[med-svn] r5908 - in trunk/packages/R/r-other-genabel/trunk/debian: . source

Steffen Möller moeller at alioth.debian.org
Sat Feb 5 17:15:44 UTC 2011 

Author: moeller
Date: 2011-02-05 17:15:41 +0000 (Sat, 05 Feb 2011)
New Revision: 5908

Added:
   trunk/packages/R/r-other-genabel/trunk/debian/TODO
   trunk/packages/R/r-other-genabel/trunk/debian/source/
   trunk/packages/R/r-other-genabel/trunk/debian/source/format
Modified:
   trunk/packages/R/r-other-genabel/trunk/debian/changelog
   trunk/packages/R/r-other-genabel/trunk/debian/control
   trunk/packages/R/r-other-genabel/trunk/debian/copyright
   trunk/packages/R/r-other-genabel/trunk/debian/rules
   trunk/packages/R/r-other-genabel/trunk/debian/watch
Log:
GenABEL is now in CRAN, bump from 1.4-0 to 1.6-4.
Changed to source/format 3.0 (quilt).


Added: trunk/packages/R/r-other-genabel/trunk/debian/TODO
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/TODO	                        (rev 0)
+++ trunk/packages/R/r-other-genabel/trunk/debian/TODO	2011-02-05 17:15:41 UTC (rev 5908)
@@ -0,0 +1,14 @@
+
+How should this be done most efficiently?
+
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/srphenos.dat
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/map.18
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/pedin.18
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/doc/index.html
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/doc/GenABEL-manual.pdf
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/doc/ABEL-tutorial.pdf
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/srgenos.dat
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/chr18.raw
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/srgenos.raw
+W: r-cran-genabel: executable-not-elf-or-script ./usr/lib/R/site-library/GenABEL/exdata/phenos.18
+

Modified: trunk/packages/R/r-other-genabel/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/changelog	2011-02-05 16:48:57 UTC (rev 5907)
+++ trunk/packages/R/r-other-genabel/trunk/debian/changelog	2011-02-05 17:15:41 UTC (rev 5908)
@@ -1,3 +1,13 @@
+r-cran-genabel (1.6-4-1) unstable; urgency=low
+
+  * New upstream release.
+  * The package has now arrived in CRAN and is taken from there,
+    which according to the R policy is also reflected by the name change.
+  * Switch to source/format 3.0 (quilt)
+  * Bumped policy-standard to 3.9.1.
+
+ -- Steffen Moeller <moeller at debian.org>  Sat, 05 Feb 2011 18:06:24 +0100
+
 r-other-genabel (1.4-0-1) unstable; urgency=low
 
   * Initial release (Closes: #492044).

Modified: trunk/packages/R/r-other-genabel/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/control	2011-02-05 16:48:57 UTC (rev 5907)
+++ trunk/packages/R/r-other-genabel/trunk/debian/control	2011-02-05 17:15:41 UTC (rev 5908)
@@ -1,15 +1,17 @@
-Source: r-other-genabel
+Source: r-cran-genabel
 Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>
 Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev (>= 2.7.0~20080408), r-recommended, r-cran-genetics, r-cran-haplo.stats, r-cran-qvalue
-Standards-Version: 3.8.0
+Standards-Version: 3.9.1
 Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
 
-Package: r-other-genabel
+Package: r-cran-genabel
 Architecture: any
 Depends: ${shlibs:Depends}, r-base-core (>= 2.7.0), r-recommended, r-cran-genetics, r-cran-haplo.stats, r-cran-qvalue
+Provides: r-other-genabel
+Conflicts: r-other-genabel
 Description: GNU R 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

Modified: trunk/packages/R/r-other-genabel/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/copyright	2011-02-05 16:48:57 UTC (rev 5907)
+++ trunk/packages/R/r-other-genabel/trunk/debian/copyright	2011-02-05 17:15:41 UTC (rev 5908)
@@ -1,20 +1,21 @@
-This is the Debian GNU/Linux r-other-geneabel package of
-GenABEL, performing statistical analyses of genome-wide SNP
-association studies. GenABEL is maintained by Yurii Aulchenko
+This is the Debian GNU/Linux r-cran-genabel (formerly r-other-geneabel)
+package of GenABEL, performing statistical analyses of genome-wide
+SNP association studies. GenABEL is maintained by Yurii Aulchenko
 <i.aoultchenko at erasmusmc.nl>.  It was written by Yurii Aulchenko, Maksim
 Struchalin, with contributions from Stephan Ripke, Terry Therneau and
 Toby Johnson.
 
+This Debian package was created by Steffen Moeller <moeller at debian.org>,
+based on work for the r-cran-rodbc package of Dirk Eddelbuettel
+<edd at debian.org>. The code associated with packaging is distributed
+under the terms of the GPL version 2 or later.
 
-This package was created by Steffen Moeller <moeller at debian.org>, based on
-work for the r-cran-rodbc package of Dirk Eddelbuettel <edd at debian.org>.
+The sources were previously downloaded from http://mga.bionet.nsc.ru/nlru/GenABEL
+and now from the CRAN (cran.r-project.org) repository.
 
-The sources were downloaded from http://mga.bionet.nsc.ru/nlru/GenABEL.
-
 The package was renamed from its upstream name 'GenABEL' to
-'r-other-genabel' to highlight the fact that is it a package for R
-outside the CRAN or other established archives, and to match Debian's
-convention of lowercase package names.
+'r-cran-genabel' to highlight the fact that is it a package for R
+in CRAN, and to match Debian's convention of lowercase package names.
 
 GenABEL is copyright 2006-2008 of Yurii Aulchenko, Maksim Struchalin, with
 contributions from Stephan Ripke, Terry Therneau and Toby Johnson and

Modified: trunk/packages/R/r-other-genabel/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/rules	2011-02-05 16:48:57 UTC (rev 5907)
+++ trunk/packages/R/r-other-genabel/trunk/debian/rules	2011-02-05 17:15:41 UTC (rev 5908)
@@ -3,5 +3,5 @@
 # debian/rules file for the Debian/GNU Linux r-cran-qtl package
 # Copyright 2003-2006 by Dirk Eddelbuettel <edd at debian.org>
 
-debRreposname=other
+debRreposname=cran
 include /usr/share/R/debian/r-cran.mk

Added: trunk/packages/R/r-other-genabel/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/R/r-other-genabel/trunk/debian/source/format	2011-02-05 17:15:41 UTC (rev 5908)
@@ -0,0 +1 @@
+3.0 (quilt)

Modified: trunk/packages/R/r-other-genabel/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/watch	2011-02-05 16:48:57 UTC (rev 5907)
+++ trunk/packages/R/r-other-genabel/trunk/debian/watch	2011-02-05 17:15:41 UTC (rev 5908)
@@ -1,3 +1,5 @@
 version=3
-http://mga.bionet.nsc.ru/nlru/GenABEL/GenABEL_(.*)\.tar\.gz
+#http://mga.bionet.nsc.ru/nlru/GenABEL/GenABEL_(.*)\.tar\.gz
+# The package has now arrived in CRAN
+http://cran.r-project.org/src/contrib/GenABEL_(.*)\.tar\.gz

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