Makefile
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####### Compiler, tools and options
CXX = g++
CXXFLAGS = -pipe -std=c++17 -O2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Wall -W -D_REENTRANT -fPIC
INCPATH = -I./src -I. -I/opt/ibm/ILOG/CPLEX_Studio221/cplex/include -I/usr/local/include
DEL_FILE = rm -f
LINK = g++
LFLAGS = -Wl,-O1 -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now
LIBS = -L/opt/ibm/ILOG/CPLEX_Studio221/cplex/lib/x86-64_linux/static_pic/ -lcplex -L/usr/local/lib/ -lRNA -lnupackconc -lnupackpfunc -lnupackutils -L/usr/lib/x86_64-linux-gnu/ -lpthread -lX11 -ldl
####### Files
OBJECTS = graph.o \
main.o \
rna.o \
structure.o \
interaction.o \
complexe.o \
solinteraction.o \
predictor.o \
utils.o \
helix.o \
hairpinloop.o \
motif.o \
multiloop.o \
pseudoknot.o \
interloop.o \
fa.o \
extract_str_inter.o \
biclique.o \
boip.o \
boipsolution.o \
findkbestparetoset.o \
ip.o \
ipcomp.o \
ipchromaticgraph.o \
complexip.o \
extract_probing_data.o \
extract_user_ct.o
TARGET = C-RCPred
####### Build rules
C-RCPred: /opt/ibm/ILOG/CPLEX_Studio221/cplex/lib/x86-64_linux/static_pic/libcplex.a /usr/local/lib/libRNA.a /usr/local/lib/libnupackconc.a /usr/local/lib/libnupackpfunc.a /usr/local/lib/libnupackutils.a $(OBJECTS)
$(LINK) $(LFLAGS) -o $(TARGET) $(OBJECTS) $(LIBS) && $(DEL_FILE) $(OBJECTS)
all: Makefile C-RCPred
####### Compile
graph.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o graph.o ./src/graph.cpp
main.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o main.o ./src/main.cpp
rna.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o rna.o ./src/rna.cpp
structure.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o structure.o ./src/structure.cpp
interaction.o: ./src/interaction.cpp ./src/interaction.h \
./src/rna.h \
./src/Extract_data/fa.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o interaction.o ./src/interaction.cpp
complexe.o: ./src/complexe.cpp ./src/complexe.h \
./src/Motifs/helix.h \
./src/Motifs/motif.h \
./src/structure.h \
./src/solinteraction.h \
./src/rna.h \
./src/Extract_data/fa.h \
./src/interaction.h \
./src/Motifs/pseudoknot.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o complexe.o ./src/complexe.cpp
solinteraction.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o solinteraction.o ./src/solinteraction.cpp
predictor.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o predictor.o ./src/predictor.cpp
utils.o:
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o utils.o ./src/utils.cpp
helix.o: ./src/Motifs/helix.cpp ./src/thermo/core.h \
./src/thermo/core/backtrack.h \
./src/thermo/core/ene.h \
./src/shared.h \
./src/shared/constants.h \
./src/shared/nupack_design_constants.h \
./src/shared/externals.h \
./src/shared/functions.h \
./src/shared/structs.h \
./src/shared/hash.h \
./src/shared/mt19937ar.h \
./src/thermo/core/pfuncUtils.h \
./src/thermo/core/mfeUtils.h \
./src/thermo/core/pknots.h \
./src/thermo/core/min.h \
./src/thermo/core/init.h \
./src/thermo/core/CalculateEnergy.h \
./src/thermo/core/GetEnergy.h \
./src/thermo/core/nsStar.h \
./src/thermo/core/pf.h \
./src/thermo/core/pairsPr.h \
./src/thermo/core/sumexp.h \
./src/thermo/core/sumexp_pk.h \
./src/thermo/core/ReadCommandLineNPK.h \
./src/RNAeval_cmdl.h \
./src/Motifs/helix.h \
./src/Motifs/motif.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o helix.o ./src/Motifs/helix.cpp
hairpinloop.o: ./src/Motifs/hairpinloop.cpp ./src/Motifs/hairpinloop.h \
./src/Motifs/motif.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o hairpinloop.o ./src/Motifs/hairpinloop.cpp
motif.o: ./src/Motifs/motif.cpp ./src/Motifs/motif.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o motif.o ./src/Motifs/motif.cpp
multiloop.o: ./src/Motifs/multiloop.cpp ./src/Motifs/multiloop.h \
./src/Motifs/motif.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o multiloop.o ./src/Motifs/multiloop.cpp
pseudoknot.o: ./src/Motifs/pseudoknot.cpp ./src/Motifs/pseudoknot.h \
./src/Motifs/motif.h \
./src/Motifs/helix.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o pseudoknot.o ./src/Motifs/pseudoknot.cpp
interloop.o: ./src/Motifs/interloop.cpp ./src/Motifs/interloop.h \
./src/Motifs/motif.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o interloop.o ./src/Motifs/interloop.cpp
fa.o: ./src/Extract_data/fa.cpp ./src/Extract_data/fa.h \
./src/rna.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o fa.o ./src/Extract_data/fa.cpp
extract_str_inter.o: ./src/Extract_data/extract_str_inter.cpp ./src/Extract_data/extract_user_ct.h \
./src/Motifs/interloop.h \
./src/Motifs/motif.h \
./src/Motifs/hairpinloop.h \
./src/Motifs/helix.h \
./src/Motifs/multiloop.h \
./src/Motifs/pseudoknot.h \
./src/rna.h \
./src/Extract_data/fa.h \
./src/structure.h \
./src/solinteraction.h \
./src/interaction.h \
./src/utils.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o extract_str_inter.o ./src/Extract_data/extract_str_inter.cpp
biclique.o: ./src/IP/biclique.cpp ./src/IP/biclique.h \
./src/IP/boip.h \
./src/IP/ip.h \
./src/IP/boipsolution.h \
./src/utils.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o biclique.o ./src/IP/biclique.cpp
boip.o: ./src/IP/boip.cpp ./src/IP/boip.h \
./src/IP/ip.h \
./src/IP/boipsolution.h \
./src/utils.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o boip.o ./src/IP/boip.cpp
boipsolution.o: ./src/IP/boipsolution.cpp ./src/IP/boipsolution.h \
./src/utils.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o boipsolution.o ./src/IP/boipsolution.cpp
findkbestparetoset.o: ./src/IP/findkbestparetoset.cpp ./src/IP/findkbestparetoset.h \
./src/IP/boip.h \
./src/IP/ip.h \
./src/IP/boipsolution.h \
./src/utils.h \
./src/IP/biclique.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o findkbestparetoset.o ./src/IP/findkbestparetoset.cpp
ip.o: ./src/IP/ip.cpp ./src/IP/ip.h \
/opt/ibm/ILOG/CPLEX_Studio221/cplex/include/ilcplex/cplex.h \
/opt/ibm/ILOG/CPLEX_Studio221/cplex/include/ilcplex/cpxconst.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o ip.o ./src/IP/ip.cpp
ipcomp.o: ./src/IP/ipcomp.cpp ./src/IP/ipcomp.h \
./src/IP/ip.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o ipcomp.o ./src/IP/ipcomp.cpp
ipchromaticgraph.o: ./src/IP/ipchromaticgraph.cpp ./src/IP/ipchromaticgraph.h \
./src/IP/ip.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o ipchromaticgraph.o ./src/IP/ipchromaticgraph.cpp
complexip.o: ./src/IP/complexip.cpp ./src/IP/complexip.h \
./src/structure.h \
./src/Motifs/motif.h \
./src/solinteraction.h \
./src/rna.h \
./src/Extract_data/fa.h \
./src/interaction.h \
./src/Motifs/pseudoknot.h \
./src/Motifs/helix.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o complexip.o ./src/IP/complexip.cpp
extract_probing_data.o: ./src/Extract_data/extract_probing_data.cpp ./src/Extract_data/extract_probing_data.h \
./src/rna.h \
./src/Extract_data/fa.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o extract_probing_data.o ./src/Extract_data/extract_probing_data.cpp
extract_user_ct.o: ./src/Extract_data/extract_user_ct.cpp ./src/Extract_data/extract_user_ct.h \
./src/Motifs/interloop.h \
./src/Motifs/motif.h \
./src/Motifs/hairpinloop.h \
./src/Motifs/helix.h \
./src/Motifs/multiloop.h \
./src/Motifs/pseudoknot.h \
./src/rna.h \
./src/Extract_data/fa.h \
./src/structure.h \
./src/solinteraction.h \
./src/interaction.h \
./src/utils.h
$(CXX) -c $(CXXFLAGS) $(INCPATH) -o extract_user_ct.o ./src/Extract_data/extract_user_ct.cpp