diff options
Diffstat (limited to 'sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch')
| -rw-r--r-- | sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch | 204 |
1 files changed, 0 insertions, 204 deletions
diff --git a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch b/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch deleted file mode 100644 index a710c2d86..000000000 --- a/sci-biology/SOAPdenovo2/files/SOAPdenovo2-r241-Makefile.patch +++ /dev/null @@ -1,204 +0,0 @@ ---- sparsePregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ sparsePregraph/Makefile 2018-04-22 22:07:47.303546845 +0200 -@@ -1,28 +1,28 @@ --CC= g++ -+CXX ?= g++ - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer -+CXXFLAGS ?= -O0 -g -fomit-frame-pointer - else --CFLAGS= -O3 -fomit-frame-pointer -w -+CXXFLAGS ?= -O3 -fomit-frame-pointer -w - endif - --DFLAGS= --OBJS= build_graph.o build_edge.o multi_threads.o \ -- build_preArc.o pregraph_sparse.o io_func.o\ -- global.o convert_soapdenovo.o --PROG= --INCLUDES= -I./inc --SUBDIRS= . --LIBPATH= -L/usr/lib64 --LIBS= -pthread -lz -L./inc -+DFLAGS = -+OBJS = build_graph.o build_edge.o multi_threads.o \ -+ build_preArc.o pregraph_sparse.o io_func.o\ -+ global.o convert_soapdenovo.o -+PROG = -+INCLUDES = -I./inc -+SUBDIRS = . -+LIBPATH = -L/usr/lib64 -+LIBS = -pthread -lz -L./inc - EXTRA_FLAGS= --VERSION = 1.0.3 -+VERSION = 1.0.3 - - ifdef 127mer --CFLAGS += -D_127MER_ -+CXXFLAGS += -D_127MER_ - PROG = pregraph_sparse_127mer.v$(VERSION) - - else --CFLAGS += -D_63MER_ -+CXXFLAGS += -D_63MER_ - PROG = pregraph_sparse_63mer.v$(VERSION) - endif - -@@ -38,22 +38,22 @@ - endif - - ifneq (,$(findstring $(shell uname -m), x86_64)) --CFLAGS += -m64 -+CXXFLAGS += -m64 - endif - - ifneq (,$(findstring $(shell uname -m), ia64)) --CFLAGS += -+CXXFLAGS += - endif - - ifneq (,$(findstring $(shell uname -m), ppc64)) --CFLAGS += -mpowerpc64 -+CXXFLAGS += -mpowerpc64 - endif - - .SUFFIXES:.cpp .o - - .cpp.o: - @printf "Compiling $<... \r" -- @$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $<" -+ @$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< || echo "Error in command: $(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $<" - - all: $(OBJS) - @printf "$(PROG) objects generated. \n" -@@ -66,7 +66,7 @@ - - pregraph_sparse: clean envTest $(OBJS) - @printf "Linking... \r" -- @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) -+ @$(CXX) $(CXXFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) - @printf "$(PROG) compilation done. \n" - - clean: ---- Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ Makefile 2018-04-22 22:09:16.526124921 +0200 -@@ -1,17 +1,17 @@ - MAKEFLAGS += --no-print-directory --CC = g++ -+CXX ?= g++ - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer -+CXXFLAGS ?= -O0 -g -fomit-frame-pointer - else --CFLAGS= -O3 -fomit-frame-pointer -+CXXFLAGS ?= -O3 -fomit-frame-pointer - endif - - SUBDIRS = sparsePregraph standardPregraph fusion --PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion --INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -+PROG = SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion -+INCLUDES = -I./sparsePregraph/inc -I./standardPregraph/inc - --LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc --LIBS= -pthread -lz -lm -+LIBPATH = -L./sparsePregraph/inc -L./standardPregraph/inc -+LIBS = -pthread -lz -lm - EXTRA_FLAGS= - - BIT_ERR = 0 -@@ -25,15 +25,15 @@ - endif - - ifneq (,$(findstring $(shell uname -m), x86_64)) --CFLAGS += -m64 -+CXXFLAGS += -m64 - endif - - ifneq (,$(findstring $(shell uname -m), ia64)) --CFLAGS += -+CXXFLAGS += - endif - - ifneq (,$(findstring $(shell uname -m), ppc64)) --CFLAGS += -mpowerpc64 -+CXXFLAGS += -mpowerpc64 - endif - - -@@ -46,20 +46,20 @@ - SOAPdenovo-63mer: - @cd sparsePregraph;make 63mer=1 debug=1;cd ..; - @cd standardPregraph;make 63mer=1 debug=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer - SOAPdenovo-127mer: - @cd sparsePregraph;make 127mer=1 debug=1;cd ..; - @cd standardPregraph;make 127mer=1 debug=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer - else - SOAPdenovo-63mer: - @cd sparsePregraph;make 63mer=1;cd ..; - @cd standardPregraph;make 63mer=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer - SOAPdenovo-127mer: - @cd sparsePregraph;make 127mer=1;cd ..; - @cd standardPregraph;make 127mer=1;cd ..; -- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CXX) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer - endif - - clean: ---- standardPregraph/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ standardPregraph/Makefile 2018-04-22 22:10:33.108337752 +0200 -@@ -5,13 +5,13 @@ - # - ################################### - --CC= gcc -+CC ?= gcc - GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4) - GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4) - ifdef debug --CFLAGS= -O0 -g -fomit-frame-pointer #-msse4.2 -+CFLAGS ?= -O0 -g -fomit-frame-pointer #-msse4.2 - else --CFLAGS= -O3 -fomit-frame-pointer -w #-msse4.2 -+CFLAGS ?= -O3 -fomit-frame-pointer -w #-msse4.2 - endif - DFLAGS= - OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \ -@@ -24,12 +24,12 @@ - prlRead2path.o prlReadFillGap.o read2scaf.o readInterval.o stack.o\ - readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \ - cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o --PROG= SOAPdenovo-63mer --INCLUDES= -Iinc --SUBDIRS= . --LIBPATH= -L/lib64 -L/usr/lib64 -L./inc --LIBS= -pthread -lz -lm --EXTRA_FLAGS= -+PROG = SOAPdenovo-63mer -+INCLUDES = -Iinc -+SUBDIRS = . -+LIBPATH = -L./inc -+LIBS = -pthread -lz -lm -+EXTRA_FLAGS = - - BIT_ERR = 0 - ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64)) ---- fusion/Makefile.ori 2017-01-03 21:34:59.000000000 +0100 -+++ fusion/Makefile 2018-04-22 22:11:21.209727636 +0200 -@@ -6,8 +6,8 @@ - libdir = - mandir = - --CC = gcc --CCOPT = -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w -+CC ?= gcc -+CCOPT ?= -O3 -fprefetch-loop-arrays -funroll-loops -fomit-frame-pointer -w - LIBS = -lm -lpthread - INCDIRS = -Iinc/ - CFLAGS = ${CCOPT} ${INCDIRS} |