r-bioc-rsamtools →
1.32.3-1 →
armhf → 2018-08-31 05:13:32
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| r-bioc-rsamtools 1.32.3-1 (armhf) Fri, 31 Aug 2018 04:46:30 +0000 |
+==============================================================================+
Package: r-bioc-rsamtools
Version: 1.32.3-1
Source Version: 1.32.3-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-a5bfbdcb-f274-40ab-a6e2-7ebe98690722' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.0 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.7 MB]
Fetched 23.7 MB in 29s (809 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'r-bioc-rsamtools' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-rsamtools.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 3075 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.32.3-1 (dsc) [2381 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.32.3-1 (tar) [3067 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-rsamtools 1.32.3-1 (diff) [6156 B]
Fetched 3075 kB in 1s (3019 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-M4xkfK/r-bioc-rsamtools-1.32.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rsamtools-M4xkfK' 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-3hNzHG/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-3hNzHG/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-3hNzHG/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-3hNzHG/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2750 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 42 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (23.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15733 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rsamtools-dummy' in '/<<BUILDDIR>>/resolver-3hNzHG/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-3hNzHG/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Sources [608 B]
Get:5 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ Packages [695 B]
Fetched 2636 B in 1s (3791 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-rsamtools build dependencies (apt-based resolver)
----------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dbus dbus-user-session e2fsprogs-l10n libnss-systemd libpam-systemd
libsasl2-modules systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils bzip2 cpp-8
dctrl-tools debhelper dh-autoreconf dh-r dh-strip-nondeterminism dwz file
fontconfig fontconfig-config fonts-dejavu-core g++-8 gcc-7-base gcc-8
gcc-8-base gettext gettext-base gfortran gfortran-8 gir1.2-glib-2.0
gir1.2-harfbuzz-0.0 groff-base icu-devtools intltool-debian
libarchive-zip-perl libasan5 libatomic1 libblas-dev libblas3 libbsd0
libbz2-1.0 libbz2-dev libcairo2 libcc1-0 libcroco3 libcurl4 libdatrie1
libelf1 libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgcc-8-dev libgcc1 libgfortran-8-dev libgfortran4
libgfortran5 libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin
libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libgomp1 libgraphite2-3
libgraphite2-dev libgssapi-krb5-2 libharfbuzz-dev libharfbuzz-gobject0
libharfbuzz-icu0 libharfbuzz0b libice6 libicu-dev libicu-le-hb-dev
libicu-le-hb0 libicu60 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 libnghttp2-14 libpango-1.0-0
libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcre16-3
libpcre3 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
libstdc++-8-dev libstdc++6 libtcl8.6 libthai-data libthai0 libtiff5
libtimedate-perl libtk8.6 libtool libubsan1 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-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation bzip2-doc gcc-8-locales debtags dh-make gcc-8-doc libstdc++6-8-dbg
libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan5-dbg
liblsan0-dbg libtsan0-dbg libubsan1-dbg libmpx2-dbg libquadmath0-dbg
gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-8-doc
libgfortran5-dbg libcoarrays-dev groff liblapack-doc libglib2.0-doc
libgraphite2-utils krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc
readline-doc libstdc++-8-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 libgdal-dev r-bioc-affy
r-bioc-deseq2 r-bioc-annotate r-cran-foreach r-cran-bbmisc r-cran-rmpi
r-bioc-variantannotation r-bioc-genomicalignments r-bioc-shortread
r-cran-codetools r-cran-knitr r-bioc-bsgenome r-bioc-genomicfeatures
r-cran-matrix r-bioc-rtracklayer r-bioc-gviz r-bioc-annotationhub
r-bioc-edger r-bioc-summarizedexperiment r-bioc-delayedarray r-bioc-graph
r-cran-data.table r-cran-shiny r-cran-rmarkdown r-cran-jsonlite r-cran-xml
r-cran-rsprng r-cran-rlecuyer
Recommended packages:
devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl
shared-mime-info xdg-user-dirs krb5-locales libpng-tools publicsuffix
libltdl-dev libmail-sendmail-perl r-recommended r-doc-html r-cran-runit
r-cran-batchjobs r-cran-doparallel r-bioc-rsamtools r-cran-digest
r-bioc-annotate r-bioc-summarizedexperiment r-cran-testit r-cran-codetools
r-cran-survival r-cran-testthat libfile-mimeinfo-perl libnet-dbus-perl
libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper
dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gcc-7-base gettext gettext-base gfortran
gfortran-8 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 libcurl4 libdatrie1 libelf1
libfile-stripnondeterminism-perl libfile-which-perl libfontconfig1
libfreetype6 libfribidi0 libgfortran-8-dev libgfortran4 libgfortran5
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 libicu60
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
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 libtcl8.6 libthai-data libthai0 libtiff5
libtimedate-perl 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:
bzip2 cpp-8 g++-8 gcc-8 gcc-8-base libasan5 libatomic1 libbz2-1.0 libcc1-0
libgcc-8-dev libgcc1 libgomp1 libpcre3 libstdc++-8-dev libstdc++6 libubsan1
16 upgraded, 157 newly installed, 0 to remove and 26 not upgraded.
Need to get 144 MB/148 MB of archives.
After this operation, 309 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-3hNzHG/apt_archive ./ sbuild-build-depends-r-bioc-rsamtools-dummy 0.invalid.0 [976 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libcc1-0 armhf 8.2.0-4+rpi1 [30.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf gcc-8-base armhf 8.2.0-4+rpi1 [187 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libgcc1 armhf 1:8.2.0-4+rpi1 [36.7 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libgomp1 armhf 8.2.0-4+rpi1 [63.9 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libatomic1 armhf 8.2.0-4+rpi1 [8104 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf libasan5 armhf 8.2.0-4+rpi1 [318 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libubsan1 armhf 8.2.0-4+rpi1 [104 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf g++-8 armhf 8.2.0-4+rpi1 [5941 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libstdc++-8-dev armhf 8.2.0-4+rpi1 [1561 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libgcc-8-dev armhf 8.2.0-4+rpi1 [596 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf gcc-8 armhf 8.2.0-4+rpi1 [5843 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf cpp-8 armhf 8.2.0-4+rpi1 [5472 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libstdc++6 armhf 8.2.0-4+rpi1 [325 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13-3 [132 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.6-1 [298 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.6-1 [688 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libpython3.6-minimal armhf 3.6.6-1 [565 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf python3.6-minimal armhf 3.6.6-1 [1383 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf python3-minimal armhf 3.6.5-3 [36.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf mime-support all 3.61 [37.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf bzip2 armhf 1.0.6-9 [46.1 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libbz2-1.0 armhf 1.0.6-9 [43.0 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libpython3.6-stdlib armhf 3.6.6-1 [1638 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf python3.6 armhf 3.6.6-1 [234 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libpython3-stdlib armhf 3.6.5-3 [19.7 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf python3 armhf 3.6.5-3 [24.1 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libpcre3 armhf 2:8.39-11+rpi1 [313 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9.3 [12.2 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1 [771 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.63-1 [96.7 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.8-2+rpi1 [860 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.0-5 [280 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.0-5 [325 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.13-3 [107 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.13-3 [98.4 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.15.12-1 [589 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.61.0-1 [282 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.0-5 [403 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 1.0.5-3 [61.9 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.28-1 [170 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.12-1 [35.8 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.28-1 [50.9 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.4-1 [165 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-1 [60.8 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-1 [50.8 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.8+dfsg-4 [863 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.9-6 [225 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.8-4 [657 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.5.1-1 [23.6 MB]
Get:95 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-4+rpi1 [206 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-4+rpi1 [248 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-4+rpi1 [5809 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.1.0-1+rpi1 [1424 B]
Get:99 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180714-1 [279 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180714-1 [940 B]
Get:103 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.34-2+rpi1 [275 kB]
Get:110 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 60.2-6 [166 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-icu0 armhf 1.8.8-2+rpi1 [641 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-gobject0 armhf 1.8.8-2+rpi1 [648 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf libgirepository-1.0-1 armhf 1.56.1-1 [77.6 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf gir1.2-glib-2.0 armhf 1.56.1-1 [142 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf gir1.2-harfbuzz-0.0 armhf 1.8.8-2+rpi1 [655 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf libglib2.0-data all 2.56.1-2 [2671 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf libglib2.0-bin armhf 2.56.1-2 [1694 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf python3-lib2to3 all 3.6.6-1 [79.1 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf python3-distutils all 3.6.6-1 [144 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev-bin armhf 2.56.1-2 [1733 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf libglib2.0-dev armhf 2.56.1-2 [2807 kB]
Get:123 http://172.17.0.1/private buster-staging/main armhf libgraphite2-dev armhf 1.3.11-2 [22.2 kB]
Get:124 http://172.17.0.1/private buster-staging/main armhf libharfbuzz-dev armhf 1.8.8-2+rpi1 [930 kB]
Get:125 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb-dev armhf 1.0.3+git161113-5 [28.3 kB]
Get:126 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 60.2-6 [8643 kB]
Get:127 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:128 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:129 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.5.1-1 [4476 B]
Get:130 http://172.17.0.1/private buster-staging/main armhf libfile-which-perl all 1.22-1 [14.6 kB]
Get:131 http://172.17.0.1/private buster-staging/main armhf dh-r all 20180823 [33.5 kB]
Get:132 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.26.0-3 [641 kB]
Get:133 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr all 1.5-3 [149 kB]
Get:134 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:135 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:136 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:137 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-2 [108 kB]
Get:138 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.14.2-2 [1052 kB]
Get:139 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.18.3-1+b1 [1799 kB]
Get:140 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.14.10-2 [2129 kB]
Get:141 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.20.0-2+b1 [592 kB]
Get:142 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.48.0-2+b1 [14.1 MB]
Get:143 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:144 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.11-1 [711 kB]
Get:145 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.1.0-3 [8213 kB]
Get:146 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.16.0-4 [3686 kB]
Get:147 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.32.6-1 [1937 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Setting up cpp-8 (8.2.0-4+rpi1) ...
Setting up libgomp1:armhf (8.2.0-4+rpi1) ...
Setting up libatomic1:armhf (8.2.0-4+rpi1) ...
Setting up libcc1-0:armhf (8.2.0-4+rpi1) ...
Setting up libbz2-dev:armhf (1.0.6-9) ...
Setting up libjpeg62-turbo:armhf (1:1.5.2-2+b1) ...
Setting up libarchive-zip-perl (1.63-1) ...
Setting up libnghttp2-14:armhf (1.32.0-1) ...
Setting up mime-support (3.61) ...
Installing new version of config file /etc/mime.types ...
Setting up libfile-which-perl (1.22-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libjbig0:armhf (2.1-3.1+b2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libpsl5:armhf (0.20.2-1) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: removed existing output file.
Setting up unzip (6.0-21) ...
Setting up dctrl-tools (2.24-2) ...
Setting up libdatrie1:armhf (0.2.12-1) ...
Setting up libtiff5:armhf (4.0.9-6) ...
Setting up gettext-base (0.19.8.1-7) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up ucf (3.0038) ...
Setting up libgirepository-1.0-1:armhf (1.56.1-1) ...
Setting up zip (3.0-11) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.34-2) ...
Setting up bzip2 (1.0.6-9) ...
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Setting up libgraphite2-3:armhf (1.3.11-2) ...
Setting up gcc-7-base:armhf (7.3.0-19) ...
Setting up pkg-config (0.29-4) ...
Setting up libpixman-1-0:armhf (0.34.0-2) ...
Setting up gir1.2-glib-2.0:armhf (1.56.1-1) ...
Setting up libssh2-1:armhf (1.8.0-2) ...
Setting up libglib2.0-data (2.56.1-2) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Processing triggers for systemd (239-7) ...
Setting up libfribidi0:armhf (1.0.5-3) ...
Setting up libpcrecpp0v5:armhf (2:8.39-11+rpi1) ...
Setting up libpcre32-3:armhf (2:8.39-11+rpi1) ...
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Setting up libtcl8.6:armhf (8.6.8+dfsg-4) ...
Setting up libthai-data (0.1.28-1) ...
Setting up libjpeg62-turbo-dev:armhf (1:1.5.2-2+b1) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libkeyutils1:armhf (1.5.9-9.3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up x11-common (1:7.7+19) ...
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Running in chroot, ignoring request.
All runlevel operations denied by policy
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Setting up xdg-utils (1.1.3-1) ...
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Setting up libglib2.0-bin (2.56.1-2) ...
Setting up libasan5:armhf (8.2.0-4+rpi1) ...
Setting up libgfortran5:armhf (8.2.0-4+rpi1) ...
Setting up libgraphite2-dev:armhf (1.3.11-2) ...
Setting up libx11-data (2:1.6.6-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
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Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libubsan1:armhf (8.2.0-4+rpi1) ...
Setting up libpaper1:armhf (1.1.24+nmu5) ...
Creating config file /etc/papersize with new version
Setting up libpython3.6-stdlib:armhf (3.6.6-1) ...
Setting up libpaper-utils (1.1.24+nmu5) ...
Setting up libpcre3-dev:armhf (2:8.39-11+rpi1) ...
Setting up fontconfig-config (2.13.0-5) ...
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Setting up libharfbuzz0b:armhf (1.8.8-2+rpi1) ...
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Setting up libncurses5-dev:armhf (6.1+20180714-1) ...
Setting up libblas3:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libjpeg-dev (1:1.5.2-2) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libreadline-dev:armhf (7.0-5) ...
Setting up libice6:armhf (2:1.0.9-2) ...
Setting up man-db (2.8.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libgcc-8-dev:armhf (8.2.0-4+rpi1) ...
Setting up libpng-dev:armhf (1.6.34-2+rpi1) ...
Setting up libgfortran-8-dev:armhf (8.2.0-4+rpi1) ...
Setting up libxcb1:armhf (1.13-3) ...
Setting up libharfbuzz-gobject0:armhf (1.8.8-2+rpi1) ...
Setting up libtool (2.4.6-2.1) ...
Setting up libpython3-stdlib:armhf (3.6.5-3) ...
Setting up libfontconfig1:armhf (2.13.0-5) ...
Setting up libstdc++-8-dev:armhf (8.2.0-4+rpi1) ...
Setting up libsm6:armhf (2:1.2.2-1+b3) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up libxcb-render0:armhf (1.13-3) ...
Setting up python3 (3.6.5-3) ...
Setting up libblas-dev:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up liblapack3:armhf (3.8.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libx11-6:armhf (2:1.6.6-1) ...
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Setting up gcc-8 (8.2.0-4+rpi1) ...
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Setting up gir1.2-harfbuzz-0.0:armhf (1.8.8-2+rpi1) ...
Setting up libxcb-shm0:armhf (1.13-3) ...
Setting up libxt6:armhf (1:1.1.5-1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libxft2:armhf (2.3.2-2) ...
Setting up python3-lib2to3 (3.6.6-1) ...
Setting up python3-distutils (3.6.6-1) ...
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 libxext6:armhf (2:1.3.3-1+b2) ...
Setting up libglib2.0-dev-bin (2.56.1-2) ...
Setting up gfortran-8 (8.2.0-4+rpi1) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libglib2.0-dev:armhf (2.56.1-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up xauth (1:1.0.10-1) ...
Setting up libpango-1.0-0:armhf (1.42.4-1) ...
Setting up gfortran (4:8.1.0-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libcairo2:armhf (1.15.12-1) ...
Setting up libtk8.6:armhf (8.6.8-4) ...
Setting up libcurl4:armhf (7.61.0-1) ...
Setting up libpangoft2-1.0-0:armhf (1.42.4-1) ...
Setting up libpangocairo-1.0-0:armhf (1.42.4-1) ...
Setting up dh-autoreconf (19) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libharfbuzz-icu0:armhf (1.8.8-2+rpi1) ...
Setting up libicu-le-hb-dev:armhf (1.0.3+git161113-5) ...
Setting up r-base-core (3.5.1-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-bioc-biocgenerics (0.26.0-3) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up r-cran-bitops (1.0-6-4) ...
Setting up r-cran-formatr (1.5-3) ...
Setting up r-cran-futile.options (1.0.1-2) ...
Setting up icu-devtools (60.2-6) ...
Setting up r-cran-rcurl (1.95-4.11-1) ...
Setting up r-cran-lambda.r (1.2.3-2) ...
Setting up r-cran-snow (1:0.4.2-2) ...
Setting up r-bioc-s4vectors (0.18.3-1+b1) ...
Setting up gettext (0.19.8.1-7) ...
Setting up r-bioc-genomeinfodbdata (1.1.0-3) ...
Setting up libicu-dev (60.2-6) ...
Setting up r-base-dev (3.5.1-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up r-cran-futile.logger (1.4.3-3) ...
Setting up libharfbuzz-dev:armhf (1.8.8-2+rpi1) ...
Setting up r-bioc-iranges (2.14.10-2) ...
Setting up r-bioc-biocparallel (1.14.2-2) ...
Setting up po-debconf (1.0.20) ...
Setting up r-bioc-genomeinfodb (1.16.0-4) ...
Setting up r-bioc-xvector (0.20.0-2+b1) ...
Setting up r-bioc-biostrings (2.48.0-2+b1) ...
Setting up r-bioc-genomicranges (1.32.6-1) ...
Setting up debhelper (11.3.5) ...
Setting up dh-r (20180823) ...
Setting up sbuild-build-depends-r-bioc-rsamtools-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.2.0-4+rpi1 gcc-8_8.2.0-4+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.2.0-4+rpi1 libstdc++6_8.2.0-4+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.2.0-4+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 dctrl-tools_2.24-2 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-r_20180823 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 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++_4:8.1.0-1+rpi1 g++-8_8.2.0-4+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-7-base_7.3.0-19 gcc-8_8.2.0-4+rpi1 gcc-8-base_8.2.0-4+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gfortran_4:8.1.0-1+rpi1 gfortran-8_8.2.0-4+rpi1 gir1.2-glib-2.0_1.56.1-1 gir1.2-harfbuzz-0.0_1.8.8-2+rpi1 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 icu-devtools_60.2-6 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.63-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-4+rpi1 libassuan0_2.5.1-2 libatomic1_8.2.0-4+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcairo2_1.15.12-1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-4+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libcurl4_7.61.0-1 libdatrie1_0.2.12-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfile-which-perl_1.22-1 libfontconfig1_2.13.0-5 libfreetype6_2.8.1-2 libfribidi0_1.0.5-3 libgcc-8-dev_8.2.0-4+rpi1 libgcc1_1:8.2.0-4+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran-8-dev_8.2.0-4+rpi1 libgfortran4_7.3.0-19 libgfortran5_8.2.0-4+rpi1 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_3.5.19-1 libgomp1_8.2.0-4+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.11-2 libgraphite2-dev_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz-dev_1.8.8-2+rpi1 libharfbuzz-gobject0_1.8.8-2+rpi1 libharfbuzz-icu0_1.8.8-2+rpi1 libharfbuzz0b_1.8.8-2+rpi1 libhogweed4_3.4-1 libice6_2:1.0.9-2 libicu-dev_60.2-6 libicu-le-hb-dev_1.0.3+git161113-5 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 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_1.5.9-9.3 libklibc_2.0.4-14+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_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180714-1 libncurses5_6.1+20180714-1 libncurses5-dev_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpango-1.0-0_1.42.4-1 libpangocairo-1.0-0_1.42.4-1 libpangoft2-1.0-0_1.42.4-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.24_5.24.1-4 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-3 libpng-dev_1.6.34-2+rpi1 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-1 libpython3-stdlib_3.6.5-3 libpython3.6-minimal_3.6.6-1 libpython3.6-stdlib_3.6.6-1 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssh2-1_1.8.0-2 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.2.0-4+rpi1 libstdc++6_8.2.0-4+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtcl8.6_8.6.8+dfsg-4 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.28-1 libthai0_0.1.28-1 libtiff5_4.0.9-6 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtk8.6_8.6.8-4 libtool_2.4.6-2.1 libubsan1_8.2.0-4+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32.1-0.1 libx11-6_2:1.6.6-1 libx11-data_2:1.6.6-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13-3 libxcb-shm0_1.13-3 libxcb1_1.13-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mime-support_3.61 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 python3_3.6.5-3 python3-distutils_3.6.6-1 python3-lib2to3_3.6.6-1 python3-minimal_3.6.5-3 python3.6_3.6.6-1 python3.6-minimal_3.6.6-1 r-base-core_3.5.1-1 r-base-dev_3.5.1-1 r-bioc-biocgenerics_0.26.0-3 r-bioc-biocparallel_1.14.2-2 r-bioc-biostrings_2.48.0-2+b1 r-bioc-genomeinfodb_1.16.0-4 r-bioc-genomeinfodbdata_1.1.0-3 r-bioc-genomicranges_1.32.6-1 r-bioc-iranges_2.14.10-2 r-bioc-s4vectors_0.18.3-1+b1 r-bioc-xvector_0.20.0-2+b1 r-cran-bitops_1.0-6-4 r-cran-formatr_1.5-3 r-cran-futile.logger_1.4.3-3 r-cran-futile.options_1.0.1-2 r-cran-lambda.r_1.2.3-2 r-cran-rcurl_1.95-4.11-1 r-cran-snow_1:0.4.2-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rsamtools-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 ucf_3.0038 udev_239-7 unzip_6.0-21 util-linux_2.32.1-0.1 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.3-1 xz-utils_5.2.2-1.3 zip_3.0-11 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue Aug 28 15:11:22 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_1.32.3-1.dsc
dpkg-source: info: extracting r-bioc-rsamtools in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rsamtools_1.32.3.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rsamtools_1.32.3-1.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-a5bfbdcb-f274-40ab-a6e2-7ebe98690722
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rsamtools
dpkg-buildpackage: info: source version 1.32.3-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-rsamtools-1.32.3
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 packages needed for DEP8: runit, shortread
I: R Package: Rsamtools Version: 1.32.3
I: Building using R version 3.5.1-1
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Tue, 28 Aug 2018 17:06:02 +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='Tue, 28 Aug 2018 17:06:02 +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-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -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-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utilities.c -o utilities.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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,
from /usr/include/limits.h:26,
from /usr/lib/gcc/arm-linux-gnueabihf/8/include-fixed/limits.h:194,
from /usr/lib/gcc/arm-linux-gnueabihf/8/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/8/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-73GQCG/r-base-3.5.1=. -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,
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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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,
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:
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-73GQCG/r-base-3.5.1=. -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,
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-73GQCG/r-base-3.5.1=. -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,
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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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,
from /usr/include/limits.h:26,
from /usr/lib/gcc/arm-linux-gnueabihf/8/include-fixed/limits.h:194,
from /usr/lib/gcc/arm-linux-gnueabihf/8/include-fixed/syslimits.h:7,
from /usr/lib/gcc/arm-linux-gnueabihf/8/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-73GQCG/r-base-3.5.1=. -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,
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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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,
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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -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-73GQCG/r-base-3.5.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tabix/bedidx.c -o tabix/bedidx.o
ar -crus libtabix.a samtools/bgzf.o samtools/kstring.o samtools/knetfile.o tabix/index.o tabix/bedidx.o samtools_patch.o
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools"
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix"
cp samtools/*.h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/"
cp samtools/bcftools/*h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/samtools/bcftools/"
cp tabix/*h "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
cp samtools/bgzf.h samtools/kstring.h samtools/knetfile.h \
"/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/include/tabix/"
mkdir -p "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
cp libbam.a libbcf.a libtabix.a "/<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib"
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o Rsamtools.so Biostrings_stubs.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam_data.o bam_mate_iter.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o -pthread -fopenmp /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbam.a /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libbcf.a /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/usrlib/libtabix.a -lz -L/usr/lib/R/lib -lR
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
installing to /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsamtools)
rm -f /<<PKGBUILDDIR>>/debian/r-bioc-rsamtools/usr/lib/R/site-library/Rsamtools/LICENSE
I: Using r-bioc-genomeinfodb for Depends:GenomeInfoDb (>= 1.1.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8)
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.47.6)
I: Using r-cran-runit for Recommends:runit
I: Using r-bioc-shortread for Recommends:shortread
I: Using r-bioc-genomicalignments for Suggests:GenomicAlignments
I: Using r-bioc-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
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-dbgsym' in '../r-bioc-rsamtools-dbgsym_1.32.3-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-rsamtools' in '../r-bioc-rsamtools_1.32.3-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-rsamtools_1.32.3-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-rsamtools-1.32.3
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-08-31T05:13:17Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-rsamtools_1.32.3-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Tue, 28 Aug 2018 17:06:02 +0200
Source: r-bioc-rsamtools
Binary: r-bioc-rsamtools
Architecture: armhf
Version: 1.32.3-1
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 (1.32.3-1) unstable; urgency=medium
.
* New upstream version
* Standards-Version: 4.2.1
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-rsamtools-dbgsym_1.32.3-1_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 1062492 bytes: control archive=544 bytes.
403 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rsamtools-dbgsym
Source: r-bioc-rsamtools
Version: 1.32.3-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 1106
Depends: r-bioc-rsamtools (= 1.32.3-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-rsamtools
Build-Ids: 34af95bf31be5e7c1d9acd6c87b5f99eb2621182
drwxr-xr-x root/root 0 2018-08-28 15:06 ./
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 1122180 2018-08-28 15:06 ./usr/lib/debug/.build-id/34/af95bf31be5e7c1d9acd6c87b5f99eb2621182.debug
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/share/
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-08-28 15:06 ./usr/share/doc/r-bioc-rsamtools-dbgsym -> r-bioc-rsamtools
r-bioc-rsamtools_1.32.3-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 3491348 bytes: control archive=4312 bytes.
1059 bytes, 16 lines control
11990 bytes, 131 lines md5sums
Package: r-bioc-rsamtools
Version: 1.32.3-1
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 5502
Depends: r-base-core (>= 3.5.1-1), r-api-3.5, r-bioc-genomeinfodb (>= 1.1.3), r-bioc-genomicranges (>= 1.31.8), r-bioc-biostrings (>= 2.47.6), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.17.25), r-bioc-iranges (>= 2.13.12), r-bioc-xvector (>= 0.19.7), r-cran-bitops, r-bioc-biocparallel, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.3)
Recommends: r-cran-runit, r-bioc-shortread
Suggests: r-bioc-genomicalignments, r-bioc-genomicfeatures
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 2018-08-28 15:06 ./
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drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/R/site-library/
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-rw-r--r-- root/root 2136 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/INDEX
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-rw-r--r-- root/root 1413 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/NAMESPACE
-rw-r--r-- root/root 14433 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/NEWS
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/R/
-rw-r--r-- root/root 1056 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools
-rw-r--r-- root/root 785690 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdb
-rw-r--r-- root/root 6512 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/R/Rsamtools.rdx
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/
-rw-r--r-- root/root 9648 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.R
-rw-r--r-- root/root 19845 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.Rnw
-rw-r--r-- root/root 180892 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-Overview.pdf
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-rw-r--r-- root/root 3843 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.Rnw
-rw-r--r-- root/root 126129 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/Rsamtools-UsingCLibraries.pdf
-rw-r--r-- root/root 1976 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/doc/index.html
drwxr-xr-x root/root 0 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/
-rw-r--r-- root/root 176 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa
-rw-r--r-- root/root 112 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ce2dict1.fa.fai
-rw-r--r-- root/root 126539 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam
-rw-r--r-- root/root 176 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bam.bai
-rw-r--r-- root/root 74700 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf
-rw-r--r-- root/root 77 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.bcf.bci
-rw-r--r-- root/root 559422 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/ex1.sam
-rw-r--r-- root/root 3778 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz
-rw-r--r-- root/root 259 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/example.gtf.gz.tbi
-rw-r--r-- root/root 348 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam
-rw-r--r-- root/root 96 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.bam.bai
-rw-r--r-- root/root 368 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/example_from_SAM_Spec.sam
-rw-r--r-- root/root 203 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.bam
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-rw-r--r-- root/root 240 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_buffered_pileup.sam
-rw-r--r-- root/root 198 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam
-rw-r--r-- root/root 176 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.bam.bai
-rw-r--r-- root/root 168 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/no_which_whole_file.sam
-rw-r--r-- root/root 1663363 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/olaps.Rda
-rw-r--r-- root/root 138598 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/pileup.txt
-rw-r--r-- root/root 181 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/querybins.bam
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-rw-r--r-- root/root 36 2018-08-28 15:06 ./usr/lib/R/site-library/Rsamtools/extdata/tophat/README
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 19620
Build-Time: 451
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 1097
Job: r-bioc-rsamtools_1.32.3-1
Machine Architecture: armhf
Package: r-bioc-rsamtools
Package-Time: 1607
Source-Version: 1.32.3-1
Space: 19620
Status: successful
Version: 1.32.3-1
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Finished at 2018-08-31T05:13:17Z
Build needed 00:26:47, 19620k disc space