[pkg-bioc] svn commit r371 r371 - in /trunk/packages/qtl/trunk/debian: changelog control copyright

Fri Feb 20 18:14:55 UTC 2009

Author: moeller
Date: Fri Feb 20 18:14:54 2009
New Revision: 371

URL: http://svn.debian.org/wsvn/pkg-bioc/?sc=1&rev=371
Log:
New upstream version.
Upstream comes with some extra documentation which is not appearing in the default install. Some work to do here.

Modified:
    trunk/packages/qtl/trunk/debian/changelog
    trunk/packages/qtl/trunk/debian/control
    trunk/packages/qtl/trunk/debian/copyright

Modified: trunk/packages/qtl/trunk/debian/changelog
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/qtl/trunk/debian/changelog?rev=371&op=diff
==============================================================================

--- trunk/packages/qtl/trunk/debian/changelog (original)
+++ trunk/packages/qtl/trunk/debian/changelog Fri Feb 20 18:14:54 2009
@@ -1,3 +1,47 @@
+qtl (1.10-28-1) unstable; urgency=low
+
+  * new upstream version
+    - resolves inconsistencies in copyright
+    - various changes affecting stability or performance
+    - more on http://www.rqtl.org/STATUS.txt
+  * debian/copyright updated
+  * removed PDFs from source tree
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 20 Feb 2009 18:50:00 +0100
+
+qtl (1.09-43-2) unstable; urgency=low
+
+  * Dirk requested to be removed from the uploaders list
+  * Allowing Debian-Med community maintenance albeit
+    package remaining under pkg-bioc control for now.
+  * Added Vcs-Browser and Vcs-Svn fields.
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 29 Sep 2008 17:18:20 +0200
+
+qtl (1.09-43-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 30 Jul 2008 16:42:46 +0200
+
+qtl (1.08-56-1) unstable; urgency=low
+
+  * New upstream release.
+  * Establishing compatibility to R release 2.7.
+
+ -- Steffen Moeller <moeller at debian.org>  Fri, 11 Apr 2008 11:48:30 +0200
+
+qtl (1.07-12-2) unstable; urgency=low
+
+  * [debian/control]
+    - updated description
+    - adhering to latest standards version
+  * [debian/copyright]
+    - updated Steffen's email adress
+  * Recompilation will induce transition to gfortran
+
+ -- Steffen Moeller <moeller at debian.org>  Tue, 11 Mar 2008 10:41:54 +0100
+
 qtl (1.07-12-1) unstable; urgency=low
 
   * New upstream version.

Modified: trunk/packages/qtl/trunk/debian/control
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/qtl/trunk/debian/control?rev=371&op=diff
==============================================================================
--- trunk/packages/qtl/trunk/debian/control (original)
+++ trunk/packages/qtl/trunk/debian/control Fri Feb 20 18:14:54 2009
@@ -1,28 +1,41 @@
 Source: qtl
 Section: math
 Priority: optional
-Maintainer: Steffen Moeller <moeller at debian.org>
-Uploaders: Dirk Eddelbuettel <edd at debian.org>
-Build-Depends: debhelper (>> 4.1.0), cdbs, r-base-dev (>= 2.5.1)
-Standards-Version: 3.7.2
+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)
+Standards-Version: 3.8.0
+Vcs-Browser: http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/qtl/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/pkg-bioc/trunk/packages/qtl/trunk/
 Homepage: http://www.rqtl.org
 
 Package: r-cran-qtl
 Architecture: any
-Depends: ${shlibs:Depends}, r-base-core (>= 2.5.1)
+Depends: ${shlibs:Depends}, r-base-core (>= 2.7.0~20080408)
 Description: GNU R package for genetic marker linkage analysis
- R/qtl is an extensible, interactive environment for
- mapping quantitative trait loci (QTLs) in experimental crosses. It is
- implemented as an add-on-package for the freely available and widely used
- statistical language/software R (see http://www.r-project.org). The
- user will benefit from the seamless integration of the QTL mapping
- software into a general statistical analysis program. 
+ R/qtl is an extensible, interactive environment for mapping quantitative
+ trait loci (QTLs) in experimental crosses. It is implemented as an
+ add-on-package for the freely available and widely used statistical
+ language/software R (see http://www.r-project.org).
+ .
+ The development of this software as an add-on to R allows to take
+ advantage of the basic mathematical and statistical functions, and
+ powerful graphics capabilities, that are provided with R. Further,
+ the user will benefit by the seamless integration of the QTL mapping
+ software into a general statistical analysis program. The goal is to
+ make complex QTL mapping methods widely accessible and allow users to
+ focus on modeling rather than computing.
+ .
+ A key component of computational methods for QTL mapping is the hidden
+ Markov model (HMM) technology for dealing with missing genotype data. We
+ have implemented the main HMM algorithms, with allowance for the presence
+ of genotyping errors, for backcrosses, intercrosses, and phase-known
+ four-way crosses.
  .
  The current version of R/qtl includes facilities for estimating
  genetic maps, identifying genotyping errors, and performing single-QTL
  genome scans and two-QTL, two-dimensional genome scans, by interval
- mapping (with EM algorithm), Haley-Knott regression, and multiple
- imputation. All of this may be done in the presence of covariates
- (such as sex, age or treatment). The fit of higher-order QTL models,
- with sophisticated techniques for model comparisons and model search,
- will be incorporated soon.
+ mapping (with the EM algorithm), Haley-Knott regression, and multiple
+ imputation. All of this may be done in the presence of covariates (such
+ as sex, age or treatment). One may also fit higher-order QTL models by
+ multiple imputation.

Modified: trunk/packages/qtl/trunk/debian/copyright
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/qtl/trunk/debian/copyright?rev=371&op=diff
==============================================================================
--- trunk/packages/qtl/trunk/debian/copyright (original)
+++ trunk/packages/qtl/trunk/debian/copyright Fri Feb 20 18:14:54 2009
@@ -3,22 +3,26 @@ performing statistical analyses of genom
 studies. R/qtl was written by Karl W. Broman <kbroman at jhsph.edu>
 with Hao Wu <haowu at jax.org> and is maintained by Karl W. Broman.
 
-This package was created by Steffen Moeller <moeller at pzr.uni-rostock.de>,
-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>,
+based on work for the r-cran-rodbc package of Dirk Eddelbuettel
+<edd at debian.org>.
+
 The sources were downloaded from 
 	http://www.rqtl.org/download
 or
 	http://cran.r-project.org/src/contrib/
+and are also available as a public git repository at
+	http://github.com/kbroman/qtl/tree/master
 
 The package was renamed from its upstream name 'R/qtl' to 'r-cran-qtl'
 to highlight the fact that is it a package for R within the CRAN archive,
 and to match Debian's convention of lowercase package names.
 
 R/qtl is copyright of Karl W. Broman and released under
-version 2 of the GNU General Public License (GPL).
+version 2 or later of the GNU General Public License (GPL).
 
 On a Debian GNU/Linux system, the GPL license is included in the file
 /usr/share/common-licenses/GPL.
 
-The author agreed to the distribution of r/qtl in debian in a personal
+The author agreed to the distribution of r/qtl in Debian in a personal
 email to the maintainer.


