[med-svn] r16311 - in trunk/packages/mothur/trunk/debian: . patches

Tue Feb 25 12:32:42 UTC 2014

Author: tille
Date: 2014-02-25 12:32:42 +0000 (Tue, 25 Feb 2014)
New Revision: 16311

Modified:
   trunk/packages/mothur/trunk/debian/changelog
   trunk/packages/mothur/trunk/debian/patches/makefile.patch
   trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
   trunk/packages/mothur/trunk/debian/patches/spelling.patch
   trunk/packages/mothur/trunk/debian/patches/uchime_hardening.patch
Log:
New upstream version (adapted patches)


Modified: trunk/packages/mothur/trunk/debian/changelog
===================================================================

--- trunk/packages/mothur/trunk/debian/changelog	2014-02-25 12:09:53 UTC (rev 16310)
+++ trunk/packages/mothur/trunk/debian/changelog	2014-02-25 12:32:42 UTC (rev 16311)
@@ -1,3 +1,10 @@
+mothur (1.33.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debian/upstream -> debian/upstream/metadata
+
+ -- Andreas Tille <tille at debian.org>  Tue, 25 Feb 2014 13:31:27 +0100
+
 mothur (1.31.2+dfsg-2) unstable; urgency=low
 
   * Team upload.

Modified: trunk/packages/mothur/trunk/debian/patches/makefile.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/makefile.patch	2014-02-25 12:09:53 UTC (rev 16310)
+++ trunk/packages/mothur/trunk/debian/patches/makefile.patch	2014-02-25 12:32:42 UTC (rev 16311)
@@ -4,7 +4,7 @@
   on all architectures (and trying to set -m64 explicitly fails on ia64).
 --- a/makefile
 +++ b/makefile
-@@ -21,14 +21,15 @@ FORTAN_COMPILER = gfortran
+@@ -20,14 +20,15 @@ FORTAN_COMPILER = gfortran
  FORTRAN_FLAGS = 
  
  # Optimize to level 3:
@@ -22,20 +22,21 @@
  	
  	#if you using cygwin to build Windows the following line
  	#CXX = x86_64-w64-mingw32-g++
-@@ -38,9 +39,11 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
+@@ -37,9 +38,12 @@ ifeq  ($(strip $(64BIT_VERSION)),yes)
  
  	#if you are a linux user use the following line
- 	#CXXFLAGS += -mtune=native -march=native -m64
+ 	#CXXFLAGS += -mtune=native -march=native 
 +	# But not if you are trying to make a generic build for
 +	# packaging, because your binary will end up being specific
 +	# to your processor.
  	
  	CXXFLAGS += -DBIT_VERSION 
--    FORTRAN_FLAGS = -m64
+-	FORTRAN_FLAGS = -m64
++	# FORTRAN_FLAGS = -m64
  endif
  
  
-@@ -120,4 +123,3 @@ install : mothur
+@@ -115,4 +119,3 @@ install : mothur
  clean :
  	@rm -f $(OBJECTS)
  	@rm -f uchime

Modified: trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch	2014-02-25 12:09:53 UTC (rev 16310)
+++ trunk/packages/mothur/trunk/debian/patches/no_lcurses.patch	2014-02-25 12:32:42 UTC (rev 16311)
@@ -3,7 +3,7 @@
 Dscription: There is no need to link against lncurses because its symbols are not used
 --- a/makefile
 +++ b/makefile
-@@ -68,8 +68,7 @@ endif
+@@ -62,8 +62,7 @@ endif
  ifeq  ($(strip $(USEREADLINE)),yes)
      CXXFLAGS += -DUSE_READLINE
      LIBS = \

Modified: trunk/packages/mothur/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/spelling.patch	2014-02-25 12:09:53 UTC (rev 16310)
+++ trunk/packages/mothur/trunk/debian/patches/spelling.patch	2014-02-25 12:32:42 UTC (rev 16311)
@@ -28,7 +28,7 @@
  		return helpString;
 --- a/matrixoutputcommand.cpp
 +++ b/matrixoutputcommand.cpp
-@@ -773,7 +773,7 @@ int MatrixOutputCommand::driver(vector<S
+@@ -777,7 +777,7 @@ int MatrixOutputCommand::driver(vector<S
  			
  			for (int l = 0; l < k; l++) {
  				
@@ -39,17 +39,8 @@
  					subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
 --- a/mgclustercommand.cpp
 +++ b/mgclustercommand.cpp
-@@ -41,7 +41,7 @@ string MGClusterCommand::getHelpString()
- 	try {
- 		string helpString = "";
- 		helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, hard,  method, merge, min, length, penalty and hcluster. The blast parameter is required.\n";
--		helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similiar to the OTUs.\n";
-+		helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similar to the OTUs.\n";
- 		helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
- 		helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
- 		helpString += "The precision parameter's default value is 100. \n";
-@@ -50,7 +50,7 @@ string MGClusterCommand::getHelpString()
- 		helpString += "The length parameter is used to specify the minimum overlap required.  The default is 5.\n";
+@@ -52,7 +52,7 @@ string MGClusterCommand::getHelpString()
+         helpString += "The adjust parameter is used to handle missing distances.  If you set a cutoff, adjust=f by default.  If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method.  Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n";
  		helpString += "The penalty parameter is used to adjust the error rate.  The default is 0.10.\n";
  		helpString += "The merge parameter allows you to shut off merging based on overlaps and just cluster.  By default merge is true, meaning you want to merge.\n";
 -		helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering.  This may be neccessary if your file is too large to fit into RAM. The default is false.\n";
@@ -103,7 +94,7 @@
  		helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
 --- a/trimseqscommand.cpp
 +++ b/trimseqscommand.cpp
-@@ -68,7 +68,7 @@ string TrimSeqsCommand::getHelpString(){
+@@ -69,7 +69,7 @@ string TrimSeqsCommand::getHelpString(){
  		helpString += "The oligos parameter allows you to provide an oligos file.\n";
  		helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
          helpString += "The count parameter allows you to provide a count file with your fasta file.\n";

Modified: trunk/packages/mothur/trunk/debian/patches/uchime_hardening.patch
===================================================================
--- trunk/packages/mothur/trunk/debian/patches/uchime_hardening.patch	2014-02-25 12:09:53 UTC (rev 16310)
+++ trunk/packages/mothur/trunk/debian/patches/uchime_hardening.patch	2014-02-25 12:32:42 UTC (rev 16311)
@@ -4,7 +4,7 @@
 
 --- a/makefile
 +++ b/makefile
-@@ -105,7 +105,9 @@ mothur : fortranSource $(OBJECTS) uchime
+@@ -99,7 +99,9 @@ mothur : fortranSource $(OBJECTS) uchime
  	strip mothur
   
  uchime:


