[med-svn] r16635 - in trunk/packages/discosnp/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2014-04-09 12:52:52 +0000 (Wed, 09 Apr 2014)
New Revision: 16635

Modified:
   trunk/packages/discosnp/trunk/debian/changelog
   trunk/packages/discosnp/trunk/debian/patches/fix_build
Log:
new upstream release 1.2.1

Modified: trunk/packages/discosnp/trunk/debian/changelog
===================================================================
--- trunk/packages/discosnp/trunk/debian/changelog	2014-04-09 11:31:20 UTC (rev 16634)
+++ trunk/packages/discosnp/trunk/debian/changelog	2014-04-09 12:52:52 UTC (rev 16635)
@@ -1,3 +1,9 @@
+discosnp (1.2.1-1) UNRELEASED; urgency=low
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 09 Apr 2014 14:41:03 +0200
+
 discosnp (1.0.1-3) unstable; urgency=low
 
   * d/rules: FTBS fix help2man command

Modified: trunk/packages/discosnp/trunk/debian/patches/fix_build
===================================================================
--- trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-04-09 11:31:20 UTC (rev 16634)
+++ trunk/packages/discosnp/trunk/debian/patches/fix_build	2014-04-09 12:52:52 UTC (rev 16635)
@@ -4,24 +4,54 @@
 Forwarded: no
 Author: Olivier Sallou <osallou at debian.org>
 Last-Updated: 2014-02-01
+--- a/kissnp2/makefile
++++ b/kissnp2/makefile
+@@ -33,7 +33,10 @@
+ #knowledge of the CeCILL license and that you accept its terms.
+ 
+ CC=g++
+-CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
++CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
++LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
++
+ #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 @@
+ all: $(EXEC)
+ 
+ ifeq ($(prof),1)
+- CFLAGS=-O3 -pg -lz
++ CFLAGS= $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -pg -lz
+ endif
+ ifeq ($(deb),1)
+  CFLAGS+=-O0 -DASSERTS -g -lz 
+@@ -79,7 +82,7 @@
+ all: $(EXEC)
+ 
+ kissnp2:  $(OBJ) kissnp2.cpp
+-	$(CC) -o $@ $^ $(CFLAGS) 
++	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
+ 
+ %.o: %.cpp %.h
+ 	$(CC) -o $@ -c $< $(CFLAGS)
 --- a/kissreads/Makefile
 +++ b/kissreads/Makefile
-@@ -19,9 +19,12 @@
+@@ -19,9 +19,10 @@
  
  # optimized flags
  
--CFLAGS=-Wall -O3 -lz -fopenmp
+-CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§
 +CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
 +CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
 +LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
-+
-+
  CFLAGS+=$(MYFLAGS)
--LDFLAGS+=-Wall -lm -O3 -lz -fopenmp
+-LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
  
  ## debug flags
  
-@@ -49,7 +52,7 @@
+@@ -49,7 +50,7 @@
  	@echo "#################"
  
  kissreads: $(OBJ) 
@@ -32,18 +62,16 @@
  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 $(INCLDIR)tree.h
 --- a/minia/makefile
 +++ b/minia/makefile
-@@ -1,5 +1,9 @@
+@@ -1,5 +1,7 @@
  CC=g++
--CFLAGS = -O4
-+
+-CFLAGS = -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
 +CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4
++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 +64,7 @@
+@@ -60,7 +62,7 @@
  all: $(EXEC)
  
  minia: clean $(OBJ) Minia.cpp
@@ -52,35 +80,3 @@
  
  %.o: %.cpp %.h
  	$(CC) -o $@ -c $< $(CFLAGS)
---- a/kissnp2/makefile
-+++ b/kissnp2/makefile
-@@ -33,7 +33,10 @@
- #knowledge of the CeCILL license and that you accept its terms.
- 
- CC=g++
--CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
-+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
-+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-+
- #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 @@
- all: $(EXEC)
- 
- ifeq ($(prof),1)
-- CFLAGS=-O3 -pg -lz
-+ CFLAGS= $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -pg -lz
- endif
- ifeq ($(deb),1)
-  CFLAGS+=-O0 -DASSERTS -g -lz 
-@@ -79,7 +82,7 @@
- all: $(EXEC)
- 
- kissnp2:  $(OBJ) kissnp2.cpp
--	$(CC) -o $@ $^ $(CFLAGS) 
-+	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
- 
- %.o: %.cpp %.h
- 	$(CC) -o $@ -c $< $(CFLAGS)