diff options
Diffstat (limited to 'sci-biology/augustus/files/augustus-2.5.5-sane-build.patch')
| -rw-r--r-- | sci-biology/augustus/files/augustus-2.5.5-sane-build.patch | 156 |
1 files changed, 156 insertions, 0 deletions
diff --git a/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch new file mode 100644 index 000000000000..39cd0762b1c1 --- /dev/null +++ b/sci-biology/augustus/files/augustus-2.5.5-sane-build.patch @@ -0,0 +1,156 @@ + Makefile | 8 +++--- + scripts/Makefile | 6 +++- + scripts/aln2wig/Makefile | 8 +++--- + scripts/compileSpliceCands/Makefile | 6 ++-- + src/Makefile | 43 ++++++++++++++++++---------------- + 5 files changed, 38 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index e23a667..64610c8 100644 +--- a/Makefile ++++ b/Makefile +@@ -3,9 +3,9 @@ + # + + all: +- cd src && ${MAKE} +- cd scripts && ${MAKE} ++ $(MAKE) -C src ++ $(MAKE) -C scripts + + clean: +- cd src && ${MAKE} clean +- cd scripts && ${MAKE} clean ++ $(MAKE) -C src clean ++ $(MAKE) -C scripts clean +diff --git a/scripts/Makefile b/scripts/Makefile +index 6d4dd67..ab6a885 100644 +--- a/scripts/Makefile ++++ b/scripts/Makefile +@@ -1,5 +1,7 @@ + all : +- cd aln2wig && ${MAKE} ++ $(MAKE) -C aln2wig ++ $(MAKE) -C compileSpliceCands + + clean : +- cd aln2wig && ${MAKE} clean ++ $(MAKE) -C aln2wig clean ++ $(MAKE) -C compileSpliceCands +diff --git a/scripts/aln2wig/Makefile b/scripts/aln2wig/Makefile +index 64d09f5..9752980 100644 +--- a/scripts/aln2wig/Makefile ++++ b/scripts/aln2wig/Makefile +@@ -1,10 +1,10 @@ +-CFLAGS := -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic -O2 -ggdb ++CFLAGS += -Wall -Wno-unused-result -Wno-sign-compare -ansi -pedantic + + psl2wig : aln2wig.o +- gcc $(CFLAGS) -o aln2wig aln2wig.o; +- cp aln2wig ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o aln2wig aln2wig.o; ++ cp aln2wig ../../bin/ + psl2wig.o : aln2wig.c +- gcc $(CFLAGS) -c aln2wig.c ++ $(CC) $(CFLAGS) -c aln2wig.c + + all : psl2wig + +diff --git a/scripts/compileSpliceCands/Makefile b/scripts/compileSpliceCands/Makefile +index cddada5..8079791 100644 +--- a/scripts/compileSpliceCands/Makefile ++++ b/scripts/compileSpliceCands/Makefile +@@ -1,8 +1,8 @@ + compileSpliceCands : compileSpliceCands.o list.h list.o +- gcc -o compileSpliceCands compileSpliceCands.o list.o; +-# cp compileSpliceCands ../../bin ++ $(CC) $(CFLAGS) $(LDFLAGS) -o compileSpliceCands compileSpliceCands.o list.o; ++ cp compileSpliceCands ../../bin/ + compileSpliceCands.o : compileSpliceCands.c +- gcc -Wall -pedantic -ansi -c compileSpliceCands.c ++ $(CC) $(CFLAGS) -Wall -pedantic -ansi -c compileSpliceCands.c + + all : compileSpliceCands + +diff --git a/src/Makefile b/src/Makefile +index 71795b6..732b953 100644 +--- a/src/Makefile ++++ b/src/Makefile +@@ -6,8 +6,8 @@ + # a strict signed-only usage strategy to avoid mistakes since we are not warned about this. + # - In the current version, the order of object files in $(OBJS) IS IMPORTANT (see lldouble.hh) + # +-CC = g++ +-CFLAGS := -Wall -Wno-sign-compare -ansi -pedantic -O2 ${CFLAGS} -static # -pg -DDEBUG -g -ggdb -static ++CXX ?= g++ ++CXXFLAGS += -Wall -Wno-sign-compare -ansi -pedantic # -pg -DDEBUG -g -ggdb -static + INCLS = -I../include -I. + LIBS = # -lcwd + OBJS = genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o \ +@@ -18,45 +18,48 @@ TOBJS = commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o # conte + PROGR = augustus etraining consensusFinder curve2hints fastBlockSearch prepareAlign + INFO = cflags + +-all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info ++all: $(OBJS) $(TOBJS) $(DUMOBJS) $(PROGR) info bin + + .SUFFIXES: + .SUFFIXES: .cc .o .so + + .cc.o: +- $(CC) -c $(CFLAGS) -o $@ $< $(INCLS) ++ $(CXX) -c $(CXXFLAGS) -o $@ $< $(INCLS) + +-augustus: augustus.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++bin: $(PROGR) ++ cp $(PROGR) ../bin/ ++ ++augustus: augustus.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp augustus ../bin/ + +-etraining: etraining.cc $(TOBJS) $(OBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++etraining: etraining.o $(TOBJS) $(OBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp etraining ../bin/ + +-evaluate: evaluate.cc $(OBJS) $(DUMOBJS) +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++evaluate: evaluate.o $(OBJS) $(DUMOBJS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-consensusFinder: consensusFinder.cc consensus.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++consensusFinder: consensusFinder.o consensus.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-curve2hints: curve2hints.cc exon_seg.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++curve2hints: curve2hints.o exon_seg.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + +-fastBlockSearch: fastBlockSearch.cc pp_fastBlockSearcher.o \ ++fastBlockSearch: fastBlockSearch.o pp_fastBlockSearcher.o \ + types.o properties.o geneticcode.o pp_profile.o lldouble.o +- $(CC) $(CFLAGS) -o $@ $^ $(INCLS) $(LIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ $(INCLS) $(LIBS) + cp fastBlockSearch ../bin/ + +-prepareAlign: pp_prepare_align.cc +- $(CC) $(CFLAGS) -o $@ $^ ++prepareAlign: pp_prepare_align.o ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ $^ + cp prepareAlign ../bin/ + + info: +- echo "$(CFLAGS)" > $(INFO) ++ echo "$(CXXFLAGS)" > $(INFO) + + clean: +- rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ++ rm -f $(PROGR) $(OBJS) $(DUMOBJS) $(TOBJS) consensus.o exon_seg.o pp_fastBlockSearcher.o $(INFO) ../bin/* + + tidy: clean + rm -f *~ *.o *.rej *.orig ../include/*~ ../include/*.orig ../include/*.rej $(INFO) |