r-bioc-shortread →
1.36.1-1 →
armhf → 2018-03-20 10:55:35
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| r-bioc-shortread 1.36.1-1 (armhf) Tue, 20 Mar 2018 10:35:32 +0000 |
+==============================================================================+
Package: r-bioc-shortread
Version: 1.36.1-1
Source Version: 1.36.1-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-ece77b58-25c3-4325-a9a6-8839b013745d' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 29s (796 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-shortread' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/r-bioc-shortread.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/r-bioc-shortread.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5191 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.36.1-1 (dsc) [2260 B]
Get:2 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.36.1-1 (tar) [5184 kB]
Get:3 http://172.17.0.1/private buster-staging/main r-bioc-shortread 1.36.1-1 (diff) [5296 B]
Fetched 5191 kB in 2s (2845 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-DA9IOL/r-bioc-shortread-1.36.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-DA9IOL' 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-hJrUkG/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-hJrUkG/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-hJrUkG/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-hJrUkG/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2831 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 3 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-hJrUkG/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 (11.9 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15694 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-biobase (>= 2.26.0), r-bioc-genomicalignments (>= 1.8.0), r-bioc-rsamtools (>= 1.28.0), r-cran-hwriter, r-cran-latticeextra
Filtered Build-Depends: debhelper (>= 11~), dh-r, r-base-dev, r-bioc-biobase (>= 2.26.0), r-bioc-genomicalignments (>= 1.8.0), r-bioc-rsamtools (>= 1.28.0), r-cran-hwriter, r-cran-latticeextra
dpkg-deb: building package 'sbuild-build-depends-r-bioc-shortread-dummy' in '/<<BUILDDIR>>/resolver-hJrUkG/apt_archive/sbuild-build-depends-r-bioc-shortread-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-shortread-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-hJrUkG/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Sources [570 B]
Get:5 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ Packages [651 B]
Fetched 2554 B in 1s (3402 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install r-bioc-shortread 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 cdbs dctrl-tools
debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbsd0 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-7-dev libgfortran4 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2
libharfbuzz0b libice6 libicu-dev libicu57 libjbig0 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1
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 libssl1.0.2 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool 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-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-hwriter
r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix
r-cran-matrixstats r-cran-rcolorbrewer 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 devscripts debtags dh-make dwz gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-7-doc libgfortran4-dbg
libcoarrays-dev groff liblapack-doc krb5-doc krb5-user 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-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-bioc-bsgenome r-bioc-genomicfeatures r-bioc-affy
r-bioc-genefilter r-bioc-rtracklayer r-bioc-deseq2 r-bioc-edger
r-bioc-annotationdbi r-bioc-annotate r-bioc-gviz r-bioc-annotationhub
r-cran-digest r-bioc-graph r-cran-data.table r-cran-jsonlite r-cran-testthat
r-cran-base64enc r-cran-ggplot2 r-cran-xml r-cran-rsprng r-cran-rlecuyer
Recommended packages:
curl | wget | lynx-cur bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libpng-tools publicsuffix
libltdl-dev libmail-sendmail-perl r-recommended r-doc-html
libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils
x11-xserver-utils
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils cdbs dctrl-tools
debhelper dh-autoreconf dh-r dh-strip-nondeterminism file fontconfig
fontconfig-config fonts-dejavu-core gettext gettext-base gfortran gfortran-7
groff-base icu-devtools intltool-debian libarchive-zip-perl libblas-dev
libblas3 libbsd0 libbz2-dev libcairo2 libcroco3 libcurl3 libdatrie1
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-7-dev libgfortran4 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2
libharfbuzz0b libice6 libicu-dev libicu57 libjbig0 libjpeg-dev
libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 liblzma-dev libmagic-mgc libmagic1
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 libssl1.0.2 libtcl8.6
libthai-data libthai0 libtiff5 libtimedate-perl libtinfo-dev libtk8.6
libtool 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-cran-bitops r-cran-futile.logger r-cran-futile.options r-cran-hwriter
r-cran-lambda.r r-cran-lattice r-cran-latticeextra r-cran-matrix
r-cran-matrixstats r-cran-rcolorbrewer r-cran-rcurl r-cran-snow
sbuild-build-depends-r-bioc-shortread-dummy ucf unzip x11-common xauth
xdg-utils zip zlib1g-dev
0 upgraded, 139 newly installed, 0 to remove and 3 not upgraded.
Need to get 98.3 MB/138 MB of archives.
After this operation, 315 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-hJrUkG/apt_archive ./ sbuild-build-depends-r-bioc-shortread-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2n-1 [887 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf cdbs all 0.4.156 [83.1 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf dctrl-tools armhf 2.24-2 [94.4 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 16 [16.3 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.5 [1007 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf zip armhf 3.0-11 [212 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf unzip armhf 6.0-21 [149 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libpaper1 armhf 1.1.24+nmu5 [20.8 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpaper-utils armhf 1.1.24+nmu5 [17.2 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf xdg-utils all 1.1.2-2 [72.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-11 [191 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libcurl3 armhf 7.58.0-2 [276 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf r-base-core armhf 3.4.4-1 [23.0 MB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libgfortran-7-dev armhf 7.3.0-11 [232 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf gfortran-7 armhf 7.3.0-11 [5456 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:7.2.0-1d1 [1352 B]
Get:37 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.1-1 [66.6 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1-1 [152 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libreadline-dev armhf 7.0-3 [109 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libpcre16-3 armhf 2:8.39-9 [234 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libpcre32-3 armhf 2:8.39-9 [226 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libpcrecpp0v5 armhf 2:8.39-9 [150 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libpcre3-dev armhf 2:8.39-9 [561 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libxmuu1 armhf 2:1.1.2-2 [23.0 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf xauth armhf 1:1.0.10-1 [36.4 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf r-base-dev all 3.4.4-1 [4488 B]
Get:50 http://172.17.0.1/private buster-staging/main armhf dh-r all 20171201 [10.0 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocgenerics all 0.24.0-1 [567 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf r-bioc-biobase armhf 2.38.0-1 [2024 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf r-cran-lambda.r all 1.2-1 [86.3 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.options all 1.0.0-3 [15.6 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf r-cran-futile.logger all 1.4.3-2 [93.8 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf r-cran-snow all 1:0.4.2-1.1 [65.4 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf r-bioc-biocparallel armhf 1.12.0-2 [765 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf r-bioc-s4vectors armhf 0.16.0-1 [1163 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf r-bioc-iranges armhf 2.12.0-2 [1467 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf r-bioc-xvector armhf 0.18.0-1 [367 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf r-bioc-biostrings armhf 2.46.0-1 [13.6 MB]
Get:62 http://172.17.0.1/private buster-staging/main armhf r-cran-matrixstats armhf 0.53.1-1 [560 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf r-bioc-delayedarray all 0.4.1-1 [615 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf r-cran-bitops armhf 1.0-6-3 [22.5 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf r-cran-rcurl armhf 1.95-4.8-4 [617 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodbdata all 1.0.0-1 [18.0 MB]
Get:67 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomeinfodb all 1.14.0-1 [3529 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicranges armhf 1.30.0-1 [1575 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf r-cran-lattice armhf 0.20-35-1+b1 [723 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf r-cran-matrix armhf 1.2-12-1 [2329 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf r-bioc-summarizedexperiment all 1.8.1-1 [1592 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf r-bioc-rsamtools armhf 1.30.0-1 [3278 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf r-bioc-genomicalignments armhf 1.14.1-1 [1693 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf r-cran-hwriter all 1.3.2-2 [137 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf r-cran-rcolorbrewer all 1.1-2-1.1 [26.3 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf r-cran-latticeextra armhf 0.6-28-2+b1 [2059 kB]
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Setting up cdbs (0.4.156) ...
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Creating config file /etc/papersize with new version
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Setting up fontconfig (2.12.6-0.1) ...
Regenerating fonts cache... done.
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Creating config file /etc/R/Renviron with new version
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Setting up r-cran-rcolorbrewer (1.1-2-1.1) ...
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Setting up r-cran-futile.options (1.0.0-3) ...
Setting up r-cran-rcurl (1.95-4.8-4) ...
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Setting up r-cran-lambda.r (1.2-1) ...
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Setting up r-bioc-s4vectors (0.16.0-1) ...
Setting up r-cran-lattice (0.20-35-1+b1) ...
Setting up r-cran-latticeextra (0.6-28-2+b1) ...
Setting up r-bioc-genomeinfodbdata (1.0.0-1) ...
Setting up r-cran-futile.logger (1.4.3-2) ...
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Setting up r-bioc-biocparallel (1.12.0-2) ...
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Setting up r-bioc-xvector (0.18.0-1) ...
Setting up r-bioc-biostrings (2.46.0-1) ...
Setting up r-bioc-genomicranges (1.30.0-1) ...
Setting up r-bioc-summarizedexperiment (1.8.1-1) ...
Setting up r-bioc-rsamtools (1.30.0-1) ...
Setting up r-bioc-genomicalignments (1.14.1-1) ...
Setting up dh-autoreconf (16) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (11.1.5) ...
Setting up dh-r (20171201) ...
Setting up sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-2+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_2.30-7+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-11 gcc-7_7.3.0-11 libc6-dev_2.27-2+rpi1 libstdc++-7-dev_7.3.0-11 libstdc++6_8-20180218-1+rpi1 linux-libc-dev_4.15.4-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-1.1 binutils_2.30-7+rpi1 binutils-arm-linux-gnueabihf_2.30-7+rpi1 binutils-common_2.30-7+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.4 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 cdbs_0.4.156 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-11 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 dctrl-tools_2.24-2 debconf_1.5.66 debhelper_11.1.5 debianutils_4.8.4 dh-autoreconf_16 dh-r_20171201 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.0-1 e2fsprogs_1.44.0-1 e2fsprogs-l10n_1.44.0-1 fakeroot_1.22-2 fdisk_2.31.1-0.4 file_1:5.32-2 findutils_4.6.0+git+20170828-2 fontconfig_2.12.6-0.1 fontconfig-config_2.12.6-0.1 fonts-dejavu-core_2.37-1 g++_4:7.2.0-1d1 g++-7_7.3.0-11 gcc_4:7.2.0-1d1 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libblkid1_2.31.1-0.4 libbsd0_0.8.7-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-2+rpi1 libc-dev-bin_2.27-2+rpi1 libc6_2.27-2+rpi1 libc6-dev_2.27-2+rpi1 libcairo2_1.15.10-1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180218-1+rpi1 libcilkrts5_7.3.0-11 libcom-err2_1.44.0-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.1-1 libcryptsetup4_2:1.7.5-1 libcurl3_7.58.0-2 libdatrie1_0.2.10-7 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.241 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.90-1+rpi1 libdrm2_2.4.90-1+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.0-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.4 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libfontconfig1_2.12.6-0.1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-11 libgcc1_1:8-20180218-1+rpi1 libgcrypt20_1.8.1-4 libgdbm-compat4_1.14.1-4 libgdbm3_1.8.3-14 libgdbm5_1.14.1-4 libgfortran-7-dev_7.3.0-11 libgfortran4_7.3.0-11 libglib2.0-0_2.54.3-2 libgmp10_2:6.1.2+dfsg-3 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libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-2 libpam0g_1.1.8-3.7 libpango-1.0-0_1.40.14-1 libpangocairo-1.0-0_1.40.14-1 libpangoft2-1.0-0_1.40.14-1 libpaper-utils_1.1.24+nmu5 libpaper1_1.1.24+nmu5 libpcre16-3_2:8.39-9 libpcre3_2:8.39-9 libpcre3-dev_2:8.39-9 libpcre32-3_2:8.39-9 libpcrecpp0v5_2:8.39-9 libperl5.24_5.24.1-4 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libpixman-1-0_0.34.0-2 libplymouth4_0.9.3-2 libpng-dev_1.6.34-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libpsl5_0.19.1-5 libreadline-dev_7.0-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsm6_2:1.2.2-1+b3 libsmartcols1_2.31.1-0.4 libsqlite3-0_3.22.0-1 libss2_1.44.0-1 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2n-1 libssl1.1_1.1.0g-2 libstdc++-7-dev_7.3.0-11 libstdc++6_8-20180218-1+rpi1 libsystemd0_238-2 libtasn1-6_4.13-2 libtcl8.6_8.6.8+dfsg-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libthai-data_0.1.27-2 libthai0_0.1.27-2 libtiff5_4.0.9-4 libtimedate-perl_2.3000-2 libtinfo-dev_6.1-1 libtinfo5_6.1-1 libtk8.6_8.6.8-3 libtool_2.4.6-2 libubsan0_7.3.0-11 libudev1_238-2 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.4 libx11-6_2:1.6.4-3 libx11-data_2:1.6.4-3 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13-1 libxcb-shm0_1.13-1 libxcb1_1.13-1 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxft2_2.3.2-1+b2 libxml2_2.9.4+dfsg1-6.1 libxmuu1_2:1.1.2-2 libxrender1_1:0.9.10-1 libxss1_1:1.2.2-1 libxt6_1:1.1.5-1 linux-base_4.5 linux-libc-dev_4.15.4-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.2-1 mawk_1.3.3-17 mount_2.31.1-0.4 multiarch-support_2.27-2+rpi1 nano_2.9.4-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 openssl_1.1.0g-2 passwd_1:4.5-1 patch_2.7.6-1 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 pkg-config_0.29-4 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 r-base-core_3.4.4-1 r-base-dev_3.4.4-1 r-bioc-biobase_2.38.0-1 r-bioc-biocgenerics_0.24.0-1 r-bioc-biocparallel_1.12.0-2 r-bioc-biostrings_2.46.0-1 r-bioc-delayedarray_0.4.1-1 r-bioc-genomeinfodb_1.14.0-1 r-bioc-genomeinfodbdata_1.0.0-1 r-bioc-genomicalignments_1.14.1-1 r-bioc-genomicranges_1.30.0-1 r-bioc-iranges_2.12.0-2 r-bioc-rsamtools_1.30.0-1 r-bioc-s4vectors_0.16.0-1 r-bioc-summarizedexperiment_1.8.1-1 r-bioc-xvector_0.18.0-1 r-cran-bitops_1.0-6-3 r-cran-futile.logger_1.4.3-2 r-cran-futile.options_1.0.0-3 r-cran-hwriter_1.3.2-2 r-cran-lambda.r_1.2-1 r-cran-lattice_0.20-35-1+b1 r-cran-latticeextra_0.6-28-2+b1 r-cran-matrix_1.2-12-1 r-cran-matrixstats_0.53.1-1 r-cran-rcolorbrewer_1.1-2-1.1 r-cran-rcurl_1.95-4.8-4 r-cran-snow_1:0.4.2-1.1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-2 systemd-sysv_238-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018c-1 ucf_3.0038 udev_238-2 unzip_6.0-21 util-linux_2.31.1-0.4 x11-common_1:7.7+19 xauth_1:1.0.10-1 xdg-utils_1.1.2-2 xz-utils_5.2.2-1.3 zip_3.0-11 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| 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 Mar 13 08:00:19 2018 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.36.1-1.dsc
dpkg-source: info: extracting r-bioc-shortread in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking r-bioc-shortread_1.36.1.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.36.1-1.debian.tar.xz
dpkg-source: info: applying use_debian_packaged_zlib.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-ece77b58-25c3-4325-a9a6-8839b013745d
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package r-bioc-shortread
dpkg-buildpackage: info: source version 1.36.1-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build r-bioc-shortread-1.36.1
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem R
dh_testdir -O--buildsystem=R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
debian/rules build-arch
dh build-arch --buildsystem R
dh_testdir -a -O--buildsystem=R
dh_update_autotools_config -a -O--buildsystem=R
dh_autoreconf -a -O--buildsystem=R
dh_auto_configure -a -O--buildsystem=R
dh_auto_build -a -O--buildsystem=R
dh_auto_test -a -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --buildsystem R
dh_testroot -a -O--buildsystem=R
dh_prep -a -O--buildsystem=R
dh_installdirs -a -O--buildsystem=R
dh_auto_install -a -O--buildsystem=R
I: R Package: ShortRead Version: 1.36.1
I: Building using R version 3.4.4-1
I: R API version: r-api-3.4
I: Using built-time from d/changelog: Tue, 13 Mar 2018 08:50:11 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library --clean . "--built-timestamp='Tue, 13 Mar 2018 08:50:11 +0100'"
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 4
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 -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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c IRanges_stubs.c -o IRanges_stubs.o
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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_init_ShortRead.c -o R_init_ShortRead.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/S4Vectors/include" -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c alphabet.c -o alphabet.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io.c -o io.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_bowtie.c -o io_bowtie.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c io_soap.c -o io_soap.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" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readBfaToc.cc -o readBfaToc.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" -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=4 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read_maq_map.cc -o read_maq_map.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sampler.c -o sampler.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.c -o util.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 -fpic -g -O2 -fdebug-prefix-map=/build/r-base-1Z1lf8/r-base-3.4.4=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c xsnap.c -o xsnap.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -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-shortread/usr/lib/R/site-library/ShortRead/libs
** R
** inst
** preparing package for lazy loading
code for methods in class "ShortReadFile" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqFileReader" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "QAData" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "Snapshot" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "SpTrellis" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqSampler" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
code for methods in class "FastqStreamer" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 290.
Use of uninitialized value $dep_line in substitution (s///) at /usr/share/perl5/Dpkg/Deps.pm line 291.
Use of uninitialized value $dep_line in split at /usr/share/perl5/Dpkg/Deps.pm line 294.
I: Using r-bioc-biocgenerics for Depends:BiocGenerics (>= 0.23.3)
I: Using r-bioc-biocparallel for Depends:BiocParallel
I: Using r-bioc-biostrings for Depends:Biostrings (>= 2.37.1)
I: Using r-bioc-rsamtools for Depends:Rsamtools (>= 1.21.4)
I: Using r-bioc-genomicalignments for Depends:GenomicAlignments (>= 1.5.4)
W: Cannot find a debian package for Suggests:BiocStyle
I: Using r-cran-runit for Suggests:RUnit
I: Using r-bioc-biomart for Suggests:biomaRt
I: Using r-bioc-genomicfeatures for Suggests:GenomicFeatures
W: Cannot find a debian package for Suggests:yeastNagalakshmi
I: Using r-bioc-biobase for Imports:Biobase
I: Using r-bioc-s4vectors for Imports:S4Vectors (>= 0.13.8)
I: Using r-bioc-iranges for Imports:IRanges (>= 2.3.7)
I: Using r-bioc-genomeinfodb for Imports:GenomeInfoDb (>= 1.1.19)
I: Using r-bioc-genomicranges for Imports:GenomicRanges (>= 1.21.6)
I: Using r-cran-hwriter for Imports:hwriter
I: Using r-cran-lattice for Imports:lattice
I: Using r-cran-latticeextra for Imports:latticeExtra
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-shortread/usr/lib/R/site-library/ShortRead/libs/ShortRead.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-shortread' in '../r-bioc-shortread_1.36.1-1_armhf.deb'.
dpkg-deb: building package 'r-bioc-shortread-dbgsym' in '../r-bioc-shortread-dbgsym_1.36.1-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-shortread_1.36.1-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build r-bioc-shortread-1.36.1
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-03-20T10:55:25Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
r-bioc-shortread_1.36.1-1_armhf.changes:
----------------------------------------
Format: 1.8
Date: Tue, 13 Mar 2018 08:50:11 +0100
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: armhf
Version: 1.36.1-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
r-bioc-shortread - GNU R classes and methods for high-throughput short-read sequenci
Changes:
r-bioc-shortread (1.36.1-1) unstable; urgency=medium
.
* New upstream version
* Standards-Version: 4.1.3
* debhelper 11
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044cd92951c952bcd5d0f736e79f3da9 8223 gnu-r optional r-bioc-shortread_1.36.1-1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
r-bioc-shortread-dbgsym_1.36.1-1_armhf.deb
------------------------------------------
new Debian package, version 2.0.
size 138864 bytes: control archive=544 bytes.
408 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: r-bioc-shortread-dbgsym
Source: r-bioc-shortread
Version: 1.36.1-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 174
Depends: r-bioc-shortread (= 1.36.1-1)
Section: debug
Priority: optional
Description: debug symbols for r-bioc-shortread
Build-Ids: be72728e1ce613c4db5d20c20a86db537e1a7eba
drwxr-xr-x root/root 0 2018-03-13 07:50 ./
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/debug/.build-id/be/
-rw-r--r-- root/root 167100 2018-03-13 07:50 ./usr/lib/debug/.build-id/be/72728e1ce613c4db5d20c20a86db537e1a7eba.debug
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/share/
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-03-13 07:50 ./usr/share/doc/r-bioc-shortread-dbgsym -> r-bioc-shortread
r-bioc-shortread_1.36.1-1_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 4291876 bytes: control archive=4120 bytes.
1259 bytes, 17 lines control
10811 bytes, 113 lines md5sums
Package: r-bioc-shortread
Version: 1.36.1-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6073
Depends: r-base-core (>= 3.4.4-1), r-api-3.4, r-bioc-biocgenerics (>= 0.23.3), r-bioc-biocparallel, r-bioc-biostrings (>= 2.37.1), r-bioc-rsamtools (>= 1.21.4), r-bioc-genomicalignments (>= 1.5.4), r-bioc-biobase, r-bioc-s4vectors (>= 0.13.8), r-bioc-iranges (>= 2.3.7), r-bioc-genomeinfodb (>= 1.1.19), r-bioc-genomicranges (>= 1.21.6), r-cran-hwriter, r-cran-lattice, r-cran-latticeextra, libc6 (>= 2.7), libgcc1 (>= 1:3.5), libgomp1 (>= 4.2.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4)
Suggests: r-cran-runit, r-bioc-biomart, r-bioc-genomicfeatures
Section: gnu-r
Priority: optional
Homepage: https://bioconductor.org/packages/ShortRead/
Description: GNU R classes and methods for high-throughput short-read sequencing data
This BioConductor module is a package for input, quality assessment,
manipulation and output of high-throughput sequencing data. ShortRead is
provided in the R and Bioconductor environments, allowing ready access
to additional facilities for advanced statistical analysis, data
transformation, visualization and integration with diverse genomic
resources.
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drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/R/site-library/
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-rw-r--r-- root/root 1321 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/DESCRIPTION
-rw-r--r-- root/root 5917 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/INDEX
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-rw-r--r-- root/root 1147 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/NAMESPACE
-rw-r--r-- root/root 12176 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/NEWS
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/R/
-rw-r--r-- root/root 1056 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/R/ShortRead
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-rw-r--r-- root/root 11884 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/R/ShortRead.rdx
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-rw-r--r-- root/root 5961 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/doc/Overview.R
-rw-r--r-- root/root 15627 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/doc/Overview.Rnw
-rw-r--r-- root/root 176266 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/doc/Overview.pdf
-rw-r--r-- root/root 1355 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/doc/index.html
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drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/
drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/
-rw-r--r-- root/root 31740 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_1_sequence.txt
-rw-r--r-- root/root 121368 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_2_export.txt
-rw-r--r-- root/root 90912 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/extdata/Data/C1-36Firecrest/Bustard/GERALD/s_5_0001_realign.txt
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drwxr-xr-x root/root 0 2018-03-13 07:50 ./usr/lib/R/site-library/ShortRead/extdata/bowtie/
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Purging /<<BUILDDIR>>
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| Summary |
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Build Architecture: armhf
Build-Space: 19600
Build-Time: 266
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 869
Job: r-bioc-shortread_1.36.1-1
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 1193
Source-Version: 1.36.1-1
Space: 19600
Status: successful
Version: 1.36.1-1
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Finished at 2018-03-20T10:55:25Z
Build needed 00:19:53, 19600k disc space