41 lines
1.4 KiB
Text
41 lines
1.4 KiB
Text
--- Makefile.orig 2018-05-09 00:33:23 UTC
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+++ Makefile
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@@ -1,7 +1,8 @@
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-OPTFLAG = -O3
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-INCLUDES = -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2
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-CXXFLAGS = -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS
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-CXX = g++
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+# ${LOCALBASE}/include must come after bundled dirs
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+INCLUDES = -I. -Ilib -Ilib/Rmath -Ilib/tclap -Ilib/pcre2 -I${LOCALBASE}/include
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+CXXFLAGS ?= -pipe -std=c++0x $(OPTFLAG) $(INCLUDES) -D__STDC_LIMIT_MACROS
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+CXXFLAGS += -std=c++0x $(INCLUDES) -D__STDC_LIMIT_MACROS
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+CXX ?= g++
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SOURCESONLY =
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@@ -139,11 +140,11 @@ SOURCESONLY = main.cpp
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TARGET = vt
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TOOLSRC = $(SOURCES:=.cpp) $(SOURCESONLY)
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TOOLOBJ = $(TOOLSRC:.cpp=.o)
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-LIBDEFLATE = lib/libdeflate/libdeflate.a
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-LIBHTS = lib/htslib/libhts.a
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+LIBDEFLATE = -ldeflate
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+LIBHTS = -lhts
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LIBRMATH = lib/Rmath/libRmath.a
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LIBPCRE2 = lib/pcre2/libpcre2.a
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-LIBSVM = lib/libsvm/libsvm.a
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+LIBSVM = -lsvm
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all : $(TARGET)
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@@ -165,8 +166,8 @@ ${LIBSVM} :
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version :
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git rev-parse HEAD | cut -c 1-8 | awk '{print "#define VERSION \"0.5772-"$$0"\""}' > version.h;
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-$(TARGET) : ${LIBHTS} ${LIBRMATH} ${LIBPCRE2} ${LIBSVM} $(TOOLOBJ)
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- $(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto
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+$(TARGET) : ${LIBRMATH} ${LIBPCRE2} $(TOOLOBJ)
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+ $(CXX) $(CXXFLAGS) -o $@ $(TOOLOBJ) -L${LOCALBASE}/lib $(LIBHTS) $(LIBRMATH) ${LIBPCRE2} ${LIBDEFLATE} -lz -lpthread -lbz2 -llzma -lcurl -lcrypto
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$(TOOLOBJ): $(HEADERSONLY)
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