[med-svn] r9020 - in trunk/packages/R/r-other-mott-happy: branches tags tags/2.1-5 tags/2.1-5/debian tags/2.1-5/debian/patches
Andreas Tille
tille at alioth.debian.org
Sat Dec 17 12:04:41 UTC 2011
Author: tille
Date: 2011-12-17 12:04:41 +0000 (Sat, 17 Dec 2011)
New Revision: 9020
Added:
trunk/packages/R/r-other-mott-happy/branches/2.3/
trunk/packages/R/r-other-mott-happy/tags/2.1-5/
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/README.source
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/changelog
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/compat
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/control
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/copyright
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/ELT_String.patch
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/debug.patch
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/happyMatrices.patch
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/series
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/validateParams.patch
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/rules
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/upstream-metadata.yaml
trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/watch
Log:
Moved existing packaging to branches/2.3 because Steffen asked for not uploading this package; injected current packaging state to propper tag
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/README.source
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/README.source (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/README.source 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,11 @@
+The following patches are being applied:
+
+ happyMatrices.patch - explicitly mentioning the test on is.null
+
+ ELT_String.patch - provides fixed for newer version of R
+
+Not applied are:
+
+ debug.patch
+
+ validateParams.patch -p0 - extra output when a marker is found
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/changelog
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/changelog (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/changelog 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,45 @@
+r-other-mott-happy (2.1-5) unstable; urgency=low
+
+ [Charles Plessy]
+ * Documented information in ‘debian/upstream-metadata.yaml’.
+ * Removed mention of the bibliographic reference in ‘debian/control’.
+
+ [Andreas Tille]
+ * debian/control:
+ - Build-Depends r-base-dev (>= 2.10), Depends r-core (>= 2.10) and
+ rebuild on current Squeeze system
+ Closes: #611008
+ - Added myself to uploaders
+ - Standards-Version: 3.9.1 (no changes needed)
+ - Fixed name of Debian Med team
+ - Debhelper 7
+ - Replaced (Build-)Depends r-cran-vr by r-cran-mass
+ - Recommends: r-cran-vr, r-cran-multicore
+ * Added watch file
+
+ -- Andreas Tille <tille at debian.org> Tue, 25 Jan 2011 08:17:57 +0100
+
+r-other-mott-happy (2.1-4) unstable; urgency=low
+
+ * Fixed build dependency on MASS library (packaged
+ as r-cran-vr) (Closes: #544836).
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 03 Sep 2009 12:57:03 +0200
+
+r-other-mott-happy (2.1-3) unstable; urgency=low
+
+ * Corrected for architecture all -> any (Closes: #530007)
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 18 Aug 2009 17:13:41 +0200
+
+r-other-mott-happy (2.1-2) UNRELEASED; urgency=low
+
+ * Added patch for not using SET_VECTOR_ELT on strings
+
+ -- Steffen Moeller <moeller at debian.org> Thu, 11 Jun 2009 18:28:33 +0200
+
+r-other-mott-happy (2.1-1) UNRELEASED; urgency=low
+
+ * Initial release.
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 22 May 2009 21:31:12 +0200
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/compat
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/compat (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/compat 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1 @@
+7
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/control
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/control (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/control 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,68 @@
+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>,
+ Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7), cdbs, r-base-dev (>= 2.10), r-cran-g.data, r-cran-mass, quilt
+Standards-Version: 3.9.1
+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-other-mott-happy
+Architecture: any
+Depends: ${shlibs:Depends}, r-base-core (>= 2.10), r-cran-g.data, r-cran-mass
+Recommends: r-cran-vr, r-cran-multicore
+Description: GNU R package for fine-mapping complex diseases
+ Most phenotypes of medical importance can be measured quantitatively,
+ and in many cases the genetic contribution is substantial, accounting
+ for 40% or more of the phenotypic variance. Considerable efforts have
+ been made to isolate the genes responsible for quantitative genetic
+ variation in human populations, but with little success, mostly
+ because genetic loci contributing to quantitative traits
+ (quantitative trait loci, QTL) have only a small effect on the
+ phenotype. Association studies have been proposed as the most
+ appropriate method for finding the genes that influence complex
+ traits. However, family-based studies may not provide the resolution
+ needed for positional cloning, unless they are very large, while
+ environmental or genetic differences between cases and controls may
+ confound population-based association studies.
+ .
+ These difficulties have led to the study of animal models of human
+ traits. Studies using experimental crosses between inbred animal
+ strains have been successful in mapping QTLs with effects on a number
+ of different phenotypes, including behaviour, but attempts to
+ fine-map QTLs in animals have often foundered on the discovery that a
+ single QTL of large effect was in fact due to multiple loci of small
+ effect positioned within the same chromosomal region. A further
+ potential difficulty with detecting QTLs between inbred crosses is
+ the significant reduction in genetic heterogeneity compared to the
+ total genetic variation present in animal populations: a QTL
+ segregating in the wild need not be present in the experimental
+ cross.
+ .
+ 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. It uses a multipoint
+ analysis which offers significant improvements in statistical power to
+ detect QTLs over that achieved by single-marker association.
+ .
+ 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.
+
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/copyright
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/copyright (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/copyright 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,16 @@
+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>.
+
+The sources were downloaded from http://www.well.ox.ac.uk/happy/happyR.shtml.
+
+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.
+
+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 version 2 is included in the file
+/usr/share/common-licenses/GPL-2.
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/ELT_String.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/ELT_String.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/ELT_String.patch 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,32 @@
+--- old/src/Rhappy.c 2009-06-11 18:15:42.156232021 +0200
++++ new/src/Rhappy.c 2009-06-11 18:21:27.890496555 +0200
+@@ -195,21 +195,21 @@
+
+
+ SET_VECTOR_ELT(ans,0,strains);
+- SET_VECTOR_ELT(names,0,mkChar("strains"));
++ SET_STRING_ELT(names,0,mkChar("strains"));
+ SET_VECTOR_ELT(ans,1,markers);
+- SET_VECTOR_ELT(names,1,mkChar("markers"));
++ SET_STRING_ELT(names,1,mkChar("markers"));
+ SET_VECTOR_ELT(ans,2,map);
+- SET_VECTOR_ELT(names,2,mkChar("map"));
++ SET_STRING_ELT(names,2,mkChar("map"));
+ SET_VECTOR_ELT(ans,3,subjects);
+- SET_VECTOR_ELT(names,3,mkChar("subjects"));
++ SET_STRING_ELT(names,3,mkChar("subjects"));
+ SET_VECTOR_ELT(ans,4,phenotypes);
+- SET_VECTOR_ELT(names,4,mkChar("phenotypes"));
++ SET_STRING_ELT(names,4,mkChar("phenotypes"));
+ SET_VECTOR_ELT(ans,5,handle);
+- SET_VECTOR_ELT(names,5,mkChar("handle"));
++ SET_STRING_ELT(names,5,mkChar("handle"));
+ SET_VECTOR_ELT(ans,6,chromosome);
+- SET_VECTOR_ELT(names,6,mkChar("chromosome"));
++ SET_STRING_ELT(names,6,mkChar("chromosome"));
+ SET_VECTOR_ELT(ans,7,family);
+- SET_VECTOR_ELT(names,7,mkChar("family"));
++ SET_STRING_ELT(names,7,mkChar("family"));
+
+ setAttrib( ans, R_NamesSymbol, names );
+
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/debug.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/debug.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/debug.patch 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,56 @@
+--- src/Rhappy.c.o 2009-06-12 01:07:11.422410263 +0200
++++ src/Rhappy.c 2009-06-12 01:44:13.589388115 +0200
+@@ -1385,20 +1388,30 @@
+ QTL_DATA *q = validateParams( handle, marker, &locus, 0 );
+ SEXP Matrix = R_NilValue;
+
++ int ttt=0;
++
++ printf("A %d\n",ttt++);
++
+ if ( locus >= 0 && q->dp_matrices != NULL) {
++ int ppppp = printf("AA %d\n",ttt++);
+ ALLELE_FREQ *af = &(q->alleles->af[locus]);
+ QTL_PRIOR ***p;
+ int S2 = q->S*(q->S+1)/2;
+
+ int i;
+
++ printf("AB %d\n",ttt++);
++
+
+ /* get the prior probabilities of the strain state combinations at the flanking marker */
+
+ p = allocate_qtl_priors( q );
++ printf("G %d\n",ttt++);
+ compute_qtl_priors( q, p, locus, af->prior );
++ printf("K %d\n",ttt++);
+
+ PROTECT( Matrix = allocMatrix( REALSXP, q->N, S2) );
++ printf("M %d\n",ttt++);
+
+ for(i=0; i<q->N; i++) {
+ int j, k,m=0;
+@@ -1410,17 +1423,22 @@
+ m++;
+ }
+ }
++ printf("N %d\n",ttt++);
+ UNPROTECT(1);
+
++ printf("X %d\n",ttt++);
++
+ for(i=0;i<q->N;i++) {
+ int s1;
+ for(s1=0;s1<q->S;s1++)
+ free(p[i][s1]);
+ free(p[i]);
+ }
++ printf("Y %d\n",ttt++);
+ free(p);
+
+ }
++ printf("Z %d\n",ttt++);
+ return Matrix;
+ }
+
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/happyMatrices.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/happyMatrices.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/happyMatrices.patch 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,17 @@
+--- old/R/happy.R 2009-06-12 00:42:32.261397270 +0200
++++ new/R/happy.R 2009-06-12 00:50:00.933433780 +0200
+@@ -72,10 +72,12 @@
+ for( m in h$markers) {
+ add <- hdesign( h, m, model='additive' )
+ full <- hdesign( h, m, model='full' )
+- if ( h$use.pedigrees || h$phase.known )
++ if ( (!is.null(h$use.pedigrees)&&h$use.pedigrees) || (!is.null(h$phase.known)&&h$phase.known) ) {
+ full.asymmetric <- hdesign( h, m, model="full.asymmetric")
+- else
++ }
++ else {
+ full.asymmetric <- NULL
++ }
+ id <- m
+ matrices[[m]] <- list( id=id, additive=add, full=full, full.asymmetric=full.asymmetric )
+ }
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/series
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/series (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/series 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,2 @@
+happyMatrices.patch
+ELT_String.patch
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/validateParams.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/validateParams.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/patches/validateParams.patch 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,15 @@
+--- src/Rhappy.c.o 2009-06-12 01:07:11.422410263 +0200
++++ src/Rhappy.c 2009-06-12 01:30:46.949375072 +0200
+@@ -1287,8 +1287,10 @@
+
+ for( i=0; i<numMarkers ; i++)
+ {
+- if ( ! strcmp( name, af[i].marker_name ) )
+- return i;
++ if ( 0 == strcmp( name, af[i].marker_name ) ) {
++ printf( "Found marker %s\n", name);
++ return i;
++ }
+ }
+
+ return NOT_FOUND;
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/rules
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/rules (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/rules 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+debRreposname=other-mott
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/R/debian/r-cran.mk
Property changes on: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/upstream-metadata.yaml (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/upstream-metadata.yaml 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,15 @@
+Contact: Richard Mott <Richard.Mott at well.ox.ac.uk>
+DOI: 10.1073/pnas.230304397
+Homepage: http://www.well.ox.ac.uk/happy/happyR
+Name: HAPPY
+PMID: 11050180
+Reference:
+ author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan
+ title: A method for fine mapping quantitative trait loci in outbred animal stocks
+ journal: Proc Natl Acad Sci U S A
+ volume: 97
+ number: 23
+ pages: 12649-12654
+ year: 2000
+ URL: http://www.pnas.org/content/97/23/12649.abstract
+ eprint: http://www.pnas.org/content/97/23/12649.full.pdf+html
Added: trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/watch
===================================================================
--- trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/watch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/tags/2.1-5/debian/watch 2011-12-17 12:04:41 UTC (rev 9020)
@@ -0,0 +1,2 @@
+version=3
+http://www.well.ox.ac.uk/happy/happyR.shtml happy.*_([\d\.]+).tar.gz
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