.org/debian unstable/main amd64 mapdamage all 2.0.9+dfsg-1 [39.6 kB] Get:153 http://deb.debian.org/debian unstable/main amd64 phylip amd64 1:3.697+dfsg-1 [910 kB] Get:154 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get:155 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.41-1 [1,157 kB] Get:156 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20180516 [15.5 kB] Get:157 http://deb.debian.org/debian unstable/main amd64 java-common all 0.71 [14.4 kB] Get:158 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.7-4+b1 [122 kB] Get:159 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.7-4+b1 [54.6 kB] Get:160 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.7-4+b1 [58.1 kB] Get:161 http://deb.debian.org/debian unstable/main amd64 libcups2 amd64 2.2.10-3 [324 kB] Get:162 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:163 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.1.7-2 [56.6 kB] Get:164 http://deb.debian.org/debian unstable/main amd64 libasound2 amd64 1.1.7-2 [362 kB] Get:165 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get:166 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:167 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:168 http://deb.debian.org/debian unstable/main amd64 openjdk-11-jre-headless amd64 11.0.1+13-3 [36.9 MB] Get:169 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get:170 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:171 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 1.10-1 [766 kB] Get:172 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.38.0+dfsg-7 [315 kB] Get:173 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-0 amd64 2.38.0+dfsg-7 [177 kB] Get:174 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.3-1 [81.6 kB] Get:175 http://deb.debian.org/debian unstable/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:176 http://deb.debian.org/debian unstable/main amd64 librsvg2-2 amd64 2.44.10-1 [1,270 kB] Get:177 http://deb.debian.org/debian unstable/main amd64 librsvg2-common amd64 2.44.10-1 [23.1 kB] Get:178 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 3.30.1-1 [11.7 MB] Get:179 http://deb.debian.org/debian unstable/main amd64 libatk1.0-data all 2.30.0-2 [145 kB] Get:180 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0 amd64 2.30.0-2 [50.6 kB] Get:181 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0 amd64 2.30.0-5 [65.1 kB] Get:182 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0 amd64 2.30.0-2 [61.5 kB] Get:183 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.16.0-2 [124 kB] Get:184 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.3-3+b1 [140 kB] Get:185 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.3-0.1 [190 kB] Get:186 http://deb.debian.org/debian unstable/main amd64 libjson-glib-1.0-common all 1.4.4-2 [52.3 kB] Get:187 http://deb.debian.org/debian unstable/main amd64 libjson-glib-1.0-0 amd64 1.4.4-2 [61.2 kB] Get:188 http://deb.debian.org/debian unstable/main amd64 libproxy1v5 amd64 0.4.15-5 [58.1 kB] Get:189 http://deb.debian.org/debian unstable/main amd64 glib-networking-common all 2.58.0-2 [59.3 kB] Get:190 http://deb.debian.org/debian unstable/main amd64 glib-networking-services amd64 2.58.0-2 [13.5 kB] Get:191 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.30.1-2 [40.7 kB] Get:192 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.12.12-1 [92.1 kB] Get:193 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.30.1-2 [36.4 kB] Get:194 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.30.1-2 [28.9 kB] Get:195 http://deb.debian.org/debian unstable/main amd64 gsettings-desktop-schemas all 3.28.1-1 [529 kB] Get:196 http://deb.debian.org/debian unstable/main amd64 glib-networking amd64 2.58.0-2 [54.4 kB] Get:197 http://deb.debian.org/debian unstable/main amd64 libsoup2.4-1 amd64 2.64.2-2 [253 kB] Get:198 http://deb.debian.org/debian unstable/main amd64 libsoup-gnome2.4-1 amd64 2.64.2-2 [18.0 kB] Get:199 http://deb.debian.org/debian unstable/main amd64 librest-0.7-0 amd64 0.8.1-1 [33.7 kB] Get:200 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.16.0-1 [26.4 kB] Get:201 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.16.0-1 [14.1 kB] Get:202 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.16.0-1 [8,204 B] Get:203 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.4-2 [16.5 kB] Get:204 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:205 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.1.15-2 [36.6 kB] Get:206 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.4-3 [14.4 kB] Get:207 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-1 [16.6 kB] Get:208 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.23.1-1 [675 kB] Get:209 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 0.8.2-1 [123 kB] Get:210 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.1-1 [37.5 kB] Get:211 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.3-1 [3,682 kB] Get:212 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0 amd64 3.24.3-1 [2,591 kB] Get:213 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.1.0-1 [48.6 kB] Get:214 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.95-1 [13.7 kB] Get:215 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.95-1 [39.5 kB] Get:216 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 18.2.8-2 [64.6 kB] Get:217 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.6.7-1 [190 kB] Get:218 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB] Get:219 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB] Get:220 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB] Get:221 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB] Get:222 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB] Get:223 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.13.1-2 [103 kB] Get:224 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1 [8,820 B] Get:225 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:226 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.95-1 [27.1 kB] Get:227 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.95-1 [69.7 kB] Get:228 http://deb.debian.org/debian unstable/main amd64 libdrm-nouveau2 amd64 2.4.95-1 [26.3 kB] Get:229 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.95-1 [31.1 kB] Get:230 http://deb.debian.org/debian unstable/main amd64 libllvm7 amd64 1:7.0.1-4 [13.0 MB] Get:231 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 18.2.8-2 [6,626 kB] Get:232 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 18.2.8-2 [177 kB] Get:233 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB] Get:234 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB] Get:235 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-glx amd64 18.2.8-2 [46.1 kB] Get:236 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.1.4-3 [43.3 kB] Get:237 http://deb.debian.org/debian unstable/main amd64 openjdk-11-jre amd64 11.0.1+13-3 [34.3 kB] Get:238 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.11-71 [1,044 B] Get:239 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5,312 B] Get:240 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-10 [26.5 kB] Get:241 http://deb.debian.org/debian unstable/main amd64 libguava-java all 19.0-1 [2,028 kB] Get:242 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 18-1 [4,676 B] Get:243 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:244 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.18-1 [532 kB] Get:245 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB] Get:246 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-4 [257 kB] Get:247 http://deb.debian.org/debian unstable/main amd64 ant all 1.10.5-2 [2,082 kB] Get:248 http://deb.debian.org/debian unstable/main amd64 ant-optional all 1.10.5-2 [379 kB] Get:249 http://deb.debian.org/debian unstable/main amd64 libactivation-java all 1.2.0-2 [84.7 kB] Get:250 http://deb.debian.org/debian unstable/main amd64 libargs4j-java all 2.33-1 [139 kB] Get:251 http://deb.debian.org/debian unstable/main amd64 libjaxen-java all 1.1.6-4 [214 kB] Get:252 http://deb.debian.org/debian unstable/main amd64 libdom4j-java all 2.1.1-2 [310 kB] Get:253 http://deb.debian.org/debian unstable/main amd64 libcommons-io-java all 2.6-2 [213 kB] Get:254 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-utils-java all 3.3.0-1 [149 kB] Get:255 http://deb.debian.org/debian unstable/main amd64 libcommons-cli-java all 1.4-1 [55.2 kB] Get:256 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.8-2 [478 kB] Get:257 http://deb.debian.org/debian unstable/main amd64 libgeronimo-annotation-1.3-spec-java all 1.0-1 [10.6 kB] Get:258 http://deb.debian.org/debian unstable/main amd64 libaopalliance-java all 20070526-6 [9,048 B] Get:259 http://deb.debian.org/debian unstable/main amd64 libguice-java all 4.2.1-1 [962 kB] Get:260 http://deb.debian.org/debian unstable/main amd64 libmaven-parent-java all 31-2 [5,100 B] Get:261 http://deb.debian.org/debian unstable/main amd64 libplexus-utils2-java all 3.1.1-1 [249 kB] Get:262 http://deb.debian.org/debian unstable/main amd64 libwagon-provider-api-java all 3.3.1-1 [50.0 kB] Get:263 http://deb.debian.org/debian unstable/main amd64 libmaven-resolver-java all 1.3.1-1 [549 kB] Get:264 http://deb.debian.org/debian unstable/main amd64 libplexus-cipher-java all 1.7-3 [15.0 kB] Get:265 http://deb.debian.org/debian unstable/main amd64 libplexus-classworlds-java all 2.6.0-1 [49.4 kB] Get:266 http://deb.debian.org/debian unstable/main amd64 libplexus-component-annotations-java all 1.7.1-7 [7,536 B] Get:267 http://deb.debian.org/debian unstable/main amd64 libplexus-interpolation-java all 1.25-1 [76.8 kB] Get:268 http://deb.debian.org/debian unstable/main amd64 libplexus-sec-dispatcher-java all 1.4-4 [28.1 kB] Get:269 http://deb.debian.org/debian unstable/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8,484 B] Get:270 http://deb.debian.org/debian unstable/main amd64 libcdi-api-java all 1.2-2 [54.5 kB] Get:271 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.25-3 [143 kB] Get:272 http://deb.debian.org/debian unstable/main amd64 libsisu-inject-java all 0.3.2-3 [345 kB] Get:273 http://deb.debian.org/debian unstable/main amd64 libsisu-plexus-java all 0.3.3-3 [182 kB] Get:274 http://deb.debian.org/debian unstable/main amd64 libmaven3-core-java all 3.6.0-1 [1,465 kB] Get:275 http://deb.debian.org/debian unstable/main amd64 libmaven-shared-io-java all 3.0.0-3 [33.3 kB] Get:276 http://deb.debian.org/debian unstable/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB] Get:277 http://deb.debian.org/debian unstable/main amd64 libplexus-io-java all 3.1.1-1 [64.6 kB] Get:278 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.1.7-1 [17.0 kB] Get:279 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.7.2-1 [7,148 B] Get:280 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.7.2-1 [73.7 kB] Get:281 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.8-2 [141 kB] Get:282 http://deb.debian.org/debian unstable/main amd64 libplexus-archiver-java all 3.6.0-2 [171 kB] Get:283 http://deb.debian.org/debian unstable/main amd64 libsisu-guice-java all 4.2.0-1 [785 kB] Get:284 http://deb.debian.org/debian unstable/main amd64 libsisu-ioc-java all 2.3.0-11 [492 kB] Get:285 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.10-1 [624 kB] Get:286 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.11-1 [271 kB] Get:287 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.6-2 [720 kB] Get:288 http://deb.debian.org/debian unstable/main amd64 libjsoup-java all 1.10.2-2 [350 kB] Get:289 http://deb.debian.org/debian unstable/main amd64 libwagon-http-java all 3.3.1-1 [50.4 kB] Get:290 http://deb.debian.org/debian unstable/main amd64 libistack-commons-java all 3.0.6-3 [144 kB] Get:291 http://deb.debian.org/debian unstable/main amd64 libcodemodel-java all 2.6+jaxb2.3.0.1-7 [163 kB] Get:292 http://deb.debian.org/debian unstable/main amd64 librelaxng-datatype-java all 1.0+ds1-3 [11.7 kB] Get:293 http://deb.debian.org/debian unstable/main amd64 librngom-java all 2.3.0.1-7 [288 kB] Get:294 http://deb.debian.org/debian unstable/main amd64 libxsom-java all 2.3.0.1-7 [396 kB] Get:295 http://deb.debian.org/debian unstable/main amd64 libtxw2-java all 2.3.0.1-7 [133 kB] Get:296 http://deb.debian.org/debian unstable/main amd64 libxml-commons-resolver1.1-java all 1.2-9 [91.6 kB] Get:297 http://deb.debian.org/debian unstable/main amd64 libdtd-parser-java all 1.2~svn20110404-1 [62.5 kB] Get:298 http://deb.debian.org/debian unstable/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB] Get:299 http://deb.debian.org/debian unstable/main amd64 libstax-ex-java all 1.7.8-3 [40.9 kB] Get:300 http://deb.debian.org/debian unstable/main amd64 libstreambuffer-java all 1.5.4-1 [71.8 kB] Get:301 http://deb.debian.org/debian unstable/main amd64 libfastinfoset-java all 1.2.12-3 [343 kB] Get:302 http://deb.debian.org/debian unstable/main amd64 libjaxb-java all 2.3.0.1-7 [1,966 kB] Get:303 http://deb.debian.org/debian unstable/main amd64 libngs-sdk2 amd64 2.9.3-1 [62.7 kB] Get:304 http://deb.debian.org/debian unstable/main amd64 libngs-sdk-dev amd64 2.9.3-1 [111 kB] Get:305 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 2.9.3-1 [79.9 kB] Get:306 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 2.16.1+dfsg-3 [1,494 kB] Get:307 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.23-9 [1,228 kB] Get:308 http://deb.debian.org/debian unstable/main amd64 libjoptsimple-java all 5.0.4-3 [73.0 kB] Get:309 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.8.5-2 [225 kB] Get:310 http://deb.debian.org/debian unstable/main amd64 liblightcouch-java all 0.0.6-1 [63.7 kB] Get:311 http://deb.debian.org/debian unstable/main amd64 liblog4j2-java all 2.11.1-2 [1,721 kB] Get:312 http://deb.debian.org/debian unstable/main amd64 libbarclay-java all 2.1.0-2 [116 kB] Get:313 http://deb.debian.org/debian unstable/main amd64 libgkl-jni amd64 0.8.5+dfsg-1 [190 kB] Get:314 http://deb.debian.org/debian unstable/main amd64 libgkl-java all 0.8.5+dfsg-1 [1,144 kB] Get:315 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-3 [2,018 kB] Get:316 http://deb.debian.org/debian unstable/main amd64 libgatk-native-bindings-java all 1.0.0-2 [7,140 B] Get:317 http://deb.debian.org/debian unstable/main amd64 libpicard-java all 2.18.23+dfsg-1 [1,417 kB] Get:318 http://deb.debian.org/debian unstable/main amd64 picard-tools all 2.18.23+dfsg-1 [311 kB] Get:319 http://deb.debian.org/debian unstable/main amd64 radiant all 2.7+dfsg-2 [159 kB] Get:320 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.12+dfsg-1 [1,275 kB] Get:321 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.9-2 [424 kB] Get:322 http://deb.debian.org/debian unstable/main amd64 python-pkg-resources all 40.6.2-1 [181 kB] Get:323 http://deb.debian.org/debian unstable/main amd64 python-coverage amd64 4.5.1+dfsg.1-1 [143 kB] Get:324 http://deb.debian.org/debian unstable/main amd64 python-flexmock all 0.10.2-2 [18.9 kB] Get:325 http://deb.debian.org/debian unstable/main amd64 paleomix amd64 1.2.13.3-1 [4,679 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 235 MB in 6s (37.5 MB/s) Selecting previously unselected package libnghttp2-14:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12153 files and directories currently installed.) Preparing to unpack .../00-libnghttp2-14_1.35.1-1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.35.1-1+b1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../01-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. 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Selecting previously unselected package libpython-stdlib:amd64. Preparing to unpack .../14-libpython-stdlib_2.7.15-3_amd64.deb ... Unpacking libpython-stdlib:amd64 (2.7.15-3) ... Setting up libpython2.7-minimal:amd64 (2.7.15-5) ... Setting up python2.7-minimal (2.7.15-5) ... Setting up python2-minimal (2.7.15-3) ... Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12980 files and directories currently installed.) Preparing to unpack .../python2_2.7.15-3_amd64.deb ... Unpacking python2 (2.7.15-3) ... Setting up python-minimal (2.7.15-3) ... Selecting previously unselected package python. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13013 files and directories currently installed.) Preparing to unpack .../000-python_2.7.15-3_amd64.deb ... Unpacking python (2.7.15-3) ... Selecting previously unselected package python-pysam. 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Setting up libmaven-resolver-java (1.3.1-1) ... Setting up libepoxy0:amd64 (1.5.3-0.1) ... Setting up libatk1.0-0:amd64 (2.30.0-2) ... Setting up libjaxen-java (1.1.6-4) ... Setting up libsnappy1v5:amd64 (1.1.7-1) ... Processing triggers for systemd (240-4) ... Setting up libltdl7:amd64 (2.4.6-8) ... Setting up libapache-pom-java (18-1) ... Setting up openssl (1.1.1a-1) ... Setting up libdconf1:amd64 (0.30.1-2) ... Setting up libfribidi0:amd64 (1.0.5-3.1) ... Setting up libpciaccess0:amd64 (0.14-1) ... Setting up shared-mime-info (1.10-1) ... Setting up libxkbcommon0:amd64 (0.8.2-1) ... Setting up libatinject-jsr330-api-java (1.0+ds1-5) ... Setting up libmaven-parent-java (31-2) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-1) ... Setting up libcolord2:amd64 (1.4.3-3+b1) ... Setting up libthai-data (0.1.28-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up ocl-icd-libopencl1:amd64 (2.2.12-2) ... Setting up libgoogle-gson-java (2.8.5-2) ... Setting up libnl-3-200:amd64 (3.4.0-1) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Setting up libgslcblas0:amd64 (2.5+dfsg-6) ... Setting up xdg-utils (1.1.3-1) ... Setting up ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 133 added, 0 removed; done. Setting up hicolor-icon-theme (0.17-2) ... Setting up libgfortran5:amd64 (8.2.0-14) ... Setting up libaopalliance-java (20070526-6) ... Setting up libwayland-cursor0:amd64 (1.16.0-1) ... Setting up libgeronimo-annotation-1.3-spec-java (1.0-1) ... Setting up libwayland-egl1:amd64 (1.16.0-1) ... Setting up libx11-data (2:1.6.7-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.15-5) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libgkl-jni (0.8.5+dfsg-1) ... Setting up librelaxng-datatype-java (1.0+ds1-3) ... Setting up libcommons-cli-java (1.4-1) ... Setting up libngs-java (2.9.3-1) ... Setting up libavahi-common-data:amd64 (0.7-4+b1) ... Setting up libplexus-sec-dispatcher-java (1.4-4) ... Setting up libwebp6:amd64 (0.6.1-2) ... Setting up libopenblas-base:amd64 (0.3.5+ds-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libdom4j-java (2.1.1-2) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libpsm2-2 (11.2.68-4) ... Setting up libgsl23:amd64 (2.5+dfsg-6) ... Setting up dconf-service (0.30.1-2) ... Setting up libgsl-dev (2.5+dfsg-6) ... Setting up libcurl3-gnutls:amd64 (7.62.0-1) ... Setting up libsnappy-jni (1.1.7.2-1) ... Setting up liblapack3:amd64 (3.8.0-2) ... Setting up libjaxb-api-java (2.3.1-1) ... Setting up libcurl4:amd64 (7.62.0-1) ... Setting up libxsom-java (2.3.0.1-7) ... Setting up libstax-ex-java (1.7.8-3) ... Setting up python2.7 (2.7.15-5) ... Setting up libguava-java (19.0-1) ... Setting up libnss3:amd64 (2:3.41-1) ... Setting up libharfbuzz0b:amd64 (2.3.0-1) ... Setting up libtiff5:amd64 (4.0.10-3) ... Setting up libnl-route-3-200:amd64 (3.4.0-1) ... Setting up libthai0:amd64 (0.1.28-1) ... Setting up libhwloc5:amd64 (1.11.12-1) ... Setting up libdrm2:amd64 (2.4.95-1) ... Setting up libgkl-java (0.8.5+dfsg-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libhwloc-plugins:amd64 (1.11.12-1) ... Setting up libcdi-api-java (1.2-2) ... Setting up libdrm-intel1:amd64 (2.4.95-1) ... Setting up libblas3:amd64 (3.8.0-2) ... Setting up libcommons-compress-java (1.18-1) ... Setting up libcommons-lang3-java (3.8-2) ... Setting up libsnappy-java (1.1.7.2-1) ... Setting up librngom-java (2.3.0.1-7) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libstreambuffer-java (1.5.4-1) ... Setting up libpython2-stdlib:amd64 (2.7.15-3) ... Setting up libsisu-guice-java (4.2.0-1) ... Setting up libavahi-common3:amd64 (0.7-4+b1) ... Setting up libdrm-radeon1:amd64 (2.4.95-1) ... Setting up libdrm-nouveau2:amd64 (2.4.95-1) ... Setting up libopenblas-dev:amd64 (0.3.5+ds-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libcommons-codec-java (1.11-1) ... Setting up libsisu-ioc-java (2.3.0-11) ... Setting up dconf-gsettings-backend:amd64 (0.30.1-2) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libhts2:amd64 (1.9-9) ... Setting up libibverbs1:amd64 (21.0-1) ... Setting up libxcb-present0:amd64 (1.13.1-2) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up libxcb-dri2-0:amd64 (1.13.1-2) ... Setting up libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libxcb-dri3-0:amd64 (1.13.1-2) ... Setting up libxcb-glx0:amd64 (1.13.1-2) ... Setting up libcommons-io-java (2.6-2) ... Setting up libxcb-xfixes0:amd64 (1.13.1-2) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up gsettings-desktop-schemas (3.28.1-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.95-1) ... Setting up libgtk-3-common (3.24.3-1) ... Setting up libguice-java (4.2.1-1) ... Setting up libx11-6:amd64 (2:1.6.7-1) ... Setting up libgl1-mesa-dri:amd64 (18.2.8-2) ... Setting up libcommons-logging-java (1.2-2) ... Setting up libpmix2:amd64 (3.1.0~rc4-1) ... Setting up librdmacm1:amd64 (21.0-1) ... Setting up libmaven-shared-utils-java (3.3.0-1) ... Setting up libfastinfoset-java (1.2.12-3) ... Setting up python2 (2.7.15-3) ... Setting up libxcb-sync1:amd64 (1.13.1-2) ... Setting up libpython-stdlib:amd64 (2.7.15-3) ... Setting up libsisu-inject-java (0.3.2-3) ... Setting up glib-networking:amd64 (2.58.0-2) ... Setting up libhttpclient-java (4.5.6-2) ... Setting up libxcomposite1:amd64 (1:0.4.4-2) ... Setting up libcommons-jexl2-java (2.1.1-4) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libavahi-client3:amd64 (0.7-4+b1) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up samtools (1.9-2) ... Setting up bcftools (1.9-1) ... Setting up python (2.7.15-3) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up python-setproctitle:amd64 (1.1.10-1+b2) ... Setting up libcups2:amd64 (2.2.10-3) ... Setting up python-flexmock (0.10.2-2) ... Setting up liblightcouch-java (0.0.6-1) ... Setting up libplexus-io-java (3.1.1-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libfabric1 (1.6.2-2) ... Setting up libsisu-plexus-java (0.3.3-3) ... Setting up libatspi2.0-0:amd64 (2.30.0-5) ... Setting up python-pysam (0.15.1+ds-1) ... Setting up libwagon-http-java (3.3.1-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.38.0+dfsg-7) ... Setting up libsoup2.4-1:amd64 (2.64.2-2) ... Setting up libsoup-gnome2.4-1:amd64 (2.64.2-2) ... Setting up python-pkg-resources (40.6.2-1) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up python-coverage (4.5.1+dfsg.1-1) ... Setting up gtk-update-icon-cache (3.24.3-1) ... Setting up libxcursor1:amd64 (1:1.1.15-2) ... Setting up libplexus-archiver-java (3.6.0-2) ... Setting up libpango-1.0-0:amd64 (1.42.4-6) ... Setting up libatk-bridge2.0-0:amd64 (2.30.0-2) ... Setting up liblog4j2-java (2.11.1-2) ... Setting up librest-0.7-0:amd64 (0.8.1-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libbarclay-java (2.1.0-2) ... Setting up libxrandr2:amd64 (2:1.5.1-1) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libcairo2:amd64 (1.16.0-2) ... Setting up libxinerama1:amd64 (2:1.1.4-1) ... Setting up libopenmpi3:amd64 (3.1.3-9) ... Setting up libxdamage1:amd64 (1:1.1.4-3) ... Setting up libmaven3-core-java (3.6.0-1) ... Setting up libmaven-shared-io-java (3.0.0-3) ... Setting up libtk8.6:amd64 (8.6.9-1) ... Setting up libcairo-gobject2:amd64 (1.16.0-2) ... Setting up openmpi-bin (3.1.3-9) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-6) ... Setting up libglx-mesa0:amd64 (18.2.8-2) ... Setting up libmaven-file-management-java (3.0.0-1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-6) ... Setting up examl (3.0.21-2) ... Setting up libglx0:amd64 (1.1.0-1) ... Setting up librsvg2-2:amd64 (2.44.10-1) ... Setting up r-base-core (3.5.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-withr (2.1.2-3) ... Setting up r-cran-littler (0.3.5-1+b1) ... Setting up littler (0.3.5-1) ... Setting up r-cran-fansi (0.4.0-1) ... Setting up r-cran-crayon (1.3.4-4) ... Setting up r-cran-gtable (0.2.0-3) ... Setting up librsvg2-common:amd64 (2.44.10-1) ... Setting up r-cran-assertthat (0.2.0-2) ... Setting up r-cran-rcolorbrewer (1.1-2-2) ... Setting up r-cran-stringi (1.2.4-2) ... Setting up r-cran-pkgkitten (0.1.4-2) ... Setting up r-cran-rcpp (1.0.0-1) ... Setting up r-cran-labeling (0.3-3) ... Setting up libgl1:amd64 (1.1.0-1) ... Setting up r-cran-r6 (2.3.0-1) ... Setting up r-cran-colorspace (1.4-0+dfsg-1) ... Setting up r-cran-utf8 (1.1.4-1+b1) ... Setting up r-cran-inline (0.3.15-2) ... Setting up r-cran-mass (7.3-51.1-1) ... Setting up r-cran-plyr (1.8.4-2) ... Setting up r-cran-rlang (0.3.1-1) ... Setting up r-cran-digest (0.6.18-1) ... Setting up r-cran-cli (1.0.1-1) ... Setting up r-cran-magrittr (1.5-5) ... Setting up r-cran-pkgconfig (2.0.2-1) ... Setting up r-cran-glue (1.3.0-1) ... Setting up adwaita-icon-theme (3.30.1-1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up r-cran-codetools (0.2-16-1) ... Setting up r-cran-rcppgsl (0.3.6-1) ... Setting up r-cran-viridislite (0.3.0-3) ... Setting up r-cran-iterators (1.0.10-1) ... Setting up r-cran-lattice (0.20-38-1) ... Setting up r-cran-lazyeval (0.2.1-3) ... Setting up r-cran-nlme (3.1.137-1+b3) ... Setting up r-cran-stringr (1.3.1-2) ... Setting up libgtk-3-0:amd64 (3.24.3-1) ... Setting up r-cran-foreach (1.4.4-2) ... Setting up r-cran-gam (1.16-1) ... Setting up libgl1-mesa-glx:amd64 (18.2.8-2) ... Setting up r-cran-munsell (0.5.0-1) ... Setting up r-cran-pillar (1.3.1-1) ... Setting up r-cran-reshape2 (1.4.3-2) ... Setting up r-cran-scales (1.0.0-2) ... Setting up r-cran-tibble (2.0.0-1) ... Setting up r-cran-matrix (1.2-15-1) ... Setting up r-cran-mgcv (1.8-26-1) ... Setting up r-cran-ggplot2 (3.1.0-1) ... Setting up mapdamage (2.0.9+dfsg-1) ... Setting up openjdk-11-jre-headless:amd64 (11.0.1+13-3) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ant (1.10.5-2) ... Setting up default-jre-headless (2:1.11-71) ... Setting up openjdk-11-jre:amd64 (11.0.1+13-3) ... Setting up ca-certificates-java (20180516) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:OpenTrust_Root_CA_G2.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:Certigna.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:Certinomis_-_Root_CA.pem Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:Visa_eCommerce_Root.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:ISRG_Root_X1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:TrustCor_ECA-1.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:Deutsche_Telekom_Root_CA_2.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:AffirmTrust_Networking.pem Adding debian:ACCVRAIZ1.pem Adding debian:AffirmTrust_Premium.pem Adding debian:OpenTrust_Root_CA_G3.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:DST_Root_CA_X3.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Certplus_Root_CA_G1.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:EC-ACC.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:SecureTrust_CA.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Certplus_Root_CA_G2.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Taiwan_GRCA.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:TÜRKTRUST_Elektronik_Sertifika_Hizmet_Sağlayıcısı_H5.pem Adding debian:OpenTrust_Root_CA_G1.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Certplus_Class_2_Primary_CA.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:Izenpe.com.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:AddTrust_External_Root.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem done. Setting up default-jre (2:1.11-71) ... Setting up ant-optional (1.10.5-2) ... Setting up libistack-commons-java (3.0.6-3) ... Setting up libcodemodel-java (2.6+jaxb2.3.0.1-7) ... Setting up libtxw2-java (2.3.0.1-7) ... Setting up libjaxb-java (2.3.0.1-7) ... Setting up libhtsjdk-java (2.16.1+dfsg-3) ... Setting up libpicard-java (2.18.23+dfsg-1) ... Setting up picard-tools (2.18.23+dfsg-1) ... Setting up paleomix (1.2.13.3-1) ... Setting up autopkgtest-satdep (0) ... Processing triggers for libc-bin (2.28-5) ... Processing triggers for systemd (240-4) ... Processing triggers for ca-certificates (20180409) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.38.0+dfsg-7) ... (Reading database ... 32733 files and directories currently installed.) Removing autopkgtest-satdep (0) ... autopkgtest [14:09:49]: test run-unit-test: [----------------------- ./tests/data/fasta_file.fasta.gz /tmp/autopkgtest-lxc.cq6ype19/downtmp/build.WWG/src/debian/tests/run-unit-test: line 25: nosetests: command not found autopkgtest [14:09:49]: test run-unit-test: -----------------------] autopkgtest [14:09:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-test FAIL non-zero exit status 127 autopkgtest [14:09:49]: @@@@@@@@@@@@@@@@@@@@ summary run-unit-test FAIL non-zero exit status 127