[med-svn] r17251 - in trunk/packages/R: . r-bioc-hilbertvis/trunk/debian r-cran-genabel.data r-cran-genabel.data/trunk r-cran-genabel.data/trunk/debian r-cran-genabel.data/trunk/debian/source
Andreas Tille
tille at moszumanska.debian.org
Fri Jun 20 08:05:11 UTC 2014
Author: tille
Date: 2014-06-20 08:05:11 +0000 (Fri, 20 Jun 2014)
New Revision: 17251
Added:
trunk/packages/R/r-cran-genabel.data/
trunk/packages/R/r-cran-genabel.data/trunk/
trunk/packages/R/r-cran-genabel.data/trunk/debian/
trunk/packages/R/r-cran-genabel.data/trunk/debian/README.source
trunk/packages/R/r-cran-genabel.data/trunk/debian/changelog
trunk/packages/R/r-cran-genabel.data/trunk/debian/compat
trunk/packages/R/r-cran-genabel.data/trunk/debian/control
trunk/packages/R/r-cran-genabel.data/trunk/debian/copyright
trunk/packages/R/r-cran-genabel.data/trunk/debian/rules
trunk/packages/R/r-cran-genabel.data/trunk/debian/source/
trunk/packages/R/r-cran-genabel.data/trunk/debian/source/format
trunk/packages/R/r-cran-genabel.data/trunk/debian/watch
Modified:
trunk/packages/R/r-bioc-hilbertvis/trunk/debian/copyright
Log:
Add precondition for r-cran-genabel update
Modified: trunk/packages/R/r-bioc-hilbertvis/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-hilbertvis/trunk/debian/copyright 2014-06-20 07:27:38 UTC (rev 17250)
+++ trunk/packages/R/r-bioc-hilbertvis/trunk/debian/copyright 2014-06-20 08:05:11 UTC (rev 17251)
@@ -1,7 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: HilbertVis
Upstream-Contact: Simon Anders <sanders at fs.tum.de>
-Source: http://www.bioconductor.org/packages/devel/bioc/html/HilbertVis.html
+Source: http://www.bioconductor.org/packages/release/bioc/src/contrib/HilbertVis_1.18.0.tar.gz
Files: *
Copyright: 2009-2012 Simon Anders <sanders at fs.tum.de>;
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/README.source (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/README.source 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1,59 @@
+Explanation for binary files inside source package according to
+ http://lists.debian.org/debian-devel/2013/09/msg00332.html
+
+This package is a pure collection of data which is needed to
+ 1. Build r-cran-genabel >= 1.8
+ 2. Run unit tests in autopkgtest for r-cran-genabel
+
+Here comes a description of the single data files:
+
+Files: data/*
+Documentation: man/GenABEL.data-package.Rd
+ GenABEL.data contains six files with data which is used by examples of GenABEL.
+ These are ge03d2.clean.RData, ge03d2c.RData, ge03d2ex.clean.RData, ge03d2ex.RData, ge03d2.RData and srdta.RData.
+
+Files: data/ge03d2.Rdata
+Documentation: man/ge03d2.Rd
+ A small data set (approximately 1,000 people and 8,000 SNPs) containing
+ data on 3 autosomes and X chromsome. Is a good set for
+ demonatration of the QC procedures (different genotyping errors
+ are introduced) and GWA analysis.
+ This data set was developed for the "Advances in population-
+ based studies" (Ge03) course of the Nihes.
+
+Files: data/ge03d2c.Rdata
+Documentation: man/ge03d2.Rd
+ A small data set (approximately 200 people and 8,000 SNPs) containing
+ data on 3 autosomes and X chromsome. This data set is
+ complementary to ge03d2.
+
+Files: data/ge03d2ex.Rdata
+Documentation: man/ge03d2.Rd
+ A small data set (approximately 150 people and 4,000 SNPs) containing
+ data on 3 autosomes and X chromsome. Is a good set for
+ demonatration of the QC procedures (different genotyping errors
+ are introduced) and GWA analysis.
+ This data set was developed for the "Advances in population-
+ based studies" (Ge03) course of the Nihes.
+ See vignette "GenABEL-tutorial.pdf" in the r-cran-genabel package
+ for details.
+
+Files: data/*.clean.Rdata
+Documentation: man/ge03d2.Rd
+ The data sets with extension ".clean" are sets after QC.
+
+Files: data/srdta.RData
+Documentation: man/srdta.Rd
+ srdta contains gwaa.data object with results
+ on a small region of
+ about 2.5 Mb. 833 SNPs are typed on 2500 people.
+ NA rate is 95\%. Sex, age, two quantitative (qt1 and
+ qt2) and one binary (bt) traits are available for
+ analysis.
+ Original data files used for this set are available as
+ srphenos.dat (phenotypes), srgenos.dat (human-readable
+ genotypes) and srgenos.raw (genotypes in internal format)
+
+
+ -- Andreas Tille <tille at debian.org> Fri, 20 Jun 2014 09:23:44 +0200
+
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/changelog 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1,5 @@
+r-cran-genabel.data (1.0.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #).
+
+ -- Andreas Tille <tille at debian.org> Fri, 20 Jun 2014 09:23:44 +0200
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/compat (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/compat 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/control 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1,28 @@
+Source: r-cran-genabel.data
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cdbs,
+ r-base-dev
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genabel.data/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genabel.data/trunk/
+Homepage: http://cran.at.r-project.org/web/packages/GenABEL.data/
+
+Package: r-cran-genabel.data
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${R:Depends}
+Description: data package for genome-wide SNP association analysis
+ The package offers the R library GenABEL for the hunt of genetic contributions
+ to a disease (or any other pheonypical trait) by so called genome-wide
+ association analysis. Additional input commonly comes from DNA mircoarray
+ experiments, performed on every individual, that determine differences
+ (polymorphisms) in the population. GenABEL finds associations between
+ quantitative or binary traits and single-nucleiotide polymorphisms
+ (SNPs).
+ .
+ GenABEL.data package consists of a data set used by GenABEL functions.
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/copyright 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: GenABEL.data
+Upstream-Contact: Maksim Struchalin <m.v.struchalin at mail.ru>
+Source: http://cran.at.r-project.org/web/packages/GenABEL.data/
+
+Files: *
+Copyright: 2013 Maksim Struchalin <m.v.struchalin at mail.ru>
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+Comment: On a Debian GNU/Linux system, the GPL license version 2 is included
+ in the file /usr/share/common-licenses/GPL-2.
+
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/rules 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1,3 @@
+#!/usr/bin/make -f
+
+include /usr/share/R/debian/r-cran.mk
Property changes on: trunk/packages/R/r-cran-genabel.data/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/source/format (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/source/format 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/R/r-cran-genabel.data/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-cran-genabel.data/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-cran-genabel.data/trunk/debian/watch 2014-06-20 08:05:11 UTC (rev 17251)
@@ -0,0 +1,2 @@
+version=3
+http://cran.r-project.org/src/contrib/GenABEL.data_(.*)\.tar\.gz
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