r-bioc-shortread →
1.20.0-1 →
armhf → 2014-01-06 07:07:49
sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-02
╔══════════════════════════════════════════════════════════════════════════════╗
║ r-bioc-shortread 1.20.0-1 (armhf) 06 Jan 2014 06:49 ║
╚══════════════════════════════════════════════════════════════════════════════╝
Package: r-bioc-shortread
Version: 1.20.0-1
Source Version: 1.20.0-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-7483h1/r-bioc-shortread-1.20.0' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/r-bioc-shortread-7483h1' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-946bff98-7e14-467c-b586-9e01d9e1167e' with '«CHROOT»'
┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot │
└──────────────────────────────────────────────────────────────────────────────┘
Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7144 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8263 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.4 MB in 30s (502 kB/s)
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files │
└──────────────────────────────────────────────────────────────────────────────┘
Check APT
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Checking available source versions...
Download source files with APT
──────────────────────────────
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'r-bioc-shortread' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-shortread/trunk/
Need to get 2098 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main r-bioc-shortread 1.20.0-1 (dsc) [1632 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main r-bioc-shortread 1.20.0-1 (tar) [2092 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main r-bioc-shortread 1.20.0-1 (diff) [4731 B]
Fetched 2098 kB in 0s (4228 kB/s)
Download complete and in download only mode
Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-3Stal9/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver) │
└──────────────────────────────────────────────────────────────────────────────┘
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 8 not upgraded.
Need to get 0 B/758 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11446 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, r-base-dev, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), cdbs, r-base-dev, r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter
dpkg-deb: building package `sbuild-build-depends-r-bioc-shortread-dummy' in `/«BUILDDIR»/resolver-wAzTMy/apt_archive/sbuild-build-depends-r-bioc-shortread-dummy.deb'.
OK
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 extra packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base
intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2
libcroco3 libdatrie1 libdrm2 libegl1-mesa libexpat1 libffi6 libfontconfig1
libfreetype6 libgbm1 libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx
libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0b libice6 libjbig0
libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm3.3 libmagic1
libncurses5-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0
libpng12-0 libpng12-dev libreadline-dev libreadline6-dev libsm6 libthai-data
libthai0 libtiff5 libtinfo-dev libunistring0 libwayland-client0
libwayland-server0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0
libxcb-glx0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-xfixes0 libxcb1
libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxml2 libxrender1
libxss1 libxt6 libxxf86vm1 man-db po-debconf r-base-core r-base-dev
r-bioc-biobase r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomicranges
r-bioc-iranges r-bioc-rsamtools r-bioc-xvector r-cran-bitops r-cran-hwriter
r-cran-lattice r-cran-latticeextra r-cran-rcolorbrewer tcl8.5 tk8.5 ucf
unzip x11-common xdg-utils zip zlib1g-dev
Suggested packages:
wamerican wordlist whois vacation devscripts dh-make gettext-doc
gfortran-doc gfortran-4.8-doc libgfortran3-dbg groff ncurses-doc ttf-baekmuk
ttf-arphic-gbsn00lp ttf-arphic-bsmi00lp ttf-arphic-gkai00mp
ttf-arphic-bkai00mp less www-browser libmail-box-perl 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
texi2html r-bioc-pasillabamsubset r-bioc-shortread tcl-tclreadline gvfs-bin
Recommended packages:
autotools-dev curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
libegl1-mesa-drivers libgl1-mesa-dri libglib2.0-data shared-mime-info
xml-core libmail-sendmail-perl r-recommended r-doc-html xterm
x-terminal-emulator libfile-mimeinfo-perl libnet-dbus-perl
libx11-protocol-perl x11-utils x11-xserver-utils
The following NEW packages will be installed:
bsdmainutils cdbs debhelper file fontconfig fontconfig-config
fonts-dejavu-core gettext gettext-base gfortran gfortran-4.8 groff-base
intltool-debian libasprintf0c2 libblas-dev libblas3 libbz2-dev libcairo2
libcroco3 libdatrie1 libdrm2 libegl1-mesa libexpat1 libffi6 libfontconfig1
libfreetype6 libgbm1 libgfortran-4.8-dev libgfortran3 libgl1-mesa-glx
libglapi-mesa libglib2.0-0 libgraphite2-3 libharfbuzz0b libice6 libjbig0
libjpeg8 libjpeg8-dev liblapack-dev liblapack3 libllvm3.3 libmagic1
libncurses5-dev libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0
libpaper-utils libpaper1 libpcre3-dev libpcrecpp0 libpipeline1 libpixman-1-0
libpng12-0 libpng12-dev libreadline-dev libreadline6-dev libsm6 libthai-data
libthai0 libtiff5 libtinfo-dev libunistring0 libwayland-client0
libwayland-server0 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0
libxcb-glx0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-xfixes0 libxcb1
libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxml2 libxrender1
libxss1 libxt6 libxxf86vm1 man-db po-debconf r-base-core r-base-dev
r-bioc-biobase r-bioc-biocgenerics r-bioc-biostrings r-bioc-genomicranges
r-bioc-iranges r-bioc-rsamtools r-bioc-xvector r-cran-bitops r-cran-hwriter
r-cran-lattice r-cran-latticeextra r-cran-rcolorbrewer
sbuild-build-depends-r-bioc-shortread-dummy tcl8.5 tk8.5 ucf unzip
x11-common xdg-utils zip zlib1g-dev
0 upgraded, 110 newly installed, 0 to remove and 8 not upgraded.
Need to get 77.2 MB/77.2 MB of archives.
After this operation, 153 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.2.6-1 [24.4 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-3 [666 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.5-2 [949 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.1-2 [29.5 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.14-2 [213 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libdrm2 armhf 2.4.50-1 [474 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.0.13-4 [19.8 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libglapi-mesa armhf 9.2.2-1 [63.2 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libllvm3.3 armhf 1:3.3-16 [5374 kB]
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Get:15 http://172.17.0.1/private/ jessie-staging/main libxdmcp6 armhf 1:1.1.1-1 [24.6 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main libxcb1 armhf 1.9.1-3.1 [42.6 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main libxcb-dri2-0 armhf 1.9.1-3.1 [12.4 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main libgbm1 armhf 9.2.2-1 [418 kB]
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Get:22 http://172.17.0.1/private/ jessie-staging/main libxcb-render0 armhf 1.9.1-3.1 [17.4 kB]
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Get:24 http://172.17.0.1/private/ jessie-staging/main libxcb-xfixes0 armhf 1.9.1-3.1 [14.0 kB]
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Get:26 http://172.17.0.1/private/ jessie-staging/main libexpat1 armhf 2.1.0-4 [117 kB]
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Get:30 http://172.17.0.1/private/ jessie-staging/main fonts-dejavu-core all 2.33+svn2514-3 [1042 kB]
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Get:35 http://172.17.0.1/private/ jessie-staging/main libxdamage1 armhf 1:1.1.4-1 [14.6 kB]
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Get:37 http://172.17.0.1/private/ jessie-staging/main libxxf86vm1 armhf 1:1.1.3-1 [20.0 kB]
Get:38 http://172.17.0.1/private/ jessie-staging/main libgl1-mesa-glx armhf 9.2.2-1 [128 kB]
Get:39 http://172.17.0.1/private/ jessie-staging/main libpixman-1-0 armhf 0.32.4-1 [476 kB]
Get:40 http://172.17.0.1/private/ jessie-staging/main libxcb-shm0 armhf 1.9.1-3.1 [10.8 kB]
Get:41 http://172.17.0.1/private/ jessie-staging/main libxrender1 armhf 1:0.9.8-1 [30.4 kB]
Get:42 http://172.17.0.1/private/ jessie-staging/main libcairo2 armhf 1.12.16-2 [998 kB]
Get:43 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.36.4-1 [1907 kB]
Get:44 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:45 http://172.17.0.1/private/ jessie-staging/main libdatrie1 armhf 0.2.7.1-1 [28.1 kB]
Get:46 http://172.17.0.1/private/ jessie-staging/main libgfortran3 armhf 4.8.2-10 [225 kB]
Get:47 http://172.17.0.1/private/ jessie-staging/main libgraphite2-3 armhf 1.2.4-1 [57.9 kB]
Get:48 http://172.17.0.1/private/ jessie-staging/main libharfbuzz0b armhf 0.9.25-1 [452 kB]
Get:49 http://172.17.0.1/private/ jessie-staging/main x11-common all 1:7.7+5 [282 kB]
Get:50 http://172.17.0.1/private/ jessie-staging/main libice6 armhf 2:1.0.8-2 [56.2 kB]
Get:51 http://172.17.0.1/private/ jessie-staging/main libjpeg8 armhf 8d-2 [133 kB]
Get:52 http://172.17.0.1/private/ jessie-staging/main libthai-data all 0.1.20-1 [157 kB]
Get:53 http://172.17.0.1/private/ jessie-staging/main libthai0 armhf 0.1.20-1 [41.4 kB]
Get:54 http://172.17.0.1/private/ jessie-staging/main fontconfig armhf 2.11.0-2 [407 kB]
Get:55 http://172.17.0.1/private/ jessie-staging/main libpango-1.0-0 armhf 1.36.0-1+b1 [257 kB]
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Get:57 http://172.17.0.1/private/ jessie-staging/main libpangocairo-1.0-0 armhf 1.36.0-1+b1 [181 kB]
Get:58 http://172.17.0.1/private/ jessie-staging/main libpaper1 armhf 1.1.24+nmu2 [20.9 kB]
Get:59 http://172.17.0.1/private/ jessie-staging/main libpcrecpp0 armhf 1:8.31-2 [125 kB]
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Get:93 http://172.17.0.1/private/ jessie-staging/main xdg-utils all 1.1.0~rc1+git20111210-7 [83.7 kB]
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Get:102 http://172.17.0.1/private/ jessie-staging/main r-bioc-biostrings armhf 2.30.1-1 [2293 kB]
Get:103 http://172.17.0.1/private/ jessie-staging/main r-bioc-genomicranges armhf 1.14.3-1 [2988 kB]
Get:104 http://172.17.0.1/private/ jessie-staging/main r-cran-bitops armhf 1.0-6-1 [23.6 kB]
Get:105 http://172.17.0.1/private/ jessie-staging/main r-bioc-rsamtools armhf 1.14.2-1 [3560 kB]
Get:106 http://172.17.0.1/private/ jessie-staging/main r-cran-hwriter all 1.3-1 [137 kB]
Get:107 http://172.17.0.1/private/ jessie-staging/main r-cran-lattice armhf 0.20-24-1 [726 kB]
Get:108 http://172.17.0.1/private/ jessie-staging/main r-cran-rcolorbrewer all 1.0-5-2 [25.5 kB]
Get:109 http://172.17.0.1/private/ jessie-staging/main r-cran-latticeextra armhf 0.6-26-1 [1469 kB]
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Setting up libdrm2:armhf (2.4.50-1) ...
Setting up libffi6:armhf (3.0.13-4) ...
Setting up libglapi-mesa:armhf (9.2.2-1) ...
Setting up libllvm3.3:armhf (1:3.3-16) ...
Setting up libwayland-client0:armhf (1.3.0-1+rpi1) ...
Setting up libwayland-server0:armhf (1.3.0-1+rpi1) ...
Setting up libxau6:armhf (1:1.0.8-1) ...
Setting up libxdmcp6:armhf (1:1.1.1-1) ...
Setting up libxcb1:armhf (1.9.1-3.1) ...
Setting up libxcb-dri2-0:armhf (1.9.1-3.1) ...
Setting up libgbm1:armhf (9.2.2-1) ...
Setting up libx11-data (2:1.6.2-1) ...
Setting up libx11-6:armhf (2:1.6.2-1) ...
Setting up libx11-xcb1:armhf (2:1.6.2-1) ...
Setting up libxcb-render0:armhf (1.9.1-3.1) ...
Setting up libxcb-shape0:armhf (1.9.1-3.1) ...
Setting up libxcb-xfixes0:armhf (1.9.1-3.1) ...
Setting up libegl1-mesa:armhf (9.2.2-1) ...
Setting up libexpat1:armhf (2.1.0-4) ...
Setting up libpng12-0:armhf (1.2.49-5) ...
Setting up libfreetype6:armhf (2.5.2-1) ...
Setting up ucf (3.0027+nmu1) ...
Setting up fonts-dejavu-core (2.33+svn2514-3) ...
Setting up fontconfig-config (2.11.0-2) ...
Setting up libfontconfig1:armhf (2.11.0-2) ...
Setting up libxcb-glx0:armhf (1.9.1-3.1) ...
Setting up libxfixes3:armhf (1:5.0.1-1) ...
Setting up libxdamage1:armhf (1:1.1.4-1) ...
Setting up libxext6:armhf (2:1.3.2-1) ...
Setting up libxxf86vm1:armhf (1:1.1.3-1) ...
Setting up libgl1-mesa-glx:armhf (9.2.2-1) ...
Setting up libpixman-1-0:armhf (0.32.4-1) ...
Setting up libxcb-shm0:armhf (1.9.1-3.1) ...
Setting up libxrender1:armhf (1:0.9.8-1) ...
Setting up libcairo2:armhf (1.12.16-2) ...
Setting up libglib2.0-0:armhf (2.36.4-1) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libdatrie1:armhf (0.2.7.1-1) ...
Setting up libgfortran3:armhf (4.8.2-10) ...
Setting up libgraphite2-3:armhf (1.2.4-1) ...
Setting up libharfbuzz0b:armhf (0.9.25-1) ...
Setting up x11-common (1:7.7+5) ...
update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
All runlevel operations denied by policy
invoke-rc.d: policy-rc.d denied execution of start.
Setting up libice6:armhf (2:1.0.8-2) ...
Setting up libjpeg8:armhf (8d-2) ...
Setting up libthai-data (0.1.20-1) ...
Setting up libthai0:armhf (0.1.20-1) ...
Setting up fontconfig (2.11.0-2) ...
Regenerating fonts cache... done.
Setting up libpango-1.0-0:armhf (1.36.0-1+b1) ...
Setting up libpangoft2-1.0-0:armhf (1.36.0-1+b1) ...
Setting up libpangocairo-1.0-0:armhf (1.36.0-1+b1) ...
Setting up libpaper1:armhf (1.1.24+nmu2) ...
Creating config file /etc/papersize with new version
Setting up libpcrecpp0:armhf (1:8.31-2) ...
Setting up libsm6:armhf (2:1.2.1-2) ...
Setting up libjbig0:armhf (2.0-2) ...
Setting up libtiff5:armhf (4.0.3-7) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libxft2:armhf (2.3.1-1) ...
Setting up libxss1:armhf (1:1.2.2-1) ...
Setting up libxt6:armhf (1:1.1.4-1) ...
Setting up file (1:5.14-2) ...
Setting up gettext-base (0.18.3.1-2) ...
Setting up cdbs (0.4.122) ...
Setting up gettext (0.18.3.1-2) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20131227) ...
Setting up libgfortran-4.8-dev:armhf (4.8.2-10) ...
Setting up gfortran-4.8 (4.8.2-10) ...
Setting up gfortran (4:4.8.2-1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
Setting up libblas3 (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libblas-dev (1.2.20110419-7) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libbz2-dev:armhf (1.0.6-5) ...
Setting up libjpeg8-dev:armhf (8d-2) ...
Setting up liblapack3 (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up liblapack-dev (3.5.0-2) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libtinfo-dev:armhf (5.9+20130608-1) ...
Setting up libncurses5-dev:armhf (5.9+20130608-1) ...
Setting up libpaper-utils (1.1.24+nmu2) ...
Setting up libpcre3-dev:armhf (1:8.31-2) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up libpng12-dev (1.2.49-5) ...
Setting up libreadline6-dev:armhf (6.2+dfsg-0.1) ...
Setting up libreadline-dev:armhf (6.2+dfsg-0.1) ...
Setting up zip (3.0-8) ...
Setting up unzip (6.0-10) ...
Setting up xdg-utils (1.1.0~rc1+git20111210-7) ...
Setting up tcl8.5 (8.5.14-2) ...
update-alternatives: using /usr/bin/tclsh8.5 to provide /usr/bin/tclsh (tclsh) in auto mode
Setting up tk8.5 (8.5.14-2) ...
update-alternatives: using /usr/bin/wish8.5 to provide /usr/bin/wish (wish) in auto mode
Setting up r-base-core (3.0.2-1) ...
Creating config file /etc/R/Renviron with new version
Setting up r-base-dev (3.0.2-1) ...
Setting up r-bioc-biocgenerics (0.8.0-1) ...
Setting up r-bioc-biobase (2.20.0-1) ...
Setting up r-bioc-iranges (1.20.6-1) ...
Setting up r-bioc-xvector (0.2.0-1) ...
Setting up r-bioc-biostrings (2.30.1-1) ...
Setting up r-bioc-genomicranges (1.14.3-1) ...
Setting up r-cran-bitops (1.0-6-1) ...
Setting up r-bioc-rsamtools (1.14.2-1) ...
Setting up r-cran-hwriter (1.3-1) ...
Setting up r-cran-lattice (0.20-24-1) ...
Setting up r-cran-rcolorbrewer (1.0-5-2) ...
Setting up r-cran-latticeextra (0.6-26-1) ...
Setting up sbuild-build-depends-r-bioc-shortread-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.17-97) ...
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment │
└──────────────────────────────────────────────────────────────────────────────┘
Kernel: Linux 3.11.0-armv7-x13 armhf (armv7l)
Toolchain package versions: binutils_2.24-2 dpkg-dev_1.17.5 g++-4.8_4.8.2-10 gcc-4.8_4.8.2-10 libc6-dev_2.17-97 libstdc++-4.8-dev_4.8.2-10 libstdc++6_4.8.2-10 linux-libc-dev_3.10.11-1+rpi1
Package versions: apt_0.9.14.1+rpi1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.2+dfsg-1 binutils_2.24-2 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.5 build-essential_11.6 bzip2_1.0.6-5 cdbs_0.4.122 coreutils_8.21-1 cpio_2.11+dfsg-1 cpp_4:4.8.2-1 cpp-4.8_4.8.2-10 dash_0.5.7-3 debconf_1.5.52 debconf-i18n_1.5.52 debfoster_2.7-1.2 debhelper_9.20131227 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.5 dpkg-dev_1.17.5 e2fslibs_1.42.8-1 e2fsprogs_1.42.8-1 fakeroot_1.18.4-2 file_1:5.14-2 findutils_4.4.2-7 fontconfig_2.11.0-2 fontconfig-config_2.11.0-2 fonts-dejavu-core_2.33+svn2514-3 g++_4:4.8.2-1 g++-4.8_4.8.2-10 gcc_4:4.8.2-1 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-9+rpi1 gcc-4.8_4.8.2-10 gcc-4.8-base_4.8.2-10 gettext_0.18.3.1-2 gettext-base_0.18.3.1-2 gfortran_4:4.8.2-1 gfortran-4.8_4.8.2-10 gnupg_1.4.15-3 gpgv_1.4.15-3 grep_2.15-2 groff-base_1.22.2-3 gzip_1.6-2 hostname_3.15 initramfs-tools_0.115 initscripts_2.88dsf-43 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_9-3 libacl1_2.2.52-1 libapt-pkg4.12_0.9.14.1+rpi1 libasan0_4.8.2-10 libasprintf0c2_0.18.3.1-2 libatomic1_4.8.2-10 libattr1_1:2.4.47-1 libaudit-common_1:2.3.2-2 libaudit1_1:2.3.2-2 libblas-dev_1.2.20110419-7 libblas3_1.2.20110419-7 libblkid1_2.20.1-5.5 libbz2-1.0_1.0.6-5 libbz2-dev_1.0.6-5 libc-bin_2.17-97 libc-dev-bin_2.17-97 libc6_2.17-97 libc6-dev_2.17-97 libcairo2_1.12.16-2 libcap2_1:2.22-1.2 libcloog-isl4_0.18.1-3 libcomerr2_1.42.8-1 libcroco3_0.6.8-2 libdatrie1_0.2.7.1-1 libdb5.1_5.1.29-6 libdbus-1-3_1.6.18-2 libdpkg-perl_1.17.5 libdrm2_2.4.50-1 libegl1-mesa_9.2.2-1 libexpat1_2.1.0-4 libffi6_3.0.13-4 libfontconfig1_2.11.0-2 libfreetype6_2.5.2-1 libgbm1_9.2.2-1 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-10 libgcc1_1:4.8.2-10 libgdbm3_1.8.3-12 libgfortran-4.8-dev_4.8.2-10 libgfortran3_4.8.2-10 libgl1-mesa-glx_9.2.2-1 libglapi-mesa_9.2.2-1 libglib2.0-0_2.36.4-1 libgmp10_2:5.1.3+dfsg-1 libgomp1_4.8.2-10 libgraphite2-3_1.2.4-1 libharfbuzz0b_0.9.25-1 libice6_2:1.0.8-2 libisl10_0.12.1-2 libjbig0_2.0-2 libjpeg8_8d-2 libjpeg8-dev_8d-2 libklibc_2.0.2-1+rpi1 libkmod2_9-3 liblapack-dev_3.5.0-2 liblapack3_3.5.0-2 libllvm3.3_1:3.3-16 liblocale-gettext-perl_1.05-7+b3 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.14-2 libmount1_2.20.1-5.5 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20130608-1 libncurses5-dev_5.9+20130608-1 libncursesw5_5.9+20130608-1 libnih-dbus1_1.0.3-4.2 libnih1_1.0.3-4.2 libpam-modules_1.1.3-9 libpam-modules-bin_1.1.3-9 libpam-runtime_1.1.3-9 libpam0g_1.1.3-9 libpango-1.0-0_1.36.0-1+b1 libpangocairo-1.0-0_1.36.0-1+b1 libpangoft2-1.0-0_1.36.0-1+b1 libpaper-utils_1.1.24+nmu2 libpaper1_1.1.24+nmu2 libpcre3_1:8.31-2 libpcre3-dev_1:8.31-2 libpcrecpp0_1:8.31-2 libpipeline1_1.2.6-1 libpixman-1-0_0.32.4-1 libpng12-0_1.2.49-5 libpng12-dev_1.2.49-5 libprocps0_1:3.3.4-2 libreadline-dev_6.2+dfsg-0.1 libreadline6_6.2+dfsg-0.1 libreadline6-dev_6.2+dfsg-0.1 libselinux1_2.2.1-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libsm6_2:1.2.1-2 libss2_1.42.8-1 libstdc++-4.8-dev_4.8.2-10 libstdc++6_4.8.2-10 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libthai-data_0.1.20-1 libthai0_0.1.20-1 libtiff5_4.0.3-7 libtimedate-perl_2.3000-1 libtinfo-dev_5.9+20130608-1 libtinfo5_5.9+20130608-1 libudev1_204-5 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.5 libwayland-client0_1.3.0-1+rpi1 libwayland-server0_1.3.0-1+rpi1 libx11-6_2:1.6.2-1 libx11-data_2:1.6.2-1 libx11-xcb1_2:1.6.2-1 libxau6_1:1.0.8-1 libxcb-dri2-0_1.9.1-3.1 libxcb-glx0_1.9.1-3.1 libxcb-render0_1.9.1-3.1 libxcb-shape0_1.9.1-3.1 libxcb-shm0_1.9.1-3.1 libxcb-xfixes0_1.9.1-3.1 libxcb1_1.9.1-3.1 libxdamage1_1:1.1.4-1 libxdmcp6_1:1.1.1-1 libxext6_2:1.3.2-1 libxfixes3_1:5.0.1-1 libxft2_2.3.1-1 libxml2_2.9.1+dfsg1-3 libxrender1_1:0.9.8-1 libxss1_1:1.2.2-1 libxt6_1:1.1.4-1 libxxf86vm1_1:1.1.3-1 linux-libc-dev_3.10.11-1+rpi1 login_1:4.1.5.1-1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.5-2 mawk_1.3.3-17 mount_2.20.1-5.5 mountall_2.52 multiarch-support_2.17-97 ncurses-base_5.9+20130608-1 ncurses-bin_5.9+20130608-1 passwd_1:4.1.5.1-1 patch_2.7.1-4 perl_5.18.1-5 perl-base_5.18.1-5 perl-modules_5.18.1-5 plymouth_0.8.8-6+deb8u3 po-debconf_1.0.16+nmu2 procps_1:3.3.4-2 r-base-core_3.0.2-1 r-base-dev_3.0.2-1 r-bioc-biobase_2.20.0-1 r-bioc-biocgenerics_0.8.0-1 r-bioc-biostrings_2.30.1-1 r-bioc-genomicranges_1.14.3-1 r-bioc-iranges_1.20.6-1 r-bioc-rsamtools_1.14.2-1 r-bioc-xvector_0.2.0-1 r-cran-bitops_1.0-6-1 r-cran-hwriter_1.3-1 r-cran-lattice_0.20-24-1 r-cran-latticeextra_0.6-26-1 r-cran-rcolorbrewer_1.0-5-2 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-r-bioc-shortread-dummy_0.invalid.0 sed_4.2.2-3 sensible-utils_0.0.9 sysv-rc_2.88dsf-43 sysvinit_2.88dsf-43 sysvinit-utils_2.88dsf-43 tar_1.26+dfsg-8 tcl8.5_8.5.14-2 tk8.5_8.5.14-2 tzdata_2013i-1 ucf_3.0027+nmu1 udev_204-5 unzip_6.0-10 util-linux_2.20.1-5.5 x11-common_1:7.7+5 xdg-utils_1.1.0~rc1+git20111210-7 xz-utils_5.1.1alpha+20120614-2 zip_3.0-8 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1
┌──────────────────────────────────────────────────────────────────────────────┐
│ Build │
└──────────────────────────────────────────────────────────────────────────────┘
Unpack source
─────────────
gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Mon Dec 2 13:24:54 2013 UTC using DSA key ID C09FD35A
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./r-bioc-shortread_1.20.0-1.dsc
dpkg-source: info: extracting r-bioc-shortread in r-bioc-shortread-1.20.0
dpkg-source: info: unpacking r-bioc-shortread_1.20.0.orig.tar.gz
dpkg-source: info: unpacking r-bioc-shortread_1.20.0-1.debian.tar.gz
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
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=root
MAIL=/var/mail/root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/root
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-946bff98-7e14-467c-b586-9e01d9e1167e
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
SHLVL=1
SSH_CLIENT=172.17.0.6 47843 22
SSH_CONNECTION=172.17.0.6 47843 172.17.2.2 22
SSH_TTY=/dev/pts/0
TERM=xterm
USER=buildd
_=/etc/init.d/buildd
dpkg-buildpackage
─────────────────
dpkg-buildpackage: source package r-bioc-shortread
dpkg-buildpackage: source version 1.20.0-1
dpkg-buildpackage: source distribution unstable
dpkg-source --before-build r-bioc-shortread-1.20.0
dpkg-buildpackage: host architecture armhf
fakeroot debian/rules clean
test -x debian/rules
dh_clean
if test -d src; then \
find src -regex ".*\.o" | \
xargs --no-run-if-empty -r rm; \
fi
rm -f config.log config.status
debian/rules build-arch
test -x debian/rules
mkdir -p "."
fakeroot debian/rules binary-arch
test -x debian/rules
dh_testroot
dh_prep
dh_installdirs -A
mkdir -p "."
dh_installdirs usr/lib/R/site-library
echo "R:Depends=r-base-core (>= 3.0.2-1)" >> debian/r-bioc-shortread.substvars
if test -f /usr/bin/xvfb-run; then \
xvfb-run -a \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library --clean \
. ; \
else \
R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library \
--clean . ;\
fi
* 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/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -O3 -pipe -g -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -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/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -O3 -pipe -g -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c alphabet.c -o alphabet.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c io.c -o io.o
io.c: In function '_count_ipar_int_recs':
io.c:115:5: warning: passing argument 1 of 'gzread' from incompatible pointer type [enabled by default]
while (*n_cycles == 0 && (bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1313:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
io.c:132:5: warning: passing argument 1 of 'gzread' from incompatible pointer type [enabled by default]
while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1313:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
io.c: In function 'count_ipar_int_recs':
io.c:167:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function 'read_prb_as_character':
io.c:193:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
if (gzgets(file, buf, LINEBUF_SIZE) == Z_NULL) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:194:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:203:5: warning: passing argument 1 of 'gzrewind' from incompatible pointer type [enabled by default]
gzrewind(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1447:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzrewind OF((gzFile file));
^
io.c:208:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
while (gzgets(file, buf, LINEBUF_SIZE) != Z_NULL) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:210:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:220:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:229:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:235:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function '_read_solexa_fastq_file':
io.c:252:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:260:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:263:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:286:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function '_io_XStringSet_columns':
io.c:347:9: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
gzgets(file, linebuf, LINEBUF_SIZE);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:349:9: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
gzgets(file, linebuf, LINEBUF_SIZE);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:351:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
while (recno < nrow && gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:372:5: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c: In function '_read_solexa_export_file':
io.c:577:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io.c:586:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:623:17: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
io.c:641:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c io_bowtie.c -o io_bowtie.o
io_bowtie.c: In function '_read_bowtie':
io_bowtie.c:35:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io_bowtie.c:2:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
io_bowtie.c:45:13: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from io_bowtie.c:2:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c io_soap.c -o io_soap.o
io_soap.c: In function '_read_soap':
io_soap.c:38:5: warning: passing argument 1 of 'gzgets' from incompatible pointer type [enabled by default]
while (gzgets(file, linebuf, LINEBUF_SIZE) != NULL) {
^
In file included from ShortRead.h:8:0,
from io_soap.c:2:
/usr/include/zlib.h:1372:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c pileup.c -o pileup.o
g++ -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c readBfaToc.cc -o readBfaToc.o
g++ -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -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/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include" -fopenmp -fpic -O3 -pipe -g -c sampler.c -o sampler.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c trim.c -o trim.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c util.c -o util.o
util.c: In function '_fopen':
util.c:225:20: warning: initialization from incompatible pointer type [enabled by default]
gzFile *file = gzopen(fname, mode);
^
util.c: In function '_linebuf_skip_p':
util.c:240:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
util.c:243:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
util.c: In function '_count_lines':
util.c:345:5: warning: passing argument 1 of 'gzread' from incompatible pointer type [enabled by default]
while ((bytes_read = gzread(file, buf, LINEBUF_SIZE)) > 0) {
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1313:21: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
^
util.c: In function 'count_lines':
util.c:381:9: warning: passing argument 1 of 'gzclose' from incompatible pointer type [enabled by default]
gzclose(file);
^
In file included from ShortRead.h:8:0,
from util.c:3:
/usr/include/zlib.h:1511:24: note: expected 'gzFile' but argument is of type 'struct gzFile_s **'
ZEXTERN int ZEXPORT gzclose OF((gzFile file));
^
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -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 -O3 -pipe -g -c xsnap.c -o xsnap.o
g++ -shared -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o pileup.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)
rm -vf /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/R.css \
/«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/COPYING \
/«PKGBUILDDIR»/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead/LICENSE.txt
if test -f debian/overrides; then \
install -d /«PKGBUILDDIR»/debian/r-bioc-shortread/usr/share/lintian/overrides ; \
install -m 0644 debian/overrides \
/«PKGBUILDDIR»/debian/r-bioc-shortread/usr/share/lintian/overrides/r-bioc-shortread; \
fi
Adding cdbs dependencies to debian/r-bioc-shortread.substvars
dh_installdirs -pr-bioc-shortread
dh_installdocs -pr-bioc-shortread ./NEWS
dh_installexamples -pr-bioc-shortread
dh_installman -pr-bioc-shortread
dh_installinfo -pr-bioc-shortread
dh_installmenu -pr-bioc-shortread
dh_installcron -pr-bioc-shortread
dh_installinit -pr-bioc-shortread
dh_installdebconf -pr-bioc-shortread
dh_installemacsen -pr-bioc-shortread
dh_installcatalogs -pr-bioc-shortread
dh_installpam -pr-bioc-shortread
dh_installlogrotate -pr-bioc-shortread
dh_installlogcheck -pr-bioc-shortread
dh_installchangelogs -pr-bioc-shortread
dh_installudev -pr-bioc-shortread
dh_lintian -pr-bioc-shortread
dh_bugfiles -pr-bioc-shortread
dh_install -pr-bioc-shortread
dh_link -pr-bioc-shortread
dh_installmime -pr-bioc-shortread
dh_installgsettings -pr-bioc-shortread
dh_strip -pr-bioc-shortread
dh_compress -pr-bioc-shortread
dh_fixperms -pr-bioc-shortread
dh_makeshlibs -pr-bioc-shortread
dh_installdeb -pr-bioc-shortread
dh_perl -pr-bioc-shortread
dh_shlibdeps -pr-bioc-shortread
dh_gencontrol -pr-bioc-shortread
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
dh_md5sums -pr-bioc-shortread
dh_builddeb -pr-bioc-shortread
dpkg-deb: building package `r-bioc-shortread' in `../r-bioc-shortread_1.20.0-1_armhf.deb'.
dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../r-bioc-shortread_1.20.0-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
dpkg-source --after-build r-bioc-shortread-1.20.0
dpkg-buildpackage: binary only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140106-0701
Finished
────────
I: Built successfully
┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-shortread_1.20.0-1_armhf.changes:
────────────────────────────────────────
Format: 1.8
Date: Mon, 04 Nov 2013 17:24:35 +0100
Source: r-bioc-shortread
Binary: r-bioc-shortread
Architecture: armhf
Version: 1.20.0-1
Distribution: jessie-staging
Urgency: low
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
Closes: 731085
Changes:
r-bioc-shortread (1.20.0-1) unstable; urgency=low
.
* Initial release (closes: #731085)
Checksums-Sha1:
29aa1503265a08ac5fe84faeae8d8cec9663a57b 1968262 r-bioc-shortread_1.20.0-1_armhf.deb
Checksums-Sha256:
378507cb0473abdde92517029463c5c3dd5d3549cf7a5c30858048e849016a3c 1968262 r-bioc-shortread_1.20.0-1_armhf.deb
Files:
821eb33b5e0ecc86740efdce015cba6a 1968262 gnu-r optional r-bioc-shortread_1.20.0-1_armhf.deb
┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents │
└──────────────────────────────────────────────────────────────────────────────┘
r-bioc-shortread_1.20.0-1_armhf.deb
───────────────────────────────────
new debian package, version 2.0.
size 1968262 bytes: control archive=4373 bytes.
1034 bytes, 16 lines control
11032 bytes, 116 lines md5sums
Package: r-bioc-shortread
Version: 1.20.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4497
Depends: r-base-core (>= 3.0.2-1), libc6 (>= 2.7), libgcc1 (>= 1:4.4.0), libgomp1 (>= 4.2.1), libstdc++6 (>= 4.3.0), zlib1g (>= 1:1.1.4), r-cran-latticeextra, r-bioc-biobase, r-bioc-biocgenerics, r-bioc-genomicranges, r-bioc-iranges, r-bioc-biostrings, r-bioc-rsamtools, r-bioc-xvector, r-cran-hwriter
Section: gnu-r
Priority: optional
Homepage: http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html
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.
drwxr-xr-x root/root 0 2014-01-06 07:00 ./
drwxr-xr-x root/root 0 2014-01-06 07:00 ./usr/
drwxr-xr-x root/root 0 2014-01-06 06:58 ./usr/lib/
drwxr-xr-x root/root 0 2014-01-06 06:58 ./usr/lib/R/
drwxr-xr-x root/root 0 2014-01-06 07:00 ./usr/lib/R/site-library/
drwxr-xr-x root/root 0 2014-01-06 07:00 ./usr/lib/R/site-library/ShortRead/
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Post Build │
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┌──────────────────────────────────────────────────────────────────────────────┐
│ Cleanup │
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Purging /«BUILDDIR»
Not cleaning session: cloned chroot in use
┌──────────────────────────────────────────────────────────────────────────────┐
│ Summary │
└──────────────────────────────────────────────────────────────────────────────┘
Build Architecture: armhf
Build-Space: 12180
Build-Time: 199
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 477
Job: r-bioc-shortread_1.20.0-1
Machine Architecture: armhf
Package: r-bioc-shortread
Package-Time: 730
Source-Version: 1.20.0-1
Space: 12180
Status: successful
Version: 1.20.0-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140106-0701
Build needed 00:12:10, 12180k disc space