[pkg-bioc] svn commit r350 r350 - in /trunk/packages/qtl/trunk/debian: ./ changelog control

Mon Oct 15 09:16:53 UTC 2007

Author: smoe-guest
Date: Mon Oct 15 09:16:53 2007
New Revision: 350

URL: http://svn.debian.org/wsvn/pkg-bioc/?sc=1&rev=350
Log:
[svn-inject] Applying Debian modifications to trunk

Added:
    trunk/packages/qtl/trunk/debian/   (with props)
    trunk/packages/qtl/trunk/debian/changelog
    trunk/packages/qtl/trunk/debian/control

Propchange: trunk/packages/qtl/trunk/debian/
------------------------------------------------------------------------------
    mergeWithUpstream = 1

Added: trunk/packages/qtl/trunk/debian/changelog
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/qtl/trunk/debian/changelog?rev=350&op=file
==============================================================================

--- trunk/packages/qtl/trunk/debian/changelog (added)
+++ trunk/packages/qtl/trunk/debian/changelog Mon Oct 15 09:16:53 2007
@@ -0,0 +1,146 @@
+qtl (1.07-12-1) unstable; urgency=low
+
+  * New upstream version.
+
+  * Major changes:
+
+    - Upstream completely rewrote the effectscan function, so that it
+    now uses multiple imputation results and deals with the X chromosome
+    appropriately.
+
+    - Upstream fixed an important bug in fitqtl, in which incorrect
+    results could be obtained if covariates were placed before QTL terms
+    in the formula.
+
+ -- Steffen Moeller <moeller at debian.org>  Wed, 10 Oct 2007 13:43:39 +0200
+
+qtl (1.06-43-1) unstable; urgency=low
+
+  * New upstream release
+  * debian/control: (Build-)Depends: updated to r-base-dev (>= 2.4.0)
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Sun, 12 Aug 2007 15:30:27 -0500
+
+qtl (1.05-2-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Thu,  9 Nov 2006 17:57:04 -0600
+
+qtl (1.04-53-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Sun, 29 Oct 2006 11:17:51 -0600
+
+qtl (1.04-52-1) unstable; urgency=low
+
+  * New upstream release
+
+  * debian/control: (Build-)Depends: updated to r-base-dev (>= 2.4.0)
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Sat, 28 Oct 2006 11:26:41 -0500
+
+qtl (1.03-14-1) unstable; urgency=low
+
+  * New upstream release
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Fri, 21 Jul 2006 18:16:41 -0500
+
+qtl (1.02-26-1) unstable; urgency=low
+
+  * New upstream release
+  
+  * New maintainer as Steffen's NM progress appears to have stalled
+  
+  * debian/rules: Simplified to cdbs-based one-liner sourcing r-cran.mk 
+  * debian/control: Hence Build-Depends: updated to r-base-dev (>= 2.3.0)
+  
+  * debian/control: Standards-Version: increased to 3.7.2
+  * debian/watch: Updated file to version: 3
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Thu,  8 Jun 2006 21:13:27 -0500
+
+qtl (1.01-9-1) unstable; urgency=low
+
+  * New upstream version.
+  
+  [ Dirk Eddelbuettel ]
+  * Rename upstream tarball correctly as .orig.tar.gz before building package 
+    to prevent accidental build as a Debian native package
+  * debian/post{inst,rm}: No longer call R to update html help index
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Thu,  1 Dec 2005 15:20:00 +0100
+
+qtl (0.99.24-1) unstable; urgency=low
+
+  * New upstream version.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Sun, 15 May 2005 23:54:03 +0200
+
+qtl (0.98.57-2.1) unstable; urgency=low
+
+  * NMU
+  * Coordinated with Maintainer as part of larger R 2.0.0 update effort
+  * Rebuilt under R 2.0.0
+  * debian/control: Updated Build-Depends: and Depends: accordingly
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Sat,  9 Oct 2004 20:55:08 -0500
+
+qtl (0.98.57-2) unstable; urgency=low
+
+  * added postinst script
+  * added postrm script too [ Dirk Eddelbuettel ]
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  19 Sep 2004 23:24:00 +0100
+
+qtl (0.98.57-1) unstable; urgency=low
+
+  * New upstream version.
+    - Proper support of the X chromosome
+    - many little improvements
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  19 Sep 2004 01:06:00 +0100
+
+qtl (0.97.22-1) unstable; urgency=low
+
+  * New upstream version.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  14 Jan 2004 10:55:00 +0100
+
+qtl (0.97.21-5) unstable; urgency=low
+
+  * Retrieval of genetical map from EnsEMBL (http://www.ensembl.org)
+  * Also implemented access to EnsEMBL via RMySQL, package r-cran-mysql
+    available on mentors.debian.net
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  11 Nov 2003 13:14:00 +0100
+
+qtl (0.97.21-4) unstable; urgency=low
+
+  * Retrieval of physical map from EnsEMBL (http://www.ensembl.org)
+    Requires RODBC.
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  11 Nov 2003 13:14:00 +0100
+
+qtl (0.97.21-3) unstable; urgency=low
+
+  * added demo, code copied from "A starting point" help to the qtl library
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  11 Nov 2003 13:14:00 +0100
+
+qtl (0.97.21-2) unstable; urgency=low
+
+  * dec and quote parameters passed to internally called R base function
+    read.table for read.cross
+  * second parameter (dir) interpreted as file if file unset
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  3 Nov 2003 22:05:03 +0100
+
+qtl (0.97.21-1) unstable; urgency=low
+
+  * Initial Debian Release (closes: #214601)
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Tue,  8 Oct 2003 09:02:03 +0100
+
+

Added: trunk/packages/qtl/trunk/debian/control
URL: http://svn.debian.org/wsvn/pkg-bioc/trunk/packages/qtl/trunk/debian/control?rev=350&op=file
==============================================================================
--- trunk/packages/qtl/trunk/debian/control (added)
+++ trunk/packages/qtl/trunk/debian/control Mon Oct 15 09:16:53 2007
@@ -0,0 +1,28 @@
+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
+Homepage: http://www.rqtl.org
+
+Package: r-cran-qtl
+Architecture: any
+Depends: ${shlibs:Depends}, r-base-core (>= 2.5.1)
+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. 
+ .
+ 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.


