[med-svn] r4862 - in trunk/packages/R: . r-cran-qtl r-cran-qtl/trunk r-cran-qtl/trunk/debian
Andreas Tille
tille at alioth.debian.org
Fri Jun 4 11:45:11 UTC 2010
Author: tille
Date: 2010-06-04 11:45:04 +0000 (Fri, 04 Jun 2010)
New Revision: 4862
Added:
trunk/packages/R/r-cran-qtl/
trunk/packages/R/r-cran-qtl/tags/
trunk/packages/R/r-cran-qtl/trunk/
trunk/packages/R/r-cran-qtl/trunk/debian/
trunk/packages/R/r-cran-qtl/trunk/debian/README.Debian
trunk/packages/R/r-cran-qtl/trunk/debian/changelog
trunk/packages/R/r-cran-qtl/trunk/debian/control
trunk/packages/R/r-cran-qtl/trunk/debian/copyright
trunk/packages/R/r-cran-qtl/trunk/debian/rules
trunk/packages/R/r-cran-qtl/trunk/debian/watch
Log:
Move qtl package from pkg-bioc to debian-med repository
Added: trunk/packages/R/r-cran-qtl/trunk/debian/README.Debian
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/README.Debian 2010-06-04 11:45:04 UTC (rev 4862)
@@ -0,0 +1,23 @@
+The debian package name was changed fom qtl on the CRAN archives to
+r-cran-qtl. This best reflects the origin of the package obvious. The
+qtl source are referred to as r/qtl on the upstream web pages
+(http://www.biostat.jhsph.edu/~kbroman/qtl/).
+
+Dirk Eddelbuettel <edd at debian.org> kindly sponsored the initial release
+and performed many smaller changes to streamline the debianisation. I
+very much thank him for this.
+
+The chromosomal linkage analyses for a longer time seemed neglected in
+the bioinformatics community. If the distribution of this package in
+Debian had some positive side effect in improving the communication
+between researchers in bioinformatics and genetics, then we have
+achieved something real good.
+
+When using the package, please cite
+ Broman KW, Wu H, Sen S, Churchill GA (2003)
+ R/qtl: QTL mapping in experimental crosses.
+ Bioinformatics 19:889-890
+in your publications.
+
+
+-- Steffen Moeller <steffen_moeller at gmx.de> Wed, 10 Oct 2007 13:43:39 +0200
Added: trunk/packages/R/r-cran-qtl/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/changelog 2010-06-04 11:45:04 UTC (rev 4862)
@@ -0,0 +1,220 @@
+qtl (1.14-2-1) unstable; urgency=low
+
+ * dependency on R 2.7.10
+ * new upstream version with only minor changes
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 28 Oct 2009 23:09:18 +0000
+
+qtl (1.13-7-1) unstable; urgency=low
+
+ * new upstream version with various bug fixes
+ * bumped standard compliance to 3.8.3 (no changes required)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 28 Sep 2009 13:39:40 +0200
+
+qtl (1.12-26-1) unstable; urgency=low
+
+ * new upstream version
+ - support for recombinant inbred lines (RIL)
+ - simpler notation to reference pseudonmarkers
+ * license change to GPL-3
+ * adapted section to gnu-r
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 09 Jul 2009 13:52:50 +0200
+
+qtl (1.11-12-1) unstable; urgency=low
+
+ * new upstream version
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 14 May 2009 13:47:06 +0200
+
+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.
+
+ * 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/R/r-cran-qtl/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/control 2010-06-04 11:45:04 UTC (rev 4862)
@@ -0,0 +1,41 @@
+Source: qtl
+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 (>= 2.10.0~20091019)
+Standards-Version: 3.8.3
+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 (>= 2.10.0~20091019)
+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 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 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.
Added: trunk/packages/R/r-cran-qtl/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/copyright 2010-06-04 11:45:04 UTC (rev 4862)
@@ -0,0 +1,30 @@
+This is the Debian GNU/Linux r-cran-qtl package of r/qtl,
+performing statistical analyses of genomic marker association
+studies. R/qtl was written by Karl W. Broman <kbroman at jhsph.edu>
+and Hao Wu <haowu at jax.org>, with ideas from Gary Churchill
+and Śaunak Sen and contributions from Brian Yandell. It is
+solely maintained and copyright 2001-2009 by Karl W. Broman.
+
+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 3 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-3.
+
+The author agreed to the distribution of R/qtl in Debian in a personal
+email to the maintainer.
Added: trunk/packages/R/r-cran-qtl/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/rules 2010-06-04 11:45:04 UTC (rev 4862)
@@ -0,0 +1,6 @@
+#!/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>
+
+include /usr/share/R/debian/r-cran.mk
Property changes on: trunk/packages/R/r-cran-qtl/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-cran-qtl/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-cran-qtl/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-cran-qtl/trunk/debian/watch 2010-06-04 11:45:04 UTC (rev 4862)
@@ -0,0 +1,3 @@
+version=3
+http://cran.r-project.org/src/contrib/qtl_([-0-9\.]*).tar.gz
+
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