Build log for r-bioc-rsamtools (1.32.0-2+b1) on armhf

r-bioc-rsamtools → 1.32.0-2+b1 → armhf → 2018-06-14 17:24:56

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| r-bioc-rsamtools 1.32.0-2+b1 (armhf)         Thu, 14 Jun 2018 17:06:56 +0000 |
+==============================================================================+

Package: r-bioc-rsamtools
Version: 1.32.0-2+b1
Source Version: 1.32.0-2
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-e0d701e5-f50e-4c6f-89ee-9647fc18e2c2' 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 13s (1755 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-rsamtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3073 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.32.0-2 (dsc) [2381 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.32.0-2 (tar) [3065 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.32.0-2 (diff) [6124 B]
Fetched 3073 kB in 8s (384 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-ZMOFpq/r-bioc-rsamtools-1.32.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-ZMOFpq' 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-gSpig3/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-gSpig3/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-gSpig3/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-gSpig3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (11.1 kB/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 49 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-gSpig3/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 ... 15727 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-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-gSpig3/apt_archive/sbuild-build-depends-r-bioc-rsamtools-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-rsamtools-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-gSpig3/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Sources [608 B]
Get:5 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ Packages [695 B]
Fetched 2636 B in 0s (14.3 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install r-bioc-rsamtools 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-biocgenerics
  r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
  r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors
  r-bioc-xvector r-cran-bitops r-cran-formatr r-cran-futile.logger
  r-cran-futile.options r-cran-lambda.r 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-biobase r-bioc-rsamtools
  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-genomicalignments r-bioc-shortread r-cran-codetools r-cran-knitr
  r-bioc-bsgenome r-bioc-genomicfeatures r-bioc-summarizedexperiment
  r-cran-matrix r-bioc-rtracklayer r-bioc-gviz r-bioc-annotationhub
  r-bioc-edger r-bioc-delayedarray r-bioc-graph r-cran-data.table r-cran-shiny
  r-cran-rmarkdown r-cran-jsonlite 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-rsamtools r-cran-digest r-bioc-annotate
  r-bioc-summarizedexperiment 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-biocgenerics
  r-bioc-biocparallel r-bioc-biostrings r-bioc-genomeinfodb
  r-bioc-genomeinfodbdata r-bioc-genomicranges r-bioc-iranges r-bioc-s4vectors
  r-bioc-xvector r-cran-bitops r-cran-formatr r-cran-futile.logger
  r-cran-futile.options r-cran-lambda.r r-cran-rcurl r-cran-snow
  sbuild-build-depends-r-bioc-rsamtools-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, 257 newly installed, 0 to remove and 36 not upgraded.
Need to get 188 MB/198 MB of archives.
After this operation, 610 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-gSpig3/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [976 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 3.6.5-9 [565 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.5-9 [1374 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 3.6.5-9 [1651 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.5-9 [229 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 libnspr4 armhf 2:4.19-3+rpi1 [90.0 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf libnss3 armhf 2:3.37.1-1 [933 kB]
Get:154 http://172.17.0.1/private buster-staging/main armhf libpoppler74 armhf 0.63.0-2 [1225 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf libpq5 armhf 10.4-2 [148 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf libxerces-c3.2 armhf 3.2.1+debian-2+b2 [710 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf odbcinst armhf 2.3.6-0.1 [47.6 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf odbcinst1debian2 armhf 2.3.6-0.1 [70.8 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf libgdal20 armhf 2.3.0+dfsg-1 [4842 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf libgeos-dev armhf 3.6.2-1 [282 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf libtiffxx5 armhf 4.0.9-5 [100 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf libtiff5-dev armhf 4.0.9-5 [337 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf libtiff-dev armhf 4.0.9-5 [96.3 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf libgeotiff-dev armhf 1.4.2-2+b2 [93.5 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf libgif-dev armhf 5.1.4-3 [43.4 kB]
Get:166 http://172.17.0.1/private buster-staging/main armhf libnetcdf-dev armhf 1:4.6.1-1 [80.5 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf libhdf4-alt-dev armhf 4.2.13-2 [310 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf libjson-c-dev armhf 0.12.1-1.3 [34.6 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf libminizip-dev armhf 1.1-8 [25.6 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf liburiparser-dev armhf 0.8.5-1 [17.8 kB]
Get:171 http://172.17.0.1/private buster-staging/main armhf libkml-dev armhf 1.3.0-5 [940 kB]
Get:172 http://172.17.0.1/private buster-staging/main armhf libltdl-dev armhf 2.4.6-2.1 [158 kB]
Get:173 http://172.17.0.1/private buster-staging/main armhf libproj-dev armhf 5.1.0-1 [225 kB]
Get:174 http://172.17.0.1/private buster-staging/main armhf libogdi3.2-dev armhf 3.2.1+ds-1+b1 [38.3 kB]
Get:175 http://172.17.0.1/private buster-staging/main armhf libopenjp2-7-dev armhf 2.3.0-1 [43.7 kB]
Get:176 http://172.17.0.1/private buster-staging/main armhf libpoppler-dev armhf 0.63.0-2 [22.5 kB]
Get:177 http://172.17.0.1/private buster-staging/main armhf libpoppler-private-dev armhf 0.63.0-2 [187 kB]
Get:178 http://172.17.0.1/private buster-staging/main armhf libpq-dev armhf 10.4-2 [145 kB]
Get:179 http://172.17.0.1/private buster-staging/main armhf libqhull-r7 armhf 2015.2-4 [171 kB]
Get:180 http://172.17.0.1/private buster-staging/main armhf libqhull-dev armhf 2015.2-4 [346 kB]
Get:181 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.24.0-1 [655 kB]
Get:182 http://172.17.0.1/private buster-staging/main armhf libspatialite-dev armhf 4.3.0a-5+b2 [1460 kB]
Get:183 http://172.17.0.1/private buster-staging/main armhf libwebpdemux2 armhf 0.6.1-2 [86.7 kB]
Get:184 http://172.17.0.1/private buster-staging/main armhf libwebp-dev armhf 0.6.1-2 [304 kB]
Get:185 http://172.17.0.1/private buster-staging/main armhf libxerces-c-dev armhf 3.2.1+debian-2+b2 [1486 kB]
Get:186 http://172.17.0.1/private buster-staging/main armhf libzstd-dev armhf 1.3.4+dfsg-3+rpi1 [209 kB]
Get:187 http://172.17.0.1/private buster-staging/main armhf unixodbc-dev armhf 2.3.6-0.1 [232 kB]
Get:188 http://172.17.0.1/private buster-staging/main armhf libgdal-dev armhf 2.3.0+dfsg-1 [6211 kB]
Get:189 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-3 [641 kB]
Get:190 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr armhf 1.5-2+b1 [149 kB]
Get:191 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:192 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:193 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:194 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-2 [108 kB]
Get:195 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.14.1-1+b1 [1051 kB]
Get:196 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.2-1+b1 [1802 kB]
Get:197 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.10-1+b1 [2127 kB]
Get:198 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2+b1 [592 kB]
Get:199 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2+b1 [14.1 MB]
Get:200 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3+b1 [24.0 kB]
Get:201 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.10-1+b2 [712 kB]
Get:202 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-3 [8213 kB]
Get:203 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.16.0-3 [3687 kB]
Get:204 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.3-1+b1 [1938 kB]
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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 libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
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 libcroco3:armhf (0.6.12-2) ...
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 libxerces-c3.2:armhf (3.2.1+debian-2+b2) ...
Setting up r-cran-lambda.r (1.2.3-2) ...
Setting up r-cran-snow (1:0.4.2-2) ...
Setting up libdap25:armhf (3.19.1-2) ...
Setting up gettext (0.19.8.1-6) ...
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 libharfbuzz-dev:armhf (1.7.6-1+b1) ...
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 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-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 sbuild-build-depends-r-bioc-rsamtools-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 4.4.0-124-generic armhf (armv8l)
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 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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 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_3.6.5-9 python3.6-minimal_3.6.5-9 r-base-core_3.5.0-5 r-base-dev_3.5.0-5 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-genomeinfodb_1.16.0-3 r-bioc-genomeinfodbdata_1.1.0-3 r-bioc-genomicranges_1.32.3-1+b1 r-bioc-iranges_2.14.10-1+b1 r-bioc-s4vectors_0.18.2-1+b1 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-lambda.r_1.2.3-2 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-rsamtools-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 05:59:33 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-rsamtools_1.32.0-2.dsc
dpkg-source: info: extracting r-bioc-rsamtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsamtools_1.32.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.32.0-2.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.patch
dpkg-source: info: applying skip_test_requiring_network.patch

Check disk space
----------------

Sufficient free space for build

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

Created changelog entry for binNMU version 1.32.0-2+b1

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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-e0d701e5-f50e-4c6f-89ee-9647fc18e2c2
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 1.32.0-2+b1
dpkg-buildpackage: info: source distribution buster-staging
 dpkg-source --before-build r-bioc-rsamtools-1.32.0
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, r-bioc-shortread
I: R Package: Rsamtools Version: 1.32.0
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 07:51:50 +0200
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 06 May 2018 07:51:50 +0200'"
* installing *source* package 'Rsamtools' ...
** 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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
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"    -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 PileupBuffer.cpp -o PileupBuffer.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"    -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 PosCacheColl.cpp -o PosCacheColl.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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_Rsamtools.c -o R_init_Rsamtools.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"    -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 ResultManager.cpp -o ResultManager.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 as_bam.c -o as_bam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bam_data.c -o bam_data.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"    -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 bam_mate_iter.cpp -o bam_mate_iter.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bambuffer.c -o bambuffer.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bamfile.c -o bamfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 bcffile.c -o bcffile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 encode.c -o encode.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 fafile.c -o fafile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 idxstats.c -o idxstats.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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_sam.c -o io_sam.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"    -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 pbuffer_wrapper.cpp -o pbuffer_wrapper.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"    -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 pileup.cpp -o pileup.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 pileupbam.c -o pileupbam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools_patch.c -o samtools_patch.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 scan_bam_data.c -o scan_bam_data.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tabixfile.c -o tabixfile.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tagfilter.c -o tagfilter.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 utilities.c -o utilities.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 zip_compression.c -o zip_compression.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bgzf.c -o samtools/bgzf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/kstring.c -o samtools/kstring.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_aux.c -o samtools/bam_aux.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam.c -o samtools/bam.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_import.c -o samtools/bam_import.o
In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0,
                 from /usr/include/limits.h:26,
                 from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:194,
                 from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:34,
                 from /usr/include/zconf.h:418,
                 from /usr/include/zlib.h:34,
                 from samtools/bam_import.c:3:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/sam.c -o samtools/sam.o
In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0,
                 from /usr/include/string.h:26,
                 from samtools/sam.c:3:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_index.c -o samtools/bam_index.o
samtools/bam_index.c: In function 'bam_index_load_core':
samtools/bam_index.c:335:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(magic, 1, 4, fp);
  ^~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:342:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
  fread(&idx->n, 4, 1, fp);
  ^~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:355:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
   fread(&size, 4, 1, fp);
   ^~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:358:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
    fread(&key, 4, 1, fp);
    ^~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:362:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
    fread(&p->n, 4, 1, fp);
    ^~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:366:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
    fread(p->list, 16, p->n, fp);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:376:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
   fread(&index2->n, 4, 1, fp);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/bam_index.c:380:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
   fread(index2->offset, index2->n, 8, fp);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_pileup.c -o samtools/bam_pileup.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_lpileup.c -o samtools/bam_lpileup.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_md.c -o samtools/bam_md.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/razf.c -o samtools/razf.o
samtools/razf.c: In function 'razf_flush':
samtools/razf.c:221:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
   write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:234:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
    write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function '_razf_write':
samtools/razf.c:201:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
   write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function 'razf_close':
samtools/razf.c:810:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
    write(rz->x.fpw, &rz->in, sizeof(int64_t));
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:811:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
    write(rz->x.fpw, &rz->out, sizeof(int64_t));
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:814:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
    write(rz->x.fpw, &v64, sizeof(int64_t));
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:816:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
    write(rz->x.fpw, &v64, sizeof(int64_t));
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function 'razf_end_flush':
samtools/razf.c:258:4: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
    write(rz->x.fpw, rz->outbuf, RZ_BUFFER_SIZE - rz->stream->avail_out);
    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c: In function 'save_zindex':
samtools/razf.c:96:12: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
  if(is_be) write(fd, &rz->index->size, sizeof(int));
            ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:99:3: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
   write(fd, &v32, sizeof(uint32_t));
   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:106:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
  write(fd, rz->index->bin_offsets, sizeof(int64_t) * v32);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
samtools/razf.c:107:2: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
  write(fd, rz->index->cell_offsets, sizeof(int32_t) * rz->index->size);
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/faidx.c -o samtools/faidx.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/knetfile.c -o samtools/knetfile.o
In file included from /usr/include/time.h:25:0,
                 from samtools/knetfile.c:33:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
In file included from samtools/knetfile.c:49:0:
samtools/knetfile.c: In function 'kftp_send_cmd':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
 #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                ^~~~~~~~~~~~~~~~~~~
samtools/knetfile.c:239:2: note: in expansion of macro 'netwrite'
  netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
  ^~~~~~~~
samtools/knetfile.c: In function 'khttp_connect_file':
samtools/knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
 #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                ^~~~~~~~~~~~~~~~~~~
samtools/knetfile.c:418:2: note: in expansion of macro 'netwrite'
  netwrite(fp->fd, buf, l);
  ^~~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_sort.c -o samtools/bam_sort.o
In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0,
                 from /usr/include/stdlib.h:25,
                 from samtools/bam_sort.c:3:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/sam_header.c -o samtools/sam_header.o
In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0,
                 from /usr/include/stdio.h:27,
                 from samtools/sam_header.c:3:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bam_reheader.c -o samtools/bam_reheader.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/kprobaln.c -o samtools/kprobaln.o
ar -crus libbam.a samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/knetfile.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcf.c -o samtools/bcftools/bcf.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/vcf.c -o samtools/bcftools/vcf.o
In file included from /usr/include/arm-linux-gnueabihf/bits/libc-header-start.h:33:0,
                 from /usr/include/limits.h:26,
                 from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:194,
                 from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/syslimits.h:7,
                 from /usr/lib/gcc/arm-linux-gnueabihf/7/include-fixed/limits.h:34,
                 from /usr/include/zconf.h:418,
                 from /usr/include/zlib.h:34,
                 from samtools/bcftools/vcf.c:3:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcfutils.c -o samtools/bcftools/bcfutils.o
In file included from /usr/include/alloca.h:21:0,
                 from samtools/bcftools/bcfutils.c:3:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/prob1.c -o samtools/bcftools/prob1.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/index.c -o samtools/bcftools/index.o
In file included from /usr/include/assert.h:35:0,
                 from samtools/bcftools/index.c:2:
/usr/include/features.h:184:3: warning: #warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp]
 # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE"
   ^~~~~~~
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/fet.c -o samtools/bcftools/fet.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 samtools/bcftools/bcf2qcall.c -o samtools/bcftools/bcf2qcall.o
ar -crus libbcf.a samtools/bcftools/bcf.o samtools/bcftools/vcf.o samtools/bcftools/bcfutils.o samtools/bcftools/prob1.o samtools/bcftools/index.o samtools/bcftools/fet.o samtools/bcftools/bcf2qcall.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tabix/index.c -o tabix/index.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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -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 tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools"
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix"
cp samtools/*.h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
	"/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -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-rsamtools/usr/lib/R/site-library/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsamtools)
	rm -f /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8)
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-shortread for Recommends:shortread
I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments
I: Using r-bioc-shortread for Suggests:ShortRead (>= 1.19.10)
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene
I: Using libgdal-dev for Suggests:TxDb.Dmelanogaster.UCSC.dm3.ensGene
W: Cannot find a debian package for Suggests:KEGG.db
I: Using libgdal-dev for Suggests:KEGG.db
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene
I: Using libgdal-dev for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene
W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14
I: Using libgdal-dev for Suggests:RNAseqData.HNRNPC.bam.chr14
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
I: Using libgdal-dev for Suggests:BSgenome.Hsapiens.UCSC.hg19
I: Using r-cran-runit for Suggests:RUnit
W: Cannot find a debian package for Suggests:BiocStyle
I: Using libgdal-dev for Suggests:BiocStyle
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.25.1)
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-xvector for Imports:XVector (>= 0.19.7)
I: Using r-cran-bitops for Imports:bitops
I: Using r-bioc-biocparallel for Imports:BiocParallel
   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
   dh_installcatalogs -a -O--buildsystem=R
   dh_installcron -a -O--buildsystem=R
   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
   dh_installmime -a -O--buildsystem=R
   dh_installmodules -a -O--buildsystem=R
   dh_installlogcheck -a -O--buildsystem=R
   dh_installlogrotate -a -O--buildsystem=R
   dh_installpam -a -O--buildsystem=R
   dh_installppp -a -O--buildsystem=R
   dh_installudev -a -O--buildsystem=R
   dh_installgsettings -a -O--buildsystem=R
   dh_bugfiles -a -O--buildsystem=R
   dh_ucf -a -O--buildsystem=R
   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-rsamtools/usr/lib/R/site-library/Rsamtools/libs/Rsamtools.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-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.32.0-2+b1_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.32.0-2+b1_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../r-bioc-rsamtools_1.32.0-2+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-rsamtools-1.32.0
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-06-14T17:24:53Z

Finished
--------

I: Built successfully

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


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


r-bioc-rsamtools_1.32.0-2+b1_armhf.changes:
-------------------------------------------

Format: 1.8
Date: Sun, 06 May 2018 07:51:50 +0200
Source: r-bioc-rsamtools (1.32.0-2)
Binary: r-bioc-rsamtools
Binary-Only: yes
Architecture: armhf
Version: 1.32.0-2+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Description:
 r-bioc-rsamtools - GNU R binary alignment (BAM), variant call (BCF), or tabix file i
Changes:
 r-bioc-rsamtools (1.32.0-2+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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 6891f92145cef3f3b7c7461c215f8fcf4b3f3cb3 12229 r-bioc-rsamtools_1.32.0-2+b1_armhf.buildinfo
 70424fe8618d4c5e5bedc3ea1fcc1abdb30f5ebe 3489192 r-bioc-rsamtools_1.32.0-2+b1_armhf.deb
Checksums-Sha256:
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 29bc2f4fd92ad777b431f07dd3db5bbf53f5af0b856beccd381e53992b88f92a 12229 r-bioc-rsamtools_1.32.0-2+b1_armhf.buildinfo
 03609457284309cc496196340490d74b49a021b848076ea0608a5e59de92a416 3489192 r-bioc-rsamtools_1.32.0-2+b1_armhf.deb
Files:
 447b4adfce5ab65d8743dc1025cb3683 821060 debug optional r-bioc-rsamtools-dbgsym_1.32.0-2+b1_armhf.deb
 fa4ffa3fdfd6b2fb87785838ee0d79a3 12229 gnu-r optional r-bioc-rsamtools_1.32.0-2+b1_armhf.buildinfo
 3ea8a4b9fef0ce36a41e03ba6afd6b4c 3489192 gnu-r optional r-bioc-rsamtools_1.32.0-2+b1_armhf.deb

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


r-bioc-rsamtools-dbgsym_1.32.0-2+b1_armhf.deb
---------------------------------------------

 new Debian package, version 2.0.
 size 821060 bytes: control archive=544 bytes.
     419 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: r-bioc-rsamtools-dbgsym
 Source: r-bioc-rsamtools (1.32.0-2)
 Version: 1.32.0-2+b1
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 868
 Depends: r-bioc-rsamtools (= 1.32.0-2+b1)
 Section: debug
 Priority: optional
 Description: debug symbols for r-bioc-rsamtools
 Build-Ids: 39480212894fac2a4015539dec4393024385fdfe

drwxr-xr-x root/root         0 2018-05-06 05:51 ./
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/debug/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/debug/.build-id/39/
-rw-r--r-- root/root    877740 2018-05-06 05:51 ./usr/lib/debug/.build-id/39/480212894fac2a4015539dec4393024385fdfe.debug
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/share/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/share/doc/
lrwxrwxrwx root/root         0 2018-05-06 05:51 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools


r-bioc-rsamtools_1.32.0-2+b1_armhf.deb
--------------------------------------

 new Debian package, version 2.0.
 size 3489192 bytes: control archive=4368 bytes.
    1142 bytes,    17 lines      control              
   12081 bytes,   132 lines      md5sums              
 Package: r-bioc-rsamtools
 Source: r-bioc-rsamtools (1.32.0-2)
 Version: 1.32.0-2+b1
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 5498
 Depends: r-base-core (>= 3.5.0-5), r-api-3.5, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
 Recommends: r-cran-runit, r-bioc-shortread
 Suggests: r-bioc-genomicalignments, r-bioc-shortread (>= 1.19.10), r-bioc-genomicfeatures, libgdal-dev
 Section: gnu-r
 Priority: optional
 Homepage: https://bioconductor.org/packages/Rsamtools/
 Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
  This package provides an interface to the 'samtools', 'bcftools', and
  'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
  binary variant call (BCF) and compressed indexed tab-delimited (tabix)
  files.

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-rw-r--r-- root/root      9648 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root     19845 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root    179914 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
-rw-r--r-- root/root       221 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.R
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-rw-r--r-- root/root    125561 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.pdf
-rw-r--r-- root/root      1976 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root       176 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root       112 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root    126539 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root       176 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root     74700 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf
-rw-r--r-- root/root        77 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci
-rw-r--r-- root/root    559422 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root      3778 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root       259 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root       348 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root        96 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root       368 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root       203 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
-rw-r--r-- root/root       176 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam.bai
-rw-r--r-- root/root       240 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root       198 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root       176 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root       168 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root   1663363 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root    138598 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root       181 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
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-rw-r--r-- root/root       770 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
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-rw-r--r-- root/root      1167 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam
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-rw-r--r-- root/root        36 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
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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: 18864
Build-Time: 118
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 929
Job: r-bioc-rsamtools_1.32.0-2
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 1077
Source-Version: 1.32.0-2
Space: 18864
Status: successful
Version: 1.32.0-2+b1
--------------------------------------------------------------------------------
Finished at 2018-06-14T17:24:53Z
Build needed 00:17:57, 18864k disk space
Raspbian Package Auto-Building

Build log for r-bioc-rsamtools (1.32.0-2+b1) on armhf
