[med-svn] r3790 - in trunk/packages/R/r-other-mott-happy/trunk/debian: . patches
Steffen Möller
smoe-guest at alioth.debian.org
Tue Aug 18 15:52:14 UTC 2009
Author: smoe-guest
Date: 2009-08-18 15:52:14 +0000 (Tue, 18 Aug 2009)
New Revision: 3790
Added:
trunk/packages/R/r-other-mott-happy/trunk/debian/README.source
trunk/packages/R/r-other-mott-happy/trunk/debian/patches/
trunk/packages/R/r-other-mott-happy/trunk/debian/patches/ELT_String.patch
trunk/packages/R/r-other-mott-happy/trunk/debian/patches/debug.patch
trunk/packages/R/r-other-mott-happy/trunk/debian/patches/happyMatrices.patch
trunk/packages/R/r-other-mott-happy/trunk/debian/patches/series
trunk/packages/R/r-other-mott-happy/trunk/debian/patches/validateParams.patch
Modified:
trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
trunk/packages/R/r-other-mott-happy/trunk/debian/control
trunk/packages/R/r-other-mott-happy/trunk/debian/rules
Log:
Latest roundup of changes for the r-other-mott-happy package.
Added: trunk/packages/R/r-other-mott-happy/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/README.source (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/README.source 2009-08-18 15:52:14 UTC (rev 3790)
@@ -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
Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/changelog 2009-08-18 14:28:37 UTC (rev 3789)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/changelog 2009-08-18 15:52:14 UTC (rev 3790)
@@ -1,5 +1,17 @@
-r-other-mott-happy (2.1-1) unstable; urgency=low
+r-other-mott-happy (2.1-3) unstable; urgency=low
- * Initial release (closes: #530007).
+ * 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
Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/control 2009-08-18 14:28:37 UTC (rev 3789)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/control 2009-08-18 15:52:14 UTC (rev 3790)
@@ -4,7 +4,7 @@
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, r-cran-g.data, quilt
-Standards-Version: 3.8.1
+Standards-Version: 3.8.3
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/
@@ -63,7 +63,7 @@
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.
-
+ .
Further details can be found in
Proc. Natl. Acad. Sci. USA, 10.1073/pnas.230304397.
Added: trunk/packages/R/r-other-mott-happy/trunk/debian/patches/ELT_String.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/patches/ELT_String.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/patches/ELT_String.patch 2009-08-18 15:52:14 UTC (rev 3790)
@@ -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/trunk/debian/patches/debug.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/patches/debug.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/patches/debug.patch 2009-08-18 15:52:14 UTC (rev 3790)
@@ -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/trunk/debian/patches/happyMatrices.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/patches/happyMatrices.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/patches/happyMatrices.patch 2009-08-18 15:52:14 UTC (rev 3790)
@@ -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/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/patches/series (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/patches/series 2009-08-18 15:52:14 UTC (rev 3790)
@@ -0,0 +1,2 @@
+happyMatrices.patch
+ELT_String.patch
Added: trunk/packages/R/r-other-mott-happy/trunk/debian/patches/validateParams.patch
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/patches/validateParams.patch (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/patches/validateParams.patch 2009-08-18 15:52:14 UTC (rev 3790)
@@ -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;
Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/rules 2009-08-18 14:28:37 UTC (rev 3789)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/rules 2009-08-18 15:52:14 UTC (rev 3790)
@@ -1,4 +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
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