diff options
Diffstat (limited to 'sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch')
| -rw-r--r-- | sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch | 173 |
1 files changed, 173 insertions, 0 deletions
diff --git a/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch new file mode 100644 index 000000000000..8f9bf4042758 --- /dev/null +++ b/sci-biology/primer3/files/primer3-2.3.7-buildsystem.patch @@ -0,0 +1,173 @@ +--- a/src/Makefile ++++ b/src/Makefile +@@ -52,15 +52,13 @@ + WINMAKE=mingw32-make + + LDLIBS = -lm +-AR = ar +-CC = gcc +-CPP = g++ +-O_OPTS = -O2 +-CC_OPTS = -g -Wall -D__USE_FIXED_PROTOTYPES__ +-P_DEFINES = +- +-CFLAGS = $(CC_OPTS) $(O_OPTS) +-LDFLAGS = -g ++O_OPTS ?= ++CC_OPTS ?= -Wall -D__USE_FIXED_PROTOTYPES__ ++P_DEFINES ?= ++ ++CFLAGS += $(CC_OPTS) $(O_OPTS) ++CXXFLAGS += $(CC_OPTS) $(O_OPTS) ++LDFLAGS += + # Note, for profiling, use + # make O_OPTS='-pg -O0' LDFLAGS='-g -pg' + +@@ -92,7 +90,6 @@ + LIBPRIMER3_DYN = libprimer3.so.1.0.0 + LIBRARIES = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) + DYNLIBS = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN) +-RANLIB = ranlib + + PRIMER_OBJECTS1=primer3_boulder_main.o\ + format_output.o\ +@@ -119,93 +116,89 @@ + ifeq ($(TESTOPTS),--windows) + cd ..\test & $(WINMAKE) clean TESTOPTS=$(TESTOPTS) + else +- cd ../test/; make clean ++ cd ../test/ && $(MAKE) clean + endif + + $(LIBOLIGOTM): oligotm.o +- $(AR) rv $@ oligotm.o +- $(RANLIB) $@ ++ $(AR) rcs $@ oligotm.o + + $(LIBOLIGOTM_LIB): oligotm.o +- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o + + $(LIBDPAL): dpal_primer.o +- $(AR) rv $@ dpal_primer.o +- $(RANLIB) $@ ++ $(AR) rcs $@ dpal_primer.o + + $(LIBDPAL_DYN): dpal_primer.o +- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o + + $(LIBTHAL): thal_primer.o +- $(AR) rv $@ thal_primer.o +- $(RANLIB) $@ ++ $(AR) rcs $@ thal_primer.o + + $(LIBTHAL_DYN): thal_primer.o +- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o + + $(LIBPRIMER3): libprimer3.o p3_seq_lib.o +- $(AR) rv $@ libprimer3.o p3_seq_lib.o +- $(RANLIB) $@ ++ $(AR) rcs $@ libprimer3.o p3_seq_lib.o + + $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o +- $(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o ++ $(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o + + $(PRIMER_EXE): $(PRIMER_OBJECTS) +- $(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS) + + libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h +- $(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c ++ $(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c + + $(NTDPAL_EXE): ntdpal_main.o dpal.o +- $(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o ++ $(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o + + $(NTTHAL_EXE): thal_main.o thal.o +- $(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) ++ $(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS) + + $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM) +- $(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS) + + $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o +- $(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) ++ $(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS) + + read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c + + print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c + + dpal.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) -o $@ dpal.c + + # We use '-ffloat-store' on windows to prevent undesirable + # precision which may lead to differences in floating point results. + thal.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c + + p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h +- $(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c ++ $(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c + + dpal_primer.o: dpal.c dpal.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c + + thal_primer.o: thal.c thal.h +- $(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c ++ $(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c + + format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c + + ntdpal_main.o: ntdpal_main.c dpal.h +- $(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c + + thal_main.o: thal_main.c thal.h +- $(CPP) -c $(CFLAGS) -o $@ thal_main.c ++ $(CXX) -c $(CXXFLAGS) -o $@ thal_main.c + # We use CC_OPTS above rather than CFLAGS because + # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2 + + oligotm.o: oligotm.c oligotm.h + + primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h +- $(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c ++ $(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c + + primer_test: test + +@@ -213,7 +206,7 @@ + ifeq ($(TESTOPTS),--windows) + cd ..\test & $(WINMAKE) TESTOPTS=$(TESTOPTS) + else +- cd ../test; make test ++ cd ../test && $(MAKE) test + endif + + # ====================================================================== +--- a/test/Makefile ++++ b/test/Makefile +@@ -86,7 +86,7 @@ + ifeq ($(TESTOPTS),--windows) + cd ..\src & $(WINMAKE) + else +- cd ../src; make ++ cd ../src && $(MAKE) + endif + + clean: |