[med-svn] r17015 - trunk/packages/discosnp/trunk/debian/patches

[Olivier Sallou]

Author: osallou
Date: 2014-05-29 13:01:27 +0000 (Thu, 29 May 2014)
New Revision: 17015

Modified:
   trunk/packages/discosnp/trunk/debian/patches/fix_build
Log:
update patch for new release

Modified: trunk/packages/discosnp/trunk/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-05-29 12:51:19 UTC (rev 17014)
+++ trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-05-29 13:01:27 UTC (rev 17015)
@@ -4,8 +4,10 @@
 Forwarded: no
 Author: Olivier Sallou <osallou at debian.org>
 Last-Updated: 2014-02-01
---- a/kissnp2/makefile
-+++ b/kissnp2/makefile
+Index: discoSnp/kissnp2/makefile
+===================================================================
+--- discoSnp.orig/kissnp2/makefile
++++ discoSnp/kissnp2/makefile
 @@ -33,7 +33,10 @@
  #knowledge of the CeCILL license and that you accept its terms.
  
@@ -18,7 +20,7 @@
  #CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -DDONTMARK
  SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp SNP.cpp filter.cpp IterativeExtensions.cpp commons.cpp
  EXEC=kissnp2
-@@ -41,7 +44,7 @@
+@@ -41,7 +44,7 @@ OBJ= $(SRC:.cpp=.o)
  all: $(EXEC)
  
  ifeq ($(prof),1)
@@ -27,7 +29,7 @@
  endif
  ifeq ($(deb),1)
   CFLAGS+=-O0 -DASSERTS -g -lz 
-@@ -79,7 +82,7 @@
+@@ -79,7 +82,7 @@ endif
  all: $(EXEC)
  
  kissnp2:  $(OBJ) kissnp2.cpp
@@ -36,9 +38,11 @@
  
  %.o: %.cpp %.h
  	$(CC) -o $@ -c $< $(CFLAGS)
---- a/kissreads/Makefile
-+++ b/kissreads/Makefile
-@@ -19,9 +19,10 @@
+Index: discoSnp/kissreads/Makefile
+===================================================================
+--- discoSnp.orig/kissreads/Makefile
++++ discoSnp/kissreads/Makefile
+@@ -19,9 +19,10 @@ CC		=gcc
  
  # optimized flags
  
@@ -51,7 +55,7 @@
  
  ## debug flags
  
-@@ -49,7 +50,7 @@
+@@ -49,7 +50,7 @@ all: $(ALL)
  	@echo "#################"
  
  kissreads: $(OBJ) 
@@ -60,21 +64,23 @@
  
  
  kissReads.o: $(INCLDIR)coherence_algorithm.h  $(INCLDIR)couple.h $(INCLDIR)extension_algorithm.h $(INCLDIR)fragment_info.h  $(INCLDIR)libchash.h  $(INCLDIR)outputs.h $(INCLDIR)commons.h $(INCLDIR)extending_fragment.h $(INCLDIR)fragment_index.h $(INCLDIR)hash.h $(INCLDIR)list.h $(INCLDIR)tree.h
---- a/minia/makefile
-+++ b/minia/makefile
+Index: discoSnp/minia/makefile
+===================================================================
+--- discoSnp.orig/minia/makefile
++++ discoSnp/minia/makefile
 @@ -1,5 +1,7 @@
  CC=g++
--CFLAGS = -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
+-CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
 +CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
 +CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -D_FILE_OFFSET_BITS=64
 +LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
  SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
  EXEC=minia
  OBJ= $(SRC:.cpp=.o)
-@@ -60,7 +62,7 @@
- all: $(EXEC)
+@@ -61,7 +63,7 @@ all:
+ 	$(MAKE) $(EXEC)
  
- minia: clean $(OBJ) Minia.cpp
+ minia: $(OBJ) Minia.cpp
 -	$(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
 +	$(CC) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz