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diff -ur vcftools_0.1.12b.orig/cpp/Makefile vcftools_0.1.12b/cpp/Makefile
--- vcftools_0.1.12b.orig/cpp/Makefile 2014-08-01 21:11:22.000000000 +0200
+++ vcftools_0.1.12b/cpp/Makefile 2015-04-03 17:24:38.830781049 +0200
@@ -3,8 +3,8 @@
# ($Revision: 1.1 $)
# Compiler
-CC = gcc
-CPP = g++
+CC ?= gcc
+CPP ?= g++
# Output executable
EXECUTABLE = vcftools
# Flag used to turn on compilation of PCA routines
@@ -12,9 +12,9 @@
VCFTOOLS_PCA = 0
endif
# Compiler flags
-CFLAGS = -O2 -m64
+CFLAGS ?= -O2 -m64
#CFLAGS = -Wall -O2 -pg -m64
-CPPFLAGS = -O2 -D_FILE_OFFSET_BITS=64
+CPPFLAGS ?= -O2 -D_FILE_OFFSET_BITS=64
#CPPFLAGS = -O2 -Wall -pg -D_FILE_OFFSET_BITS=64
# Included libraries (zlib)
LIB = -lz
@@ -29,13 +29,13 @@
# Define flag for PCA routine compilation
CPPFLAGS += -DVCFTOOLS_PCA
# Add LAPACK library
- LIB += -llapack
+ LIB += `$(PKG_CONFIG) --libs lapack`
# Add PCA source code
OBJS+= dgeev.o
endif
vcftools: $(OBJS)
- $(CPP) $(CPPFLAGS) $(OBJS) -o vcftools $(LIB)
+ $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(OBJS) -o vcftools $(LIB)
ifdef BINDIR
cp $(CURDIR)/$@ $(BINDIR)/$@
endif
@@ -47,8 +47,8 @@
-include $(OBJS:.o=.d)
%.o: %.cpp
- $(CPP) -c $(CPPFLAGS) $*.cpp -o $*.o
- $(CPP) -MM $(CPPFLAGS) $*.cpp > $*.d
+ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) $*.cpp -o $*.o
+ $(CXX) -MM $(CXXFLAGS) $(CPPFLAGS) $*.cpp > $*.d
# remove compilation products
clean:
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