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

r-bioc-rsamtools → 1.32.0-2 → armhf → 2018-05-24 22:59:28

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01

+==============================================================================+
| r-bioc-rsamtools 1.32.0-2 (armhf)            Thu, 24 May 2018 22:32:46 +0000 |
+==============================================================================+

Package: r-bioc-rsamtools
Version: 1.32.0-2
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/run/schroot/mount/buster-staging-armhf-sbuild-b399b84a-8f24-4c2a-a433-c0fc842a24c0' 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 [12.5 MB]
Fetched 23.3 MB in 28s (827 kB/s)
Reading package lists...

+------------------------------------------------------------------------------+
| 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 0s (7424 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-4z2Try/r-bioc-rsamtools-1.32.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-4z2Try' 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-GZSDFH/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-GZSDFH/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-GZSDFH/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (3250 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-GZSDFH/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 62 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (43.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15506 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) ...

+------------------------------------------------------------------------------+
| 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-GZSDFH/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-GZSDFH/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Sources [608 B]
Get:5 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Packages [695 B]
Fetched 2636 B in 1s (3571 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-GZSDFH/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
  e2fsprogs-l10n libsasl2-modules
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils cdbs cpp-7
  dctrl-tools debhelper dh-autoreconf dh-python dh-r dh-strip-nondeterminism
  file fontconfig fontconfig-config fonts-dejavu-core g++-7 gcc-7 gcc-7-base
  gettext gettext-base gfortran gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0
  groff-base icu-devtools intltool-debian libarchive-zip-perl libasan4
  libblas-dev libblas3 libbsd0 libbz2-dev libcairo2 libcilkrts5 libcroco3
  libcurl3 libdatrie1 libelf1 libexpat1 libfile-stripnondeterminism-perl
  libfontconfig1 libfreetype6 libfribidi0 libgcc-7-dev libgfortran-7-dev
  libgfortran4 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 libice6 libicu-dev libicu-le-hb-dev
  libicu-le-hb0 libicu57 libicu60 libisl19 libjbig0 libjpeg-dev
  libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3
  libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1
  libmpdec2 libncurses-dev libncurses5-dev libncurses6 libncursesw6
  libnghttp2-14 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 libpsl5 libpython3-stdlib
  libpython3.6-minimal libpython3.6-stdlib libreadline-dev libreadline7
  librtmp1 libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libstdc++-7-dev libtcl8.6
  libthai-data libthai0 libtiff5 libtimedate-perl libtinfo6 libtk8.6 libtool
  libubsan0 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1
  libxdmcp6 libxext6 libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4
  man-db mime-support pkg-config po-debconf 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 unzip x11-common xauth xdg-utils zip zlib1g zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation devscripts gcc-7-locales debtags dh-make dwz gcc-7-doc
  libstdc++6-7-dbg 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
  liblapack-doc libglib2.0-doc libgraphite2-utils krb5-doc krb5-user icu-doc
  liblzma-doc ncurses-doc readline-doc libstdc++-7-doc tcl8.6 tk8.6
  libtool-doc gcj-jdk 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-runit
  r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel 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-cran-digest r-bioc-delayedarray
  r-bioc-graph r-cran-data.table r-cran-shiny r-cran-testit r-cran-testthat
  r-cran-jsonlite r-cran-xml r-cran-rsprng r-cran-rlecuyer
Recommended packages:
  curl | wget | lynx bzip2-doc libarchive-cpio-perl shared-mime-info
  xdg-user-dirs krb5-locales libgpm2 libpng-tools publicsuffix libltdl-dev
  libmail-sendmail-perl r-recommended r-doc-html 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 cdbs dctrl-tools
  debhelper dh-autoreconf dh-python dh-r dh-strip-nondeterminism file
  fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base gfortran
  gfortran-7 gir1.2-glib-2.0 gir1.2-harfbuzz-0.0 groff-base icu-devtools
  intltool-debian libarchive-zip-perl libblas-dev libblas3 libbsd0 libbz2-dev
  libcairo2 libcroco3 libcurl3 libdatrie1 libelf1 libexpat1
  libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libfribidi0
  libgfortran-7-dev libgfortran4 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 libice6 libicu-dev
  libicu-le-hb-dev libicu-le-hb0 libicu57 libicu60 libisl19 libjbig0
  libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1
  libkrb5-3 libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc
  libmagic1 libmpdec2 libncurses-dev libncurses5-dev libncurses6 libncursesw6
  libnghttp2-14 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 libpsl5 libpython3-stdlib
  libpython3.6-minimal libpython3.6-stdlib libreadline-dev librtmp1
  libsigsegv2 libsm6 libssh2-1 libssl1.0.2 libtcl8.6 libthai-data libthai0
  libtiff5 libtimedate-perl libtinfo6 libtk8.6 libtool libx11-6 libx11-data
  libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2
  libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db mime-support
  pkg-config po-debconf 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 unzip x11-common
  xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
  cpp-7 g++-7 gcc-7 gcc-7-base libasan4 libcilkrts5 libgcc-7-dev libreadline7
  libstdc++-7-dev libubsan0 zlib1g
11 upgraded, 162 newly installed, 0 to remove and 51 not upgraded.
Need to get 151 MB/151 MB of archives.
After this operation, 337 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-GZSDFH/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [980 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.7-1 [96.8 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 zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13-1 [131 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.5-1 [292 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.5-1 [683 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.2-1 [16.8 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.5~rc1-1 [565 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.5~rc1-1 [1234 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-3 [307 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libreadline7 armhf 7.0-5 [130 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.5~rc1-1 [1585 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.5~rc1-1 [79.0 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.5~rc1-1 [147 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.5~rc1-1 [229 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.4-1 [19.3 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf dh-python all 3.20180326 [93.2 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.4-1 [22.3 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libasan4 armhf 7.3.0-19 [301 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libisl19 armhf 0.19-1 [427 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf g++-7 armhf 7.3.0-19 [5593 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf gcc-7 armhf 7.3.0-19 [5488 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf cpp-7 armhf 7.3.0-19 [5139 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libubsan0 armhf 7.3.0-19 [106 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libcilkrts5 armhf 7.3.0-19 [35.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libstdc++-7-dev armhf 7.3.0-19 [1506 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libgcc-7-dev armhf 7.3.0-19 [671 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gcc-7-base armhf 7.3.0-19 [187 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2o-1 [888 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.2 [12.1 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0038 [67.8 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf cdbs all 0.4.156 [83.1 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-9 [7414 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-6.1 [602 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-2 [132 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.2-2 [72.8 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.8.1-2 [402 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libpixman-1-0 armhf 0.34.0-2 [451 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.13-1 [107 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.13-1 [98.3 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.10-3 [575 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.16-2 [59.0 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.16-2 [116 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.16-2 [265 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.16-2 [135 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.58.0-2 [276 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-5 [403 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 0.19.7-2 [44.1 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.27-2 [168 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.11-1 [34.6 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.27-2 [50.2 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.0-1 [158 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.11-2 [73.5 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.7.6-1 [799 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.0-1 [53.2 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.0-1 [43.3 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libsm6 armhf 2:1.2.2-1+b3 [31.2 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libjbig0 armhf 2.1-3.1+b2 [27.6 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-5 [224 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf libxt6 armhf 1:1.1.5-1 [155 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.4.4-1 [23.0 MB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-19 [232 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-19 [5459 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:116 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20180210-3 [78.3 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-3 [103 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-3 [278 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-3 [924 B]
Get:122 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:130 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.34-1 [274 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf liblzma-dev armhf 5.2.2-1.3 [284 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.7.6-1 [584 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.7.6-1 [590 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.7.6-1 [597 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.4 [160 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:143 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf pkg-config armhf 0.29-4 [59.2 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:148 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.7.6-1 [879 kB]
Get:149 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:150 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:151 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:152 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:153 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.4.4-1 [4488 B]
Get:154 http://172.17.0.1/private buster-staging/main armhf dh-r all 20180514 [20.2 kB]
Get:155 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-2 [582 kB]
Get:156 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr armhf 1.5-2 [126 kB]
Get:157 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-1 [87.7 kB]
Get:158 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-1 [16.0 kB]
Get:159 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-2 [93.8 kB]
Get:160 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-1.1 [65.4 kB]
Get:161 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.14.1-1 [955 kB]
Get:162 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.2-1 [1353 kB]
Get:163 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.10-1 [1466 kB]
Get:164 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2 [378 kB]
Get:165 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2 [13.6 MB]
Get:166 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3 [22.5 kB]
Get:167 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.10-1 [618 kB]
Get:168 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-2 [8213 kB]
Get:169 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.16.0-2 [3529 kB]
Get:170 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.3-1 [1566 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up zlib1g:armhf (1:1.2.11.dfsg-1) ...
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Unpacking libxss1:armhf (1:1.2.2-1) ...
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Selecting previously unselected package libpython3.6-stdlib:armhf.
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Setting up libtiff5:armhf (4.0.9-5) ...
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Setting up libfribidi0:armhf (0.19.7-2) ...
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Creating config file /etc/papersize with new version
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
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update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
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Setting up libice6:armhf (2:1.0.9-2) ...
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up po-debconf (1.0.20) ...
Setting up gcc-7 (7.3.0-19) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up g++-7 (7.3.0-19) ...
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Setting up libx11-6:armhf (2:1.6.5-1) ...
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Setting up libreadline-dev:armhf (7.0-5) ...
Setting up libxcb-shm0:armhf (1.13-1) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up gfortran-7 (7.3.0-19) ...
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Setting up libxft2:armhf (2.3.2-2) ...
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 gfortran (4:7.2.0-1d1) ...
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update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libpango-1.0-0:armhf (1.42.0-1) ...
Setting up libcairo2:armhf (1.15.10-3) ...
Setting up libcurl3:armhf (7.58.0-2) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libpangoft2-1.0-0:armhf (1.42.0-1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.0-1) ...
Setting up r-base-core (3.4.4-1) ...

Creating config file /etc/R/Renviron with new version
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Setting up r-cran-bitops (1.0-6-3) ...
Setting up r-cran-formatr (1.5-2) ...
Setting up r-cran-futile.options (1.0.1-1) ...
Setting up r-cran-rcurl (1.95-4.10-1) ...
Setting up r-cran-lambda.r (1.2.3-1) ...
Setting up r-cran-snow (1:0.4.2-1.1) ...
Setting up r-bioc-s4vectors (0.18.2-1) ...
Setting up r-bioc-genomeinfodbdata (1.1.0-2) ...
Setting up r-cran-futile.logger (1.4.3-2) ...
Setting up r-bioc-iranges (2.14.10-1) ...
Setting up r-bioc-biocparallel (1.14.1-1) ...
Setting up r-bioc-genomeinfodb (1.16.0-2) ...
Setting up r-bioc-xvector (0.20.0-2) ...
Setting up r-bioc-biostrings (2.48.0-2) ...
Setting up r-bioc-genomicranges (1.32.3-1) ...
Setting up python3.6 (3.6.5~rc1-1) ...
Setting up python3 (3.6.4-1) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up python3-lib2to3 (3.6.5~rc1-1) ...
Setting up dh-python (3.20180326) ...
Setting up python3-distutils (3.6.5~rc1-1) ...
Setting up debhelper (11.2.1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up dh-autoreconf (17) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up icu-devtools (60.2-6) ...
Setting up libharfbuzz-dev:armhf (1.7.6-1) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up libicu-dev (60.2-6) ...
Setting up r-base-dev (3.4.4-1) ...
Setting up dh-r (20180514) ...
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Processing triggers for libc-bin (2.27-3+rpi1) ...
Processing triggers for systemd (238-4) ...

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

Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+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_1:2.31.1-0.5 build-essential_12.4+b1 bzip2_1.0.6-8.1 ca-certificates_20170717 cdbs_0.4.156 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dctrl-tools_2.24-2 debconf_1.5.66 debhelper_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-python_3.20180326 dh-r_20180514 dh-strip-nondeterminism_0.041-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 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_4:7.2.0-1d1 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_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gfortran_4:7.2.0-1d1 gfortran-7_7.3.0-19 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.7.6-1 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 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 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8-20180414-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbinutils_2.30-15+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.31.1-0.5 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcairo2_1.15.10-3 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.1-2 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.58.0-2 libdatrie1_0.2.11-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libelf1_0.170-0.4 libexpat1_2.2.5-3 libext2fs2_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libfontconfig1_2.13.0-5 libfreetype6_2.8.1-2 libfribidi0_0.19.7-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-7-dev_7.3.0-19 libgfortran4_7.3.0-19 libgirepository-1.0-1_1.56.1-1 libglib2.0-0_2.56.1-2 libglib2.0-bin_2.56.1-2 libglib2.0-data_2.56.1-2 libglib2.0-dev_2.56.1-2 libglib2.0-dev-bin_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.7.6-1 libharfbuzz-gobject0_1.7.6-1 libharfbuzz-icu0_1.7.6-1 libharfbuzz0b_1.7.6-1 libhogweed4_3.4-1 libice6_2:1.0.9-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu57_57.1-9 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libisl19_0.19-1 libjbig0_2.1-3.1+b2 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblz4-1_1.8.1.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-3 libncurses5_6.1-1 libncurses5-dev_6.1+20180210-3 libncurses6_6.1+20180210-3 libncursesw5_6.1-1 libncursesw6_6.1+20180210-3 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-3 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam0g_1.1.8-3.7 libpango-1.0-0_1.42.0-1 libpangocairo-1.0-0_1.42.0-1 libpangoft2-1.0-0_1.42.0-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-2 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 libpsl5_0.20.1-1 libpython3-stdlib_3.6.4-1 libpython3.6-minimal_3.6.5~rc1-1 libpython3.6-stdlib_3.6.5~rc1-1 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-1 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_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.31.1-0.5 libsqlite3-0_3.23.1-1 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2o-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-19 libstdc++6_8-20180414-1+rpi1 libsystemd0_238-4 libtasn1-6_4.13-2 libtcl8.6_8.6.8+dfsg-4 libthai-data_0.1.27-2 libthai0_0.1.27-2 libtiff5_4.0.9-5 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-3 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 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 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 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-6.1 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+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_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 python3_3.6.4-1 python3-distutils_3.6.5~rc1-1 python3-lib2to3_3.6.5~rc1-1 python3-minimal_3.6.4-1 python3.6_3.6.5~rc1-1 python3.6-minimal_3.6.5~rc1-1 r-base-core_3.4.4-1 r-base-dev_3.4.4-1 r-bioc-biocgenerics_0.26.0-2 r-bioc-biocparallel_1.14.1-1 r-bioc-biostrings_2.48.0-2 r-bioc-genomeinfodb_1.16.0-2 r-bioc-genomeinfodbdata_1.1.0-2 r-bioc-genomicranges_1.32.3-1 r-bioc-iranges_2.14.10-1 r-bioc-s4vectors_0.18.2-1 r-bioc-xvector_0.20.0-2 r-cran-bitops_1.0-6-3 r-cran-formatr_1.5-2 r-cran-futile.logger_1.4.3-2 r-cran-futile.options_1.0.1-1 r-cran-lambda.r_1.2.3-1 r-cran-rcurl_1.95-4.10-1 r-cran-snow_1:0.4.2-1.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 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 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 ucf_3.0038 udev_238-4 unzip_6.0-21 util-linux_2.31.1-0.5 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.2-2 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 disc space
----------------

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-b399b84a-8f24-4c2a-a433-c0fc842a24c0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd

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

dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 1.32.0-2
dpkg-buildpackage: info: source distribution unstable
 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: R Package: Rsamtools Version: 1.32.0
I: Building using R version 3.4.4-1
I: R API version: r-api-3.4
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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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-1Z1lf8/r-base-3.4.4=. -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
** preparing 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
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 290.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 291.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 294.
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-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
W: Cannot find a debian package for Suggests:KEGG.db
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg18.knownGene
W: Cannot find a debian package for Suggests:RNAseqData.HNRNPC.bam.chr14
W: Cannot find a debian package 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 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' in '../r-bioc-rsamtools_1.32.0-2_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.32.0-2_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_1.32.0-2_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 2018-05-24T22:58:22Z

Finished
--------

I: Built successfully

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


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


r-bioc-rsamtools_1.32.0-2_armhf.changes:
----------------------------------------

Format: 1.8
Date: Sun, 06 May 2018 07:51:50 +0200
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.32.0-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.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) unstable; urgency=medium
 .
   * Fix Maintainer and Vcs-fields
Checksums-Sha1:
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 53aa31de7a355cbbe09906a753ec725d409df31d 8909 r-bioc-rsamtools_1.32.0-2_armhf.buildinfo
 a3b52d61e078a04e5558d02daac10ae27ae13bf5 3280512 r-bioc-rsamtools_1.32.0-2_armhf.deb
Checksums-Sha256:
 c8353d128c7d1a620a5359123ac2ad4d5145f4971438d29a7aa67619cf006b83 821052 r-bioc-rsamtools-dbgsym_1.32.0-2_armhf.deb
 effb53cd339bbd0a953b0d54b2135a9da6dd9ba95f1c7213abb3b7217b0a5187 8909 r-bioc-rsamtools_1.32.0-2_armhf.buildinfo
 71ca1a69adefa2397f09c3067239b4fdd22ac8f6274720c68df36db481140878 3280512 r-bioc-rsamtools_1.32.0-2_armhf.deb
Files:
 cd9db92931b20e681b65c6fed550f763 821052 debug optional r-bioc-rsamtools-dbgsym_1.32.0-2_armhf.deb
 a82ec2850b4834a0c8f46522f6392c4f 8909 gnu-r optional r-bioc-rsamtools_1.32.0-2_armhf.buildinfo
 d6043f4eba9a74560e80a34d149bcd79 3280512 gnu-r optional r-bioc-rsamtools_1.32.0-2_armhf.deb

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


r-bioc-rsamtools-dbgsym_1.32.0-2_armhf.deb
------------------------------------------

 new Debian package, version 2.0.
 size 821052 bytes: control archive=544 bytes.
     402 bytes,    12 lines      control              
     106 bytes,     1 lines      md5sums              
 Package: r-bioc-rsamtools-dbgsym
 Source: r-bioc-rsamtools
 Version: 1.32.0-2
 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)
 Section: debug
 Priority: optional
 Description: debug symbols for r-bioc-rsamtools
 Build-Ids: 47a0d01a055a91a1989cfbc89d4f4e6d4c0aa27f

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/47/
-rw-r--r-- root/root    877736 2018-05-06 05:51 ./usr/lib/debug/.build-id/47/a0d01a055a91a1989cfbc89d4f4e6d4c0aa27f.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_armhf.deb
-----------------------------------

 new Debian package, version 2.0.
 size 3280512 bytes: control archive=4312 bytes.
    1061 bytes,    15 lines      control              
   11990 bytes,   131 lines      md5sums              
 Package: r-bioc-rsamtools
 Version: 1.32.0-2
 Architecture: armhf
 Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
 Installed-Size: 5149
 Depends: r-base-core (>= 3.4.4-1), r-api-3.4, 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)
 Suggests: r-bioc-genomicalignments, r-bioc-shortread (>= 1.19.10), r-bioc-genomicfeatures, r-cran-runit
 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.

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/R/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/
-rw-r--r-- root/root      1529 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/DESCRIPTION
-rw-r--r-- root/root      2136 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/INDEX
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/
-rw-r--r-- root/root      3178 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/Rd.rds
-rw-r--r-- root/root       112 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/features.rds
-rw-r--r-- root/root      3309 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/hsearch.rds
-rw-r--r-- root/root      2433 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/links.rds
-rw-r--r-- root/root       766 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/nsInfo.rds
-rw-r--r-- root/root      1561 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/package.rds
-rw-r--r-- root/root       283 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/Meta/vignette.rds
-rw-r--r-- root/root      1413 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root     14271 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root      1056 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root    428274 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root      6442 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/
-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
-rw-r--r-- root/root      3843 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.Rnw
-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
-rw-r--r-- root/root        96 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam.bai
-rw-r--r-- root/root       117 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.sam
-rw-r--r-- root/root       381 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam
-rw-r--r-- root/root       416 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.bam.bai
-rw-r--r-- root/root       770 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/revbins.sam
-rw-r--r-- root/root        31 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/samtools-github.txt
-rw-r--r-- root/root      2808 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/slxMaq09_urls.txt
-rw-r--r-- root/root       333 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam
-rw-r--r-- root/root       656 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.bam.bai
-rw-r--r-- root/root       804 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tagfilter.sam
-rw-r--r-- root/root      1167 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam
-rw-r--r-- root/root      2336 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.bam.bai
-rw-r--r-- root/root      4102 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tiny.sam
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/
-rw-r--r-- root/root        36 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
-rw-r--r-- root/root     36039 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/accepted_hits.sam
-rw-r--r-- root/root      4381 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/coverage.wig
-rw-r--r-- root/root       196 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/junctions.bed
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/help/
-rw-r--r-- root/root     11422 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/help/AnIndex
-rw-r--r-- root/root    174499 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/help/Rsamtools.rdb
-rw-r--r-- root/root       769 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/help/Rsamtools.rdx
-rw-r--r-- root/root      2475 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/help/aliases.rds
-rw-r--r-- root/root       368 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/help/paths.rds
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/html/
-rw-r--r-- root/root     42444 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/html/00Index.html
-rw-r--r-- root/root      1335 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/html/R.css
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/include/
drwxr-xr-x root/root         0 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/include/samtools/
-rw-r--r-- root/root     25788 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam.h
-rw-r--r-- root/root      1064 2018-05-06 05:51 ./usr/lib/R/site-library/Rsamtools/include/samtools/bam_endian.h
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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: 18052
Build-Time: 371
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1107
Job: r-bioc-rsamtools_1.32.0-2
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 1536
Source-Version: 1.32.0-2
Space: 18052
Status: successful
Version: 1.32.0-2
--------------------------------------------------------------------------------
Finished at 2018-05-24T22:58:22Z
Build needed 00:25:36, 18052k disc space
Raspbian Package Auto-Building

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