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|
Description: propagate Debian standard build flags.
Author: Étienne Mollier <emollier@debian.org>
Forwarded: not-needed
Last-Update: 2022-07-09
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- primer3.orig/src/Makefile
+++ primer3/src/Makefile
@@ -52,9 +52,9 @@
WINMAKE=mingw32-make
LDLIBS = -lm
-AR = ar
-CC = gcc
-CXX = g++
+AR ?= ar
+CC ?= gcc
+CXX ?= g++
O_OPTS = -O2
CC_OPTS = -g -Wall
P_DEFINES =
@@ -153,108 +153,108 @@
$(RANLIB) $@
$(LIBOLIGOTM_LIB): oligotm.o
- $(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
$(LIBAMPTM): amplicontm.o
$(AR) rv $@ amplicontm.o
$(RANLIB) $@
$(LIBAMPTM_LIB): amplicontm.o
- $(CC) -shared -W1,-soname,libamplicontm.so.1 -o $(LIBAMPTM_DYN) amplicontm.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libamplicontm.so.1 -o $(LIBAMPTM_DYN) amplicontm.o
$(LIBDPAL): dpal_primer.o
$(AR) rv $@ dpal_primer.o
$(RANLIB) $@
$(LIBDPAL_DYN): dpal_primer.o
- $(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
$(LIBTHAL): thal_primer.o
$(AR) rv $@ thal_primer.o
$(RANLIB) $@
$(LIBTHAL_DYN): thal_primer.o
- $(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
$(LIBTHALPARA): thal_parameters.o
$(AR) rv $@ thal_parameters.o
$(RANLIB) $@
$(LIBTHALPARA_DYN): thal_parameters.o
- $(CC) -shared -W1,-soname,libthalpara.so.1 -o $(LIBTHALPARA_DYN_LIB) thal_parameters.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libthalpara.so.1 -o $(LIBTHALPARA_DYN_LIB) thal_parameters.o
$(LIBPRIMER3): libprimer3.o p3_seq_lib.o
$(AR) rv $@ libprimer3.o p3_seq_lib.o
$(RANLIB) $@
$(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) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
$(LIBMASKER): masker.o
$(AR) rv $@ masker.o
$(RANLIB) $@
$(LIBMASKER_DYN): masker.o
- $(CC) -shared -W1,-soname,libmasker.so.1 -o $(LIBMASKER_DYN) masker.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) -shared $(LDFLAGS) -W1,-soname,libmasker.so.1 -o $(LIBMASKER_DYN) masker.o
$(PRIMER_EXE): $(PRIMER_OBJECTS)
- $(CXX) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
libprimer3.o: libprimer3.cc libprimer3.h p3_seq_lib.h dpal.h thal.h thal_parameters.h oligotm.h
- $(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ libprimer3.cc
+ $(CXX) $(CPPFLAGS) -c $(CXXFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ libprimer3.cc
$(NTDPAL_EXE): ntdpal_main.o dpal.o
- $(CC) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
$(NTTHAL_EXE): thal_main.o thal.o thal_parameters.o
- $(CC) $(LDFLAGS) -o $@ thal_main.o thal.o thal_parameters.o $(LDLIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ thal_main.o thal.o thal_parameters.o $(LDLIBS)
$(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
- $(CC) $(CFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
$(AMPLICONTM_EXE): amplicontm_main.c amplicontm.h $(LIBAMPTM)
- $(CC) $(CFLAGS) -o $@ amplicontm_main.c $(LIBAMPTM) $(LIBOPTS) $(LDLIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ amplicontm_main.c $(LIBAMPTM) $(LIBOPTS) $(LDLIBS)
$(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
- $(CC) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
$(MASKER_EXE): masker_main.c $(LIBRARIES)
- $(CXX) $(CXXFLAGS) -lstdc++ -o $@ masker_main.c $(LIBRARIES) $(LIBOPTS) $(LDLIBS)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) -lstdc++ $(LDFLAGS) -o $@ masker_main.c $(LIBRARIES) $(LIBOPTS) $(LDLIBS)
read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h thal_parameters.h p3_seq_lib.h
- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ read_boulder.c
print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h
- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ print_boulder.c
dpal.o: dpal.c dpal.h
- $(CC) -c $(CFLAGS) -o $@ dpal.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -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 thal_parameters.h
- $(CC) -c $(CFLAGS) -ffloat-store -o $@ thal.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) -ffloat-store $(LDFLAGS) -o $@ thal.c
thal_parameters.o: thal_parameters.c thal_parameters.h thal.h
- $(CC) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal_parameters.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) -ffloat-store $(P_DEFINES) $(LDFLAGS) -o $@ thal_parameters.c
p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
- $(CC) -c $(CFLAGS) -o $@ p3_seq_lib.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -o $@ p3_seq_lib.c
dpal_primer.o: dpal.c dpal.h
- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ dpal.c
thal_primer.o: thal.c thal.h thal_parameters.h
- $(CC) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) -ffloat-store $(P_DEFINES) $(LDFLAGS) -o $@ thal.c
format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h
- $(CC) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) -o $@ format_output.c
ntdpal_main.o: ntdpal_main.c dpal.h
- $(CC) -c $(CC_OPTS) -o $@ ntdpal_main.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(CC_OPTS) $(LDFLAGS) -o $@ ntdpal_main.c
thal_main.o: thal_main.c thal.h thal_parameters.h
- $(CC) -c $(CFLAGS) -o $@ thal_main.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -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
@@ -263,10 +263,10 @@
oligotm.o: oligotm.c oligotm.h
primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h thal_parameters.h oligotm.h format_output.h print_boulder.h read_boulder.h
- $(CC) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) primer3_boulder_main.c
masker.o: masker.c masker.h libprimer3.h
- $(CC) -c $(CFLAGS) $(P_DEFINES) masker.c
+ $(CC) -c $(CPPFLAGS) $(CFLAGS) $(P_DEFINES) $(LDFLAGS) masker.c
primer_test: test
|
