[med-svn] r3413 - in trunk/packages/R: . r-other-mott-happy r-other-mott-happy/trunk r-other-mott-happy/trunk/debian

Fri May 22 21:34:13 UTC 2009

Author: smoe-guest
Date: 2009-05-22 21:34:13 +0000 (Fri, 22 May 2009)
New Revision: 3413

Added:
   trunk/packages/R/r-other-mott-happy/
   trunk/packages/R/r-other-mott-happy/trunk/
   trunk/packages/R/r-other-mott-happy/trunk/debian/
Removed:
   trunk/packages/R/r-other-mott-happy/trunk/debian/watch
Modified:
   trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
   trunk/packages/R/r-other-mott-happy/trunk/debian/control
   trunk/packages/R/r-other-mott-happy/trunk/debian/copyright
   trunk/packages/R/r-other-mott-happy/trunk/debian/rules
Log:
This package is a sister-program to R/qtl, allowing for the
analysis of disease-associated loci.


Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
===================================================================

--- trunk/packages/R/r-cran-combinat/trunk/debian/changelog	2009-05-13 07:47:49 UTC (rev 3377)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/changelog	2009-05-22 21:34:13 UTC (rev 3413)
@@ -1,12 +1,5 @@
-r-cran-combinat (0.0-6-2) unstable; urgency=low
+r-other-mott-happy (2.1-1) unstable; urgency=low
 
-  * Obeying Dirk's pledge to be removed from the uploaders list
-  * debian/control adheres better to policy 3.8.0
+  * Initial release (closes: #530007).
 
- -- Steffen Moeller <moeller at debian.org>  Thu, 15 Jan 2009 14:23:54 +0100
-
-r-cran-combinat (0.0-6-1) unstable; urgency=low
-
-  * Initial release (closes: #492112).
-
- -- Steffen Moeller <moeller at debian.org>  Wed, 23 Jul 2008 18:27:42 +0200
+ -- Steffen Moeller <moeller at debian.org>  Fri, 22 May 2009 21:31:12 +0200

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-combinat/trunk/debian/control	2009-05-13 07:47:49 UTC (rev 3377)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/control	2009-05-22 21:34:13 UTC (rev 3413)
@@ -1,16 +1,34 @@
-Source: r-cran-combinat
-Section: math
+Source: r-other-mott-happy
+Section: gnu-r
 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
-Standards-Version: 3.8.0
-Homepage: http://cran.r-project.org/web/packages/combinat
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-combinat/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-cran-combinat/trunk/
+Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev, r-cran-g.data
+Standards-Version: 3.8.1
+Homepage: http://www.well.ox.ac.uk/happy/happyR.shtml
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/
 
-Package: r-cran-combinat
-Architecture: all
-Depends: ${shlibs:Depends}, r-base-core
-Description: GNU R package with utilities for combinatorics
- The R library provides routines for combinatorics.
+Package: r-other-mott-happy
+Architecture: any
+Depends: ${shlibs:Depends}, r-base-core, r-cran-g.data
+Description: GNU R package for fine-mapping complex diseases
+ The idea behind this package is that when multiple strains of
+ animals that differ in their susceptibility to multiple diseases
+ are bread over multiple generations, then one can analyse the
+ contribution that a particular genetic locus has to each of those
+ diseases. While in the past this approach has been performed
+ for one disease at a time, this tool extends the statistics
+ for allowing multiple crosses and thus save animal lifes. A larger
+ stock of animals with more generations to keep them will further
+ help producing larger numbers of observable cross-over events
+ and thus help increasing the resolution of the mapping.
+ .
+ happy is an R interface into the HAPPY C package for fine-mapping
+ Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is
+ an advanced intercross between (usually eight) founder inbred strains
+ of mice. HS are suitable for fine-mapping QTL. The happy package is
+ an extension of the original C program happy; it uses the C code to
+ compute the probability of descent from each of the founders, at each
+ locus position, but the happy packager allows a much richer range of
+ models to be fit to the data.

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-cran-combinat/trunk/debian/copyright	2009-05-13 07:47:49 UTC (rev 3377)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/copyright	2009-05-22 21:34:13 UTC (rev 3413)
@@ -1,20 +1,16 @@
-The R library combinat was written by Scott Chasalow
-<Scott.Chasalow at users.pv.wau.nl> with contributions by Alan Zaslavsky
-and is maintained by Vince Carey <stvjc at channing.harvard.edu>.
+The R library combinat was written by Richard Mott
+<Richard.Mott at well.ox.ac.uk> and is also maintained by him.
 
-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>.
+This package was created by Steffen Moeller <moeller at debian.org>.
 
-The sources were downloaded from http://cran.r-project.org/src/contrib/.
+The sources were downloaded from http://www.well.ox.ac.uk/happy/happyR.shtml.
 
-The package was renamed from its upstream name 'combinat' to
-'r-cran-combinat' to highlight the fact that is it a package for R within
-the CRAN archive.
+The package was renamed from its upstream name 'happy' to
+'r-other-mott-happy' in harmony with the R packaging policy to indicate
+that the package is external to the CRAN or BioC repositories.
 
-Combinat is copyright 1994-1997 of Scott Chasalow, with contributions
-from Alan Zaslavsky and released under the GNU General Public License
-(GPL) version 2.
+happy is copyright 1995-2008 of Richard Mott, and released under the
+GNU General Public License (GPL) version 2 or later versions.
 
-On a Debian GNU/Linux system, the GPL license is included in the file
-/usr/share/common-licenses/GPL.
+On a Debian GNU/Linux system, the GPL license version 2 is included in the file
+/usr/share/common-licenses/GPL-2.

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-cran-combinat/trunk/debian/rules	2009-05-13 07:47:49 UTC (rev 3377)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/rules	2009-05-22 21:34:13 UTC (rev 3413)
@@ -1,6 +1,4 @@
 #!/usr/bin/make -f
 # 							-*- makefile -*-
-# debian/rules file for the Debian/GNU Linux r-cran-qtl package
-# Copyright 2003-2006 by Dirk Eddelbuettel <edd at debian.org>
-
+debRreposname=other-mott
 include /usr/share/R/debian/r-cran.mk

Deleted: trunk/packages/R/r-other-mott-happy/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-cran-combinat/trunk/debian/watch	2009-05-13 07:47:49 UTC (rev 3377)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/watch	2009-05-22 21:34:13 UTC (rev 3413)
@@ -1,3 +0,0 @@
-version=3
-http://cran.r-project.org/src/contrib/combinat_([-0-9\.]*)\.tar\.gz
-


