r-bioc-rtracklayer →
1.42.1-2 →
armhf → 2019-01-12 05:22:08
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| r-bioc-rtracklayer 1.42.1-2 (armhf) Sat, 12 Jan 2019 05:09:25 +0000 |
+==============================================================================+
Package: r-bioc-rtracklayer
Version: 1.42.1-2
Source Version: 1.42.1-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-da77a4b9-967b-426b-93b1-e8464a338f68' 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 [11.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.1 MB]
Fetched 24.5 MB in 9s (2691 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-rtracklayer' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/r-pkg-team/r-bioc-rtracklayer.git
Please use:
git clone https://salsa.debian.org/r-pkg-team/r-bioc-rtracklayer.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1410 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-rtracklayer 1.42.1-2 (dsc) [2439 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-rtracklayer 1.42.1-2 (tar) [1382 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-rtracklayer 1.42.1-2 (diff) [26.4 kB]
Fetched 1410 kB in 0s (7508 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-rtracklayer-Y4F0oQ/r-bioc-rtracklayer-1.42.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-rtracklayer-Y4F0oQ' 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-AD4JPi/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-AD4JPi/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-AD4JPi/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (10.9 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session e2fsprogs-l10n krb5-locales libexpat1
libgpg-error-l10n libnss-systemd libpam-systemd 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 11 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-AD4JPi/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15815 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-genomicranges (>= 1.31.8), r-cran-xml, r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.19.22), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-biostrings (>= 2.47.6), r-bioc-zlibbioc, r-cran-rcurl, r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6)
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-genomicranges (>= 1.31.8), r-cran-xml, r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.19.22), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-biostrings (>= 2.47.6), r-bioc-zlibbioc, r-cran-rcurl, r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6)
dpkg-deb: building package 'sbuild-build-depends-r-bioc-rtracklayer-dummy' in '/<<BUILDDIR>>/resolver-AD4JPi/apt_archive/sbuild-build-depends-r-bioc-rtracklayer-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-rtracklayer-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-AD4JPi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Sources [643 B]
Get:5 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ Packages [726 B]
Fetched 2702 B in 0s (13.8 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-rtracklayer build dependencies (apt-based resolver)
------------------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
dbus dbus-user-session e2fsprogs-l10n krb5-locales libgpg-error-l10n
libnss-systemd libpam-systemd systemd-sysv
Use 'apt autoremove' to remove them.
The following additional 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 gettext gettext-base gfortran gfortran-8
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 libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libice6 libicu-dev libicu63 libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
liblzma-dev libmagic-mgc libmagic1 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 libpng16-16 libpsl5 libreadline-dev
librtmp1 libsigsegv2 libsm6 libssh2-1 libswitch-perl libtcl8.6 libthai-data
libthai0 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libx11-6
libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6
libxft2 libxml2 libxmuu1 libxrender1 libxss1 libxt6 m4 man-db pkg-config
po-debconf r-base-core r-base-dev r-bioc-biobase r-bioc-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray
r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors
r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-bitops
r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-lambda.r
r-cran-lattice r-cran-matrix r-cran-matrixstats r-cran-rcurl r-cran-snow
r-cran-xml ucf unzip x11-common xauth xdg-utils zip zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation debtags dh-make gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-8-doc libgfortran5-dbg libcoarrays-dev groff
liblapack-doc icu-doc liblzma-doc ncurses-doc readline-doc tcl8.6 tk8.6
libtool-doc gcj-jdk m4-doc apparmor less www-browser libmail-box-perl ess
r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base
texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra
texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo
r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate
r-cran-foreach r-cran-batchjobs r-cran-bbmisc r-cran-doparallel r-cran-rmpi
r-bioc-variantannotation r-bioc-shortread r-cran-codetools r-cran-runit
r-cran-knitr r-cran-batchtools r-cran-data.table r-bioc-bsgenome
r-bioc-genomicfeatures r-bioc-rtracklayer r-bioc-edger r-bioc-gviz
r-bioc-annotationhub r-bioc-graph r-cran-rmarkdown r-cran-jsonlite
r-cran-testthat r-cran-shiny r-cran-base64enc r-cran-ggplot2 r-cran-rsprng
r-cran-rlecuyer
Recommended packages:
devscripts curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs libpng-tools publicsuffix libltdl-dev
libmail-sendmail-perl r-recommended r-doc-html r-cran-runit
r-bioc-genefilter r-bioc-shortread r-cran-digest r-bioc-annotate
r-cran-testit r-cran-codetools r-cran-survival r-cran-testthat
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils dctrl-tools debhelper
dh-autoreconf dh-r dh-strip-nondeterminism dwz file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-8
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 libgfortran5 libglib2.0-0
libgraphite2-3 libharfbuzz0b libice6 libicu-dev libicu63 libjbig0
libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblapack-dev liblapack3
liblzma-dev libmagic-mgc libmagic1 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 libreadline-dev librtmp1
libsigsegv2 libsm6 libssh2-1 libswitch-perl libtcl8.6 libthai-data libthai0
libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libx11-6 libx11-data libxau6
libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2
libxmuu1 libxrender1 libxss1 libxt6 m4 man-db pkg-config po-debconf
r-base-core r-base-dev r-bioc-biobase r-bioc-biocgenerics
r-bioc-biocparallel r-bioc-biostrings r-bioc-delayedarray
r-bioc-genomeinfodb r-bioc-genomeinfodbdata r-bioc-genomicalignments
r-bioc-genomicranges r-bioc-iranges r-bioc-rsamtools r-bioc-s4vectors
r-bioc-summarizedexperiment r-bioc-xvector r-bioc-zlibbioc r-cran-bitops
r-cran-formatr r-cran-futile.logger r-cran-futile.options r-cran-lambda.r
r-cran-lattice r-cran-matrix r-cran-matrixstats r-cran-rcurl r-cran-snow
r-cran-xml sbuild-build-depends-r-bioc-rtracklayer-dummy ucf unzip
x11-common xauth xdg-utils zip zlib1g-dev
The following packages will be upgraded:
libpng16-16
1 upgraded, 138 newly installed, 0 to remove and 10 not upgraded.
Need to get 125 MB/128 MB of archives.
After this operation, 292 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-AD4JPi/apt_archive ./ sbuild-build-depends-r-bioc-rtracklayer-dummy 0.invalid.0 [1008 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 libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-2 [25.1 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libswitch-perl all 2.17-2 [20.5 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-3 [94.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-6 [547 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.0.0-1 [19.5 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.0.0-1 [12.5 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.2-3 [1076 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-5 [7976 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.26 [20.0 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.26 [17.5 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.3-1 [73.3 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libgfortran5 armhf 8.2.0-13+rpi1 [205 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-2 [103 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libpng16-16 armhf 1.6.36-2 [273 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libfreetype6 armhf 2.9.1-3 [318 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libcairo2 armhf 1.16.0-2 [602 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.35.1-1 [70.8 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-2 [52.6 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-2 [125 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.62.0-1 [286 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-2 [1493 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf fontconfig armhf 2.13.1-2 [404 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libfribidi0 armhf 1.0.5-3 [61.9 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libthai-data all 0.1.28-1 [170 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libdatrie1 armhf 0.2.12-1 [35.8 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libthai0 armhf 0.1.28-1 [50.9 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libpango-1.0-0 armhf 1.42.4-6 [168 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 2.3.0-1 [1130 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libpangoft2-1.0-0 armhf 1.42.4-6 [61.9 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libpangocairo-1.0-0 armhf 1.42.4-6 [51.6 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libtcl8.6 armhf 8.6.9+dfsg-1 [878 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libtiff5 armhf 4.0.10-3 [235 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libxft2 armhf 2.3.2-2 [49.3 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libxss1 armhf 1:1.2.3-1 [17.3 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libtk8.6 armhf 8.6.9-1 [666 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.5.2-1 [23.6 MB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libgfortran-8-dev armhf 8.2.0-13+rpi1 [248 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf gfortran-8 armhf 8.2.0-13+rpi1 [5816 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:8.2.0-2+rpi1 [1432 B]
Get:79 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-2 [113 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-2 [1551 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20181013-1 [278 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20181013-1 [940 B]
Get:83 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-5 [110 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-11+rpi1 [234 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-11+rpi1 [227 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-11+rpi1 [150 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-11+rpi1 [565 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libpng-dev armhf 1.6.36-2 [280 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-9 [27.7 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 63.1-5 [166 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 63.1-5 [8845 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.5.2-1 [4480 B]
Get:96 http://172.17.0.1/private buster-staging/main armhf libfile-which-perl all 1.23-1 [16.6 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf dh-r all 20181206 [34.9 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.28.0-2 [644 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf r-bioc-biobase armhf 2.42.0-1 [2215 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf r-cran-formatr all 1.5-3 [149 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2.3-2 [117 kB]
Get:102 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.1-2 [19.8 kB]
Get:103 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-3 [102 kB]
Get:104 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.3-1 [108 kB]
Get:105 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.16.5-1 [1057 kB]
Get:106 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.20.1-2 [1807 kB]
Get:107 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.16.0-1 [2121 kB]
Get:108 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.22.0-1 [596 kB]
Get:109 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.50.1-1 [14.1 MB]
Get:110 http://172.17.0.1/private buster-staging/main armhf r-cran-matrixstats armhf 0.54.0-1 [551 kB]
Get:111 http://172.17.0.1/private buster-staging/main armhf r-bioc-delayedarray armhf 0.8.0+dfsg-2 [1286 kB]
Get:112 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-4 [23.9 kB]
Get:113 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.11-1 [711 kB]
Get:114 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.2.0-1 [9196 kB]
Get:115 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.18.1-1 [3692 kB]
Get:116 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.34.0+dfsg-1 [1765 kB]
Get:117 http://172.17.0.1/private buster-staging/main armhf r-cran-lattice armhf 0.20-38-1 [1120 kB]
Get:118 http://172.17.0.1/private buster-staging/main armhf r-cran-matrix armhf 1.2-15-1 [3356 kB]
Get:119 http://172.17.0.1/private buster-staging/main armhf r-bioc-summarizedexperiment all 1.12.0+dfsg-1 [1886 kB]
Get:120 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.34.0-1 [3492 kB]
Get:121 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicalignments armhf 1.18.1-1 [2097 kB]
Get:122 http://172.17.0.1/private buster-staging/main armhf r-bioc-zlibbioc all 1.28.0+dfsg-1 [8540 B]
Get:123 http://172.17.0.1/private buster-staging/main armhf r-cran-xml armhf 3.98-1.16-1 [1938 kB]
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W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-13+rpi1 gcc-8_8.2.0-13+rpi1 libc6-dev_2.28-2 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~alpha3 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33-0.2 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-13+rpi1 dash_0.5.10.2-4 dbus_1.12.12-1 dbus-user-session_1.12.12-1 dctrl-tools_2.24-3 debconf_1.5.69 debhelper_12 debianutils_4.8.6 dh-autoreconf_19 dh-r_20181206 dh-strip-nondeterminism_1.0.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.145-4.1+b5 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 e2fsprogs-l10n_1.44.5-1 fakeroot_1.23-1 fdisk_2.33-0.2 file_1:5.34-2 findutils_4.6.0+git+20181018-1 fontconfig_2.13.1-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-13+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-8_8.2.0-13+rpi1 gcc-8-base_8.2.0-13+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gfortran_4:8.2.0-2+rpi1 gfortran-8_8.2.0-13+rpi1 gnupg_2.2.12-1+rpi1 gnupg-agent_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.1-3 groff-base_1.22.4-2 gzip_1.9-2.1 hostname_3.21 icu-devtools_63.1-5 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-2 krb5-locales_1.16.2-1 libacl1_2.2.52-3 libapparmor1_2.13.1-3+b1 libapt-pkg5.0_1.8.0~alpha3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-13+rpi1 libassuan0_2.5.2-1 libatomic1_8.2.0-13+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblas-dev_3.8.0-2 libblas3_3.8.0-2 libblkid1_2.33-0.2 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libbz2-dev_1.0.6-9 libc-bin_2.28-2 libc-dev-bin_2.28-2 libc6_2.28-2 libc6-dev_2.28-2 libcairo2_1.16.0-2 libcap-ng0_0.7.9-1+b1 libcap2_1:2.25-1.2 libcc1-0_8.2.0-13+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libcurl4_7.62.0-1 libdatrie1_0.2.12-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.145-4.1+b5 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33-0.2 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.0.0-1 libfile-which-perl_1.23-1 libfontconfig1_2.13.1-2 libfreetype6_2.9.1-3 libfribidi0_1.0.5-3 libgcc-8-dev_8.2.0-13+rpi1 libgcc1_1:8.2.0-13+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran-8-dev_8.2.0-13+rpi1 libgfortran5_8.2.0-13+rpi1 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-13+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgraphite2-3_1.3.12-1 libgssapi-krb5-2_1.16.2-1 libharfbuzz0b_2.3.0-1 libhogweed4_3.4.1~rc1-1 libice6_2:1.0.9-2 libicu-dev_63.1-5 libicu63_63.1-5 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 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_1.16.2-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-14+rpi1 libkmod2_25-2 libkrb5-3_1.16.2-1 libkrb5support0_1.16.2-1 libksba8_1.3.5-2 liblapack-dev_3.8.0-2 liblapack3_3.8.0-2 libldap-2.4-2_2.4.47+dfsg-1 libldap-common_2.4.47+dfsg-1 liblz4-1_1.8.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.33-0.2 libmpc3_1.1.0-1 libmpfr6_4.0.1-2 libncurses-dev_6.1+20181013-1 libncurses5_6.1+20181013-1 libncurses5-dev_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnghttp2-14_1.35.1-1 libnpth0_1.6-1 libnss-systemd_240-2+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-3.8 libpam-modules-bin_1.1.8-3.8 libpam-runtime_1.1.8-3.8 libpam-systemd_240-2+rpi1 libpam0g_1.1.8-3.8 libpango-1.0-0_1.42.4-6 libpangocairo-1.0-0_1.42.4-6 libpangoft2-1.0-0_1.42.4-6 libpaper-utils_1.1.26 libpaper1_1.1.26 libpcre16-3_2:8.39-11+rpi1 libpcre3_2:8.39-11+rpi1 libpcre3-dev_2:8.39-11+rpi1 libpcre32-3_2:8.39-11+rpi1 libpcrecpp0v5_2:8.39-11+rpi1 libperl5.24_5.24.1-7 libperl5.28_5.28.1-3 libpipeline1_1.5.0-2 libpixman-1-0_0.36.0-1 libplymouth4_0.9.4-1 libpng-dev_1.6.36-2 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libpsl5_0.20.2-2 libreadline-dev_7.0-5 libreadline7_7.0-5 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~rc8-1 libsasl2-modules-db_2.1.27~rc8-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-1 libsemanage1_2.8-1+b1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsm6_2:1.2.2-1+b3 libsmartcols1_2.33-0.2 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssh2-1_1.8.0-2 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-13+rpi1 libstdc++6_8.2.0-13+rpi1 libswitch-perl_2.17-2 libsystemd0_240-2+rpi1 libtasn1-6_4.13-3 libtcl8.6_8.6.9+dfsg-1 libthai-data_0.1.28-1 libthai0_0.1.28-1 libtiff5_4.0.10-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtk8.6_8.6.9-1 libtool_2.4.6-6 libubsan1_8.2.0-13+rpi1 libuchardet0_0.0.6-3 libudev1_240-2+rpi1 libunistring2_0.9.10-1 libustr-1.0-1_1.0.4-6 libuuid1_2.33-0.2 libwebp6_0.6.1-2 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-2 libxml2_2.9.4+dfsg1-7+b1 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libxt6_1:1.1.5-1 libzstd1_1.3.5+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-1 mawk_1.3.3-17 mount_2.33-0.2 multiarch-support_2.28-2 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.24_5.24.1-7 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 r-base-core_3.5.2-1 r-base-dev_3.5.2-1 r-bioc-biobase_2.42.0-1 r-bioc-biocgenerics_0.28.0-2 r-bioc-biocparallel_1.16.5-1 r-bioc-biostrings_2.50.1-1 r-bioc-delayedarray_0.8.0+dfsg-2 r-bioc-genomeinfodb_1.18.1-1 r-bioc-genomeinfodbdata_1.2.0-1 r-bioc-genomicalignments_1.18.1-1 r-bioc-genomicranges_1.34.0+dfsg-1 r-bioc-iranges_2.16.0-1 r-bioc-rsamtools_1.34.0-1 r-bioc-s4vectors_0.20.1-2 r-bioc-summarizedexperiment_1.12.0+dfsg-1 r-bioc-xvector_0.22.0-1 r-bioc-zlibbioc_1.28.0+dfsg-1 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-lattice_0.20-38-1 r-cran-matrix_1.2-15-1 r-cran-matrixstats_0.54.0-1 r-cran-rcurl_1.95-4.11-1 r-cran-snow_1:0.4.3-1 r-cran-xml_3.98-1.16-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-rtracklayer-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-2+rpi1 systemd-sysv_240-2+rpi1 sysvinit-utils_2.93-2 tar_1.30+dfsg-3+rpi1 tzdata_2018i-1 ucf_3.0038+nmu1 udev_240-2+rpi1 unzip_6.0-21 util-linux_2.33-0.2 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 Thu Jan 10 07:23:03 2019 UTC
gpgv: using RSA key 9A3C07BD06DE2F416E813A5D612EF1613E050F54
gpgv: issuer "daissi@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-rtracklayer_1.42.1-2.dsc
dpkg-source: info: extracting r-bioc-rtracklayer in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-rtracklayer_1.42.1.orig.tar.gz
dpkg-source: info: unpacking r-bioc-rtracklayer_1.42.1-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying delete_configure.patch
Check disk 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=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-da77a4b9-967b-426b-93b1-e8464a338f68
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-rtracklayer
dpkg-buildpackage: info: source version 1.42.1-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: rtracklayer Version: 1.42.1
I: Building using R version 3.5.2-1
I: R API version: r-api-3.5
I: Using built-time from d/changelog: Thu, 10 Jan 2019 08:18:08 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean . "--built-timestamp='Thu, 10 Jan 2019 08:18:08 +0100'"
* installing *source* package 'rtracklayer' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... no
configure: creating ./config.status
config.status: creating src/Makevars
** libs
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -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 -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readGFF.c -o readGFF.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c bigWig.c -o bigWig.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c chain_io.c -o chain_io.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c twoBit.c -o twoBit.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c handlers.c -o handlers.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.c -o utils.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/common.c -o ucsc/common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:331:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
write(STDERR_FILENO, errMsg, strlen(errMsg));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/hash.c -o ucsc/hash.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/linefile.c -o ucsc/linefile.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/localmem.c -o ucsc/localmem.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dystring.c -o ucsc/dystring.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/obscure.c -o ucsc/obscure.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/dlist.c -o ucsc/dlist.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/udc.c -o ucsc/udc.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/net.c -o ucsc/net.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/internet.c -o ucsc/internet.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/https.c -o ucsc/https.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/verbose.c -o ucsc/verbose.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/os.c -o ucsc/os.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-xoRi9J/r-base-3.5.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -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-rtracklayer/usr/lib/R/site-library/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)
rm -f /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/LICENSE
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 292.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 293.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 296.
W: Ignoring specified R dependency: R (>= 3.3)
I: Using r-bioc-genomicranges for Depends:GenomicRanges (>= 1.31.8)
I: Using r-bioc-bsgenome for Suggests:BSgenome (>= 1.33.4)
W: Cannot find a debian package for Suggests:humanStemCell
W: Cannot find a debian package for Suggests:microRNA (>= 1.1.1)
I: Using r-bioc-genefilter for Suggests:genefilter
I: Using r-bioc-limma for Suggests:limma
W: Cannot find a debian package for Suggests:org.Hs.eg.db
W: Cannot find a debian package for Suggests:hgu133plus2.db
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:BSgenome.Hsapiens.UCSC.hg19
W: Cannot find a debian package for Suggests:TxDb.Hsapiens.UCSC.hg19.knownGene
I: Using r-cran-runit for Suggests:RUnit
I: Using r-cran-xml for Imports:XML (>= 1.98-0)
I: Using r-bioc-biocgenerics for Imports:BiocGenerics (>= 0.25.1)
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.19.22)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.13.13)
I: Using r-bioc-xvector for Imports:XVector (>= 0.19.7)
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.15.2)
I: Using r-bioc-biostrings for Imports:Biostrings (>= 2.47.6)
I: Using r-bioc-zlibbioc for Imports:zlibbioc
I: Using r-cran-rcurl for Imports:RCurl (>= 1.4-2)
I: Using r-bioc-rsamtools for Imports:Rsamtools (>= 1.31.2)
I: Using r-bioc-genomicalignments for Imports:GenomicAlignments (>= 1.15.6)
I: BioConductor API version: r-api-bioc-3.8
Create lintian-override for package-contains-documentation-outside-usr-share-doc
dh_installdocs -a -O--buildsystem=R
dh_installchangelogs -a -O--buildsystem=R
dh_installinit -a -O--buildsystem=R
dh_lintian -a -O--buildsystem=R
dh_perl -a -O--buildsystem=R
dh_link -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
dh_installdeb -a -O--buildsystem=R
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dpkg-deb: building package 'r-bioc-rtracklayer-dbgsym' in '../r-bioc-rtracklayer-dbgsym_1.42.1-2_armhf.deb'.
dpkg-deb: building package 'r-bioc-rtracklayer' in '../r-bioc-rtracklayer_1.42.1-2_armhf.deb'.
dpkg-genbuildinfo --build=any
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Build finished at 2019-01-12T05:22:06Z
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r-bioc-rtracklayer_1.42.1-2_armhf.changes:
------------------------------------------
Format: 1.8
Date: Thu, 10 Jan 2019 08:18:08 +0100
Source: r-bioc-rtracklayer
Binary: r-bioc-rtracklayer
Architecture: armhf
Version: 1.42.1-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Dylan Aïssi <daissi@debian.org>
Description:
r-bioc-rtracklayer - GNU R interface to genome browsers and their annotation tracks
Changes:
r-bioc-rtracklayer (1.42.1-2) unstable; urgency=medium
.
* Team upload.
* dh-update-R: Remove build-dep libgdal-dev and add r-bioc-zlibbioc.
* Standards-Version: 4.3.0
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r-bioc-rtracklayer-dbgsym_1.42.1-2_armhf.deb
--------------------------------------------
new Debian package, version 2.0.
size 435036 bytes: control archive=544 bytes.
410 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-rtracklayer-dbgsym
Source: r-bioc-rtracklayer
Version: 1.42.1-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 498
Depends: r-bioc-rtracklayer (= 1.42.1-2)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-rtracklayer
Build-Ids: 8876cc888efb27de4cd4fad9aadd1966dd580bd5
drwxr-xr-x root/root 0 2019-01-10 07:18 ./
drwxr-xr-x root/root 0 2019-01-10 07:18 ./usr/
drwxr-xr-x root/root 0 2019-01-10 07:18 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-10 07:18 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-01-10 07:18 ./usr/lib/debug/.build-id/
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lrwxrwxrwx root/root 0 2019-01-10 07:18 ./usr/share/doc/r-bioc-rtracklayer-dbgsym -> r-bioc-rtracklayer
r-bioc-rtracklayer_1.42.1-2_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 2412216 bytes: control archive=3004 bytes.
1260 bytes, 17 lines control
6631 bytes, 75 lines md5sums
Package: r-bioc-rtracklayer
Version: 1.42.1-2
Architecture: armhf
Maintainer: Debian R Packages Maintainers <r-pkg-team@alioth-lists.debian.net>
Installed-Size: 3723
Depends: r-base-core (>= 3.5.2-1), r-api-3.5, r-api-bioc-3.8, r-bioc-genomicranges (>= 1.31.8), r-cran-xml (>= 1.98-0), r-bioc-biocgenerics (>= 0.25.1), r-bioc-s4vectors (>= 0.19.22), r-bioc-iranges (>= 2.13.13), r-bioc-xvector (>= 0.19.7), r-bioc-genomeinfodb (>= 1.15.2), r-bioc-biostrings (>= 2.47.6), r-bioc-zlibbioc, r-cran-rcurl (>= 1.4-2), r-bioc-rsamtools (>= 1.31.2), r-bioc-genomicalignments (>= 1.15.6), libc6 (>= 2.28), zlib1g (>= 1:1.1.4)
Suggests: r-bioc-bsgenome (>= 1.33.4), r-bioc-genefilter, r-bioc-limma, r-bioc-genomicfeatures, r-cran-runit
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/rtracklayer/
Description: GNU R interface to genome browsers and their annotation tracks
Extensible framework for interacting with multiple genome browsers
(currently UCSC built-in) and manipulating annotation tracks in various
formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
built-in). The user may export/import tracks to/from the supported
browsers, as well as query and modify the browser state, such as the
current viewport.
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Build Architecture: armhf
Build-Space: 11256
Build-Time: 116
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 627
Job: r-bioc-rtracklayer_1.42.1-2
Machine Architecture: armhf
Package: r-bioc-rtracklayer
Package-Time: 761
Source-Version: 1.42.1-2
Space: 11256
Status: successful
Version: 1.42.1-2
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Finished at 2019-01-12T05:22:06Z
Build needed 00:12:41, 11256k disk space