Raspbian Package Auto-Building

r-bioc-shortread → 1.38.0-2+b1 → armhf → 2018-06-15 23:10:54

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard

+==============================================================================+
| r-bioc-shortread 1.38.0-2+b1 (armhf)         Fri, 15 Jun 2018 22:33:08 +0000 |
+==============================================================================+

Package: r-bioc-shortread
Version: 1.38.0-2+b1
Source Version: 1.38.0-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-3edd2524-e0a9-4901-9ffd-68cf02cebf01' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.8 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.6 MB]
Fetched 23.4 MB in 29s (810 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'r-bioc-shortread' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-shortread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5192 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.38.0-2 (dsc) [2458 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.38.0-2 (tar) [5184 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.38.0-2 (diff) [5416 B]
Fetched 5192 kB in 2s (2900 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-iBmx7W/r-bioc-shortread-1.38.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-iBmx7W' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-HlmV9T/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-HlmV9T/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-HlmV9T/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3270 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
  libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
  systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 50 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15771 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.47.6), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), r-bioc-biobase, r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-cran-hwriter, r-cran-lattice, r-cran-latticeextra
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.47.6), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), r-bioc-biobase, r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-cran-hwriter, r-cran-lattice, r-cran-latticeextra
dpkg-deb: building package 'sbuild-build-depends-r-bioc-shortread-dummy' in '/<<BUILDDIR>>/resolver-HlmV9T/apt_archive/sbuild-build-depends-r-bioc-shortread-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-r-bioc-shortread-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Sources [647 B]
Get:5 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ Packages [728 B]
Fetched 2708 B in 1s (4199 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install r-bioc-shortread build dependencies (apt-based resolver)
----------------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  dbus dbus-user-session e2fsprogs-l10n libnss-systemd libpam-systemd
  libsasl2-modules systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils cpp cpp-7 dctrl-tools
  debhelper default-libmysqlclient-dev dh-autoreconf dh-r
  dh-strip-nondeterminism dwz file fontconfig fontconfig-config
  fonts-dejavu-core g++-7 gcc gcc-7 gcc-7-base gdal-data gettext gettext-base
  gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base
  hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0
  libarchive-zip-perl libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev
  libasan4 libblas-dev libblas3 libboost-dev libboost1.62-dev libbsd0
  libbz2-dev libcairo2 libcharls-dev libcharls1 libcilkrts5 libcroco3
  libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdap-dev libdap25
  libdapclient6v5 libdapserver7v5 libdatrie1 libelf1 libepsilon-dev
  libepsilon1 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1
  libfreetype6 libfreexl-dev libfreexl1 libfribidi0 libfyba-dev libfyba0
  libgcc-7-dev libgdal-dev libgdal20 libgeos-3.6.2 libgeos-c1v5 libgeos-dev
  libgeotiff-dev libgeotiff2 libgfortran-7-dev libgfortran4 libgif-dev libgif7
  libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
  libglib2.0-dev libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev
  libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0
  libharfbuzz0b libhdf4-0-alt libhdf4-alt-dev libhdf5-100 libhdf5-cpp-100
  libhdf5-dev libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60
  libisl19 libjbig-dev libjbig0 libjpeg-dev libjpeg62-turbo
  libjpeg62-turbo-dev libjson-c-dev libk5crypto3 libkeyutils1 libkml-dev
  libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1
  libkmlxsd1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2
  libltdl-dev libltdl7 liblzma-dev libmagic-mgc libmagic1 libmariadbclient-dev
  libmariadbclient-dev-compat libmariadbclient18 libminizip-dev libminizip1
  libmpdec2 libncurses-dev libncurses5-dev libnetcdf-dev libnetcdf13
  libnghttp2-14 libnspr4 libnss3 libodbc1 libogdi3.2 libogdi3.2-dev
  libopenjp2-7 libopenjp2-7-dev libpango-1.0-0 libpangocairo-1.0-0
  libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev
  libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev
  libpoppler-dev libpoppler-private-dev libpoppler74 libpopt0 libpq-dev libpq5
  libproj-dev libproj13 libpsl5 libpython3-stdlib libpython3.6-minimal
  libpython3.6-stdlib libqhull-dev libqhull-r7 libqhull7 libreadline-dev
  libreadline7 librtmp1 libsigsegv2 libsm6 libspatialite-dev libspatialite7
  libsqlite3-0 libsqlite3-dev libssh2-1 libstdc++-7-dev libsuperlu-dev
  libsuperlu5 libsz2 libtcl8.6 libthai-data libthai0 libtiff-dev libtiff5
  libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6 libtool libubsan0
  liburiparser-dev liburiparser1 libwebp-dev libwebp6 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxerces-c-dev libxerces-c3.2 libxext6 libxft2 libxml2
  libxml2-dev libxmuu1 libxrender1 libxss1 libxt6 libzstd-dev m4 man-db
  mime-support mysql-common odbcinst odbcinst1debian2 pkg-config po-debconf
  proj-data python3 python3-distutils python3-lib2to3 python3-minimal
  python3.6 python3.6-minimal r-base-core r-base-dev r-bioc-biobase
  r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
  r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata
  r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges
  r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector
  r-cran-bitops r-cran-formatr r-cran-futile.logger r-cran-futile.options
  r-cran-hwriter r-cran-lambda.r r-cran-lattice r-cran-latticeextra
  r-cran-matrix r-cran-matrixstats r-cran-rcolorbrewer r-cran-rcurl
  r-cran-snow ucf unixodbc-dev unzip uuid-dev x11-common xauth xdg-utils zip
  zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation cpp-doc gcc-7-locales debtags dh-make gcc-7-doc libstdc++6-7-dbg
  gcc-multilib manpages-dev flex bison gdb gcc-doc libgcc1-dbg libgomp1-dbg
  libitm1-dbg libatomic1-dbg libasan4-dbg liblsan0-dbg libtsan0-dbg
  libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg gettext-doc
  libasprintf-dev libgettextpo-dev gfortran-doc gfortran-7-doc
  libgfortran4-dbg libcoarrays-dev groff libitpp-dev liblapack-doc
  libboost-doc libboost1.62-doc libboost-atomic1.62-dev
  libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
  libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
  libboost-filesystem1.62-dev libboost-graph1.62-dev
  libboost-graph-parallel1.62-dev libboost-iostreams1.62-dev
  libboost-locale1.62-dev libboost-log1.62-dev libboost-math1.62-dev
  libboost-mpi1.62-dev libboost-mpi-python1.62-dev
  libboost-program-options1.62-dev libboost-python1.62-dev
  libboost-random1.62-dev libboost-regex1.62-dev
  libboost-serialization1.62-dev libboost-signals1.62-dev
  libboost-system1.62-dev libboost-test1.62-dev libboost-thread1.62-dev
  libboost-timer1.62-dev libboost-type-erasure1.62-dev libboost-wave1.62-dev
  libboost1.62-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc
  libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
  libssh2-1-dev libgdal-doc libgeotiff-epsg geotiff-bin gdal-bin
  libglib2.0-doc libgraphite2-utils krb5-doc krb5-user libhdf4-doc hdf4-tools
  libhdf5-doc icu-doc liblcms2-utils libtool-doc liblzma-doc ncurses-doc
  netcdf-bin netcdf-doc libmyodbc odbc-postgresql tdsodbc unixodbc-bin
  ogdi-bin libfreetype6-dev postgresql-doc-10 proj-bin readline-doc
  sqlite3-doc libstdc++-7-doc libsuperlu-doc tcl8.6 tk8.6 gcj-jdk
  libxerces-c-doc m4-doc apparmor less www-browser libmail-box-perl
  python3-doc python3-tk python3-venv python3.6-venv python3.6-doc
  binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base
  texlive-latex-base texlive-generic-recommended texlive-fonts-recommended
  texlive-fonts-extra texlive-extra-utils texlive-latex-recommended
  texlive-latex-extra texinfo r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2
  r-bioc-annotate r-cran-foreach r-cran-bbmisc r-cran-rmpi
  r-bioc-variantannotation r-bioc-shortread r-cran-codetools r-cran-knitr
  r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-rtracklayer r-bioc-edger
  r-bioc-gviz r-bioc-annotationhub r-bioc-graph r-cran-data.table
  r-cran-rmarkdown r-cran-jsonlite r-cran-shiny r-cran-base64enc
  r-cran-ggplot2 r-cran-xml r-cran-rsprng r-cran-rlecuyer
Recommended packages:
  curl | wget | lynx bzip2-doc libarchive-cpio-perl proj-bin shared-mime-info
  xdg-user-dirs krb5-locales libpng-tools poppler-data publicsuffix
  libmail-sendmail-perl r-recommended r-doc-html r-cran-runit r-cran-batchjobs
  r-cran-doparallel r-bioc-genefilter r-bioc-shortread r-cran-digest
  r-bioc-annotate r-cran-testit r-cran-codetools r-cran-survival
  r-cran-testthat libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl
  x11-utils x11-xserver-utils
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper
  default-libmysqlclient-dev dh-autoreconf dh-r dh-strip-nondeterminism dwz
  file fontconfig fontconfig-config fonts-dejavu-core gdal-data gettext
  gettext-base gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0
  groff-base hdf5-helpers icu-devtools intltool-debian libaec-dev libaec0
  libarchive-zip-perl libarmadillo-dev libarmadillo8 libarpack2 libarpack2-dev
  libblas-dev libblas3 libboost-dev libboost1.62-dev libbsd0 libbz2-dev
  libcairo2 libcharls-dev libcharls1 libcroco3 libcurl3-gnutls libcurl4
  libcurl4-gnutls-dev libdap-dev libdap25 libdapclient6v5 libdapserver7v5
  libdatrie1 libelf1 libepsilon-dev libepsilon1 libexpat1-dev
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfreexl-dev
  libfreexl1 libfribidi0 libfyba-dev libfyba0 libgdal-dev libgdal20
  libgeos-3.6.2 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff2
  libgfortran-7-dev libgfortran4 libgif-dev libgif7 libgirepository-1.0-1
  libglib2.0-0 libglib2.0-bin libglib2.0-data libglib2.0-dev
  libglib2.0-dev-bin libgraphite2-3 libgraphite2-dev libgssapi-krb5-2
  libharfbuzz-dev libharfbuzz-gobject0 libharfbuzz-icu0 libharfbuzz0b
  libhdf4-0-alt libhdf4-alt-dev libhdf5-100 libhdf5-cpp-100 libhdf5-dev
  libice6 libicu-dev libicu-le-hb-dev libicu-le-hb0 libicu60 libisl19
  libjbig-dev libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
  libjson-c-dev libk5crypto3 libkeyutils1 libkml-dev libkmlbase1
  libkmlconvenience1 libkmldom1 libkmlengine1 libkmlregionator1 libkmlxsd1
  libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblcms2-2 libltdl-dev
  libltdl7 liblzma-dev libmagic-mgc libmagic1 libmariadbclient-dev
  libmariadbclient-dev-compat libmariadbclient18 libminizip-dev libminizip1
  libmpdec2 libncurses-dev libncurses5-dev libnetcdf-dev libnetcdf13
  libnghttp2-14 libnspr4 libnss3 libodbc1 libogdi3.2 libogdi3.2-dev
  libopenjp2-7 libopenjp2-7-dev libpango-1.0-0 libpangocairo-1.0-0
  libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3 libpcre3-dev
  libpcre32-3 libpcrecpp0v5 libpipeline1 libpixman-1-0 libpng-dev
  libpoppler-dev libpoppler-private-dev libpoppler74 libpopt0 libpq-dev libpq5
  libproj-dev libproj13 libpsl5 libpython3-stdlib libpython3.6-minimal
  libpython3.6-stdlib libqhull-dev libqhull-r7 libqhull7 libreadline-dev
  librtmp1 libsigsegv2 libsm6 libspatialite-dev libspatialite7 libsqlite3-dev
  libssh2-1 libsuperlu-dev libsuperlu5 libsz2 libtcl8.6 libthai-data libthai0
  libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtimedate-perl libtk8.6
  libtool liburiparser-dev liburiparser1 libwebp-dev libwebp6 libwebpdemux2
  libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxerces-c-dev libxerces-c3.2 libxext6 libxft2 libxml2
  libxml2-dev libxmuu1 libxrender1 libxss1 libxt6 libzstd-dev m4 man-db
  mime-support mysql-common odbcinst odbcinst1debian2 pkg-config po-debconf
  proj-data python3 python3-distutils python3-lib2to3 python3-minimal
  python3.6 python3.6-minimal r-base-core r-base-dev r-bioc-biobase
  r-bioc-biocgenerics r-bioc-biocparallel r-bioc-biostrings
  r-bioc-delayedarray r-bioc-genomeinfodb r-bioc-genomeinfodbdata
  r-bioc-genomicalignments r-bioc-genomicranges r-bioc-iranges
  r-bioc-rsamtools r-bioc-s4vectors r-bioc-summarizedexperiment r-bioc-xvector
  r-cran-bitops r-cran-formatr r-cran-futile.logger r-cran-futile.options
  r-cran-hwriter r-cran-lambda.r r-cran-lattice r-cran-latticeextra
  r-cran-matrix r-cran-matrixstats r-cran-rcolorbrewer r-cran-rcurl
  r-cran-snow sbuild-build-depends-r-bioc-shortread-dummy ucf unixodbc-dev
  unzip uuid-dev x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
  cpp cpp-7 g++-7 gcc gcc-7 gcc-7-base libasan4 libcilkrts5 libgcc-7-dev
  libreadline7 libsqlite3-0 libstdc++-7-dev libubsan0
13 upgraded, 268 newly installed, 0 to remove and 37 not upgraded.
Need to get 206 MB/217 MB of archives.
After this operation, 638 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-HlmV9T/apt_archive ./ sbuild-build-depends-r-bioc-shortread-dummy 0.invalid.0 [1004 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.5-1 [292 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.5-1 [683 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6~rc1-1 [565 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6~rc1-1 [1384 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libreadline7 armhf 7.0-5 [130 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.24.0-1 [521 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6~rc1-1 [1637 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6~rc1-1 [234 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libisl19 armhf 0.19-1 [427 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.3.0-19 [5593 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.3.0-19 [5488 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.3.0-19 [5139 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.3.0-19 [301 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.3.0-19 [106 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.3.0-19 [35.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.3.0-19 [1506 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.3.0-19 [671 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.3.0-19 [187 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf cpp armhf 4:7.3.0-3+rpi1 [19.2 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf gcc armhf 4:7.3.0-3+rpi1 [5192 B]
Get:42 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-2 [20.0 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-2 [12.0 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1+b1 [799 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.2 [994 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libmariadbclient-dev armhf 1:10.1.29-6+b1 [1528 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libmariadbclient-dev-compat armhf 1:10.1.29-6+b1 [27.6 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf default-libmysqlclient-dev armhf 1.0.4 [3708 B]
Get:63 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.60.0-2 [281 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-5 [403 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 0.19.7-2 [44.1 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.11-1 [34.6 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.0-1 [158 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.0-1 [53.2 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.0-1 [43.3 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-5 [224 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.5.0-5 [23.6 MB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-19 [232 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-19 [5459 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.3.0-3+rpi1 [1436 B]
Get:92 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-4 [278 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-4 [936 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.7.6-1+b1 [584 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.7.6-1+b1 [591 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.7.6-1+b1 [597 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.5-4 [79.0 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.5-4 [144 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.7.6-1+b1 [879 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.5.0-5 [4484 B]
Get:121 http://172.17.0.1/private buster-staging/main armhf dh-r all 20180601 [32.0 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf gdal-data all 2.3.0+dfsg-1 [729 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4+b2 [36.4 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libarpack2 armhf 3.5.0+real-2+b2 [80.6 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libarmadillo8 armhf 1:8.400.0+dfsg-3 [83.7 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libarpack2-dev armhf 3.5.0+real-2+b2 [87.0 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-4+b2 [1216 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4+b2 [117 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4+b2 [2150 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-3 [18.2 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libarmadillo-dev armhf 1:8.400.0+dfsg-3 [344 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-5.1 [7003 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:135 http://172.17.0.1/private buster-staging/main armhf libcharls-dev armhf 1.1.0+dfsg-2 [21.6 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.60.0-2 [279 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.60.0-2 [352 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf libxml2-dev armhf 2.9.4+dfsg1-7 [672 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.32-0.1 [91.3 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf libdap-dev armhf 3.19.1-2 [760 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf libpopt0 armhf 1.16-11 [45.9 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf libepsilon-dev armhf 0.9.2+dfsg-2 [46.8 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf libfreexl-dev armhf 1.0.5-1 [30.2 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf libfyba-dev armhf 4.1.1-3 [425 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf proj-data all 5.1.0-1 [7002 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf libproj13 armhf 5.1.0-1 [182 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf libgif7 armhf 5.1.4-3 [41.0 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf liburiparser1 armhf 0.8.5-1 [34.7 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf libnetcdf13 armhf 1:4.6.1-1 [344 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-2.1 [386 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf libodbc1 armhf 2.3.6-0.1 [186 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.9-2 [117 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf libnspr4 armhf 2:4.19-3+rpi1 [90.0 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.37.1-1 [933 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf libpoppler74 armhf 0.63.0-2 [1225 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf libpq5 armhf 10.4-2 [148 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf libxerces-c3.2 armhf 3.2.1+debian-2+b2 [710 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf odbcinst armhf 2.3.6-0.1 [47.6 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf odbcinst1debian2 armhf 2.3.6-0.1 [70.8 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf libgdal20 armhf 2.3.0+dfsg-1 [4842 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf libgeos-dev armhf 3.6.2-1 [282 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf libtiffxx5 armhf 4.0.9-5 [100 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf libtiff5-dev armhf 4.0.9-5 [337 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf libtiff-dev armhf 4.0.9-5 [96.3 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf libgeotiff-dev armhf 1.4.2-2+b2 [93.5 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf libgif-dev armhf 5.1.4-3 [43.4 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf libnetcdf-dev armhf 1:4.6.1-1 [80.5 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf libhdf4-alt-dev armhf 4.2.13-2 [310 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf libjson-c-dev armhf 0.12.1-1.3 [34.6 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf libminizip-dev armhf 1.1-8 [25.6 kB]
Get:171 http://172.17.0.1/private buster-staging/main armhf liburiparser-dev armhf 0.8.5-1 [17.8 kB]
Get:172 http://172.17.0.1/private buster-staging/main armhf libkml-dev armhf 1.3.0-5 [940 kB]
Get:173 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2.1 [158 kB]
Get:174 http://172.17.0.1/private buster-staging/main armhf libproj-dev armhf 5.1.0-1 [225 kB]
Get:175 http://172.17.0.1/private buster-staging/main armhf libogdi3.2-dev armhf 3.2.1+ds-1+b1 [38.3 kB]
Get:176 http://172.17.0.1/private buster-staging/main armhf libopenjp2-7-dev armhf 2.3.0-1 [43.7 kB]
Get:177 http://172.17.0.1/private buster-staging/main armhf libpoppler-dev armhf 0.63.0-2 [22.5 kB]
Get:178 http://172.17.0.1/private buster-staging/main armhf libpoppler-private-dev armhf 0.63.0-2 [187 kB]
Get:179 http://172.17.0.1/private buster-staging/main armhf libpq-dev armhf 10.4-2 [145 kB]
Get:180 http://172.17.0.1/private buster-staging/main armhf libqhull-r7 armhf 2015.2-4 [171 kB]
Get:181 http://172.17.0.1/private buster-staging/main armhf libqhull-dev armhf 2015.2-4 [346 kB]
Get:182 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.24.0-1 [655 kB]
Get:183 http://172.17.0.1/private buster-staging/main armhf libspatialite-dev armhf 4.3.0a-5+b2 [1460 kB]
Get:184 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.6.1-2 [86.7 kB]
Get:185 http://172.17.0.1/private buster-staging/main armhf libwebp-dev armhf 0.6.1-2 [304 kB]
Get:186 http://172.17.0.1/private buster-staging/main armhf libxerces-c-dev armhf 3.2.1+debian-2+b2 [1486 kB]
Get:187 http://172.17.0.1/private buster-staging/main armhf libzstd-dev armhf 1.3.4+dfsg-3+rpi1 [209 kB]
Get:188 http://172.17.0.1/private buster-staging/main armhf unixodbc-dev armhf 2.3.6-0.1 [232 kB]
Get:189 http://172.17.0.1/private buster-staging/main armhf libgdal-dev armhf 2.3.0+dfsg-1 [6211 kB]
Get:190 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-3 [641 kB]
Get:191 http://172.17.0.1/private buster-staging/main armhf r-bioc-biobase armhf 2.40.0-2+b1 [2215 kB]
Get:192 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr armhf 1.5-2+b1 [149 kB]
Get:193 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:194 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:195 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:196 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-2 [108 kB]
Get:197 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.14.1-1+b1 [1051 kB]
Get:198 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.2-1+b1 [1802 kB]
Get:199 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.10-1+b1 [2127 kB]
Get:200 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2+b1 [592 kB]
Get:201 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2+b1 [14.1 MB]
Get:202 http://172.17.0.1/private buster-staging/main armhf r-cran-matrixstats armhf 0.53.1-1+b1 [559 kB]
Get:203 http://172.17.0.1/private buster-staging/main armhf r-bioc-delayedarray all 0.6.0+dfsg-1 [1049 kB]
Get:204 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3+b1 [24.0 kB]
Get:205 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.10-1+b2 [712 kB]
Get:206 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-3 [8213 kB]
Get:207 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.16.0-3 [3687 kB]
Get:208 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.3-1+b1 [1938 kB]
Get:209 http://172.17.0.1/private buster-staging/main armhf r-cran-lattice armhf 0.20-35-1+b2 [1138 kB]
Get:210 http://172.17.0.1/private buster-staging/main armhf r-cran-matrix armhf 1.2-14-1+b1 [3310 kB]
Get:211 http://172.17.0.1/private buster-staging/main armhf r-bioc-summarizedexperiment all 1.10.1+dfsg-1 [1882 kB]
Get:212 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.32.0-2+b1 [3489 kB]
Get:213 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicalignments armhf 1.16.0-2+b1 [2089 kB]
Get:214 http://172.17.0.1/private buster-staging/main armhf r-cran-hwriter all 1.3.2-3 [162 kB]
Get:215 http://172.17.0.1/private buster-staging/main armhf r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB]
Get:216 http://172.17.0.1/private buster-staging/main armhf r-cran-latticeextra armhf 0.6-28-2+b2 [2182 kB]
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Setting up libproj13:armhf (5.1.0-1) ...
Setting up libgeos-dev (3.6.2-1) ...
Setting up libharfbuzz0b:armhf (1.7.6-1+b1) ...
Setting up autoconf (2.69-11) ...
Setting up libthai0:armhf (0.1.27-2) ...
Setting up file (1:5.33-3) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up libkmlbase1:armhf (1.3.0-5) ...
Setting up libgcc-7-dev:armhf (7.3.0-19) ...
Setting up cpp-7 (7.3.0-19) ...
Setting up libqhull-dev:armhf (2015.2-4) ...
Setting up libstdc++-7-dev:armhf (7.3.0-19) ...
Setting up libncurses5-dev:armhf (6.1+20180210-4) ...
Setting up libogdi3.2 (3.2.1+ds-1+b1) ...
Setting up libkmlxsd1:armhf (1.3.0-5) ...
Setting up libblas3:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libjpeg-dev (1:1.5.2-2) ...
Setting up libwebpmux3:armhf (0.6.1-2) ...
Setting up libgeotiff2:armhf (1.4.2-2+b2) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up libgfortran-7-dev:armhf (7.3.0-19) ...
Setting up libreadline-dev:armhf (7.0-5) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up libwebpdemux2:armhf (0.6.1-2) ...
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liburiparser-dev (0.8.5-1) ...
Setting up libkmldom1:armhf (1.3.0-5) ...
Setting up default-libmysqlclient-dev:armhf (1.0.4) ...
Setting up libpng-dev:armhf (1.6.34-1) ...
Setting up libxcb1:armhf (1.13-1) ...
Setting up libharfbuzz-gobject0:armhf (1.7.6-1+b1) ...
Setting up libpython3-stdlib:armhf (3.6.5-3) ...
Setting up cpp (4:7.3.0-3+rpi1) ...
Setting up libtiff-dev (4.0.9-5) ...
Setting up libfontconfig1:armhf (2.13.0-5) ...
Setting up libsm6:armhf (2:1.2.2-1+b3) ...
Setting up libgeotiff-dev:armhf (1.4.2-2+b2) ...
Setting up libproj-dev:armhf (5.1.0-1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up libxcb-render0:armhf (1.13-1) ...
Setting up libhdf5-100:armhf (1.10.0-patch1+docs-4+b2) ...
Setting up python3 (3.6.5-3) ...
Setting up libboost1.62-dev:armhf (1.62.0+dfsg-5.1) ...
Setting up gcc-7 (7.3.0-19) ...
Setting up libblas-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up g++-7 (7.3.0-19) ...
Setting up liblapack3:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libx11-6:armhf (2:1.6.5-1) ...
Setting up gcc (4:7.3.0-3+rpi1) ...
Setting up libpoppler74:armhf (0.63.0-2) ...
Setting up libsuperlu5:armhf (5.2.1+dfsg1-3) ...
Setting up libxmuu1:armhf (2:1.1.2-2) ...
Setting up libogdi3.2-dev (3.2.1+ds-1+b1) ...
Setting up libwebp-dev:armhf (0.6.1-2) ...
Setting up libkmlengine1:armhf (1.3.0-5) ...
Setting up libsuperlu-dev:armhf (5.2.1+dfsg1-3) ...
Setting up gir1.2-harfbuzz-0.0:armhf (1.7.6-1+b1) ...
Setting up libxcb-shm0:armhf (1.13-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libarpack2:armhf (3.5.0+real-2+b2) ...
Setting up gfortran-7 (7.3.0-19) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up python3-lib2to3 (3.6.5-4) ...
Setting up python3-distutils (3.6.5-4) ...
Setting up fontconfig (2.13.0-5) ...
Regenerating fonts cache... done.
Setting up liblapack-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-2.1) ...
Setting up gfortran (4:7.3.0-3+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4+b2) ...
Setting up libpoppler-dev:armhf (0.63.0-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libhdf5-dev (1.10.0-patch1+docs-4+b2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
Setting up libkmlconvenience1:armhf (1.3.0-5) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libarmadillo8 (1:8.400.0+dfsg-3) ...
Setting up libpq5:armhf (10.4-2) ...
Setting up libkmlregionator1:armhf (1.3.0-5) ...
Setting up libpango-1.0-0:armhf (1.42.0-1) ...
Setting up libarpack2-dev:armhf (3.5.0+real-2+b2) ...
Setting up libarmadillo-dev (1:8.400.0+dfsg-3) ...
Setting up libcairo2:armhf (1.15.10-3) ...
Setting up libpoppler-private-dev:armhf (0.63.0-2) ...
Setting up libpq-dev (10.4-2) ...
Setting up libcurl3-gnutls:armhf (7.60.0-2) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libcurl4:armhf (7.60.0-2) ...
Setting up libkml-dev:armhf (1.3.0-5) ...
Setting up libpangoft2-1.0-0:armhf (1.42.0-1) ...
Setting up libnetcdf13:armhf (1:4.6.1-1) ...
Setting up libcurl4-gnutls-dev:armhf (7.60.0-2) ...
Setting up libnetcdf-dev (1:4.6.1-1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.0-1) ...
Setting up libhdf4-alt-dev (4.2.13-2) ...
Setting up dh-autoreconf (19) ...
Setting up odbcinst (2.3.6-0.1) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.041-2) ...
Setting up odbcinst1debian2:armhf (2.3.6-0.1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up unixodbc-dev:armhf (2.3.6-0.1) ...
Setting up libharfbuzz-icu0:armhf (1.7.6-1+b1) ...
Setting up r-base-core (3.5.0-5) ...

Creating config file /etc/R/Renviron with new version
Setting up r-bioc-biocgenerics (0.26.0-3) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up r-bioc-biobase (2.40.0-2+b1) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up r-cran-rcolorbrewer (1.1-2-2) ...
Setting up r-cran-bitops (1.0-6-3+b1) ...
Setting up r-cran-formatr (1.5-2+b1) ...
Setting up r-cran-futile.options (1.0.1-2) ...
Setting up libspatialite7:armhf (4.3.0a-5+b2) ...
Setting up icu-devtools (60.2-6) ...
Setting up r-cran-rcurl (1.95-4.10-1+b2) ...
Setting up libspatialite-dev:armhf (4.3.0a-5+b2) ...
Setting up r-cran-hwriter (1.3.2-3) ...
Setting up libharfbuzz-dev:armhf (1.7.6-1+b1) ...
Setting up libxerces-c3.2:armhf (3.2.1+debian-2+b2) ...
Setting up r-cran-lambda.r (1.2.3-2) ...
Setting up r-cran-matrixstats (0.53.1-1+b1) ...
Setting up r-cran-snow (1:0.4.2-2) ...
Setting up libdap25:armhf (3.19.1-2) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up gettext (0.19.8.1-6) ...
Setting up r-cran-lattice (0.20-35-1+b2) ...
Setting up r-cran-latticeextra (0.6-28-2+b2) ...
Setting up r-bioc-genomeinfodbdata (1.1.0-3) ...
Setting up libicu-dev (60.2-6) ...
Setting up r-base-dev (3.5.0-5) ...
Setting up libxml2-dev:armhf (2.9.4+dfsg1-7) ...
Setting up libdapclient6v5:armhf (3.19.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libdapserver7v5:armhf (3.19.1-2) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up libxerces-c-dev (3.2.1+debian-2+b2) ...
Setting up libdap-dev:armhf (3.19.1-2) ...
Setting up r-bioc-biocparallel (1.14.1-1+b1) ...
Setting up po-debconf (1.0.20) ...
Setting up r-cran-matrix (1.2-14-1+b1) ...
Setting up libgdal20 (2.3.0+dfsg-1) ...
Setting up debhelper (11.3.2) ...
Setting up dh-r (20180601) ...
Setting up libgdal-dev (2.3.0+dfsg-1) ...
Setting up r-bioc-s4vectors (0.18.2-1+b1) ...
Setting up r-bioc-iranges (2.14.10-1+b1) ...
Setting up r-bioc-delayedarray (0.6.0+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.16.0-3) ...
Setting up r-bioc-xvector (0.20.0-2+b1) ...
Setting up r-bioc-biostrings (2.48.0-2+b1) ...
Setting up r-bioc-genomicranges (1.32.3-1+b1) ...
Setting up r-bioc-summarizedexperiment (1.10.1+dfsg-1) ...
Setting up r-bioc-rsamtools (1.32.0-2+b1) ...
Setting up r-bioc-genomicalignments (1.16.0-2+b1) ...
Setting up sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-3+rpi1 linux-libc-dev_4.16.5-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-2 dbus-user-session_1.12.8-2 dctrl-tools_2.24-2 debconf_1.5.66 debhelper_11.3.2 debianutils_4.8.6 default-libmysqlclient-dev_1.0.4 dh-autoreconf_19 dh-r_20180601 dh-strip-nondeterminism_0.041-2 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-3 findutils_4.6.0+git+20171230-2 fontconfig_2.13.0-5 fontconfig-config_2.13.0-5 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-3+rpi1 gdal-data_2.3.0+dfsg-1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.3.0-3+rpi1 gfortran-7_7.3.0-19 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.7.6-1+b1 gnupg_2.2.5-1 gnupg-agent_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hdf5-helpers_1.10.0-patch1+docs-4+b2 hostname_3.20 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libarmadillo-dev_1:8.400.0+dfsg-3 libarmadillo8_1:8.400.0+dfsg-3 libarpack2_3.5.0+real-2+b2 libarpack2-dev_3.5.0+real-2+b2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-3+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-15+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.32-0.1 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-5.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcairo2_1.15.10-3 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-3+rpi1 libcharls-dev_1.1.0+dfsg-2 libcharls1_1.1.0+dfsg-2 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.60.0-2 libcurl4_7.60.0-2 libcurl4-gnutls-dev_7.60.0-2 libdap-dev_3.19.1-2 libdap25_3.19.1-2 libdapclient6v5_3.19.1-2 libdapserver7v5_3.19.1-2 libdatrie1_0.2.11-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libepsilon-dev_0.9.2+dfsg-2 libepsilon1_0.9.2+dfsg-2 libexpat1_2.2.5-3 libexpat1-dev_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-2 libfontconfig1_2.13.0-5 libfreetype6_2.8.1-2 libfreexl-dev_1.0.5-1 libfreexl1_1.0.5-1 libfribidi0_0.19.7-2 libfyba-dev_4.1.1-3 libfyba0_4.1.1-3 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-3+rpi1 libgcrypt20_1.8.2-2 libgdal-dev_2.3.0+dfsg-1 libgdal20_2.3.0+dfsg-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgeos-3.6.2_3.6.2-1 libgeos-c1v5_3.6.2-1 libgeos-dev_3.6.2-1 libgeotiff-dev_1.4.2-2+b2 libgeotiff2_1.4.2-2+b2 libgfortran-7-dev_7.3.0-19 libgfortran4_7.3.0-19 libgif-dev_5.1.4-3 libgif7_5.1.4-3 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2 libglib2.0-bin_2.56.1-2 libglib2.0-data_2.56.1-2 libglib2.0-dev_2.56.1-2 libglib2.0-dev-bin_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8.1.0-3+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.7.6-1+b1 libharfbuzz-gobject0_1.7.6-1+b1 libharfbuzz-icu0_1.7.6-1+b1 libharfbuzz0b_1.7.6-1+b1 libhdf4-0-alt_4.2.13-2 libhdf4-alt-dev_4.2.13-2 libhdf5-100_1.10.0-patch1+docs-4+b2 libhdf5-cpp-100_1.10.0-patch1+docs-4+b2 libhdf5-dev_1.10.0-patch1+docs-4+b2 libhogweed4_3.4-1 libice6_2:1.0.9-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libisl19_0.19-1 libjbig-dev_2.1-3.1+b2 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c-dev_0.12.1-1.3 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkml-dev_1.3.0-5 libkmlbase1_1.3.0-5 libkmlconvenience1_1.3.0-5 libkmldom1_1.3.0-5 libkmlengine1_1.3.0-5 libkmlregionator1_1.3.0-5 libkmlxsd1_1.3.0-5 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 liblcms2-2_2.9-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 libltdl-dev_2.4.6-2.1 libltdl7_2.4.6-2.1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmariadbclient-dev_1:10.1.29-6+b1 libmariadbclient-dev-compat_1:10.1.29-6+b1 libmariadbclient18_1:10.1.29-6+b1 libminizip-dev_1.1-8 libminizip1_1.1-8 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-4 libncurses5_6.1+20180210-4 libncurses5-dev_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnetcdf-dev_1:4.6.1-1 libnetcdf13_1:4.6.1-1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-3 libnspr4_2:4.19-3+rpi1 libnss-systemd_238-4 libnss3_2:3.37.1-1 libodbc1_2.3.6-0.1 libogdi3.2_3.2.1+ds-1+b1 libogdi3.2-dev_3.2.1+ds-1+b1 libopenjp2-7_2.3.0-1 libopenjp2-7-dev_2.3.0-1 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpango-1.0-0_1.42.0-1 libpangocairo-1.0-0_1.42.0-1 libpangoft2-1.0-0_1.42.0-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.24_5.24.1-4 libperl5.26_5.26.2-5 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-3 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libpoppler-dev_0.63.0-2 libpoppler-private-dev_0.63.0-2 libpoppler74_0.63.0-2 libpopt0_1.16-11 libpq-dev_10.4-2 libpq5_10.4-2 libprocps7_2:3.3.15-1 libproj-dev_5.1.0-1 libproj13_5.1.0-1 libpsl5_0.20.2-1 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.6~rc1-1 libpython3.6-stdlib_3.6.6~rc1-1 libqhull-dev_2015.2-4 libqhull-r7_2015.2-4 libqhull7_2015.2-4 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-2 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32-0.1 libspatialite-dev_4.3.0a-5+b2 libspatialite7_4.3.0a-5+b2 libsqlite3-0_3.24.0-1 libsqlite3-dev_3.24.0-1 libss2_1.44.2-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-3+rpi1 libsuperlu-dev_5.2.1+dfsg1-3 libsuperlu5_5.2.1+dfsg1-3 libsystemd0_238-4 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtcl8.6_8.6.8+dfsg-4 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.27-2 libthai0_0.1.27-2 libtiff-dev_4.0.9-5 libtiff5_4.0.9-5 libtiff5-dev_4.0.9-5 libtiffxx5_4.0.9-5 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtk8.6_8.6.8-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 liburiparser-dev_0.8.5-1 liburiparser1_0.8.5-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libwebp-dev_0.6.1-2 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libx11-6_2:1.6.5-1 libx11-data_2:1.6.5-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxerces-c-dev_3.2.1+debian-2+b2 libxerces-c3.2_3.2.1+debian-2+b2 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7 libxml2-dev_2.9.4+dfsg1-7 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libzstd-dev_1.3.4+dfsg-3+rpi1 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.5-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mime-support_3.60 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 mysql-common_5.8+1.0.4 nano_2.9.5-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1-1 netbase_5.4 odbcinst_2.3.6-0.1 odbcinst1debian2_2.3.6-0.1 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-5 perl-base_5.26.2-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-5 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-1 proj-data_5.1.0-1 python3_3.6.5-3 python3-distutils_3.6.5-4 python3-lib2to3_3.6.5-4 python3-minimal_3.6.5-3 python3.6_3.6.6~rc1-1 python3.6-minimal_3.6.6~rc1-1 r-base-core_3.5.0-5 r-base-dev_3.5.0-5 r-bioc-biobase_2.40.0-2+b1 r-bioc-biocgenerics_0.26.0-3 r-bioc-biocparallel_1.14.1-1+b1 r-bioc-biostrings_2.48.0-2+b1 r-bioc-delayedarray_0.6.0+dfsg-1 r-bioc-genomeinfodb_1.16.0-3 r-bioc-genomeinfodbdata_1.1.0-3 r-bioc-genomicalignments_1.16.0-2+b1 r-bioc-genomicranges_1.32.3-1+b1 r-bioc-iranges_2.14.10-1+b1 r-bioc-rsamtools_1.32.0-2+b1 r-bioc-s4vectors_0.18.2-1+b1 r-bioc-summarizedexperiment_1.10.1+dfsg-1 r-bioc-xvector_0.20.0-2+b1 r-cran-bitops_1.0-6-3+b1 r-cran-formatr_1.5-2+b1 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-hwriter_1.3.2-3 r-cran-lambda.r_1.2.3-2 r-cran-lattice_0.20-35-1+b2 r-cran-latticeextra_0.6-28-2+b2 r-cran-matrix_1.2-14-1+b1 r-cran-matrixstats_0.53.1-1+b1 r-cran-rcolorbrewer_1.1-2-2 r-cran-rcurl_1.95-4.10-1+b2 r-cran-snow_1:0.4.2-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_238-4 unixodbc-dev_2.3.6-0.1 unzip_6.0-21 util-linux_2.31.1-0.5 uuid-dev_2.32-0.1 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.2-1.3 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun May  6 06:13:46 2018 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 ./r-bioc-shortread_1.38.0-2.dsc
dpkg-source: info: extracting r-bioc-shortread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-shortread_1.38.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.38.0-2.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch

Check disc space
----------------

Sufficient free space for build

Hack binNMU version
-------------------

Created changelog entry for binNMU version 1.38.0-2+b1

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-3edd2524-e0a9-4901-9ffd-68cf02cebf01
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package r-bioc-shortread
dpkg-buildpackage: info: source version 1.38.0-2+b1
dpkg-buildpackage: info: source distribution buster-staging
 dpkg-source --before-build r-bioc-shortread-1.38.0
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean --buildsystem R
   dh_testdir -O--buildsystem=R
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules build-arch
dh build-arch --buildsystem R
   dh_testdir -a -O--buildsystem=R
   dh_update_autotools_config -a -O--buildsystem=R
   dh_autoreconf -a -O--buildsystem=R
   dh_auto_configure -a -O--buildsystem=R
   dh_auto_build -a -O--buildsystem=R
   dh_auto_test -a -O--buildsystem=R
   create-stamp debian/debhelper-build-stamp
 fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
   dh_testroot -a -O--buildsystem=R
   dh_prep -a -O--buildsystem=R
   dh_installdirs -a -O--buildsystem=R
   dh_auto_install -a -O--buildsystem=R
I: Add Depends of DEP8 test to Recommends: r-cran-runit
I: R Package: ShortRead Version: 1.38.0
I: Building using R version 3.5.0-5
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Sun, 06 May 2018 08:02:34 +0200
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 06 May 2018 08:02:34 +0200'"
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 4
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io.c -o io.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_bowtie.c -o io_bowtie.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_soap.c -o io_soap.o
g++  -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c readBfaToc.cc -o readBfaToc.o
readBfaToc.cc: In function 'SEXPREC* readBfaToc(SEXP)':
readBfaToc.cc:35:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       (void) fread( seq_name, sizeof(char), name_len, fp );
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       (void) fread( &seq_ori_len, sizeof(int), 1, fp );
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
       (void) fread( &seq_len, sizeof(int), 1, fp );
       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++  -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_maq_map.cc -o read_maq_map.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sampler.c -o sampler.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c trim.c -o trim.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG  -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"   -fopenmp -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-iXuhKy/r-base-3.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xsnap.c -o xsnap.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/libs
** R
** inst
** byte-compile and prepare package for lazy loading
code for methods in class "ShortReadFile" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqFileReader" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "QAData" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "Snapshot" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "SpTrellis" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqSampler" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqStreamer" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.23.3)
I: Using r-bioc-biocparallel for Depends:BiocParallel
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.31.2)
I: Using r-bioc-genomicalignments for Depends:GenomicAlignments (>= 1.15.6)
I: Using r-cran-runit for Recommends:runit
W: Cannot find a debian package for Suggests:BiocStyle
I: Using libgdal-dev for Suggests:BiocStyle
I: Using r-cran-runit for Suggests:RUnit
I: Using r-bioc-biomart for Suggests:biomaRt
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:yeastNagalakshmi
I: Using libgdal-dev for Suggests:yeastNagalakshmi
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.25)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.12)
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.15.2)
I: Using r-bioc-genomicranges for Imports:GenomicRanges (>= 1.31.8)
I: Using r-cran-hwriter for Imports:hwriter
I: Using r-cran-lattice for Imports:lattice
I: Using r-cran-latticeextra for Imports:latticeExtra
   dh_install -a -O--buildsystem=R
   dh_installdocs -a -O--buildsystem=R
   dh_installchangelogs -a -O--buildsystem=R
   dh_installexamples -a -O--buildsystem=R
   dh_installman -a -O--buildsystem=R
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   dh_installdebconf -a -O--buildsystem=R
   dh_installemacsen -a -O--buildsystem=R
   dh_installifupdown -a -O--buildsystem=R
   dh_installinfo -a -O--buildsystem=R
   dh_installinit -a -O--buildsystem=R
   dh_installsystemd -a -O--buildsystem=R
   dh_installmenu -a -O--buildsystem=R
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   dh_installmodules -a -O--buildsystem=R
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   dh_installgsettings -a -O--buildsystem=R
   dh_bugfiles -a -O--buildsystem=R
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   dh_lintian -a -O--buildsystem=R
   dh_gconf -a -O--buildsystem=R
   dh_icons -a -O--buildsystem=R
   dh_perl -a -O--buildsystem=R
   dh_usrlocal -a -O--buildsystem=R
   dh_link -a -O--buildsystem=R
   dh_installwm -a -O--buildsystem=R
   dh_installxfonts -a -O--buildsystem=R
   dh_strip_nondeterminism -a -O--buildsystem=R
   dh_compress -a -O--buildsystem=R
   dh_fixperms -a -O--buildsystem=R
   dh_missing -a -O--buildsystem=R
   dh_strip -a -O--buildsystem=R
   dh_makeshlibs -a -O--buildsystem=R
   dh_shlibdeps -a -O--buildsystem=R
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/libs/ShortRead.so was not linked against libgomp.so.1 (it uses none of the library's symbols)
   dh_installdeb -a -O--buildsystem=R
   dh_gencontrol -a -O--buildsystem=R
   dh_md5sums -a -O--buildsystem=R
   dh_builddeb -a -O--buildsystem=R
dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.38.0-2+b1_armhf.deb'.
dpkg-deb: building package 'r-bioc-shortread' in '../r-bioc-shortread_1.38.0-2+b1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-shortread_1.38.0-2+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build r-bioc-shortread-1.38.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-06-15T23:10:44Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Post Build Chroot                                                            |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


r-bioc-shortread_1.38.0-2+b1_armhf.changes:
-------------------------------------------

Format: 1.8
Date: Sun, 06 May 2018 08:02:34 +0200
Source: r-bioc-shortread (1.38.0-2)
Binary: r-bioc-shortread
Binary-Only: yes
Architecture: armhf
Version: 1.38.0-2+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
 r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci
Changes:
 r-bioc-shortread (1.38.0-2+b1) buster-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
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Files:
 876d4f821a8beeac6a13d11a41863030 139232 debug optional r-bioc-shortread-dbgsym_1.38.0-2+b1_armhf.deb
 09957a1679b3db8f6ba4cd80ce14507a 12649 gnu-r optional r-bioc-shortread_1.38.0-2+b1_armhf.buildinfo
 1ec3f269eb9468639637a81e05f707d0 5011640 gnu-r optional r-bioc-shortread_1.38.0-2+b1_armhf.deb

+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


r-bioc-shortread-dbgsym_1.38.0-2+b1_armhf.deb
---------------------------------------------

 new Debian package, version 2.0.
 size 139232 bytes: control archive=548 bytes.
     419 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: r-bioc-shortread-dbgsym
 Source: r-bioc-shortread (1.38.0-2)
 Version: 1.38.0-2+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 174
 Depends: r-bioc-shortread (= 1.38.0-2+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for r-bioc-shortread
 Build-Ids: bddc95f250f397c187f81d1235a81f3f0d51894b

drwxr-xr-x root/root         0 2018-05-06 06:02 ./
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/lib/
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/lib/debug/
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/lib/debug/.build-id/bd/
-rw-r--r-- root/root    167092 2018-05-06 06:02 ./usr/lib/debug/.build-id/bd/dc95f250f397c187f81d1235a81f3f0d51894b.debug
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/share/
drwxr-xr-x root/root         0 2018-05-06 06:02 ./usr/share/doc/
lrwxrwxrwx root/root         0 2018-05-06 06:02 ./usr/share/doc/r-bioc-shortread-dbgsym -> r-bioc-shortread


r-bioc-shortread_1.38.0-2+b1_armhf.deb
--------------------------------------

 new Debian package, version 2.0.
 size 5011640 bytes: control archive=4172 bytes.
    1320 bytes,    19 lines      control              
   10902 bytes,   114 lines      md5sums              
 Package: r-bioc-shortread
 Source: r-bioc-shortread (1.38.0-2)
 Version: 1.38.0-2+b1
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 7315
 Depends: r-base-core (>= 3.5.0-5), r-api-3.5, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.47.6), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), r-bioc-biobase, r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-cran-hwriter, r-cran-lattice, r-cran-latticeextra, libc6 (>= 2.7), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
 Recommends: r-cran-runit
 Suggests: libgdal-dev, r-bioc-biomart, r-bioc-genomicfeatures
 Section: gnu-r
 Priority: optional
 Homepage: https://bioconductor.org/packages/ShortRead/
 Description: GNU R classes and methods for high-throughput short-read sequencing data
  This BioConductor module is a package for input, quality assessment,
  manipulation and output of high-throughput sequencing data. ShortRead is
  provided in the R and Bioconductor environments, allowing ready access
  to additional facilities for advanced statistical analysis, data
  transformation, visualization and integration with diverse genomic
  resources.

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-rw-r--r-- root/root       846 2018-05-06 06:02 ./usr/lib/R/site-library/ShortRead/Meta/nsInfo.rds
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-rw-r--r-- root/root       261 2018-05-06 06:02 ./usr/lib/R/site-library/ShortRead/Meta/vignette.rds
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-rw-r--r-- root/root     31740 2018-05-06 06:02 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
-rw-r--r-- root/root    121368 2018-05-06 06:02 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
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| Post Build                                                                   |
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| Cleanup                                                                      |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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| Summary                                                                      |
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Build Architecture: armhf
Build-Space: 21556
Build-Time: 467
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1729
Job: r-bioc-shortread_1.38.0-2
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 2256
Source-Version: 1.38.0-2
Space: 21556
Status: successful
Version: 1.38.0-2+b1
--------------------------------------------------------------------------------
Finished at 2018-06-15T23:10:44Z
Build needed 00:37:36, 21556k disc space

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