[med-svn] r2300 - in trunk/packages/R: . r-cran-haplo.stats r-cran-haplo.stats/trunk r-cran-haplo.stats/trunk/debian r-cran-qvalue r-cran-qvalue/trunk r-cran-qvalue/trunk/debian r-other-genabel/trunk/debian
smoe-guest at alioth.debian.org
smoe-guest at alioth.debian.org
Wed Jul 23 21:52:53 UTC 2008
Author: smoe-guest
Date: 2008-07-23 21:52:52 +0000 (Wed, 23 Jul 2008)
New Revision: 2300
Added:
trunk/packages/R/r-cran-haplo.stats/
trunk/packages/R/r-cran-haplo.stats/trunk/
trunk/packages/R/r-cran-haplo.stats/trunk/debian/
trunk/packages/R/r-cran-haplo.stats/trunk/debian/changelog
trunk/packages/R/r-cran-haplo.stats/trunk/debian/control
trunk/packages/R/r-cran-haplo.stats/trunk/debian/copyright
trunk/packages/R/r-cran-haplo.stats/trunk/debian/rules
trunk/packages/R/r-cran-haplo.stats/trunk/debian/watch
trunk/packages/R/r-cran-qvalue/
trunk/packages/R/r-cran-qvalue/trunk/
trunk/packages/R/r-cran-qvalue/trunk/debian/
trunk/packages/R/r-cran-qvalue/trunk/debian/changelog
trunk/packages/R/r-cran-qvalue/trunk/debian/control
trunk/packages/R/r-cran-qvalue/trunk/debian/copyright
trunk/packages/R/r-cran-qvalue/trunk/debian/rules
trunk/packages/R/r-cran-qvalue/trunk/debian/watch
Modified:
trunk/packages/R/r-other-genabel/trunk/debian/
trunk/packages/R/r-other-genabel/trunk/debian/control
trunk/packages/R/r-other-genabel/trunk/debian/copyright
Log:
Added R package qvalue.
Various fixes to GenABEL.
Property changes on: trunk/packages/R/r-cran-haplo.stats/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/R/r-cran-haplo.stats/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/changelog 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,5 @@
+r-cran-haplo.stats (1.3.8-1) unstable; urgency=low
+
+ * Initial release (closes: #492122).
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 23 Jul 2008 18:27:42 +0200
Added: trunk/packages/R/r-cran-haplo.stats/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/control 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,19 @@
+Source: r-cran-haplo.stats
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Uploaders: Dirk Eddelbuettel <edd at debian.org>
+Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev (>= 2.7.0~20080408)
+Standards-Version: 3.8.0
+Homepage: http://cran.r-project.org/web/packages/haplo.stats
+
+Package: r-cran-haplo.stats
+Architecture: any
+Depends: ${shlibs:Depends}, r-base-core (>= 2.7.0~20080408)
+Description: GNU R package for haplotype analysis
+ The package provides routines for the GNU R statistics environment
+ for statistical Analysis of indirectly measured Haplotypes with Traits
+ and Covariates when Linkage Phase is Ambiguous. The statistical methods
+ assume that all subjects are unrelated and that haplotypes are ambiguous
+ (due to unknown linkage phase of the genetic markers). The main functions
+ are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap.
Added: trunk/packages/R/r-cran-haplo.stats/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/copyright 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,22 @@
+The R library genetics was written and maintained by Jason P. Sinnwell
+<sinnwell.jason at mayo.edu> and written together with Daniel J. Schaid
+<schaid at mayo.edu> and Z. Yu.
+
+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://cran.r-project.org/web/packages/haplo.stats.
+
+The package was renamed from its upstream name 'haplo.stats' to
+'r-cran-haplo.stats' to highlight the fact that is it a package for R within
+the CRAN archive.
+
+Genetics is copyright 2003-2008 of Mayo Foundation for Medical Education
+and Research, and released under the GNU General Public License (GPL)
+version 2 or any later version.
+
+On a Debian GNU/Linux system, the GPL license is included in the file
+/usr/share/common-licenses/GPL.
+
Added: trunk/packages/R/r-cran-haplo.stats/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/rules 2008-07-23 21:52:52 UTC (rev 2300)
@@ -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-haplo.stats/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/R/r-cran-haplo.stats/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-cran-haplo.stats/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-cran-haplo.stats/trunk/debian/watch 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,3 @@
+version=3
+http://cran.r-project.org/src/contrib/haplo.stats_([-0-9\.]*)\.tar\.gz
+
Property changes on: trunk/packages/R/r-cran-qvalue/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/R/r-cran-qvalue/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/changelog 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,5 @@
+r-cran-qvalue (1.1-1) unstable; urgency=low
+
+ * Initial release (closes: #49212).
+
+ -- Steffen Moeller <moeller at debian.org> Wed, 23 Jul 2008 23:29:22 +0200
Added: trunk/packages/R/r-cran-qvalue/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/control 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,22 @@
+Source: r-cran-qvalue
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at debian.org>
+Uploaders: Dirk Eddelbuettel <edd at debian.org>
+Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev (>= 2.7.0~20080408)
+Standards-Version: 3.8.0
+Homepage: http://cran.r-project.org/web/packages/qvalue
+
+Package: r-cran-qvalue
+Architecture: all
+Depends: ${shlibs:Depends}, r-base-core (>= 2.7.0~20080408)
+Description: GNU R package for Q-value estimation for FDR control
+ This package takes a list of p-values resulting from the simultaneous
+ testing of many hypotheses and estimates their q-values. The
+ q-value of a test measures the proportion of false positives incurred
+ (called the false discovery rate) when that particular test is called
+ significant. Various plots are automatically generated, allowing one
+ to make sensible significance cut-offs. Several mathematical results
+ have recently been shown on the conservative accuracy of the estimated
+ q-values from this software. The software can be applied to problems
+ in genomics, brain imaging, astrophysics, and data mining.
Added: trunk/packages/R/r-cran-qvalue/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/copyright 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,22 @@
+The R library qvalue is maintained by John D. Storey
+<jstorey at u.washington.edu>, authored by Alan
+Dabney <adabney at u.washington.edu> and John D. Storey
+<jstorey at u.washington.edu>, with assistance from Gregory R. Warnes
+<gregory_r_warnes at groton.pfizer.com>.
+
+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://cran.r-project.org/web/packages/qvalue/.
+
+The package was renamed from its upstream name 'qvalue' to
+'r-cran-qvalue' to highlight the fact that is it a package for R within
+the CRAN archive.
+
+Qvalue is copyright 2008 by the above listed authors
+and released under the Lesser GNU General Public License (LGPL).
+
+On a Debian GNU/Linux system, the LGPL license is included in the file
+/usr/share/common-licenses/LGPL.
Added: trunk/packages/R/r-cran-qvalue/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/rules 2008-07-23 21:52:52 UTC (rev 2300)
@@ -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-qvalue/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/R/r-cran-qvalue/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-cran-qvalue/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-cran-qvalue/trunk/debian/watch 2008-07-23 21:52:52 UTC (rev 2300)
@@ -0,0 +1,3 @@
+version=3
+http://cran.r-project.org/src/contrib/qvalue_([-0-9\.]*)\.tar\.gz
+
Property changes on: trunk/packages/R/r-other-genabel/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Modified: trunk/packages/R/r-other-genabel/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/control 2008-07-23 20:07:58 UTC (rev 2299)
+++ trunk/packages/R/r-other-genabel/trunk/debian/control 2008-07-23 21:52:52 UTC (rev 2300)
@@ -3,7 +3,7 @@
Priority: optional
Maintainer: Steffen Moeller <moeller at debian.org>
Uploaders: Dirk Eddelbuettel <edd at debian.org>
-Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev (>= 2.7.0~20080408)
+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
Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
Modified: trunk/packages/R/r-other-genabel/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-other-genabel/trunk/debian/copyright 2008-07-23 20:07:58 UTC (rev 2299)
+++ trunk/packages/R/r-other-genabel/trunk/debian/copyright 2008-07-23 21:52:52 UTC (rev 2300)
@@ -1,8 +1,11 @@
-This is the Debian GNU/Linux r-other-geneabel package of GenABEL,
-performing statistical analyses of genome-wide SNP association
-studies. GenABEL 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 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
+<i.aoultchenko at erasmusmc.nl>. It was written by Yurii Aulchenko, Maksim
+Struchalin, with contributions from Stephan Ripke, Terry Therneau and
+Toby Johnson.
+
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>.
@@ -13,9 +16,9 @@
outside the CRAN or other established archives, and to match Debian's
convention of lowercase package names.
-GenABEL is copyright of Yurii Aulchenko, Maksim Struchalin, with
-contributions from Stephan Ripke and Toby Johnson and released under
-version 2 or later of the GNU General Public License (GPL).
+GenABEL is copyright 2006-2008 of Yurii Aulchenko, Maksim Struchalin, with
+contributions from Stephan Ripke, Terry Therneau and Toby Johnson and
+released under 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.
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