autopkgtest [07:34:20]: version 5.6
autopkgtest [07:34:20]: host ci-worker02; command line: /usr/bin/autopkgtest --no-built-binaries --user debci --apt-upgrade --output-dir /tmp/tmp.r6ltnYoamu/autopkgtest-incoming/unstable/amd64/p/paleomix/1266744 paleomix -- lxc --sudo --name ci-1541403260 autopkgtest-unstable-amd64
autopkgtest [07:34:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup
Hit:1 http://deb.debian.org/debian unstable InRelease
Hit:2 http://deb.debian.org/debian-debug unstable-debug InRelease
Get:3 http://incoming.debian.org/debian-buildd buildd-unstable InRelease [55.3 kB]
Get:4 http://incoming.debian.org/debian-buildd buildd-unstable/main Sources [287 kB]
Get:5 http://incoming.debian.org/debian-buildd buildd-unstable/contrib Sources [2,348 B]
Get:6 http://incoming.debian.org/debian-buildd buildd-unstable/contrib amd64 Packages [2,664 B]
Get:7 http://incoming.debian.org/debian-buildd buildd-unstable/main amd64 Packages [117 kB]
Fetched 464 kB in 1s (339 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
autopkgtest [07:34:38]: testbed dpkg architecture: amd64
autopkgtest [07:34:39]: testbed running kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.110-3+deb9u6 (2018-10-08)
autopkgtest [07:34:39]: @@@@@@@@@@@@@@@@@@@@ apt-source paleomix
Get:1 http://deb.debian.org/debian unstable/main paleomix 1.2.13.2-1 (dsc) [2,175 B]
Get:2 http://deb.debian.org/debian unstable/main paleomix 1.2.13.2-1 (tar) [5,149 kB]
Get:3 http://deb.debian.org/debian unstable/main paleomix 1.2.13.2-1 (diff) [10.9 kB]
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/home/debci/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu 03 May 2018 11:25:32 AM 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_1.2.13.2-1.dsc
autopkgtest [07:34:41]: testing package paleomix version 1.2.13.2-1
autopkgtest [07:34:41]: build not needed
autopkgtest [07:34:41]: 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 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 libapache-pom-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 libcolord2 libcommons-codec-java
  libcommons-compress-java libcommons-jexl2-java libcommons-lang3-java
  libcommons-logging-java libcommons-math3-java libcommons-parent-java
  libcroco3 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdconf1
  libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
  libdrm2 libepoxy0 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
  libfabric1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0
  libgatk-native-bindings-java libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common
  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 libharfbuzz0b libhts2
  libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins
  libhwloc5 libibverbs1 libice6 libicu-le-hb0 libicu60 libjbig0
  libjoptsimple-java libjpeg62-turbo libjs-jquery libjs-sphinxdoc
  libjs-underscore libjson-glib-1.0-0 libjson-glib-1.0-common libjsr305-java
  liblapack3 liblcms2-2 liblightcouch-java libllvm6.0 liblog4j2-java libltdl7
  libmongodb-java libmpdec2 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 libpmix2 libpng16-16 libproxy1v5
  libpsl5 libpsm-infinipath1 libpsm2-2 libpython-stdlib libpython2-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.6-stdlib libquadmath0 librdmacm1 librest-0.7-0 librsvg2-2
  librsvg2-common librtmp1 libsensors4 libslf4j-java libsm6 libsnappy-java
  libsnappy-jni libsnappy1v5 libsoup-gnome2.4-1 libsoup2.4-1 libssh2-1 libtbb2
  libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 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 libxml2 libxrandr2 libxrender1
  libxshmfence1 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-pip-whl python-pkg-resources python-pysam python-setproctitle python2
  python2-minimal python2.7 python2.7-minimal python3 python3-distutils
  python3-lib2to3 python3-pkg-resources python3-pluggy python3-py
  python3-setuptools python3-virtualenv python3.6 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-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 tox unzip virtualenv x11-common xdg-utils xkb-data zip
Suggested packages:
  python-numpy python-matplotlib texlive-latex-recommended bowtie2-examples
  libasound2-plugins alsa-utils libatinject-jsr330-api-java-doc colord
  libcommons-jexl2-java-doc libcommons-lang3-java-doc libavalon-framework-java
  libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java
  cups-common jython libdom4j-java libjaxen-java libjdom1-java librhino-java
  libxalan2-java libgoogle-gson-java-doc gsl-ref-psdoc | gsl-doc-pdf
  | gsl-doc-info | gsl-ref-html gvfs libhwloc-contrib-plugins
  libjoptsimple-java-doc libjsr305-java-doc liblcms2-utils liblog4j2-java-doc
  pciutils pcscd librsvg2-bin lm-sensors tcl8.6 tk8.6 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 python3-doc python3-tk python3-venv subversion
  python3-pytest python-setuptools-doc python3.6-venv python3.6-doc 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-dichromat
  r-cran-shiny r-cran-shinyjs r-cran-rstudioapi r-cran-knitr r-cran-rmarkdown
  r-cran-dplyr 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-doparallel
Recommended packages:
  at-spi2-core libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgtk-3-bin
  ibverbs-providers javascript-common publicsuffix 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 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 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 libapache-pom-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 libcolord2 libcommons-codec-java
  libcommons-compress-java libcommons-jexl2-java libcommons-lang3-java
  libcommons-logging-java libcommons-math3-java libcommons-parent-java
  libcroco3 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdconf1
  libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1
  libdrm2 libepoxy0 libevent-2.1-6 libevent-core-2.1-6 libevent-pthreads-2.1-6
  libfabric1 libfontconfig1 libfreemarker-java libfreetype6 libfribidi0
  libgatk-native-bindings-java libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common
  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 libharfbuzz0b libhts2
  libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins
  libhwloc5 libibverbs1 libice6 libicu-le-hb0 libicu60 libjbig0
  libjoptsimple-java libjpeg62-turbo libjs-jquery libjs-sphinxdoc
  libjs-underscore libjson-glib-1.0-0 libjson-glib-1.0-common libjsr305-java
  liblapack3 liblcms2-2 liblightcouch-java libllvm6.0 liblog4j2-java libltdl7
  libmongodb-java libmpdec2 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 libpmix2 libpng16-16 libproxy1v5
  libpsl5 libpsm-infinipath1 libpsm2-2 libpython-stdlib libpython2-stdlib
  libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
  libpython3.6-stdlib libquadmath0 librdmacm1 librest-0.7-0 librsvg2-2
  librsvg2-common librtmp1 libsensors4 libslf4j-java libsm6 libsnappy-java
  libsnappy-jni libsnappy1v5 libsoup-gnome2.4-1 libsoup2.4-1 libssh2-1 libtbb2
  libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 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 libxml2 libxrandr2 libxrender1
  libxshmfence1 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-pip-whl python-pkg-resources python-pysam python-setproctitle python2
  python2-minimal python2.7 python2.7-minimal python3 python3-distutils
  python3-lib2to3 python3-pkg-resources python3-pluggy python3-py
  python3-setuptools python3-virtualenv python3.6 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-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 tox unzip virtualenv x11-common xdg-utils xkb-data zip
0 upgraded, 298 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
Need to get 219 MB of archives.
After this operation, 883 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.34.0-1 [84.9 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 1.9-3 [320 kB]
Get:7 http://deb.debian.org/debian unstable/main amd64 libpython2.7-minimal amd64 2.7.15-4 [394 kB]
Get:8 http://deb.debian.org/debian unstable/main amd64 python2.7-minimal amd64 2.7.15-4 [1,361 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 2.7.15-4 [1,907 kB]
Get:13 http://deb.debian.org/debian unstable/main amd64 python2.7 amd64 2.7.15-4 [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 8.2.0-9 [8,884 B]
Get:23 http://deb.debian.org/debian unstable/main amd64 libtbb2 amd64 2017~U7-8 [140 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://deb.debian.org/debian unstable/main amd64 bcftools amd64 1.9-1 [527 kB]
Get:27 http://deb.debian.org/debian unstable/main amd64 libgomp1 amd64 8.2.0-9 [75.7 kB]
Get:28 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB]
Get:29 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB]
Get:30 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB]
Get:31 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB]
Get:32 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB]
Get:33 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 20.0-1 [50.3 kB]
Get:34 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-5 [172 kB]
Get:35 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB]
Get:36 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.68-2 [177 kB]
Get:37 http://deb.debian.org/debian unstable/main amd64 librdmacm1 amd64 20.0-1 [65.0 kB]
Get:38 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.6.1-5 [392 kB]
Get:39 http://deb.debian.org/debian unstable/main amd64 libquadmath0 amd64 8.2.0-9 [133 kB]
Get:40 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 8.2.0-9 [580 kB]
Get:41 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.6-6 [390 kB]
Get:42 http://deb.debian.org/debian unstable/main amd64 libhwloc5 amd64 1.11.11-2 [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 libpng16-16 amd64 1.6.34-2 [288 kB]
Get:45 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.8.1-2 [461 kB]
Get:46 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0 amd64 2.58.1-2 [1,223 kB]
Get:47 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.12-1 [80.2 kB]
Get:48 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 1.9.0-1 [923 kB]
Get:49 http://deb.debian.org/debian unstable/main amd64 libicu-le-hb0 amd64 1.0.3+git161113-5 [14.6 kB]
Get:50 http://deb.debian.org/debian unstable/main amd64 libicu60 amd64 60.2-6 [8,073 kB]
Get:51 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-7+b1 [725 kB]
Get:52 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.2.12-1 [37.1 kB]
Get:53 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 1.11.11-2 [17.5 kB]
Get:54 http://deb.debian.org/debian unstable/main amd64 libpmix2 amd64 3.0.2-2 [409 kB]
Get:55 http://deb.debian.org/debian unstable/main amd64 libopenmpi3 amd64 3.1.3-2 [2,175 kB]
Get:56 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 3.1.3-2 [164 kB]
Get:57 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 3.1.3-2 [200 kB]
Get:58 http://deb.debian.org/debian unstable/main amd64 examl amd64 3.0.21-2 [922 kB]
Get:59 http://deb.debian.org/debian unstable/main amd64 mafft amd64 7.402-1 [996 kB]
Get:60 http://deb.debian.org/debian unstable/main amd64 zip amd64 3.0-11+b1 [234 kB]
Get:61 http://deb.debian.org/debian unstable/main amd64 unzip amd64 6.0-21 [170 kB]
Get:62 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB]
Get:63 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB]
Get:64 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.1.3-1 [73.3 kB]
Get:65 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.8.0-1+b1 [148 kB]
Get:66 http://deb.debian.org/debian unstable/main amd64 libopenblas-base amd64 0.3.3+ds-1 [4,054 kB]
Get:67 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-1 [1,068 kB]
Get:68 http://deb.debian.org/debian unstable/main amd64 fontconfig-config all 2.13.1-1 [280 kB]
Get:69 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.13.1-1 [346 kB]
Get:70 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.34.0-2 [529 kB]
Get:71 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB]
Get:72 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get:73 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.13.1-1 [137 kB]
Get:74 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.6.7-1 [298 kB]
Get:75 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.6.7-1 [754 kB]
Get:76 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.13.1-1 [109 kB]
Get:77 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.13.1-1 [99.1 kB]
Get:78 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB]
Get:79 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB]
Get:80 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.16.0-1 [689 kB]
Get:81 http://deb.debian.org/debian unstable/main amd64 libcurl4 amd64 7.62.0-1 [324 kB]
Get:82 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+19 [251 kB]
Get:83 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB]
Get:84 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+b1 [134 kB]
Get:85 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.8.0-1+b1 [2,112 kB]
Get:86 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.13.1-1 [405 kB]
Get:87 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.5-3 [63.3 kB]
Get:88 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.28-1 [170 kB]
Get:89 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.12-1 [39.1 kB]
Get:90 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.28-1 [53.9 kB]
Get:91 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.42.4-3 [184 kB]
Get:92 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.42.4-3 [67.5 kB]
Get:93 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.42.4-3 [55.4 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 8.6.8+dfsg-4 [988 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 4.0.9+git181026-1 [250 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 8.6.8-4 [752 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 1.1.1-2 [833 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 3.5.1-1+b1 [23.9 MB]
Get:106 http://deb.debian.org/debian unstable/main amd64 r-cran-codetools all 0.2-15-2 [89.8 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 0.20-35-1+b2 [1,137 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 1.2-14-1+b3 [3,398 kB]
Get:117 http://deb.debian.org/debian unstable/main amd64 r-cran-mgcv amd64 1.8-25-1 [2,585 kB]
Get:118 http://deb.debian.org/debian unstable/main amd64 r-cran-littler amd64 0.3.5-1 [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 0.12.19-1 [3,457 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 1.2.4-1 [680 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 0.3.0.1-1 [1,034 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-colorspace amd64 1.3-2-3 [474 kB]
Get:131 http://deb.debian.org/debian unstable/main amd64 r-cran-munsell all 0.5.0-1 [235 kB]
Get:132 http://deb.debian.org/debian unstable/main amd64 r-cran-r6 all 2.3.0-1 [73.5 kB]
Get:133 http://deb.debian.org/debian unstable/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB]
Get:134 http://deb.debian.org/debian unstable/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB]
Get:135 http://deb.debian.org/debian unstable/main amd64 r-cran-scales amd64 1.0.0-2 [546 kB]
Get:136 http://deb.debian.org/debian unstable/main amd64 r-cran-assertthat all 0.2.0-2 [54.4 kB]
Get:137 http://deb.debian.org/debian unstable/main amd64 r-cran-crayon all 1.3.4-4 [750 kB]
Get:138 http://deb.debian.org/debian unstable/main amd64 r-cran-cli all 1.0.1-1 [519 kB]
Get:139 http://deb.debian.org/debian unstable/main amd64 r-cran-fansi amd64 0.4.0-1 [339 kB]
Get:140 http://deb.debian.org/debian unstable/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB]
Get:141 http://deb.debian.org/debian unstable/main amd64 r-cran-pillar all 1.3.0-1 [200 kB]
Get:142 http://deb.debian.org/debian unstable/main amd64 r-cran-tibble amd64 1.4.2-3 [232 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-5 [101 kB]
Get:148 http://deb.debian.org/debian unstable/main amd64 libgsl23 amd64 2.5+dfsg-5 [879 kB]
Get:149 http://deb.debian.org/debian unstable/main amd64 libgsl-dev amd64 2.5+dfsg-5 [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 0.3.3+ds-1 [4,129 kB]
Get:152 http://deb.debian.org/debian unstable/main amd64 mapdamage all 2.0.8+dfsg-2 [39.5 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 2:3.39-1 [1,151 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 0.70 [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 2.2.8-5 [322 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 1.1.7-1 [56.5 kB]
Get:164 http://deb.debian.org/debian unstable/main amd64 libasound2 amd64 1.1.7-1 [361 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+13-2 [36.9 MB]
Get:169 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.11-70 [10.8 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-6 [314 kB]
Get:173 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-0 amd64 2.38.0+dfsg-6 [177 kB]
Get:174 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 3.24.1-2 [81.1 kB]
Get:175 http://deb.debian.org/debian unstable/main amd64 libcroco3 amd64 0.6.12-2 [144 kB]
Get:176 http://deb.debian.org/debian unstable/main amd64 librsvg2-2 amd64 2.44.8-3 [1,272 kB]
Get:177 http://deb.debian.org/debian unstable/main amd64 librsvg2-common amd64 2.44.8-3 [23.0 kB]
Get:178 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 3.30.0-1 [11.7 MB]
Get:179 http://deb.debian.org/debian unstable/main amd64 libatk1.0-data all 2.30.0-1 [145 kB]
Get:180 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0 amd64 2.30.0-1 [50.5 kB]
Get:181 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0 amd64 2.30.0-4 [64.9 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 1.16.0-1 [124 kB]
Get:184 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.3-3 [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 1.4.4-1 [52.3 kB]
Get:187 http://deb.debian.org/debian unstable/main amd64 libjson-glib-1.0-0 amd64 1.4.4-1 [60.9 kB]
Get:188 http://deb.debian.org/debian unstable/main amd64 libproxy1v5 amd64 0.4.15-3 [57.2 kB]
Get:189 http://deb.debian.org/debian unstable/main amd64 glib-networking-common all 2.58.0-1 [59.2 kB]
Get:190 http://deb.debian.org/debian unstable/main amd64 glib-networking-services amd64 2.58.0-1 [13.5 kB]
Get:191 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.30.0-1 [40.5 kB]
Get:192 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.12.10-1 [91.0 kB]
Get:193 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.30.0-1 [36.1 kB]
Get:194 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.30.0-1 [28.8 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 2.58.0-1 [54.3 kB]
Get:197 http://deb.debian.org/debian unstable/main amd64 libsoup2.4-1 amd64 2.64.1-3 [253 kB]
Get:198 http://deb.debian.org/debian unstable/main amd64 libsoup-gnome2.4-1 amd64 2.64.1-3 [17.9 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 1:1.1.15-1 [36.4 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 3.24.1-2 [3,661 kB]
Get:212 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0 amd64 3.24.1-2 [2,585 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 18.1.9-1 [62.3 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 1.13.1-1 [101 kB]
Get:219 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.13.1-1 [100 kB]
Get:220 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.13.1-1 [116 kB]
Get:221 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.13.1-1 [99.1 kB]
Get:222 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.13.1-1 [103 kB]
Get:223 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.13.1-1 [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 libllvm6.0 amd64 1:6.0.1-9.2 [14.7 MB]
Get:231 http://deb.debian.org/debian unstable/main amd64 libsensors4 amd64 1:3.4.0-4 [53.3 kB]
Get:232 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 18.1.9-1 [6,288 kB]
Get:233 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 18.1.9-1 [174 kB]
Get:234 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB]
Get:235 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB]
Get:236 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-glx amd64 18.1.9-1 [43.7 kB]
Get:237 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.1.4-3 [43.3 kB]
Get:238 http://deb.debian.org/debian unstable/main amd64 openjdk-11-jre amd64 11.0.1+13-2 [34.2 kB]
Get:239 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.11-70 [1,040 B]
Get:240 http://deb.debian.org/debian unstable/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5,312 B]
Get:241 http://deb.debian.org/debian unstable/main amd64 libjsr305-java all 0.1~+svn49-10 [26.5 kB]
Get:242 http://deb.debian.org/debian unstable/main amd64 libguava-java all 19.0-1 [2,028 kB]
Get:243 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 18-1 [4,676 B]
Get:244 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 43-1 [10.8 kB]
Get:245 http://deb.debian.org/debian unstable/main amd64 libcommons-compress-java all 1.18-1 [532 kB]
Get:246 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.2-2 [62.2 kB]
Get:247 http://deb.debian.org/debian unstable/main amd64 libcommons-jexl2-java all 2.1.1-4 [257 kB]
Get:248 http://deb.debian.org/debian unstable/main amd64 libngs-sdk2 amd64 2.9.0-1 [52.9 kB]
Get:249 http://deb.debian.org/debian unstable/main amd64 libngs-sdk-dev amd64 2.9.0-1 [94.3 kB]
Get:250 http://deb.debian.org/debian unstable/main amd64 libngs-java amd64 2.9.0-1 [79.2 kB]
Get:251 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.1.7-1 [17.0 kB]
Get:252 http://deb.debian.org/debian unstable/main amd64 libsnappy-jni amd64 1.1.7.2-1 [7,148 B]
Get:253 http://deb.debian.org/debian unstable/main amd64 libsnappy-java all 1.1.7.2-1 [73.7 kB]
Get:254 http://deb.debian.org/debian unstable/main amd64 libxz-java all 1.8-2 [141 kB]
Get:255 http://deb.debian.org/debian unstable/main amd64 libhtsjdk-java all 2.16.1+dfsg-1 [1,495 kB]
Get:256 http://deb.debian.org/debian unstable/main amd64 libfreemarker-java all 2.3.23-8 [1,228 kB]
Get:257 http://deb.debian.org/debian unstable/main amd64 libjoptsimple-java all 5.0.4-3 [73.0 kB]
Get:258 http://deb.debian.org/debian unstable/main amd64 libgoogle-gson-java all 2.8.2-1 [222 kB]
Get:259 http://deb.debian.org/debian unstable/main amd64 libcommons-codec-java all 1.11-1 [271 kB]
Get:260 http://deb.debian.org/debian unstable/main amd64 libhttpcore-java all 4.4.10-1 [624 kB]
Get:261 http://deb.debian.org/debian unstable/main amd64 libhttpclient-java all 4.5.6-1 [720 kB]
Get:262 http://deb.debian.org/debian unstable/main amd64 liblightcouch-java all 0.0.6-1 [63.7 kB]
Get:263 http://deb.debian.org/debian unstable/main amd64 libmongodb-java all 3.6.3-1 [1,901 kB]
Get:264 http://deb.debian.org/debian unstable/main amd64 libslf4j-java all 1.7.25-3 [143 kB]
Get:265 http://deb.debian.org/debian unstable/main amd64 liblog4j2-java all 2.11.1-1 [1,737 kB]
Get:266 http://deb.debian.org/debian unstable/main amd64 libbarclay-java all 2.1.0-2 [116 kB]
Get:267 http://deb.debian.org/debian unstable/main amd64 libgkl-jni amd64 0.8.5+dfsg-1 [190 kB]
Get:268 http://deb.debian.org/debian unstable/main amd64 libgkl-java all 0.8.5+dfsg-1 [1,144 kB]
Get:269 http://deb.debian.org/debian unstable/main amd64 libcommons-lang3-java all 3.8-1 [478 kB]
Get:270 http://deb.debian.org/debian unstable/main amd64 libcommons-math3-java all 3.6.1-3 [2,018 kB]
Get:271 http://deb.debian.org/debian unstable/main amd64 libgatk-native-bindings-java all 1.0.0-2 [7,140 B]
Get:272 http://deb.debian.org/debian unstable/main amd64 libpicard-java all 2.18.14+dfsg-1 [1,408 kB]
Get:273 http://deb.debian.org/debian unstable/main amd64 picard-tools all 2.18.14+dfsg-1 [311 kB]
Get:274 http://deb.debian.org/debian unstable/main amd64 radiant all 2.7+dfsg-2 [159 kB]
Get:275 http://deb.debian.org/debian unstable/main amd64 raxml amd64 8.2.12+dfsg-1 [1,275 kB]
Get:276 http://deb.debian.org/debian unstable/main amd64 samtools amd64 1.9-1 [424 kB]
Get:277 http://deb.debian.org/debian unstable/main amd64 python-pkg-resources all 40.4.3-1 [180 kB]
Get:278 http://deb.debian.org/debian unstable/main amd64 python-coverage amd64 4.5.1+dfsg.1-1 [143 kB]
Get:279 http://deb.debian.org/debian unstable/main amd64 python-flexmock all 0.10.2-2 [18.9 kB]
Get:280 http://deb.debian.org/debian unstable/main amd64 paleomix amd64 1.2.13.2-1 [4,684 kB]
Get:281 http://deb.debian.org/debian unstable/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB]
Get:282 http://deb.debian.org/debian unstable/main amd64 libpython3.6-stdlib amd64 3.6.7-1 [1,707 kB]
Get:283 http://deb.debian.org/debian unstable/main amd64 python3.6 amd64 3.6.7-1 [240 kB]
Get:284 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.6.7-1 [19.9 kB]
Get:285 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.6.7-1 [61.4 kB]
Get:286 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 40.4.3-1 [150 kB]
Get:287 http://deb.debian.org/debian unstable/main amd64 python3-pluggy all 0.6.0-1 [12.2 kB]
Get:288 http://deb.debian.org/debian unstable/main amd64 python3-py all 1.6.0-1 [86.2 kB]
Get:289 http://deb.debian.org/debian unstable/main amd64 python3-lib2to3 all 3.7.1-1 [78.7 kB]
Get:290 http://deb.debian.org/debian unstable/main amd64 python3-distutils all 3.7.1-1 [144 kB]
Get:291 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 40.4.3-1 [301 kB]
Get:292 http://deb.debian.org/debian unstable/main amd64 python-pip-whl all 9.0.1-2.3 [1,678 kB]
Get:293 http://deb.debian.org/debian unstable/main amd64 python3-virtualenv all 15.1.0+ds-1.1 [57.9 kB]
Get:294 http://deb.debian.org/debian unstable/main amd64 virtualenv all 15.1.0+ds-1.1 [19.9 kB]
Get:295 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.2.1-1 [154 kB]
Get:296 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.8.3~dfsg-1 [63.8 kB]
Get:297 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 1.7.9-1 [92.3 kB]
Get:298 http://deb.debian.org/debian unstable/main amd64 tox all 2.5.0-1 [180 kB]
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Setting up adapterremoval (2.2.2-2) ...
Setting up libgraphite2-3:amd64 (1.3.12-1) ...
Setting up libpsm-infinipath1 (3.3+20.604758e7-5) ...
update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode
Setting up raxml (8.2.12+dfsg-1) ...
Setting up libjsr305-java (0.1~+svn49-10) ...
Setting up libatk1.0-data (2.30.0-1) ...
Setting up libx11-xcb1:amd64 (2:1.6.7-1) ...
Setting up libpixman-1-0:amd64 (0.34.0-2) ...
Setting up libssh2-1:amd64 (1.8.0-2) ...
Setting up libngs-sdk-dev (2.9.0-1) ...
Setting up libevent-pthreads-2.1-6:amd64 (2.1.8-stable-4) ...
Setting up libxz-java (1.8-2) ...
Setting up openmpi-common (3.1.3-2) ...
Processing triggers for libc-bin (2.27-8) ...
Setting up libepoxy0:amd64 (1.5.3-0.1) ...
Setting up libmongodb-java (3.6.3-1) ...
Setting up libatk1.0-0:amd64 (2.30.0-1) ...
Setting up libsnappy1v5:amd64 (1.1.7-1) ...
Processing triggers for systemd (239-11) ...
Setting up libltdl7:amd64 (2.4.6-6) ...
Setting up libapache-pom-java (18-1) ...
Setting up openssl (1.1.1-2) ...
Setting up libdconf1:amd64 (0.30.0-1) ...
Setting up libfribidi0:amd64 (1.0.5-3) ...
Setting up libpciaccess0:amd64 (0.14-1) ...
Setting up libsensors4:amd64 (1:3.4.0-4) ...
Setting up libxkbcommon0:amd64 (0.8.2-1) ...
Setting up libatinject-jsr330-api-java (1.0+ds1-5) ...
Setting up libtcl8.6:amd64 (8.6.8+dfsg-4) ...
Setting up libcolord2:amd64 (1.4.3-3) ...
Setting up libthai-data (0.1.28-1) ...
Setting up libxdmcp6:amd64 (1:1.1.2-3) ...
Setting up ocl-icd-libopencl1:amd64 (2.2.12-1) ...
Setting up libgoogle-gson-java (2.8.2-1) ...
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-5) ...
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 (8.2.0-9) ...
Setting up libwayland-cursor0:amd64 (1.16.0-1) ...
Setting up libwayland-egl1:amd64 (1.16.0-1) ...
Setting up libx11-data (2:1.6.7-1) ...
Setting up libpython2.7-stdlib:amd64 (2.7.15-4) ...
Setting up libxau6:amd64 (1:1.0.8-1+b2) ...
Setting up libmpdec2:amd64 (2.4.2-2) ...
Setting up libgkl-jni (0.8.5+dfsg-1) ...
Setting up libngs-java (2.9.0-1) ...
Setting up libavahi-common-data:amd64 (0.7-4+b1) ...
Setting up libwebp6:amd64 (0.6.1-2) ...
Setting up libopenblas-base:amd64 (0.3.3+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 python-pip-whl (9.0.1-2.3) ...
Setting up libpython3.6-stdlib:amd64 (3.6.7-1) ...
Setting up fontconfig-config (2.13.1-1) ...
Setting up python3.6 (3.6.7-1) ...
Setting up libpsm2-2 (11.2.68-2) ...
Setting up libgsl23:amd64 (2.5+dfsg-5) ...
Setting up dconf-service (0.30.0-1) ...
Setting up libgsl-dev (2.5+dfsg-5) ...
Setting up libcurl3-gnutls:amd64 (7.62.0-1) ...
Setting up libsnappy-jni (1.1.7.2-1) ...
Setting up liblapack3:amd64 (3.8.0-1+b1) ...
Setting up libcurl4:amd64 (7.62.0-1) ...
Setting up python2.7 (2.7.15-4) ...
Setting up libguava-java (19.0-1) ...
Setting up libnss3:amd64 (2:3.39-1) ...
Setting up libharfbuzz0b:amd64 (1.9.0-1) ...
Setting up libtiff5:amd64 (4.0.9+git181026-1) ...
Setting up libnl-route-3-200:amd64 (3.4.0-1) ...
Setting up libthai0:amd64 (0.1.28-1) ...
Setting up libhwloc5:amd64 (1.11.11-2) ...
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 libdrm-intel1:amd64 (2.4.95-1) ...
Setting up libblas3:amd64 (3.8.0-1+b1) ...
Setting up libcommons-compress-java (1.18-1) ...
Setting up libcommons-lang3-java (3.8-1) ...
Setting up libsnappy-java (1.1.7.2-1) ...
Setting up libice6:amd64 (2:1.0.9-2) ...
Setting up libpython2-stdlib:amd64 (2.7.15-3) ...
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 (0.3.3+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 dconf-gsettings-backend:amd64 (0.30.0-1) ...
Setting up libxcb1:amd64 (1.13.1-1) ...
Setting up libhts2:amd64 (1.9-3) ...
Setting up libpython3-stdlib:amd64 (3.6.7-1) ...
Setting up libibverbs1:amd64 (20.0-1) ...
Setting up libxcb-present0:amd64 (1.13.1-1) ...
Setting up libfontconfig1:amd64 (2.13.1-1) ...
Setting up libxcb-dri2-0:amd64 (1.13.1-1) ...
Setting up libsm6:amd64 (2:1.2.2-1+b3) ...
Setting up libxcb-dri3-0:amd64 (1.13.1-1) ...
Setting up libxcb-glx0:amd64 (1.13.1-1) ...
Setting up libxcb-xfixes0:amd64 (1.13.1-1) ...
Setting up libxcb-render0:amd64 (1.13.1-1) ...
Setting up gsettings-desktop-schemas (3.28.1-1) ...
Setting up python3 (3.6.7-1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.95-1) ...
Setting up libgtk-3-common (3.24.1-2) ...
Setting up libx11-6:amd64 (2:1.6.7-1) ...
Setting up libgl1-mesa-dri:amd64 (18.1.9-1) ...
Setting up libcommons-logging-java (1.2-2) ...
Setting up librdmacm1:amd64 (20.0-1) ...
Setting up python3-pkg-resources (40.4.3-1) ...
Setting up python3-pluggy (0.6.0-1) ...
Setting up python2 (2.7.15-3) ...
Setting up libxcb-sync1:amd64 (1.13.1-1) ...
Setting up libpython-stdlib:amd64 (2.7.15-3) ...
Setting up glib-networking:amd64 (2.58.0-1) ...
Setting up libhttpclient-java (4.5.6-1) ...
Setting up libxcomposite1:amd64 (1:0.4.4-2) ...
Setting up libcommons-jexl2-java (2.1.1-4) ...
Setting up libxcb-shm0:amd64 (1.13.1-1) ...
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 (1.9-1) ...
Setting up python3-lib2to3 (3.7.1-1) ...
Setting up bcftools (1.9-1) ...
Setting up python3-distutils (3.7.1-1) ...
Setting up python (2.7.15-3) ...
Setting up fontconfig (2.13.1-1) ...
Regenerating fonts cache... done.
Setting up python-setproctitle:amd64 (1.1.10-1+b2) ...
Setting up libcups2:amd64 (2.2.8-5) ...
Setting up python-flexmock (0.10.2-2) ...
Setting up liblightcouch-java (0.0.6-1) ...
Setting up libxext6:amd64 (2:1.3.3-1+b2) ...
Setting up libxfixes3:amd64 (1:5.0.3-1) ...
Setting up python3-py (1.6.0-1) ...
Setting up libfabric1 (1.6.1-5) ...
Setting up libatspi2.0-0:amd64 (2.30.0-4) ...
Setting up python-pysam (0.15.1+ds-1) ...
Setting up libxss1:amd64 (1:1.2.3-1) ...
Setting up python-pkg-resources (40.4.3-1) ...
Setting up bowtie2 (2.3.4.3-1) ...
Setting up python-coverage (4.5.1+dfsg.1-1) ...
Setting up libhtsjdk-java (2.16.1+dfsg-1) ...
Setting up libxcursor1:amd64 (1:1.1.15-1) ...
Setting up python3-virtualenv (15.1.0+ds-1.1) ...
Setting up libpango-1.0-0:amd64 (1.42.4-3) ...
Setting up libatk-bridge2.0-0:amd64 (2.30.0-2) ...
Setting up liblog4j2-java (2.11.1-1) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up python3-setuptools (40.4.3-1) ...
Setting up libbarclay-java (2.1.0-2) ...
Setting up virtualenv (15.1.0+ds-1.1) ...
Setting up libxrandr2:amd64 (2:1.5.1-1) ...
Setting up libxi6:amd64 (2:1.7.9-1) ...
Setting up libcairo2:amd64 (1.16.0-1) ...
Setting up tox (2.5.0-1) ...
Setting up libxinerama1:amd64 (2:1.1.4-1) ...
Setting up libxdamage1:amd64 (1:1.1.4-3) ...
Setting up libtk8.6:amd64 (8.6.8-4) ...
Setting up libcairo-gobject2:amd64 (1.16.0-1) ...
Setting up libxtst6:amd64 (2:1.2.3-1) ...
Setting up libpangoft2-1.0-0:amd64 (1.42.4-3) ...
Setting up libpicard-java (2.18.14+dfsg-1) ...
Setting up libglx-mesa0:amd64 (18.1.9-1) ...
Setting up libpangocairo-1.0-0:amd64 (1.42.4-3) ...
Setting up libglx0:amd64 (1.1.0-1) ...
Setting up libgl1:amd64 (1.1.0-1) ...
Setting up libgl1-mesa-glx:amd64 (18.1.9-1) ...
Setting up libicu-le-hb0:amd64 (1.0.3+git161113-5) ...
Setting up openjdk-11-jre-headless:amd64 (11.0.1+13-2) ...
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 default-jre-headless (2:1.11-70) ...
Setting up libicu60:amd64 (60.2-6) ...
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 r-base-core (3.5.1-1+b1) ...

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) ...
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 libxml2:amd64 (2.9.4+dfsg1-7+b1) ...
Setting up r-cran-assertthat (0.2.0-2) ...
Setting up libcroco3:amd64 (0.6.12-2) ...
Setting up r-cran-rcolorbrewer (1.1-2-2) ...
Setting up libhwloc-plugins:amd64 (1.11.11-2) ...
Setting up r-cran-stringi (1.2.4-1) ...
Setting up r-cran-pkgkitten (0.1.4-2) ...
Setting up r-cran-rcpp (0.12.19-1) ...
Setting up r-cran-labeling (0.3-3) ...
Setting up r-cran-r6 (2.3.0-1) ...
Setting up r-cran-colorspace (1.3-2-3) ...
Setting up shared-mime-info (1.10-1) ...
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 (0.3.0.1-1) ...
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-glue (1.3.0-1) ...
Setting up r-cran-codetools (0.2-15-2) ...
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 (0.20-35-1+b2) ...
Setting up r-cran-lazyeval (0.2.1-3) ...
Setting up libgdk-pixbuf2.0-0:amd64 (2.38.0+dfsg-6) ...
Setting up r-cran-nlme (3.1.137-1+b3) ...
Setting up r-cran-stringr (1.3.1-2) ...
Setting up libsoup2.4-1:amd64 (2.64.1-3) ...
Setting up libsoup-gnome2.4-1:amd64 (2.64.1-3) ...
Setting up libpmix2:amd64 (3.0.2-2) ...
Setting up r-cran-foreach (1.4.4-2) ...
Setting up gtk-update-icon-cache (3.24.1-2) ...
Setting up r-cran-gam (1.16-1) ...
Setting up r-cran-munsell (0.5.0-1) ...
Setting up r-cran-pillar (1.3.0-1) ...
Setting up librest-0.7-0:amd64 (0.8.1-1) ...
Setting up r-cran-reshape2 (1.4.3-2) ...
Setting up r-cran-scales (1.0.0-2) ...
Setting up r-cran-tibble (1.4.2-3) ...
Setting up libopenmpi3:amd64 (3.1.3-2) ...
Setting up librsvg2-2:amd64 (2.44.8-3) ...
Setting up r-cran-matrix (1.2-14-1+b3) ...
Setting up openmpi-bin (3.1.3-2) ...
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 librsvg2-common:amd64 (2.44.8-3) ...
Setting up r-cran-mgcv (1.8-25-1) ...
Setting up r-cran-ggplot2 (3.1.0-1) ...
Setting up mapdamage (2.0.8+dfsg-2) ...
Setting up adwaita-icon-theme (3.30.0-1) ...
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 examl (3.0.21-2) ...
Setting up libgtk-3-0:amd64 (3.24.1-2) ...
Setting up openjdk-11-jre:amd64 (11.0.1+13-2) ...
Setting up default-jre (2:1.11-70) ...
Setting up picard-tools (2.18.14+dfsg-1) ...
Setting up paleomix (1.2.13.2-1) ...
Setting up autopkgtest-satdep (0) ...
Processing triggers for libc-bin (2.27-8) ...
Processing triggers for systemd (239-11) ...
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-6) ...
(Reading database ... 32065 files and directories currently installed.)
Removing autopkgtest-satdep (0) ...
autopkgtest [07:35:39]: test run-unit-test: [-----------------------
./tests/data/fasta_file.fasta.gz
ERROR: toxini file 'tox.ini' not found
autopkgtest [07:35:40]: test run-unit-test: -----------------------]
autopkgtest [07:35:40]: test run-unit-test:  - - - - - - - - - - results - - - - - - - - - -
run-unit-test        FAIL non-zero exit status 1
autopkgtest [07:35:40]: @@@@@@@@@@@@@@@@@@@@ summary
run-unit-test        FAIL non-zero exit status 1