[med-svn] r5402 - in trunk/packages/mrbayes/trunk/debian: . patches patches/misc

[Steffen Möller]

Author: moeller
Date: 2010-11-01 01:29:49 +0000 (Mon, 01 Nov 2010)
New Revision: 5402

Removed:
   trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch
Modified:
   trunk/packages/mrbayes/trunk/debian/
   trunk/packages/mrbayes/trunk/debian/changelog
   trunk/packages/mrbayes/trunk/debian/control
   trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff
   trunk/packages/mrbayes/trunk/debian/patches/series
Log:
Further updates to get it finally compiled.



Property changes on: trunk/packages/mrbayes/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Modified: trunk/packages/mrbayes/trunk/debian/changelog
===================================================================
--- trunk/packages/mrbayes/trunk/debian/changelog	2010-11-01 00:45:33 UTC (rev 5401)
+++ trunk/packages/mrbayes/trunk/debian/changelog	2010-11-01 01:29:49 UTC (rev 5402)
@@ -3,7 +3,7 @@
   * Adjustments for latest Debian policy.
     - build dependencies
     - Debian source code management with Debian Med
-  * Added -mpi package
+  * Added mb-mpi binary
   * Initial upload to Debian.
 
  -- Steffen Moeller <moeller at debian.org>  Mon, 01 Nov 2010 01:32:14 +0100

Modified: trunk/packages/mrbayes/trunk/debian/control
===================================================================
--- trunk/packages/mrbayes/trunk/debian/control	2010-11-01 00:45:33 UTC (rev 5401)
+++ trunk/packages/mrbayes/trunk/debian/control	2010-11-01 01:29:49 UTC (rev 5402)
@@ -4,7 +4,7 @@
 Maintainer: Fernando Ribeiro <fernando at staff.nerdgroup.org>
 Uploaders: Steffen Moeller <moeller at debian.org>, Dominique Belhachemi <domibel at debian.org>, Pjotr Prins <pjotr.debian at thebird.nl>
 Standards-Version: 3.9.1
-Build-Depends: libncurses-dev, libreadline-dev
+Build-Depends: libncurses-dev, libreadline-dev, mpi-default-dev, quilt
 Homepage: http://mrbayes.csit.fsu.edu/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mrbayes/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mrbayes/trunk/
@@ -13,6 +13,7 @@
 Package: mrbayes
 Architecture: any
 Depends: ${shlibs:Depends}, bash (>=3.1)
+Suggests: mpi-default
 Description: A program for the Bayesian estimation of phylogeny
  Bayesian inference of phylogeny is based upon a quantity called the posterior
  probability distribution of trees, which is the probability of a tree 
@@ -21,15 +22,6 @@
  impossible to calculate analytically; instead, MrBayes uses a simulation 
  technique called Markov chain Monte Carlo (or MCMC) to approximate the 
  posterior probabilities of trees.
-
-Package: mrbayes-mpi
-Architecture: any
-Depends: ${shlibs:Depends}, bash (>=3.1)
-Description: A program for the Bayesian estimation of phylogeny
- Bayesian inference of phylogeny is based upon a quantity called the posterior
- probability distribution of trees, which is the probability of a tree 
- conditioned on the observations. The conditioning is accomplished using 
- Bayes's theorem. The posterior probability distribution of trees is 
- impossible to calculate analytically; instead, MrBayes uses a simulation 
- technique called Markov chain Monte Carlo (or MCMC) to approximate the 
- posterior probabilities of trees.
+ .
+ The package offers both a regular compilation and such for parallel 
+ computation with MPI.

Deleted: trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch	2010-11-01 00:45:33 UTC (rev 5401)
+++ trunk/packages/mrbayes/trunk/debian/patches/fix_Makefile_clean.patch	2010-11-01 01:29:49 UTC (rev 5402)
@@ -1,12 +0,0 @@
-Index: mrbayes-3.1.2/Makefile
-===================================================================
---- mrbayes-3.1.2.orig/Makefile	2010-11-01 01:38:20.624266148 +0100
-+++ mrbayes-3.1.2/Makefile	2010-11-01 01:39:17.808266148 +0100
-@@ -88,6 +88,7 @@
- 
- clean:		
- 		rm -f *.o
-+		rm -f $(PROGS)
- 
- showdep: 
- 	@$(CC) -MM bayes.c command.c mbmath.c mcmc.c model.c plot.c sump.c sumt.c

Modified: trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff	2010-11-01 00:45:33 UTC (rev 5401)
+++ trunk/packages/mrbayes/trunk/debian/patches/misc/makefile_clean_binary.diff	2010-11-01 01:29:49 UTC (rev 5402)
@@ -1,10 +1,10 @@
---- Makefile-old	2006-11-16 02:29:23.000000000 -0200
-+++ Makefile	2006-11-16 02:29:51.000000000 -0200
+--- ./Makefile-old	2006-11-16 02:29:23.000000000 -0200
++++ ./Makefile	2006-11-16 02:29:51.000000000 -0200
 @@ -88,6 +88,7 @@
  
  clean:		
  		rm -f *.o
-+		rm $(PROGS)
++		rm -f $(PROGS)
  
  showdep: 
  	@$(CC) -MM bayes.c command.c mbmath.c mcmc.c model.c plot.c sump.c sumt.c

Modified: trunk/packages/mrbayes/trunk/debian/patches/series
===================================================================
--- trunk/packages/mrbayes/trunk/debian/patches/series	2010-11-01 00:45:33 UTC (rev 5401)
+++ trunk/packages/mrbayes/trunk/debian/patches/series	2010-11-01 01:29:49 UTC (rev 5402)
@@ -1,3 +1,2 @@
-fix_Makefile_clean.patch
 misc/makefile_clean_binary.diff -p0
 misc/man1.diff -p1