Author: tille
Date: 2011-04-05 13:54:26 +0000 (Tue, 05 Apr 2011)
New Revision: 6463

Added:
   trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch
   trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch
Removed:
   trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff
Modified:
   trunk/packages/velvet/trunk/debian/changelog
   trunk/packages/velvet/trunk/debian/compat
   trunk/packages/velvet/trunk/debian/control
   trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch
   trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch
   trunk/packages/velvet/trunk/debian/patches/series
   trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch
   trunk/packages/velvet/trunk/debian/rules
Log:
New upstream version, adapted patches to this new version; debhlper 8; prepare 
building of meta-velvet (whatever this is - needs to be clarified); TODO: 
exclude contrib/MetaVelvet-v0.3.1 directory from binary package ... and clarify 
the sense of meta-velvet (separate binary package????)


Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog        2011-04-05 13:51:47 UTC 
(rev 6462)
+++ trunk/packages/velvet/trunk/debian/changelog        2011-04-05 13:54:26 UTC 
(rev 6463)
@@ -1,3 +1,16 @@
+velvet (1.1.02~nozlibcopy-1) UNRELEASED; urgency=low
+
+  * New upstream version
+    upgraded patches, tweak $(LIBS) into Z_LIB_FILES variable
+    of Makefile which makes patch more robust against upstream
+    changes
+  * Debhelper 8 (control+compat)
+  * debian/rules: Leave out Z_LIB_FILES in parameter list
+  * debian/patches/meta-velvet.patch: Enable building meta-velvet
+    in contrib
+
+ -- Andreas Tille <ti...@debian.org>  Tue, 05 Apr 2011 14:18:24 +0200
+
 velvet (1.0.18~nozlibcopy-1) unstable; urgency=low
 
   * New upstream version

Modified: trunk/packages/velvet/trunk/debian/compat
===================================================================
--- trunk/packages/velvet/trunk/debian/compat   2011-04-05 13:51:47 UTC (rev 
6462)
+++ trunk/packages/velvet/trunk/debian/compat   2011-04-05 13:54:26 UTC (rev 
6463)
@@ -1 +1 @@
-7
+8

Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control  2011-04-05 13:51:47 UTC (rev 
6462)
+++ trunk/packages/velvet/trunk/debian/control  2011-04-05 13:54:26 UTC (rev 
6463)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <ple...@debian.org>,
  Andreas Tille <ti...@debian.org>
-Build-Depends: cdbs, debhelper (>= 7.1), zlib1g-dev, help2man, quilt
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev, help2man, quilt
 Standards-Version: 3.9.1
 Homepage: http://www.ebi.ac.uk/~zerbino/velvet/
 Vcs-Browser: 
http://svn.debian.org/wsvn/debian-med/trunk/packages/velvet/trunk/?rev=0&sc=0

Modified: trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch      
2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/fix-perl-path.patch      
2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,8 +1,8 @@
 Description: s?/usr/local/perl?/usr/perl?
 Author: Andreas Tille <ti...@debian.org>
 Forwarded: No
---- velvet_1.0.15~nozlibcopy.orig/contrib/select_paired/select_paired.pl
-+++ velvet_1.0.15~nozlibcopy/contrib/select_paired/select_paired.pl
+--- velvet_1.1.02~nozlibcopy.orig/contrib/select_paired/select_paired.pl
++++ velvet_1.1.02~nozlibcopy/contrib/select_paired/select_paired.pl
 @@ -1,4 +1,4 @@
 -#!/usr/local/bin/perl -w
 +#!/usr/bin/perl -w

Modified: trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch       
2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/include_debians_zlib.patch       
2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,9 +1,9 @@
 Description: Use the zlib distributed by Debian, not the one in 
third-party/zlib-1.2.3/.
 Author: Charles Plessy <ple...@debian.org>
 Forwarded: no
---- velvet_1.0.02~nozlibcopy.orig/src/readSet.c
-+++ velvet_1.0.02~nozlibcopy/src/readSet.c
-@@ -32,7 +32,7 @@
+--- velvet_1.1.02~nozlibcopy.orig/src/readSet.c
++++ velvet_1.1.02~nozlibcopy/src/readSet.c
+@@ -33,7 +33,7 @@
  #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
  #include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
  #else

Deleted: trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff        
2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/ld-as-needed.diff        
2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,53 +0,0 @@
-Author: Matthias Klose <d...@ubuntu.com>
-Description: Enable ld --as-needed (basically by using LIBS instead of LDFLAGS.
- Adding libraries in LDFLAGS is almost always a bad idea.
-Closes: #607582
-
-Index: velvet-1.0.15~nozlibcopy/Makefile
-===================================================================
---- velvet-1.0.15~nozlibcopy.orig/Makefile     2010-12-19 21:09:32.228228999 
+0000
-+++ velvet-1.0.15~nozlibcopy/Makefile  2010-12-19 21:10:14.818229004 +0000
-@@ -1,7 +1,7 @@
- CC = gcc
- CFLAGS = -Wall
- DEBUG = -g
--LDFLAGS = -lm
-+LIBS = -lm
- OPT = -O3
- MAXKMERLENGTH=31
- CATEGORIES=2
-@@ -44,26 +44,26 @@
-       cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
- 
- velveth : obj 
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o 
obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o 
obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth obj/tightString.o 
obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o 
obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o $(Z_LIB_FILES) $(LIBS)
- 
- 
- velvetg : obj
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o 
obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o 
obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o 
obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o 
obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o 
obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o 
obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o 
obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg obj/tightString.o 
obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o 
obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o 
obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o 
obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o 
obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o 
obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o 
obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS)
- 
- debug : override DEF := $(DEF) -D DEBUG 
- debug : cleanobj obj/dbg
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o 
obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o 
obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o 
obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o 
obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o 
obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o 
obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o 
obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o 
obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o 
obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o 
obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o 
obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth obj/dbg/tightString.o 
obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o 
obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o 
obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg obj/dbg/tightString.o 
obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o 
obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o 
obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o 
obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o 
obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o 
obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o 
obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o 
obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) 
$(LIBS)
- 
- color : override DEF := $(DEF) -D COLOR
- color : cleanobj obj_de
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o 
obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o 
obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o 
$(Z_LIB_FILES)
--      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o 
obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o 
obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o 
obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o 
obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o 
obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o 
obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o 
obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velveth_de obj/tightString.o 
obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o 
obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o 
$(Z_LIB_FILES) $(LIBS)
-+      $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o velvetg_de obj/tightString.o 
obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o 
obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o 
obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o 
obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o 
obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o 
obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o 
obj/kmerOccurenceTable.o obj/allocArray.o $(Z_LIB_FILES) $(LIBS)
- 
- colordebug : override DEF := $(DEF) -D COLOR -D DEBUG
- colordebug : cleanobj obj/dbg_de
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o 
obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o 
obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o 
obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
--      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o 
obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o 
obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o 
obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o 
obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o 
obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o 
obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o 
obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o 
obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velveth_de obj/dbg/tightString.o 
obj/dbg/run.o obj/dbg/recycleBin.o obj/dbg/splay.o obj/dbg/splayTable.o 
obj/dbg/readSet.o obj/dbg/crc.o obj/dbg/utility.o obj/dbg/kmer.o 
obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) $(LIBS)
-+      $(CC) $(CFLAGS) $(LDFLAGS) $(DEBUG) -o velvetg_de obj/dbg/tightString.o 
obj/dbg/graph.o obj/dbg/run2.o obj/dbg/fibHeap.o obj/dbg/fib.o 
obj/dbg/concatenatedGraph.o obj/dbg/passageMarker.o obj/dbg/graphStats.o 
obj/dbg/correctedGraph.o obj/dbg/dfib.o obj/dbg/dfibHeap.o obj/dbg/recycleBin.o 
obj/dbg/readSet.o obj/dbg/shortReadPairs.o obj/dbg/scaffold.o 
obj/dbg/locallyCorrectedGraph.o obj/dbg/graphReConstruction.o obj/dbg/roadMap.o 
obj/dbg/preGraph.o obj/dbg/preGraphConstruction.o 
obj/dbg/concatenatedPreGraph.o obj/dbg/readCoherentGraph.o obj/dbg/utility.o 
obj/dbg/kmer.o obj/dbg/kmerOccurenceTable.o obj/dbg/allocArray.o $(Z_LIB_FILES) 
$(LIBS)
- 
- objdir:
-       mkdir -p obj

Added: trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch               
                (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/ld-as-needed.patch       
2011-04-05 13:54:26 UTC (rev 6463)
@@ -0,0 +1,25 @@
+Author: Matthias Klose <d...@ubuntu.com>
+Description: Enable ld --as-needed (basically by using LIBS instead of LDFLAGS.
+ Adding libraries in LDFLAGS is almost always a bad idea.
+Closes: #607582
+
+--- velvet_1.1.02~nozlibcopy.orig/Makefile
++++ velvet_1.1.02~nozlibcopy/Makefile
+@@ -1,14 +1,15 @@
+ CC = gcc
+ CFLAGS = -Wall
+ DEBUG = -g
+-LDFLAGS = -lm
++LIBS = -lm
+ OPT = -O3
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+ 
+ Z_LIB_DIR=third-party/zlib-1.2.3
+-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
++# In Debian we do not use local zlib copy, however, we need to add $(LIBS) to 
compile options and thus we tweak this in here:
++Z_LIB_FILES=$(LIBS)
+ 
+ # Mac OS users: uncomment the following lines
+ # Z_LIB_FILES=

Added: trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch                
                (rev 0)
+++ trunk/packages/velvet/trunk/debian/patches/meta-velvet.patch        
2011-04-05 13:54:26 UTC (rev 6463)
@@ -0,0 +1,50 @@
+--- velvet_1.1.02~nozlibcopy.orig/contrib/MetaVelvet-v0.3.1/Makefile
++++ velvet_1.1.02~nozlibcopy/contrib/MetaVelvet-v0.3.1/Makefile
+@@ -1,14 +1,15 @@
+ CC = gcc
+ CFLAGS = -Wall
+ DEBUG = -g
+-LDFLAGS = -lm
++LIBS = -lm
+ OPT = -O3
+ MAXKMERLENGTH=31
+ CATEGORIES=2
+ DEF = -D MAXKMERLENGTH=$(MAXKMERLENGTH) -D CATEGORIES=$(CATEGORIES)
+ 
+ Z_LIB_DIR=../../third-party/zlib-1.2.3
+-Z_LIB_FILES=$(Z_LIB_DIR)/*.o
++# In Debian we do not use local zlib copy, however, we need to add $(LIBS) to 
compile options and thus we tweak this in here:
++Z_LIB_FILES=$(LIBS)
+ 
+ # Mac OS users: uncomment the following lines
+ # Z_LIB_FILES=
+@@ -21,7 +22,7 @@
+ OBJ = obj/tightString.o obj/run.o obj/splay.o obj/splayTable.o obj/graph.o 
obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o 
obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o 
obj/recycleBin.o obj/readSet.o obj/shortReadPairs.o obj/locallyCorrectedGraph.o 
obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o 
obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o 
obj/crc.o obj/utility.o obj/kmer.o obj/scaffold.o
+ OBJDBG = $(subst obj,obj/dbg,$(OBJ))
+ 
+-default : cleanobj zlib obj meta-velveth meta-velvetg
++default : cleanobj obj meta-velveth meta-velvetg
+ 
+ clean :
+       -rm obj/*.o obj/dbg/*.o ./meta-velvet* 
+@@ -31,7 +32,8 @@
+       -rm obj/*.o obj/dbg/*.o 
+ 
+ zlib : 
+-      cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++      # cd $(Z_LIB_DIR); ./configure; make; rm minigzip.o; rm example.o
++      echo "Use Debian packaged version of zlib"
+ 
+ meta-velveth : obj 
+       $(CC) $(CFLAGS) $(OPT) $(LDFLAGS) -o meta-velveth obj/tightString.o 
obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/crc.o 
obj/utility.o obj/kmer.o $(Z_LIB_FILES)
+--- velvet_1.1.02~nozlibcopy.orig/contrib/MetaVelvet-v0.3.1/src/readSet.c
++++ velvet_1.1.02~nozlibcopy/contrib/MetaVelvet-v0.3.1/src/readSet.c
+@@ -32,7 +32,7 @@
+ #if defined(_WIN32) || defined(__WIN32__) || defined(WIN32)
+ #include "../third-party/zlib-1.2.3/Win32/include/zlib.h"
+ #else
+-#include "../third-party/zlib-1.2.3/zlib.h"
++#include <zlib.h>
+ #endif
+ 
+ #if defined(MSDOS) || defined(OS2) || defined(WIN32) || defined(__CYGWIN__)

Modified: trunk/packages/velvet/trunk/debian/patches/series
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/series   2011-04-05 13:51:47 UTC 
(rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/series   2011-04-05 13:54:26 UTC 
(rev 6463)
@@ -1,4 +1,5 @@
 include_debians_zlib.patch
 shuffleSequences_fasta.patch
 fix-perl-path.patch
-ld-as-needed.diff
+ld-as-needed.patch
+meta-velvet.patch

Modified: 
trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch
===================================================================
--- trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch     
2011-04-05 13:51:47 UTC (rev 6462)
+++ trunk/packages/velvet/trunk/debian/patches/shuffleSequences_fasta.patch     
2011-04-05 13:54:26 UTC (rev 6463)
@@ -1,8 +1,8 @@
 Description: Scripts need to specify interpreter in the first line
 Author: Andreas Tille <ti...@debian.org>
 Forwarded: not yet
---- 
velvet_1.0.02~nozlibcopy.orig/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
-+++ 
velvet_1.0.02~nozlibcopy/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
+--- 
velvet_1.1.02~nozlibcopy.orig/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
++++ 
velvet_1.1.02~nozlibcopy/contrib/shuffleSequences_fasta/shuffleSequences_fasta.py
 @@ -1,3 +1,4 @@
 +#!/usr/bin/python
  import sys

Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules    2011-04-05 13:51:47 UTC (rev 
6462)
+++ trunk/packages/velvet/trunk/debian/rules    2011-04-05 13:54:26 UTC (rev 
6463)
@@ -14,10 +14,10 @@
 
 pkg=velvet
 
-DEB_MAKE_BUILD_TARGET = obj velveth velvetg Z_LIB_FILES='' LIBS='-lm -lz' 
OPT=''
+DEB_MAKE_BUILD_TARGET = obj velveth velvetg LIBS='-lm -lz' OPT=''
 
 build/velvet::
-       make color CFLAGS='$(CFLAGS)' Z_LIB_FILES='' LIBS='-lm -lz' OPT=''
+       make color CFLAGS='$(CFLAGS)' LIBS='-lm -lz' OPT=''
        mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
        help2man --no-info --name="simple hashing program" \
                 $(CURDIR)/velveth > 
$(CURDIR)/debian/$(pkg)/usr/share/man/man1/velveth.1


_______________________________________________
debian-med-commit mailing list
debian-med-commit@lists.alioth.debian.org
http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit

Reply via email to