r-bioc-variantannotation →
1.28.1-1 →
armhf → 2018-11-15 05:43:43
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| r-bioc-variantannotation 1.28.1-1 (armhf) Thu, 15 Nov 2018 04:53:40 +0000 |
+==============================================================================+
Package: r-bioc-variantannotation
Version: 1.28.1-1
Source Version: 1.28.1-1
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-c198e088-83e8-4c3d-ad6c-fb5749b2fdfe' 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 [11.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.9 MB]
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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-variantannotation' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-variantannotation.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-variantannotation.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1733 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-variantannotation 1.28.1-1 (dsc) [2683 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-variantannotation 1.28.1-1 (tar) [1723 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-variantannotation 1.28.1-1 (diff) [7684 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-LGB5f0/r-bioc-variantannotation-1.28.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-variantannotation-LGB5f0' 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-16Tsl3/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-16Tsl3/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-16Tsl3/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-16Tsl3/apt_archive ./ InRelease
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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 krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd libperl5.26 libsasl2-modules
libssl1.1 openssl perl-modules-5.26 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 61 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
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(Reading database ... 17652 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 (>= 0.15.3), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-bioc-summarizedexperiment (>= 1.9.9), r-bioc-rsamtools (>= 1.33.6), r-cran-dbi, libgdal-dev, r-bioc-biobase, r-bioc-s4vectors (>= 0.17.24), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3)
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-biocgenerics (>= 0.15.3), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-bioc-summarizedexperiment (>= 1.9.9), r-bioc-rsamtools (>= 1.33.6), r-cran-dbi, libgdal-dev, r-bioc-biobase, r-bioc-s4vectors (>= 0.17.24), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3)
dpkg-deb: building package 'sbuild-build-depends-r-bioc-variantannotation-dummy' in '/<<BUILDDIR>>/resolver-16Tsl3/apt_archive/sbuild-build-depends-r-bioc-variantannotation-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-variantannotation-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-16Tsl3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-16Tsl3/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-16Tsl3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-16Tsl3/apt_archive ./ Sources [692 B]
Get:5 copy:/<<BUILDDIR>>/resolver-16Tsl3/apt_archive ./ Packages [777 B]
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Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-variantannotation 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 krb5-locales libgpg-error-l10n
libnss-systemd libpam-systemd libperl5.26 libsasl2-modules perl-modules-5.26
systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cpp cpp-8 dctrl-tools
debhelper default-libmysqlclient-dev dh-autoreconf dh-r
dh-strip-nondeterminism dwz file fontconfig fontconfig-config
fonts-dejavu-core g++ g++-8 gcc gcc-7-base gcc-8 gcc-8-base gdal-data
gettext gettext-base gfortran gfortran-8 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 libarmadillo9 libarpack2 libarpack2-dev
libasan5 libatomic1 libblas-dev libblas3 libboost-dev libboost1.62-dev
libbsd0 libbz2-dev libcairo2 libcc1-0 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
libfile-which-perl libfontconfig1 libfreetype6 libfreexl-dev libfreexl1
libfribidi0 libfyba-dev libfyba0 libgcc-8-dev libgcc1 libgdal-dev libgdal20
libgeos-3.7.0 libgeos-c1v5 libgeos-dev libgeotiff-dev libgeotiff2
libgfortran-8-dev libgfortran4 libgfortran5 libgif-dev libgif7
libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libglib2.0-data
libglib2.0-dev libglib2.0-dev-bin libgomp1 libgraphite2-3 libgraphite2-dev
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 libjbig-dev
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjson-c-dev
libkml-dev libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1
libkmlregionator1 libkmlxsd1 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 libncurses6 libncursesw6
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 libpoppler80 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 libsqlite3-0
libsqlite3-dev libssh2-1 libstdc++-8-dev libstdc++6 libsuperlu-dev
libsuperlu5 libswitch-perl libsz2 libtcl8.6 libthai-data libthai0
libtiff-dev libtiff5 libtiff5-dev libtiffxx5 libtinfo6 libtk8.6 libtool
libubsan1 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 littler 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-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel
r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray
r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools
r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment
r-bioc-xvector r-cran-assertthat r-cran-bit r-cran-bit64 r-cran-bitops
r-cran-blob r-cran-crayon r-cran-curl r-cran-dbi r-cran-digest
r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue
r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice
r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats
r-cran-memoise r-cran-mime r-cran-openssl r-cran-pkgconfig r-cran-pkgkitten
r-cran-prettyunits r-cran-progress r-cran-r6 r-cran-rcpp r-cran-rcurl
r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr
r-cran-xml 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-8-locales debtags dh-make gcc-8-doc libstdc++6-8-dbg
gcc-multilib manpages-dev flex bison gdb gcc-doc libgcc1-dbg libgomp1-dbg
libitm1-dbg libatomic1-dbg libasan5-dbg liblsan0-dbg libtsan0-dbg
libubsan1-dbg libmpx2-dbg libquadmath0-dbg gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-8-doc libgfortran5-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 libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils
libgraphite2-utils 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-11 proj-bin readline-doc sqlite3-doc libstdc++-8-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-graph r-cran-knitr r-bioc-affy r-bioc-deseq2 r-bioc-annotate
r-cran-foreach r-cran-bbmisc r-bioc-variantannotation r-bioc-shortread
r-cran-codetools r-cran-data.table r-cran-rmarkdown r-cran-testthat
r-cran-biocmanager r-cran-runit r-bioc-edger r-bioc-ensembldb r-bioc-gviz
r-bioc-annotationhub r-bioc-genefilter r-bioc-limma r-cran-pillar
r-cran-rstudioapi r-cran-rmysql r-cran-shiny r-cran-r.utils r-cran-forcats
r-cran-ggplot2 r-cran-dplyr r-cran-withr r-cran-lubridate r-cran-httpuv
r-cran-png r-cran-readr r-cran-xml2 r-cran-plyr r-cran-getopt
r-cran-base64enc r-cran-scales r-cran-inline r-cran-rmpi r-cran-rsprng
r-cran-rlecuyer
Recommended packages:
devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl proj-bin
shared-mime-info xdg-user-dirs libgpm2 libpng-tools poppler-data
publicsuffix libmail-sendmail-perl r-recommended r-doc-html r-bioc-go.db
r-cran-runit r-cran-batchjobs r-cran-doparallel r-cran-batchtools
r-cran-rmpi r-bioc-biovizbase r-bioc-genefilter r-bioc-shortread
r-bioc-annotate r-cran-testthat r-cran-withr r-cran-mockery r-cran-httpuv
r-cran-webutils r-cran-testit r-cran-codetools r-cran-survival r-cran-pillar
r-cran-sp r-cran-dbitest r-cran-htmltools r-cran-htmlwidgets
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 gcc-7-base gdal-data
gettext gettext-base gfortran gfortran-8 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 libarmadillo9 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 libfile-which-perl libfontconfig1
libfreetype6 libfreexl-dev libfreexl1 libfribidi0 libfyba-dev libfyba0
libgdal-dev libgdal20 libgeos-3.7.0 libgeos-c1v5 libgeos-dev libgeotiff-dev
libgeotiff2 libgfortran-8-dev libgfortran4 libgfortran5 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
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 libjbig-dev
libjbig0 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjson-c-dev
libkml-dev libkmlbase1 libkmlconvenience1 libkmldom1 libkmlengine1
libkmlregionator1 libkmlxsd1 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 libpoppler80 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 libswitch-perl libsz2 libtcl8.6
libthai-data libthai0 libtiff-dev libtiff5 libtiff5-dev libtiffxx5 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 littler 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-annotationdbi r-bioc-biobase r-bioc-biocgenerics r-bioc-biocparallel
r-bioc-biomart r-bioc-biostrings r-bioc-bsgenome r-bioc-delayedarray
r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
r-bioc-genomicfeatures r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools
r-bioc-rtracklayer r-bioc-s4vectors r-bioc-summarizedexperiment
r-bioc-xvector r-cran-assertthat r-cran-bit r-cran-bit64 r-cran-bitops
r-cran-blob r-cran-crayon r-cran-curl r-cran-dbi r-cran-digest
r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-glue
r-cran-hms r-cran-httr r-cran-jsonlite r-cran-lambda.r r-cran-lattice
r-cran-littler r-cran-magrittr r-cran-matrix r-cran-matrixstats
r-cran-memoise r-cran-mime r-cran-openssl r-cran-pkgconfig r-cran-pkgkitten
r-cran-prettyunits r-cran-progress r-cran-r6 r-cran-rcpp r-cran-rcurl
r-cran-rlang r-cran-rsqlite r-cran-snow r-cran-stringi r-cran-stringr
r-cran-xml sbuild-build-depends-r-bioc-variantannotation-dummy ucf
unixodbc-dev unzip uuid-dev x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
cpp cpp-8 g++ g++-8 gcc gcc-8 gcc-8-base libasan5 libatomic1 libcc1-0
libgcc-8-dev libgcc1 libgomp1 libncurses6 libncursesw6 libsqlite3-0
libstdc++-8-dev libstdc++6 libtinfo6 libubsan1
20 upgraded, 296 newly installed, 0 to remove and 41 not upgraded.
Need to get 232 MB/238 MB of archives.
After this operation, 689 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-16Tsl3/apt_archive ./ sbuild-build-depends-r-bioc-variantannotation-dummy 0.invalid.0 [1052 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 libcc1-0 armhf 8.2.0-9+rpi1 [30.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-9+rpi1 [188 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-9+rpi1 [36.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-9+rpi1 [64.2 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-9+rpi1 [8096 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-9+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-9+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-9+rpi1 [5942 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-9+rpi1 [1564 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-9+rpi1 [598 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-9+rpi1 [5847 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-9+rpi1 [5474 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-9+rpi1 [325 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-3 [1160 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.7-1 [567 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.7-1 [1380 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.7-1 [36.4 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20181013-1 [78.3 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20181013-1 [311 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20181013-1 [103 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.25.3-1 [544 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.7-1 [1639 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.7-1 [240 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.7-1 [19.9 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.7-1 [61.4 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-8 [117 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-8 [434 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf g++ armhf 4:8.2.0-2+rpi1 [1628 B]
Get:45 http://172.17.0.1/private buster-staging/main armhf gcc armhf 4:8.2.0-2+rpi1 [5196 B]
Get:46 http://172.17.0.1/private buster-staging/main armhf cpp armhf 4:8.2.0-2+rpi1 [19.5 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.45.0-1 [20.5 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.45.0-1 [12.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-8 [1220 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.5.3 [1002 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libmariadbclient18 armhf 1:10.1.37-1 [683 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libmariadbclient-dev armhf 1:10.1.37-1 [1533 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libmariadbclient-dev-compat armhf 1:10.1.37-1 [28.2 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf default-libmysqlclient-dev armhf 1.0.4 [3708 B]
Get:70 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-9+rpi1 [205 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1+b1 [104 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13.1-1 [132 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.13.1-1 [108 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.13.1-1 [99.2 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.16.0-1 [600 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.34.0-1 [73.4 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.61.0-1 [282 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1+b1 [1493 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.1-2 [404 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 1.0.5-3 [61.9 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.28-1 [170 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.12-1 [35.8 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.28-1 [50.9 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.4-3 [166 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-3 [61.8 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-3 [51.4 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9+git181026-1 [229 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.5.1-1 [23.6 MB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-9+rpi1 [248 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-9+rpi1 [5812 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.2.0-2+rpi1 [1432 B]
Get:109 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1+b1 [113 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1+b1 [1550 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20181013-1 [278 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20181013-1 [940 B]
Get:113 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.34-2+rpi1 [275 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.9.0-1+rpi1 [650 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.9.0-1+rpi1 [657 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.58.0-1 [78.2 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.58.0-1 [143 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.9.0-1+rpi1 [665 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.58.1-2 [1105 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.58.1-2 [114 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.7.1-1 [78.7 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.7.1-1 [144 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.58.1-2 [151 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.58.1-2 [1237 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.12-1 [22.6 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.9.0-1+rpi1 [944 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.5.1-1 [4476 B]
Get:139 http://172.17.0.1/private buster-staging/main armhf libfile-which-perl all 1.22-1 [14.6 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf dh-r all 20181101 [34.0 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf gdal-data all 2.3.2+dfsg-2 [733 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf hdf5-helpers armhf 1.10.0-patch1+docs-4+b2 [36.4 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf libaec-dev armhf 1.0.2-1 [19.1 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf libarpack2 armhf 3.6.3-1+rpi1 [81.2 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf libarmadillo9 armhf 1:9.100.6+dfsg-1 [86.3 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf libarpack2-dev armhf 3.6.3-1+rpi1 [89.3 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf libhdf5-100 armhf 1.10.0-patch1+docs-4+b2 [1216 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf libhdf5-cpp-100 armhf 1.10.0-patch1+docs-4+b2 [117 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf libhdf5-dev armhf 1.10.0-patch1+docs-4+b2 [2150 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf libsuperlu-dev armhf 5.2.1+dfsg1-3 [18.2 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf libarmadillo-dev armhf 1:9.100.6+dfsg-1 [357 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-10+b1 [7003 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf libboost-dev armhf 1.62.0.1+b8 [3918 B]
Get:154 http://172.17.0.1/private buster-staging/main armhf libcharls1 armhf 1.1.0+dfsg-3 [44.4 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf libcharls-dev armhf 1.1.0+dfsg-3 [21.8 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.61.0-1 [281 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf libcurl4-gnutls-dev armhf 7.61.0-1 [353 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf libdap25 armhf 3.20.0-1 [468 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf libdapserver7v5 armhf 3.20.0-1 [126 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf libdapclient6v5 armhf 3.20.0-1 [183 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf libxml2-dev armhf 2.9.4+dfsg1-7 [672 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf uuid-dev armhf 2.32.1-0.1 [91.9 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf libdap-dev armhf 3.20.0-1 [768 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf libpopt0 armhf 1.16-11 [45.9 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf libepsilon1 armhf 0.9.2+dfsg-4 [36.4 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf libepsilon-dev armhf 0.9.2+dfsg-4 [46.0 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf libexpat1-dev armhf 2.2.6-1 [127 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf libfreexl1 armhf 1.0.5-3 [31.8 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf libfreexl-dev armhf 1.0.5-3 [30.3 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf libfyba0 armhf 4.1.1-6 [97.8 kB]
Get:171 http://172.17.0.1/private buster-staging/main armhf libfyba-dev armhf 4.1.1-6 [161 kB]
Get:172 http://172.17.0.1/private buster-staging/main armhf libgeos-3.7.0 armhf 3.7.0-1 [630 kB]
Get:173 http://172.17.0.1/private buster-staging/main armhf libgeos-c1v5 armhf 3.7.0-1 [284 kB]
Get:174 http://172.17.0.1/private buster-staging/main armhf proj-data all 5.2.0-1 [6986 kB]
Get:175 http://172.17.0.1/private buster-staging/main armhf libproj13 armhf 5.2.0-1 [185 kB]
Get:176 http://172.17.0.1/private buster-staging/main armhf libgeotiff2 armhf 1.4.2-4 [66.2 kB]
Get:177 http://172.17.0.1/private buster-staging/main armhf libgif7 armhf 5.1.4-3 [41.0 kB]
Get:178 http://172.17.0.1/private buster-staging/main armhf libhdf4-0-alt armhf 4.2.13-4 [234 kB]
Get:179 http://172.17.0.1/private buster-staging/main armhf liburiparser1 armhf 0.8.6-1 [36.0 kB]
Get:180 http://172.17.0.1/private buster-staging/main armhf libkmlbase1 armhf 1.3.0-7 [42.1 kB]
Get:181 http://172.17.0.1/private buster-staging/main armhf libkmldom1 armhf 1.3.0-7 [144 kB]
Get:182 http://172.17.0.1/private buster-staging/main armhf libkmlengine1 armhf 1.3.0-7 [67.4 kB]
Get:183 http://172.17.0.1/private buster-staging/main armhf libkmlconvenience1 armhf 1.3.0-7 [44.4 kB]
Get:184 http://172.17.0.1/private buster-staging/main armhf libkmlregionator1 armhf 1.3.0-7 [22.2 kB]
Get:185 http://172.17.0.1/private buster-staging/main armhf libkmlxsd1 armhf 1.3.0-7 [28.7 kB]
Get:186 http://172.17.0.1/private buster-staging/main armhf libnetcdf13 armhf 1:4.6.1-3 [344 kB]
Get:187 http://172.17.0.1/private buster-staging/main armhf libltdl7 armhf 2.4.6-6 [387 kB]
Get:188 http://172.17.0.1/private buster-staging/main armhf libodbc1 armhf 2.3.6-0.1 [186 kB]
Get:189 http://172.17.0.1/private buster-staging/main armhf libogdi3.2 armhf 3.2.1+ds-4 [194 kB]
Get:190 http://172.17.0.1/private buster-staging/main armhf liblcms2-2 armhf 2.9-3 [116 kB]
Get:191 http://172.17.0.1/private buster-staging/main armhf libnspr4 armhf 2:4.20-1 [89.6 kB]
Get:192 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.39-1 [937 kB]
Get:193 http://172.17.0.1/private buster-staging/main armhf libpoppler80 armhf 0.69.0-2 [1322 kB]
Get:194 http://172.17.0.1/private buster-staging/main armhf libpq5 armhf 11.1-1 [146 kB]
Get:195 http://172.17.0.1/private buster-staging/main armhf libxerces-c3.2 armhf 3.2.2+debian-1 [707 kB]
Get:196 http://172.17.0.1/private buster-staging/main armhf odbcinst armhf 2.3.6-0.1 [47.6 kB]
Get:197 http://172.17.0.1/private buster-staging/main armhf odbcinst1debian2 armhf 2.3.6-0.1 [70.8 kB]
Get:198 http://172.17.0.1/private buster-staging/main armhf libgdal20 armhf 2.3.2+dfsg-2+b2 [4847 kB]
Get:199 http://172.17.0.1/private buster-staging/main armhf libgeos-dev armhf 3.7.0-1 [306 kB]
Get:200 http://172.17.0.1/private buster-staging/main armhf libtiffxx5 armhf 4.0.9+git181026-1 [100 kB]
Get:201 http://172.17.0.1/private buster-staging/main armhf libtiff5-dev armhf 4.0.9+git181026-1 [340 kB]
Get:202 http://172.17.0.1/private buster-staging/main armhf libtiff-dev armhf 4.0.9+git181026-1 [96.6 kB]
Get:203 http://172.17.0.1/private buster-staging/main armhf libgeotiff-dev armhf 1.4.2-4 [93.4 kB]
Get:204 http://172.17.0.1/private buster-staging/main armhf libgif-dev armhf 5.1.4-3 [43.4 kB]
Get:205 http://172.17.0.1/private buster-staging/main armhf libnetcdf-dev armhf 1:4.6.1-3 [80.6 kB]
Get:206 http://172.17.0.1/private buster-staging/main armhf libhdf4-alt-dev armhf 4.2.13-4 [310 kB]
Get:207 http://172.17.0.1/private buster-staging/main armhf libjson-c-dev armhf 0.12.1-1.3 [34.6 kB]
Get:208 http://172.17.0.1/private buster-staging/main armhf libminizip-dev armhf 1.1-8 [25.6 kB]
Get:209 http://172.17.0.1/private buster-staging/main armhf liburiparser-dev armhf 0.8.6-1 [18.3 kB]
Get:210 http://172.17.0.1/private buster-staging/main armhf libkml-dev armhf 1.3.0-7 [939 kB]
Get:211 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-6 [159 kB]
Get:212 http://172.17.0.1/private buster-staging/main armhf libproj-dev armhf 5.2.0-1 [228 kB]
Get:213 http://172.17.0.1/private buster-staging/main armhf libogdi3.2-dev armhf 3.2.1+ds-4 [38.2 kB]
Get:214 http://172.17.0.1/private buster-staging/main armhf libopenjp2-7-dev armhf 2.3.0-1 [43.7 kB]
Get:215 http://172.17.0.1/private buster-staging/main armhf libpoppler-dev armhf 0.69.0-2 [23.0 kB]
Get:216 http://172.17.0.1/private buster-staging/main armhf libpoppler-private-dev armhf 0.69.0-2 [190 kB]
Get:217 http://172.17.0.1/private buster-staging/main armhf libpq-dev armhf 11.1-1 [146 kB]
Get:218 http://172.17.0.1/private buster-staging/main armhf libqhull-r7 armhf 2015.2-4 [171 kB]
Get:219 http://172.17.0.1/private buster-staging/main armhf libqhull-dev armhf 2015.2-4 [346 kB]
Get:220 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.25.3-1 [677 kB]
Get:221 http://172.17.0.1/private buster-staging/main armhf libspatialite-dev armhf 4.3.0a-5+b2 [1460 kB]
Get:222 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.6.1-2 [86.7 kB]
Get:223 http://172.17.0.1/private buster-staging/main armhf libwebp-dev armhf 0.6.1-2 [304 kB]
Get:224 http://172.17.0.1/private buster-staging/main armhf libxerces-c-dev armhf 3.2.2+debian-1 [1466 kB]
Get:225 http://172.17.0.1/private buster-staging/main armhf libzstd-dev armhf 1.3.5+dfsg-1+rpi1 [226 kB]
Get:226 http://172.17.0.1/private buster-staging/main armhf unixodbc-dev armhf 2.3.6-0.1 [232 kB]
Get:227 http://172.17.0.1/private buster-staging/main armhf libgdal-dev armhf 2.3.2+dfsg-2+b2 [6274 kB]
Get:228 http://172.17.0.1/private buster-staging/main armhf r-cran-littler armhf 0.3.5-1 [301 kB]
Get:229 http://172.17.0.1/private buster-staging/main armhf littler all 0.3.5-1 [13.4 kB]
Get:230 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.28.0-1 [644 kB]
Get:231 http://172.17.0.1/private buster-staging/main armhf r-bioc-biobase armhf 2.42.0-1 [2215 kB]
Get:232 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.3-1+b1 [1799 kB]
Get:233 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.12-1 [2130 kB]
Get:234 http://172.17.0.1/private buster-staging/main armhf r-cran-dbi all 1.0.0-2 [789 kB]
Get:235 http://172.17.0.1/private buster-staging/main armhf r-cran-bit armhf 1.1-14-1 [218 kB]
Get:236 http://172.17.0.1/private buster-staging/main armhf r-cran-bit64 armhf 0.9-7-3 [433 kB]
Get:237 http://172.17.0.1/private buster-staging/main armhf r-cran-magrittr all 1.5-5 [152 kB]
Get:238 http://172.17.0.1/private buster-staging/main armhf r-cran-assertthat all 0.2.0-2 [54.4 kB]
Get:239 http://172.17.0.1/private buster-staging/main armhf r-cran-prettyunits all 1.0.2-3 [32.4 kB]
Get:240 http://172.17.0.1/private buster-staging/main armhf r-cran-blob all 1.1.1-2 [25.0 kB]
Get:241 http://172.17.0.1/private buster-staging/main armhf r-cran-digest armhf 0.6.18-1 [133 kB]
Get:242 http://172.17.0.1/private buster-staging/main armhf r-cran-memoise all 1.1.0-2 [38.6 kB]
Get:243 http://172.17.0.1/private buster-staging/main armhf r-cran-pkgconfig all 2.0.2-1 [19.4 kB]
Get:244 http://172.17.0.1/private buster-staging/main armhf r-cran-pkgkitten all 0.1.4-2 [22.4 kB]
Get:245 http://172.17.0.1/private buster-staging/main armhf r-cran-rcpp armhf 1.0.0-1 [3356 kB]
Get:246 http://172.17.0.1/private buster-staging/main armhf r-cran-rsqlite armhf 2.1.1-2+b2 [763 kB]
Get:247 http://172.17.0.1/private buster-staging/main armhf r-bioc-annotationdbi all 1.44.0-1 [4629 kB]
Get:248 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr all 1.5-3 [149 kB]
Get:249 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:250 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:251 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:252 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.3-1 [108 kB]
Get:253 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.16.0-1 [1056 kB]
Get:254 http://172.17.0.1/private buster-staging/main armhf r-cran-xml armhf 3.98-1.16-1 [1938 kB]
Get:255 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:256 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.11-1 [711 kB]
Get:257 http://172.17.0.1/private buster-staging/main armhf r-cran-rlang armhf 0.2.2-1 [807 kB]
Get:258 http://172.17.0.1/private buster-staging/main armhf r-cran-hms all 0.4.2-2 [59.1 kB]
Get:259 http://172.17.0.1/private buster-staging/main armhf r-cran-r6 all 2.3.0-1 [73.5 kB]
Get:260 http://172.17.0.1/private buster-staging/main armhf r-cran-crayon all 1.3.4-4 [750 kB]
Get:261 http://172.17.0.1/private buster-staging/main armhf r-cran-progress all 1.2.0-1 [80.3 kB]
Get:262 http://172.17.0.1/private buster-staging/main armhf r-cran-glue armhf 1.3.0-1 [91.5 kB]
Get:263 http://172.17.0.1/private buster-staging/main armhf r-cran-stringi armhf 1.2.4-1 [646 kB]
Get:264 http://172.17.0.1/private buster-staging/main armhf r-cran-stringr all 1.3.1-2 [179 kB]
Get:265 http://172.17.0.1/private buster-staging/main armhf r-cran-jsonlite armhf 1.5-3 [632 kB]
Get:266 http://172.17.0.1/private buster-staging/main armhf r-cran-mime armhf 0.6-1 [34.8 kB]
Get:267 http://172.17.0.1/private buster-staging/main armhf r-cran-curl armhf 3.2-2 [361 kB]
Get:268 http://172.17.0.1/private buster-staging/main armhf r-cran-openssl armhf 1.0.2+dfsg-1 [340 kB]
Get:269 http://172.17.0.1/private buster-staging/main armhf r-cran-httr all 1.3.1-2 [428 kB]
Get:270 http://172.17.0.1/private buster-staging/main armhf r-bioc-biomart all 2.38.0+dfsg-1 [261 kB]
Get:271 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2+b1 [592 kB]
Get:272 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2+b1 [14.1 MB]
Get:273 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.2.0-1 [9196 kB]
Get:274 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.18.0-1 [3694 kB]
Get:275 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.7-1 [1941 kB]
Get:276 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.34.0-1 [3492 kB]
Get:277 http://172.17.0.1/private buster-staging/main armhf r-cran-matrixstats armhf 0.54.0-1 [551 kB]
Get:278 http://172.17.0.1/private buster-staging/main armhf r-bioc-delayedarray all 0.6.6+dfsg-1 [1056 kB]
Get:279 http://172.17.0.1/private buster-staging/main armhf r-cran-lattice armhf 0.20-38-1 [1120 kB]
Get:280 http://172.17.0.1/private buster-staging/main armhf r-cran-matrix armhf 1.2-15-1 [3356 kB]
Get:281 http://172.17.0.1/private buster-staging/main armhf r-bioc-summarizedexperiment all 1.10.1+dfsg-1 [1882 kB]
Get:282 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicalignments armhf 1.16.0-2+b1 [2089 kB]
Get:283 http://172.17.0.1/private buster-staging/main armhf r-bioc-rtracklayer armhf 1.40.6-1 [2401 kB]
Get:284 http://172.17.0.1/private buster-staging/main armhf r-bioc-bsgenome all 1.50.0-1 [6995 kB]
Get:285 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicfeatures all 1.34.1+dfsg-1 [1556 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package libbsd0:armhf.
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Preparing to unpack .../libbsd0_0.9.1-1_armhf.deb ...
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Unpacking gcc-8-base:armhf (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
Setting up gcc-8-base:armhf (8.2.0-9+rpi1) ...
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Unpacking libgcc1:armhf (1:8.2.0-9+rpi1) over (1:8.2.0-7+rpi1) ...
Setting up libgcc1:armhf (1:8.2.0-9+rpi1) ...
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Preparing to unpack .../0-libgomp1_8.2.0-9+rpi1_armhf.deb ...
Unpacking libgomp1:armhf (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
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Unpacking libubsan1:armhf (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
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Unpacking g++-8 (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
Preparing to unpack .../5-libstdc++-8-dev_8.2.0-9+rpi1_armhf.deb ...
Unpacking libstdc++-8-dev:armhf (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
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Unpacking libgcc-8-dev:armhf (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
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Unpacking gcc-8 (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
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Unpacking cpp-8 (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
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Unpacking libstdc++6:armhf (8.2.0-9+rpi1) over (8.2.0-7+rpi1) ...
Setting up libstdc++6:armhf (8.2.0-9+rpi1) ...
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Unpacking groff-base (1.22.3-10) ...
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Unpacking python3.6-minimal (3.6.7-1) ...
Setting up libpython3.6-minimal:armhf (3.6.7-1) ...
Setting up python3.6-minimal (3.6.7-1) ...
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Unpacking mime-support (3.61) ...
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Unpacking libtinfo6:armhf (6.1+20181013-1) over (6.1+20180714-1) ...
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Unpacking libsqlite3-0:armhf (3.25.3-1) over (3.25.2-1) ...
Setting up libsqlite3-0:armhf (3.25.3-1) ...
Selecting previously unselected package libpython3.6-stdlib:armhf.
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Setting up python3-minimal (3.6.7-1) ...
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Unpacking libmagic1:armhf (1:5.34-2) ...
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Unpacking file (1:5.34-2) ...
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Setting up libxcb-shm0:armhf (1.13.1-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libarpack2:armhf (3.6.3-1+rpi1) ...
Setting up libpoppler80:armhf (0.69.0-2) ...
Setting up libboost-dev:armhf (1.62.0.1+b8) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up python3-lib2to3 (3.7.1-1) ...
Setting up python3-distutils (3.7.1-1) ...
Setting up fontconfig (2.13.1-2) ...
Regenerating fonts cache... done.
Setting up liblapack-dev:armhf (3.8.0-1+b1) ...
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 (2.4.6-6) ...
Setting up libtiff-dev (4.0.9+git181026-1) ...
Setting up libgeotiff-dev:armhf (1.4.2-4) ...
Setting up libhdf5-cpp-100:armhf (1.10.0-patch1+docs-4+b2) ...
Setting up libpoppler-dev:armhf (0.69.0-2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libglib2.0-dev-bin (2.58.1-2) ...
Setting up libarmadillo9 (1:9.100.6+dfsg-1) ...
Setting up gfortran-8 (8.2.0-9+rpi1) ...
Setting up libxss1:armhf (1:1.2.3-1) ...
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 gcc (4:8.2.0-2+rpi1) ...
Setting up libkmlconvenience1:armhf (1.3.0-7) ...
Setting up libglib2.0-dev:armhf (2.58.1-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libkmlregionator1:armhf (1.3.0-7) ...
Setting up libpango-1.0-0:armhf (1.42.4-3) ...
Setting up libarpack2-dev:armhf (3.6.3-1+rpi1) ...
Setting up g++ (4:8.2.0-2+rpi1) ...
Setting up libnetcdf-dev (1:4.6.1-3) ...
Setting up libarmadillo-dev (1:9.100.6+dfsg-1) ...
Setting up gfortran (4:8.2.0-2+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 libcairo2:armhf (1.16.0-1) ...
Setting up libpoppler-private-dev:armhf (0.69.0-2) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libkml-dev:armhf (1.3.0-7) ...
Setting up libhdf4-alt-dev (4.2.13-4) ...
Setting up libpangoft2-1.0-0:armhf (1.42.4-3) ...
Setting up libpangocairo-1.0-0:armhf (1.42.4-3) ...
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 (0.45.0-1) ...
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 (1.9.0-1+rpi1) ...
Setting up r-base-core (3.5.1-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-cran-littler (0.3.5-1) ...
Setting up littler (0.3.5-1) ...
Setting up r-cran-crayon (1.3.4-4) ...
Setting up r-cran-curl (3.2-2) ...
Setting up r-bioc-biocgenerics (0.28.0-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up r-cran-assertthat (0.2.0-2) ...
Setting up r-bioc-biobase (2.42.0-1) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up r-cran-jsonlite (1.5-3) ...
Setting up r-cran-bitops (1.0-6-4) ...
Setting up r-cran-formatr (1.5-3) ...
Setting up r-cran-dbi (1.0.0-2) ...
Setting up r-cran-stringi (1.2.4-1) ...
Setting up r-cran-pkgkitten (0.1.4-2) ...
Setting up r-cran-futile.options (1.0.1-2) ...
Setting up r-cran-rcpp (1.0.0-1) ...
Setting up r-cran-r6 (2.3.0-1) ...
Setting up libspatialite7:armhf (4.3.0a-5+b2) ...
Setting up icu-devtools (60.2-6) ...
Setting up r-cran-rcurl (1.95-4.11-1) ...
Setting up r-cran-mime (0.6-1) ...
Setting up libspatialite-dev:armhf (4.3.0a-5+b2) ...
Setting up libharfbuzz-dev:armhf (1.9.0-1+rpi1) ...
Setting up r-cran-rlang (0.2.2-1) ...
Setting up r-cran-digest (0.6.18-1) ...
Setting up libxerces-c3.2:armhf (3.2.2+debian-1) ...
Setting up r-cran-bit (1.1-14-1) ...
Setting up r-cran-magrittr (1.5-5) ...
Setting up r-cran-pkgconfig (2.0.2-1) ...
Setting up r-cran-lambda.r (1.2.3-2) ...
Setting up r-cran-matrixstats (0.54.0-1) ...
Setting up r-cran-snow (1:0.4.3-1) ...
Setting up r-cran-glue (1.3.0-1) ...
Setting up r-cran-memoise (1.1.0-2) ...
Setting up r-bioc-s4vectors (0.18.3-1+b1) ...
Setting up r-cran-bit64 (0.9-7-3) ...
Setting up r-cran-xml (3.98-1.16-1) ...
Setting up libdap25:armhf (3.20.0-1) ...
Setting up r-cran-openssl (1.0.2+dfsg-1) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up gettext (0.19.8.1-8) ...
Setting up r-cran-lattice (0.20-38-1) ...
Setting up r-bioc-genomeinfodbdata (1.2.0-1) ...
Setting up r-cran-stringr (1.3.1-2) ...
Setting up r-cran-prettyunits (1.0.2-3) ...
Setting up libicu-dev (60.2-6) ...
Setting up r-base-dev (3.5.1-1) ...
Setting up libxml2-dev:armhf (2.9.4+dfsg1-7) ...
Setting up libdapclient6v5:armhf (3.20.0-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libdapserver7v5:armhf (3.20.0-1) ...
Setting up r-cran-hms (0.4.2-2) ...
Setting up r-cran-blob (1.1.1-2) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up r-cran-rsqlite (2.1.1-2+b2) ...
Setting up r-cran-httr (1.3.1-2) ...
Setting up r-bioc-iranges (2.14.12-1) ...
Setting up libxerces-c-dev (3.2.2+debian-1) ...
Setting up libdap-dev:armhf (3.20.0-1) ...
Setting up r-bioc-biocparallel (1.16.0-1) ...
Setting up po-debconf (1.0.20) ...
Setting up r-cran-progress (1.2.0-1) ...
Setting up r-cran-matrix (1.2-15-1) ...
Setting up r-bioc-delayedarray (0.6.6+dfsg-1) ...
Setting up r-bioc-genomeinfodb (1.18.0-1) ...
Setting up libgdal20 (2.3.2+dfsg-2+b2) ...
Setting up r-bioc-xvector (0.20.0-2+b1) ...
Setting up r-bioc-biostrings (2.48.0-2+b1) ...
Setting up r-bioc-annotationdbi (1.44.0-1) ...
Setting up r-bioc-genomicranges (1.32.7-1) ...
Setting up debhelper (11.5.3) ...
Setting up dh-r (20181101) ...
Setting up libgdal-dev (2.3.2+dfsg-2+b2) ...
Setting up r-bioc-summarizedexperiment (1.10.1+dfsg-1) ...
Setting up r-bioc-biomart (2.38.0+dfsg-1) ...
Setting up r-bioc-rsamtools (1.34.0-1) ...
Setting up r-bioc-genomicalignments (1.16.0-2+b1) ...
Setting up r-bioc-rtracklayer (1.40.6-1) ...
Setting up r-bioc-genomicfeatures (1.34.1+dfsg-1) ...
Setting up r-bioc-bsgenome (1.50.0-1) ...
Setting up sbuild-build-depends-r-bioc-variantannotation-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-6+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-6+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-9+rpi1 gcc-8_8.2.0-9+rpi1 libc6-dev_2.27-6+rpi1 libstdc++-8-dev_8.2.0-9+rpi1 libstdc++6_8.2.0-9+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.118 apt_1.7.0 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-8 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-6+rpi1 binutils-arm-linux-gnueabihf_2.31.1-6+rpi1 binutils-common_2.31.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-9+rpi1 dash_0.5.10.2-1 dbus_1.12.10-1 dbus-user-session_1.12.10-1 dctrl-tools_2.24-3 debconf_1.5.69 debhelper_11.5.3 debianutils_4.8.6 default-libmysqlclient-dev_1.0.4 dh-autoreconf_19 dh-r_20181101 dh-strip-nondeterminism_0.45.0-1 diffutils_1:3.6-1 dirmngr_2.2.10-3+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.4-2 e2fsprogs_1.44.4-2 e2fsprogs-l10n_1.44.4-2 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-9+rpi1 gcc_4:8.2.0-2+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+b19 gcc-5-base_5.5.0-8 gcc-7-base_7.3.0-19 gcc-8_8.2.0-9+rpi1 gcc-8-base_8.2.0-9+rpi1 gdal-data_2.3.2+dfsg-2 gettext_0.19.8.1-8 gettext-base_0.19.8.1-8 gfortran_4:8.2.0-2+rpi1 gfortran-8_8.2.0-9+rpi1 gir1.2-glib-2.0_1.58.0-1 gir1.2-harfbuzz-0.0_1.9.0-1+rpi1 gnupg_2.2.10-3+rpi1 gnupg-agent_2.2.10-3+rpi1 gnupg-l10n_2.2.10-3+rpi1 gnupg-utils_2.2.10-3+rpi1 gpg_2.2.10-3+rpi1 gpg-agent_2.2.10-3+rpi1 gpg-wks-client_2.2.10-3+rpi1 gpg-wks-server_2.2.10-3+rpi1 gpgconf_2.2.10-3+rpi1 gpgsm_2.2.10-3+rpi1 gpgv_2.2.10-3+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2.1 hdf5-helpers_1.10.0-patch1+docs-4+b2 hostname_3.21 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-5 init-system-helpers_1.54 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 krb5-locales_1.16.1-1 libacl1_2.2.52-3 libaec-dev_1.0.2-1 libaec0_1.0.2-1 libapparmor1_2.13.1-3 libapt-pkg5.0_1.7.0 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libarmadillo-dev_1:9.100.6+dfsg-1 libarmadillo9_1:9.100.6+dfsg-1 libarpack2_3.6.3-1+rpi1 libarpack2-dev_3.6.3-1+rpi1 libasan5_8.2.0-9+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2 libbinutils_2.31.1-6+rpi1 libblas-dev_3.8.0-1+b1 libblas3_3.8.0-1+b1 libblkid1_2.32.1-0.1 libboost-dev_1.62.0.1+b8 libboost1.62-dev_1.62.0+dfsg-10+b1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.27-6+rpi1 libc-dev-bin_2.27-6+rpi1 libc6_2.27-6+rpi1 libc6-dev_2.27-6+rpi1 libcairo2_1.16.0-1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-9+rpi1 libcharls-dev_1.1.0+dfsg-3 libcharls1_1.1.0+dfsg-3 libcom-err2_1.44.4-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.5-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.61.0-1 libcurl4_7.61.0-1 libcurl4-gnutls-dev_7.61.0-1 libdap-dev_3.20.0-1 libdap25_3.20.0-1 libdapclient6v5_3.20.0-1 libdapserver7v5_3.20.0-1 libdatrie1_0.2.12-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.10-1 libdebconfclient0_0.245 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.94-1+rpi1 libdrm2_2.4.94-1+rpi1 libelf1_0.170-0.5 libepsilon-dev_0.9.2+dfsg-4 libepsilon1_0.9.2+dfsg-4 libexpat1_2.2.6-1 libexpat1-dev_2.2.6-1 libext2fs2_1.44.4-2 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.45.0-1 libfile-which-perl_1.22-1 libfontconfig1_2.13.1-2 libfreetype6_2.8.1-2 libfreexl-dev_1.0.5-3 libfreexl1_1.0.5-3 libfribidi0_1.0.5-3 libfyba-dev_4.1.1-6 libfyba0_4.1.1-6 libgcc-8-dev_8.2.0-9+rpi1 libgcc1_1:8.2.0-9+rpi1 libgcrypt20_1.8.4-3 libgdal-dev_2.3.2+dfsg-2+b2 libgdal20_2.3.2+dfsg-2+b2 libgdbm-compat4_1.18-2 libgdbm3_1.8.3-14 libgdbm6_1.18-2 libgeos-3.7.0_3.7.0-1 libgeos-c1v5_3.7.0-1 libgeos-dev_3.7.0-1 libgeotiff-dev_1.4.2-4 libgeotiff2_1.4.2-4 libgfortran-8-dev_8.2.0-9+rpi1 libgfortran4_7.3.0-19 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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_1.16.1-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkml-dev_1.3.0-7 libkmlbase1_1.3.0-7 libkmlconvenience1_1.3.0-7 libkmldom1_1.3.0-7 libkmlengine1_1.3.0-7 libkmlregionator1_1.3.0-7 libkmlxsd1_1.3.0-7 libkmod2_25-1 libkrb5-3_1.16.1-1 libkrb5support0_1.16.1-1 libksba8_1.3.5-2 liblapack-dev_3.8.0-1+b1 liblapack3_3.8.0-1+b1 liblcms2-2_2.9-3 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libltdl-dev_2.4.6-6 libltdl7_2.4.6-6 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmariadbclient-dev_1:10.1.37-1 libmariadbclient-dev-compat_1:10.1.37-1 libmariadbclient18_1:10.1.37-1 libminizip-dev_1.1-8 libminizip1_1.1-8 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20181013-1 libncurses5_6.1+20180714-1 libncurses5-dev_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20181013-1 libnetcdf-dev_1:4.6.1-3 libnetcdf13_1:4.6.1-3 libnettle6_3.4-1 libnghttp2-14_1.34.0-1 libnpth0_1.6-1 libnspr4_2:4.20-1 libnss-systemd_239-10+rpi1 libnss3_2:3.39-1 libodbc1_2.3.6-0.1 libogdi3.2_3.2.1+ds-4 libogdi3.2-dev_3.2.1+ds-4 libopenjp2-7_2.3.0-1 libopenjp2-7-dev_2.3.0-1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_239-10+rpi1 libpam0g_1.1.8-3.8 libpango-1.0-0_1.42.4-3 libpangocairo-1.0-0_1.42.4-3 libpangoft2-1.0-0_1.42.4-3 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7+b1 libperl5.28_5.28.0-3 libpipeline1_1.5.0-2 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-3 libpng-dev_1.6.34-2+rpi1 libpng16-16_1.6.34-2+rpi1 libpoppler-dev_0.69.0-2 libpoppler-private-dev_0.69.0-2 libpoppler80_0.69.0-2 libpopt0_1.16-11 libpq-dev_11.1-1 libpq5_11.1-1 libprocps7_2:3.3.15-2 libproj-dev_5.2.0-1 libproj13_5.2.0-1 libpsl5_0.20.2-2 libpython3-stdlib_3.6.7-1 libpython3.6-minimal_3.6.7-1 libpython3.6-stdlib_3.6.7-1 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~rc8-1 libsasl2-modules_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32.1-0.1 libspatialite-dev_4.3.0a-5+b2 libspatialite7_4.3.0a-5+b2 libsqlite3-0_3.25.3-1 libsqlite3-dev_3.25.3-1 libss2_1.44.4-2 libssh2-1_1.8.0-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-9+rpi1 libstdc++6_8.2.0-9+rpi1 libsuperlu-dev_5.2.1+dfsg1-3 libsuperlu5_5.2.1+dfsg1-3 libswitch-perl_2.17-2 libsystemd0_239-10+rpi1 libsz2_1.0.2-1 libtasn1-6_4.13-3 libtcl8.6_8.6.8+dfsg-4 libthai-data_0.1.28-1 libthai0_0.1.28-1 libtiff-dev_4.0.9+git181026-1 libtiff5_4.0.9+git181026-1 libtiff5-dev_4.0.9+git181026-1 libtiffxx5_4.0.9+git181026-1 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20181013-1 libtk8.6_8.6.8-4 libtool_2.4.6-6 libubsan1_8.2.0-9+rpi1 libudev1_239-10+rpi1 libunistring2_0.9.10-1 liburiparser-dev_0.8.6-1 liburiparser1_0.8.6-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libwebp-dev_0.6.1-2 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-1 libxcb-shm0_1.13.1-1 libxcb1_1.13.1-1 libxdmcp6_1:1.1.2-3 libxerces-c-dev_3.2.2+debian-1 libxerces-c3.2_3.2.2+debian-1 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_1:1.2.3-1 libxt6_1:1.1.5-1 libzstd-dev_1.3.5+dfsg-1+rpi1 libzstd1_1.3.5+dfsg-1+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 littler_0.3.5-1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.4-3 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-6+rpi1 mysql-common_5.8+1.0.4 nano_3.1-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 odbcinst_2.3.6-0.1 odbcinst1debian2_2.3.6-0.1 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.0-3 perl-base_5.28.0-3 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 perl-modules-5.28_5.28.0-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 proj-data_5.2.0-1 python3_3.6.7-1 python3-distutils_3.7.1-1 python3-lib2to3_3.7.1-1 python3-minimal_3.6.7-1 python3.6_3.6.7-1 python3.6-minimal_3.6.7-1 r-base-core_3.5.1-1 r-base-dev_3.5.1-1 r-bioc-annotationdbi_1.44.0-1 r-bioc-biobase_2.42.0-1 r-bioc-biocgenerics_0.28.0-1 r-bioc-biocparallel_1.16.0-1 r-bioc-biomart_2.38.0+dfsg-1 r-bioc-biostrings_2.48.0-2+b1 r-bioc-bsgenome_1.50.0-1 r-bioc-delayedarray_0.6.6+dfsg-1 r-bioc-genomeinfodb_1.18.0-1 r-bioc-genomeinfodbdata_1.2.0-1 r-bioc-genomicalignments_1.16.0-2+b1 r-bioc-genomicfeatures_1.34.1+dfsg-1 r-bioc-genomicranges_1.32.7-1 r-bioc-iranges_2.14.12-1 r-bioc-rsamtools_1.34.0-1 r-bioc-rtracklayer_1.40.6-1 r-bioc-s4vectors_0.18.3-1+b1 r-bioc-summarizedexperiment_1.10.1+dfsg-1 r-bioc-xvector_0.20.0-2+b1 r-cran-assertthat_0.2.0-2 r-cran-bit_1.1-14-1 r-cran-bit64_0.9-7-3 r-cran-bitops_1.0-6-4 r-cran-blob_1.1.1-2 r-cran-crayon_1.3.4-4 r-cran-curl_3.2-2 r-cran-dbi_1.0.0-2 r-cran-digest_0.6.18-1 r-cran-formatr_1.5-3 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-glue_1.3.0-1 r-cran-hms_0.4.2-2 r-cran-httr_1.3.1-2 r-cran-jsonlite_1.5-3 r-cran-lambda.r_1.2.3-2 r-cran-lattice_0.20-38-1 r-cran-littler_0.3.5-1 r-cran-magrittr_1.5-5 r-cran-matrix_1.2-15-1 r-cran-matrixstats_0.54.0-1 r-cran-memoise_1.1.0-2 r-cran-mime_0.6-1 r-cran-openssl_1.0.2+dfsg-1 r-cran-pkgconfig_2.0.2-1 r-cran-pkgkitten_0.1.4-2 r-cran-prettyunits_1.0.2-3 r-cran-progress_1.2.0-1 r-cran-r6_2.3.0-1 r-cran-rcpp_1.0.0-1 r-cran-rcurl_1.95-4.11-1 r-cran-rlang_0.2.2-1 r-cran-rsqlite_2.1.1-2+b2 r-cran-snow_1:0.4.3-1 r-cran-stringi_1.2.4-1 r-cran-stringr_1.3.1-2 r-cran-xml_3.98-1.16-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-variantannotation-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-10+rpi1 systemd-sysv_239-10+rpi1 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_239-10+rpi1 unixodbc-dev_2.3.6-0.1 unzip_6.0-21 util-linux_2.32.1-0.1 uuid-dev_2.32.1-0.1 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 Mon Nov 12 21:02:30 2018 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-variantannotation_1.28.1-1.dsc
dpkg-source: info: extracting r-bioc-variantannotation in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-variantannotation_1.28.1.orig.tar.gz
dpkg-source: info: unpacking r-bioc-variantannotation_1.28.1-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
dpkg-source: info: applying drop_tests_requiring_large_data_sets.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
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-c198e088-83e8-4c3d-ad6c-fb5749b2fdfe
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-variantannotation
dpkg-buildpackage: info: source version 1.28.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-variantannotation-1.28.1
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --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_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: R packages needed for DEP8: runit, snpstats
I: R Package: VariantAnnotation Version: 1.28.1
I: Building using R version 3.5.1-1
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Mon, 12 Nov 2018 21:54:49 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-variantannotation/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-variantannotation/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 12 Nov 2018 21:54:49 +0100'"
* installing *source* package 'VariantAnnotation' ...
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -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 -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dna_hash.c -o dna_hash.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rle.c -o rle.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c strhash.c -o strhash.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vcffile.c -o vcffile.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c vcftype.c -o vcftype.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -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" -I"/usr/lib/R/site-library/Rsamtools/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c writevcf.c -o writevcf.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /usr/lib/R/site-library/Rsamtools/usrlib//libbam.a /usr/lib/R/site-library/Rsamtools/usrlib//libbcf.a /usr/lib/R/site-library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
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** R
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** help
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** building package indices
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* DONE (VariantAnnotation)
W: Ignoring specified R dependency: R (>= 2.8.0)
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.15.3)
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.15.2)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8)
I: Using r-bioc-summarizedexperiment for Depends:SummarizedExperiment (>= 1.9.9)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.33.6)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-snpstats for Recommends:snpstats
I: Using r-bioc-annotationhub for Suggests:AnnotationHub
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I: Using r-cran-ggplot2 for Suggests:ggplot2
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-cran-dbi for Imports:DBI
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.17.24)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.13)
I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7)
I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.47.6)
I: Using r-bioc-annotationdbi for Imports:AnnotationDbi (>= 1.27.9)
I: Using r-bioc-rtracklayer for Imports:rtracklayer (>= 1.39.7)
I: Using r-bioc-bsgenome for Imports:BSgenome (>= 1.47.3)
I: Using r-bioc-genomicfeatures for Imports:GenomicFeatures (>= 1.31.3)
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dpkg-deb: building package 'r-bioc-variantannotation' in '../r-bioc-variantannotation_1.28.1-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-variantannotation-dbgsym' in '../r-bioc-variantannotation-dbgsym_1.28.1-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-variantannotation_1.28.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-variantannotation-1.28.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-11-15T05:43:34Z
Finished
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I: Built successfully
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| Post Build Chroot |
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| Changes |
+------------------------------------------------------------------------------+
r-bioc-variantannotation_1.28.1-1_armhf.changes:
------------------------------------------------
Format: 1.8
Date: Mon, 12 Nov 2018 21:54:49 +0100
Source: r-bioc-variantannotation
Binary: r-bioc-variantannotation
Architecture: armhf
Version: 1.28.1-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
r-bioc-variantannotation - BioConductor annotation of genetic variants
Changes:
r-bioc-variantannotation (1.28.1-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
* Standards-Version: 4.2.1
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-variantannotation-dbgsym_1.28.1-1_armhf.deb
--------------------------------------------------
new Debian package, version 2.0.
size 75868 bytes: control archive=548 bytes.
434 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-variantannotation-dbgsym
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lrwxrwxrwx root/root 0 2018-11-12 20:54 ./usr/share/doc/r-bioc-variantannotation-dbgsym -> r-bioc-variantannotation
r-bioc-variantannotation_1.28.1-1_armhf.deb
-------------------------------------------
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1086 bytes, 14 lines control
7291 bytes, 73 lines md5sums
Package: r-bioc-variantannotation
Version: 1.28.1-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 4009
Depends: r-base-core (>= 3.5.1-1), r-api-3.5, r-bioc-biocgenerics (>= 0.15.3), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-genomicranges (>= 1.31.8), r-bioc-summarizedexperiment (>= 1.9.9), r-bioc-rsamtools (>= 1.33.6), r-cran-dbi, r-bioc-biobase, r-bioc-s4vectors (>= 0.17.24), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-biostrings (>= 2.47.6), r-bioc-annotationdbi (>= 1.27.9), r-bioc-rtracklayer (>= 1.39.7), r-bioc-bsgenome (>= 1.47.3), r-bioc-genomicfeatures (>= 1.31.3), libc6 (>= 2.15), zlib1g (>= 1:1.2.3.3)
Recommends: r-cran-runit, r-bioc-snpstats
Suggests: r-bioc-annotationhub, r-cran-ggplot2
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/VariantAnnotation/
Description: BioConductor annotation of genetic variants
This BioConductor package provides R functions to annotate variants,
compute amino acid coding changess and to predict coding outcomes.
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Build Architecture: armhf
Build-Space: 9852
Build-Time: 604
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 2342
Job: r-bioc-variantannotation_1.28.1-1
Machine Architecture: armhf
Package: r-bioc-variantannotation
Package-Time: 2994
Source-Version: 1.28.1-1
Space: 9852
Status: successful
Version: 1.28.1-1
--------------------------------------------------------------------------------
Finished at 2018-11-15T05:43:34Z
Build needed 00:49:54, 9852k disc space