Compile error on Centos7, fixed it by modifying two Makefiles

[ld32]

I first got a lot of errors when running these commands on our cluster with CentOS7: $ module load gcc/6.2.0 cmake/3.7.1 perl/5.30.0 R/3.6.1 $ git clone --recursive https://github.com/grenaud/schmutzi.git $ cd schmutzi $ make

Then I have to modify two Makefiles to compile the software. Hope this helps some one.

$ less src/splitEndoVsCont/Makefile

CXX = g++ # -g -pg BAMTOOLS = ../../lib/bamtools/ LIBGAB = ../../lib/libgab/

CXXFLAGS = -lm -O3 -Wall -I${LIBGAB} -I${LIBGAB}/gzstream/ -I${BAMTOOLS}/include/ -I${BAMTOOLS}/src/ -c LDLIBS += ${BAMTOOLS}/build/src/utils/CMakeFiles/BamTools-utils.dir/*cpp.o ${BAMTOOLS}build/src/api/libbamtools.a -lm -lz

all: poshap2splitbam

poshap2splitbam.o: poshap2splitbam.cpp ${CXX} ${CXXFLAGS} poshap2splitbam.cpp

poshap2splitbam: poshap2splitbam.o ${LIBGAB}libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

clean : rm -f poshap2splitbam.o poshap2splitbam

############################################# $ less src/Makefile CXX = g++ #-g -pg BAMTOOLS = ../lib/bamtools/ LIBGAB = ../lib/libgab/

CXXFLAGS = -lm -O3 -Wall -I${LIBGAB} -I${LIBGAB}/gzstream/ -I${BAMTOOLS}/include/ -I${BAMTOOLS}/src/

CXXFLAGS = -static -lm -O3 -Wall -I${LIBGAB} -I${LIBGAB}/gzstream/ -I${BAMTOOLS}/include/ -I${BAMTOOLS}/src/ -c

LDLIBS += ${BAMTOOLS}/build/src/utils/CMakeFiles/BamTools-utils.dir/*cpp.o ${BAMTOOLS}/build/src/api/libbamtools.a -lpthread -lm -lz

all: endoCaller mtCont damage2profile log2freq log2fasta contDeam msa2freq bam2prof insertSize splitEndoVsCont/poshap2splitbam logs2pos countRecords ${LIBGAB}/libgab.a ${BAMTOOLS}/build/src/api/libbamtools.a jointFreqDeaminated jointFreqDeaminatedDouble msa2log log2ConsensusLog logdiff logmask filterlog msa2singlefreq subSampleBAM addXACircular

splitEndoVsCont/poshap2splitbam: make -C splitEndoVsCont/

${LIBGAB}/libgab.h: rm -rf ${LIBGAB} git clone --recursive https://github.com/grenaud/libgab.git ${LIBGAB}

${LIBGAB}/libgab.a: ${BAMTOOLS}/build/src/api/libbamtools.a ${LIBGAB}/libgab.h make -C ${LIBGAB}

${BAMTOOLS}/src/api/BamAlignment.h: rm -rf ${BAMTOOLS} git clone --recursive https://github.com/pezmaster31/bamtools.git ${BAMTOOLS}/ && cd ${BAMTOOLS}/ && git reset --hard d24d850de17134fe4e7984b26493c5c0a1844b35

${BAMTOOLS}/build/src/api/libbamtools.a: ${BAMTOOLS}/src/api/BamAlignment.h cd ${BAMTOOLS}/ && mkdir -p build/ && cd build/ && if cmake ..; then echo ""; else if cmake3 ..; then echo ""; else echo "cmake failed, please install cmake v3"; fi fi && make && cd ../../../src/

miscfunc.o: ${LIBGAB}/libgab.a miscfunc.cpp ${CXX} ${CXXFLAGS} -c miscfunc.cpp

insertSize.o: ${LIBGAB}/libgab.a insertSize.cpp ${CXX} ${CXXFLAGS} -c insertSize.cpp

insertSize: insertSize.o ${LIBGAB}/libgab.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS)

countRecords.o: ${LIBGAB}/libgab.a countRecords.cpp ${CXX} ${CXXFLAGS} -c countRecords.cpp

countRecords: countRecords.o ${LIBGAB}/libgab.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS)

jointFreqDeaminated.o: ${LIBGAB}/libgab.a jointFreqDeaminated.cpp ${CXX} ${CXXFLAGS} -c jointFreqDeaminated.cpp

jointFreqDeaminatedDouble.o: ${LIBGAB}/libgab.a jointFreqDeaminatedDouble.cpp ${CXX} ${CXXFLAGS} -c jointFreqDeaminatedDouble.cpp

jointFreqDeaminated: jointFreqDeaminated.o ${LIBGAB}/libgab.a ${LIBGAB}/ReconsReferenceBAM.o ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS)

jointFreqDeaminatedDouble: jointFreqDeaminatedDouble.o ${LIBGAB}/libgab.a ${LIBGAB}/ReconsReferenceBAM.o ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS)

mtCont.o: ${LIBGAB}/libgab.a mtCont.cpp ${CXX} ${CXXFLAGS} -c mtCont.cpp

mtCont: ${LIBGAB}/libgab.a miscfunc.o mtCont.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

bam2prof.o: ${LIBGAB}/libgab.a bam2prof.cpp ${CXX} ${CXXFLAGS} -c bam2prof.cpp

bam2prof: ${LIBGAB}/libgab.a miscfunc.o bam2prof.o ${LIBGAB}/libgab.a ${LIBGAB}/ReconsReferenceBAM.o ${LIBGAB}gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

subSampleBAM.o: ${LIBGAB}/libgab.a subSampleBAM.cpp ${CXX} ${CXXFLAGS} -c subSampleBAM.cpp

subSampleBAM: ${LIBGAB}/libgab.a subSampleBAM.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

addXACircular.o: ${LIBGAB}/libgab.a addXACircular.cpp ${CXX} ${CXXFLAGS} -c addXACircular.cpp

addXACircular: ${LIBGAB}/libgab.a addXACircular.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

contDeam.o: ${LIBGAB}/libgab.a contDeam.cpp ${CXX} ${CXXFLAGS} -c contDeam.cpp

contDeam: ${LIBGAB}/libgab.a ${LIBGAB}/ReconsReferenceBAM.o miscfunc.o contDeam.o ${LIBGAB}/libgab.a ${LIBGAB}gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

endoCaller.o: ${LIBGAB}/libgab.a endoCaller.cpp ${CXX} ${CXXFLAGS} -c endoCaller.cpp

endoCaller: ${LIBGAB}/libgab.a ${LIBGAB}/ReconsReferenceBAM.o endoCaller.o miscfunc.o ${LIBGAB}/libgab.a ${LIBGAB}gzstream/libgzstream.a ${CXX} $(LDFLAGS) -o $@ $^ $(LDLIBS)

log2freq.o: ${LIBGAB}/libgab.a log2freq.cpp ${CXX} ${CXXFLAGS} -c log2freq.cpp

log2freq: ${LIBGAB}/libgab.a log2freq.o ${LIBGAB}/libgab.a ${LIBGAB}gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

log2fasta.o: ${LIBGAB}/libgab.a log2fasta.cpp ${CXX} ${CXXFLAGS} -c log2fasta.cpp

log2fasta: ${LIBGAB}/libgab.a log2fasta.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

filterlog.o: ${LIBGAB}/libgab.a filterlog.cpp ${CXX} ${CXXFLAGS} -c filterlog.cpp

filterlog: ${LIBGAB}/libgab.a filterlog.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

logs2pos.o: ${LIBGAB}/libgab.a logs2pos.cpp ${CXX} ${CXXFLAGS} -c logs2pos.cpp

logs2pos: ${LIBGAB}/libgab.a logs2pos.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

log2ConsensusLog.o: ${LIBGAB}/libgab.a log2ConsensusLog.cpp ${CXX} ${CXXFLAGS} -c log2ConsensusLog.cpp

log2ConsensusLog: ${LIBGAB}/libgab.a log2ConsensusLog.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

logdiff.o: ${LIBGAB}/libgab.a logdiff.cpp ${CXX} ${CXXFLAGS} -c logdiff.cpp

logdiff: ${LIBGAB}/libgab.a logdiff.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

logmask.o: ${LIBGAB}/libgab.a logmask.cpp ${CXX} ${CXXFLAGS} -c logmask.cpp

logmask: ${LIBGAB}/libgab.a logmask.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

msa2freq.o: ${LIBGAB}/libgab.a msa2freq.cpp ${CXX} ${CXXFLAGS} -c msa2freq.cpp

msa2freq: ${LIBGAB}/libgab.a msa2freq.o ${LIBGAB}/libgab.a ${LIBGAB}/FastQParser.o ${LIBGAB}/FastQObj.o ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

msa2singlefreq.o: ${LIBGAB}/libgab.a msa2singlefreq.cpp ${CXX} ${CXXFLAGS} -c msa2singlefreq.cpp

msa2singlefreq: ${LIBGAB}/libgab.a msa2singlefreq.o ${LIBGAB}/libgab.a ${LIBGAB}/FastQParser.o ${LIBGAB}/FastQObj.o ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

msa2log.o: ${LIBGAB}/libgab.a msa2log.cpp ${CXX} ${CXXFLAGS} -c msa2log.cpp

msa2log: ${LIBGAB}/libgab.a msa2log.o ${LIBGAB}/libgab.a ${LIBGAB}/FastQParser.o ${LIBGAB}/FastQObj.o ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

damage2profile.o: ${LIBGAB}/libgab.a damage2profile.cpp ${CXX} ${CXXFLAGS} -c damage2profile.cpp

damage2profile: ${LIBGAB}/libgab.a damage2profile.o ${LIBGAB}/libgab.a ${LIBGAB}/gzstream/libgzstream.a ${CXX} ${CXXFLAGS} -o $@ $^ $(LDLIBS) $(LDFLAGS)

clean : rm -f *.o endoCaller mtCont damage2profile log2freq log2fasta contDeam msa2freq msa2log bam2prof subSampleBAM addXACircular insertSize splitEndoVsCont/poshap2splitbam logs2pos countRecords ${LIBGAB}/libgab.a bamtools/lib/libbamtools.a jointFreqDeaminated jointFreqDeaminatedDouble log2ConsensusLog logdiff logmask filterlog msa2singlefreq make -C splitEndoVsCont/ clean make -C ${LIBGAB}/ clean

[ld32]

Here is the patch. So you can directly apply the modifications: centos7.patch

[grenaud]

@ld32 thanks a lot! BTW, how do you work with these patch files, I tried: patch --dry-run -ruN -d . < centos7.patch But I get: can't find file to patch at input line 4

How would I go about this?

[ld32]

Not sure. Let me attach the two Makefiles: src.slash.Makefile.txt src.slash.splitEndoVsCont.slash.Makefile.txt

You need rename the fist file to Makefile and copy to src folder, and rename the second file to Makefile and copy to src/splitEndoVsCont/

[grenaud]

I just changed the makefiles for yours, they are building fine on Ubuntu. thank you so much for contributing!