[med-svn] r9021 - in trunk/packages/R/r-other-mott-happy/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Sat Dec 17 12:15:07 UTC 2011 

Author: tille
Date: 2011-12-17 12:15:07 +0000 (Sat, 17 Dec 2011)
New Revision: 9021

Added:
   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/happyMatrices.patch
   trunk/packages/R/r-other-mott-happy/trunk/debian/patches/series
Removed:
   trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian
   trunk/packages/R/r-other-mott-happy/trunk/debian/README.source
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:
Bring trunk to the status of the released package


Deleted: trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian	2011-12-17 12:04:41 UTC (rev 9020)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian	2011-12-17 12:15:07 UTC (rev 9021)
@@ -1,6 +0,0 @@
-Upstream changed the package name from happy to happy.hbrem,
-with a version change from 2.1 to 2.2. We follow that change
-for the binary package name, but expect the package to
-fall back to plain happy with one of its upcoming releases.
-
--- Steffen Moeller <moeller at debian.org>  Fri, 23 Apr 2010 22:50:53 +0200

Deleted: trunk/packages/R/r-other-mott-happy/trunk/debian/README.source
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/README.source	2011-12-17 12:04:41 UTC (rev 9020)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/README.source	2011-12-17 12:15:07 UTC (rev 9021)
@@ -1,5 +0,0 @@
-No patches are applied to sources.
-
-Upstream refers to the package as happy.hbrem, but this is only so for
-an iterim period. Nevertheless, for that period the name of the binary
-also changes.

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/changelog	2011-12-17 12:04:41 UTC (rev 9020)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/changelog	2011-12-17 12:15:07 UTC (rev 9021)
@@ -1,13 +1,9 @@
-r-other-mott-happy (2.3~beta-1) UNRELEASED; urgency=low
+r-other-mott-happy (2.1-6) unstable; urgency=low
 
-  [Steffen Moeller]
-  * debian/README.Debian
-
-  [Andreas Tille]
-  * New upstream beta release
   * Source Format 3.0 (quilt)
+  * debian/README.source (no need to tell what pacth is applied or not)
 
- -- Andreas Tille <tille at debian.org>  Mon, 24 Jan 2011 14:52:31 +0100
+ -- Andreas Tille <tille at debian.org>  Sat, 17 Dec 2011 13:05:47 +0100
 
 r-other-mott-happy (2.1-5) unstable; urgency=low
 
@@ -32,9 +28,10 @@
 
 r-other-mott-happy (2.1-4) unstable; urgency=low
 
-  * Rebuilt for R 2.10.
+  * Fixed build dependency on MASS library (packaged
+    as r-cran-vr) (Closes: #544836).
 
- -- Steffen Moeller <moeller at debian.org>  Wed, 28 Oct 2009 23:51:08 +0000
+ -- Steffen Moeller <moeller at debian.org>  Thu, 03 Sep 2009 12:57:03 +0200
 
 r-other-mott-happy (2.1-3) unstable; urgency=low
 

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/control	2011-12-17 12:04:41 UTC (rev 9020)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/control	2011-12-17 12:15:07 UTC (rev 9021)
@@ -10,9 +10,7 @@
 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.hbrem
-Replaces: r-other-mott-happy (<< 2.2-1)
-Conflicts: r-other-mott-happy
+Package: r-other-mott-happy
 Architecture: any
 Depends: ${shlibs:Depends}, r-base-core (>= 2.10.0), r-cran-g.data, r-cran-multicore, r-cran-mass
 Description: GNU R package for fine-mapping complex diseases
@@ -66,13 +64,3 @@
  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.
-
-
-Package: r-other-mott-happy.hbrem-dbg
-Architecture: any
-Depends: r-other-mott-happy.hbrem
-Description: Debug information for package r-other-mott-happy.hbrem
- In Debian, the debug information is typically stripped out from the
- regular libraries. This package provides it.  When experiencing an
- abort while executing the R library, this package will help interpreting
- the core.

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	2011-12-17 12:15:07 UTC (rev 9021)
@@ -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/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	2011-12-17 12:15:07 UTC (rev 9021)
@@ -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	2011-12-17 12:15:07 UTC (rev 9021)
@@ -0,0 +1,2 @@
+happyMatrices.patch
+ELT_String.patch

Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/rules	2011-12-17 12:04:41 UTC (rev 9020)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/rules	2011-12-17 12:15:07 UTC (rev 9021)
@@ -1,8 +1,5 @@
 #!/usr/bin/make -f
 # 							-*- makefile -*-
 debRreposname=other-mott
-
-#cranName=happy
-cranName=happy.hbrem
-
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
 include /usr/share/R/debian/r-cran.mk

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