duplicate symbol: AverageLinkage::updateDistance(PDistCell&, PDistCell&)

yurivict commented 4 years ago

ld: error: duplicate symbol: AverageLinkage::updateDistance(PDistCell&, PDistCell&)
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(AverageLinkage::updateDistance(PDistCell&, PDistCell&))
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.text+0xE0)

ld: error: duplicate symbol: AverageLinkage::getTag()
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(AverageLinkage::getTag())
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.text+0xC0)

ld: error: duplicate symbol: AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, float)
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, float))
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.text+0x0)

ld: error: duplicate symbol: AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, float)
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, float))
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.text+0x0)

ld: error: duplicate symbol: typeinfo for AverageLinkage
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(typeinfo for AverageLinkage)
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.rodata+0x78)

ld: error: duplicate symbol: typeinfo name for AverageLinkage
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(typeinfo name for AverageLinkage)
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.rodata+0x60)

ld: error: duplicate symbol: vtable for AverageLinkage
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(vtable for AverageLinkage)
>>> defined at averagelinkage.cpp
>>>            source/averagelinkage.o:(.rodata+0x0)

ld: error: duplicate symbol: CalcSparcc::getD_Matrix()
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getD_Matrix())
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x20F0)

ld: error: duplicate symbol: CalcSparcc::getT_Matrix(std::__1::vector<float, std::__1::allocator<float> >)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getT_Matrix(std::__1::vector<float, std::__1::allocator<float> >))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x1BB0)

ld: error: duplicate symbol: CalcSparcc::getT_Vector()
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getT_Vector())
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x1F60)

ld: error: duplicate symbol: CalcSparcc::excludeValues(int, int)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::excludeValues(int, int))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x2BD0)

ld: error: duplicate symbol: CalcSparcc::addPseudoCount(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >&)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::addPseudoCount(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >&))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x1440)

ld: error: duplicate symbol: CalcSparcc::getLogFractions(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getLogFractions(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x14D0)

ld: error: duplicate symbol: CalcSparcc::getExcludedPairs(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, int&, int&)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getExcludedPairs(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, int&, int&))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x2B20)

ld: error: duplicate symbol: CalcSparcc::getBasisVariances()
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getBasisVariances())
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x2320)

ld: error: duplicate symbol: CalcSparcc::getBasisCorrelations(std::__1::vector<float, std::__1::allocator<float> >)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getBasisCorrelations(std::__1::vector<float, std::__1::allocator<float> >))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x2800)

ld: error: duplicate symbol: CalcSparcc::getMedian(std::__1::vector<std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > > > >)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::getMedian(std::__1::vector<std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, std::__1::allocator<std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > > > >))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x2CD0)

ld: error: duplicate symbol: CalcSparcc::CalcSparcc(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, int, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::CalcSparcc(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, int, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x0)

ld: error: duplicate symbol: CalcSparcc::CalcSparcc(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, int, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >)
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(CalcSparcc::CalcSparcc(std::__1::vector<std::__1::vector<float, std::__1::allocator<float> >, std::__1::allocator<std::__1::vector<float, std::__1::allocator<float> > > >, int, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >))
>>> defined at calcsparcc.cpp
>>>            source/calcsparcc.o:(.text+0x0)

ld: error: duplicate symbol: Cluster::clusterBins()
>>> defined at cluster.cpp
>>>            source/cluster.o:(Cluster::clusterBins())
>>> defined at cluster.cpp
>>>            source/cluster.o:(.text+0x230)

ld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
c++: error: linker command failed with exit code 1 (use -v to see invocation)

Version: 1.44.3 OS: FreeBSD 12.2 clang-10

mothur-westcott commented 4 years ago

We have not seen this in our other OS builds. Could you tell me more about the build?

What settings did you set in the makefile?
Could you have old .o files from previous builds? If so, try make clean, make.

yurivict commented 4 years ago

What settings did you set in the makefile?

All usual variables are set by the framework: CFLAGS/CXXFLAGS/LDFLAGS.

Could you have old .o files from previous builds? If so, try make clean, make.

No, the build is clean. It is done by the ports framework, as for all other ports.

mothur-westcott commented 4 years ago

`INSTALL_DIR ?= "\"Enter_your_mothur_install_path_here\""

OPTIMIZE ?= yes USEREADLINE ?= no USEBOOST ?= no USEHDF5 ?= no USEGSL ?= no LOGFILE_NAME ?= no

BOOST_LIBRARY_DIR ?= "\"Enter_your_boost_library_path_here\"" BOOST_INCLUDE_DIR ?= "\"Enter_your_boost_include_path_here\"" HDF5_LIBRARY_DIR ?= "\"Enter_your_HDF5_library_path_here\"" HDF5_INCLUDE_DIR ?= "\"Enter_your_HDF5_include_path_here\"" GSL_LIBRARY_DIR ?= "\"Enter_your_GSL_library_path_here\"" GSL_INCLUDE_DIR ?= "\"Enter_your_GSL_include_path_here\"" MOTHUR_FILES="\"Enter_your_default_path_here\"" MOTHUR_TOOLS="\"Enter_your_mothur_tools_path_here\"" VERSION = "\"1.44.3\""

ifeq ($(strip $(LOGFILE_NAME)),yes) LOGFILE_NAME="\"silent\"" endif

ifeq ($(strip $(OPTIMIZE)),yes) CXXFLAGS += -O3 endif

CXXFLAGS += -std=c++11 -pthread -DVERSION=${VERSION} LDFLAGS += -std=c++11 -pthread

ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"") else CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES} endif

ifeq ($(strip $(MOTHUR_TOOLS)),"\"Enter_your_mothur_tools_path_here\"") else CXXFLAGS += -DMOTHUR_TOOLS=${MOTHUR_TOOLS} endif

ifeq ($(strip $(USEREADLINE)),yes) CXXFLAGS += -DUSE_READLINE LIBS += -lreadline endif

ifeq ($(strip $(USEBOOST)),yes)

LDFLAGS += -L ${BOOST_LIBRARY_DIR}

LIBS += -lboost_iostreams -lz
CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}

endif

ifeq ($(strip $(USEHDF5)),yes)

LDFLAGS += -L ${HDF5_LIBRARY_DIR} LIBS += -lhdf5 -lhdf5_cpp CXXFLAGS += -DUSE_HDF5 -I ${HDF5_INCLUDE_DIR}

endif

ifeq ($(strip $(USEGSL)),yes)

LDFLAGS += -L ${GSL_LIBRARY_DIR} LIBS += -lgsl -lgslcblas -lm CXXFLAGS += -DUSE_GSL -I ${GSL_INCLUDE_DIR}

endif

VPATH=source/calculators:source/chimera:source/classifier:source/clearcut:source/commands:source/communitytype:source/datastructures:source/engines:source/metastats:source/read:source/svm:source/ skipUchime := source/uchime_src/ subdirs := $(sort $(dir $(filter-out $(skipUchime), source/, $(wildcard source/*/)))) subDirIncludes = $(patsubst %, -I %, $(subdirs)) subDirLinking = $(patsubst %, -L%, $(subdirs)) CXXFLAGS += -I. $(subDirIncludes) LDFLAGS += $(subDirLinking)

OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))

mothur : $(OBJECTS) uchime $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)

uchime : cd source/uchime_src && export CXX=$(CXX) && make clean && make && mv uchime ../../ && cd ..

install : mothur

ifeq ($(strip $(INSTALL_DIR)),"\"Enter_your_mothur_install_path_here\"") else mkdir -p ${INSTALL_DIR} mv mothur ${INSTALL_DIR}/mothur endif

%.o : %.c %.h $(COMPILE.c) $(OUTPUT_OPTION) $< %.o : %.cpp %.h $(COMPILE.cpp) $(OUTPUT_OPTION) $< %.o : %.cpp %.hpp $(COMPILE.cpp) $(OUTPUT_OPTION) $<

clean : @rm -f $(OBJECTS)'

Can you try compiling with the this makefile?

yurivict commented 4 years ago

The link line simply contains source/averagelinkage.o twice:

c++  -L/usr/local/lib -fstack-protector-strong  -std=c++11 -pthread  -Lsource/  -Lsource/calculators/  -Lsource/chimera/  -Lsource/classifier/  -Lsource/clearcut/  -Lsource/commands/  -Lsource/communitytype/  -Lsource/datastructures/  -Lsource/engines/  -Lsource/metastats/  -Lsource/read/  -Lsource/svm/  -o mothur source/averagelinkage.o source/calcsparcc.o source/cluster.o source/clusterclassic.o source/collect.o source/commandfactory.o source/commandoptionparser.o source/completelinkage.o source/consensus.o source/currentfile.o source/dlibshuff.o source/fileoutput.o source/gotohoverlap.o source/heatmap.o source/heatmapsim.o source/inputdata.o source/libshuff.o source/linearalgebra.o source/mothur.o source/mothurout.o source/myseqdist.o source/nast.o source/nastreport.o source/needlemanoverlap.o source/noalign.o source/opticluster.o source/optifitcluster.o source/optionparser.o source/overlap.o source/raredisplay.o source/rarefact.o source/refchimeratest.o source/sensspeccalc.o source/seqnoise.o source/singlelinkage.o source/slibshuff.o source/subsample.o source/summary.o source/trialSwap2.o source/trimoligos.o source/utils.o source/validcalculator.o source/validparameter.o source/venn.o source/vsearchfileparser.o source/weightedlinkage.o source/wilcox.o source/calculators/accuracy.o source/calculators/ace.o source/calculators/bergerparker.o source/calculators/boneh.o source/calculators/bootstrap.o source/calculators/bstick.o source/calculators/calculator.o source/calculators/canberra.o source/calculators/chao1.o source/calculators/coverage.o source/calculators/diversityutils.o source/calculators/eachgapdist.o source/calculators/eachgapignore.o source/calculators/efron.o source/calculators/erarefaction.o source/calculators/f1score.o source/calculators/fdr.o source/calculators/fn.o source/calculators/fp.o source/calculators/fpfn.o source/calculators/geom.o source/calculators/goodscoverage.o source/calculators/gower.o source/calculators/hamming.o source/calculators/heip.o source/calculators/hellinger.o source/calculators/igabundance.o source/calculators/ignoregaps.o source/calculators/igrarefaction.o source/calculators/invsimpson.o source/calculators/jackknife.o source/calculators/lnabundance.o source/calculators/lnrarefaction.o source/calculators/lnshift.o source/calculators/logsd.o source/calculators/lsabundance.o source/calculators/lsrarefaction.o source/calculators/manhattan.o source/calculators/mcc.o source/calculators/memchi2.o source/calculators/memchord.o source/calculators/memeuclidean.o source/calculators/mempearson.o source/calculators/metroig.o source/calculators/metrolognormal.o source/calculators/metrologstudent.o source/calculators/metrosichel.o source/calculators/npshannon.o source/calculators/npv.o source/calculators/odum.o source/calculators/onegapdist.o source/calculators/onegapignore.o source/calculators/parsimony.o source/calculators/ppv.o source/calculators/prng.o source/calculators/qstat.o source/calculators/sensitivity.o source/calculators/shannon.o source/calculators/shannoneven.o source/calculators/shannonrange.o source/calculators/sharedace.o source/calculators/sharedanderbergs.o source/calculators/sharedbraycurtis.o source/calculators/sharedchao1.o source/calculators/sharedjabund.o source/calculators/sharedjackknife.o source/calculators/sharedjclass.o source/calculators/sharedjest.o source/calculators/sharedjsd.o source/calculators/sharedkstest.o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynskicody.o source/calculators/sharedlennon.o source/calculators/sharedmarczewski.o source/calculators/sharedmorisitahorn.o source/calculators/sharedochiai.o source/calculators/sharedrjsd.o source/calculators/sharedsobs.o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsorabund.o source/calculators/sharedsorclass.o source/calculators/sharedsorest.o source/calculators/sharedthetan.o source/calculators/sharedthetayc.o source/calculators/shen.o source/calculators/siabundance.o source/calculators/simpson.o source/calculators/simpsoneven.o source/calculators/sirarefaction.o source/calculators/sishift.o source/calculators/smithwilson.o source/calculators/soergel.o source/calculators/solow.o source/calculators/spearman.o source/calculators/speciesprofile.o source/calculators/specificity.o source/calculators/structchi2.o source/calculators/structchord.o source/calculators/structeuclidean.o source/calculators/structkulczynski.o source/calculators/structpearson.o source/calculators/tn.o source/calculators/tp.o source/calculators/tptn.o source/calculators/unweighted.o source/calculators/uvest.o source/calculators/weighted.o source/calculators/whittaker.o source/chimera/bellerophon.o source/chimera/ccode.o source/chimera/chimeracheckrdp.o source/chimera/chimerarealigner.o source/chimera/chimeraslayer.o source/chimera/decalc.o source/chimera/maligner.o source/chimera/mothurchimera.o source/chimera/myPerseus.o source/chimera/pintail.o source/chimera/slayer.o source/classifier/alignnode.o source/classifier/aligntree.o source/classifier/bayesian.o source/classifier/classify.o source/classifier/kmernode.o source/classifier/kmertree.o source/classifier/knn.o source/classifier/opticlassifier.o source/classifier/phylosummary.o source/classifier/phylotree.o source/classifier/taxonomyequalizer.o source/classifier/taxonomynode.o source/clearcut/clearcut.o source/clearcut/cmdargs.o source/clearcut/distclearcut.o source/clearcut/dmat.o source/clearcut/fasta.o source/clearcut/getopt_long.o source/commands/aligncheckcommand.o source/commands/aligncommand.o source/commands/amovacommand.o source/commands/anosimcommand.o source/commands/binsequencecommand.o source/commands/biominfocommand.o source/commands/chimerabellerophoncommand.o source/commands/chimeraccodecommand.o source/commands/chimeracheckcommand.o source/commands/chimeraperseuscommand.o source/commands/chimerapintailcommand.o source/commands/chimeraslayercommand.o source/commands/chimerauchimecommand.o source/commands/chimeravsearchcommand.o source/commands/chopseqscommand.o source/commands/classifyotucommand.o source/commands/classifyseqscommand.o source/commands/classifysvmsharedcommand.o source/commands/classifytreecommand.o source/commands/clearcutcommand.o source/commands/clustercommand.o source/commands/clusterdoturcommand.o source/commands/clusterfitcommand.o source/commands/clusterfragmentscommand.o source/commands/clustersplitcommand.o source/commands/collectcommand.o source/commands/collectsharedcommand.o source/commands/consensusseqscommand.o source/commands/cooccurrencecommand.o source/commands/corraxescommand.o source/commands/countgroupscommand.o source/commands/countseqscommand.o source/commands/createdatabasecommand.o source/commands/deconvolutecommand.o source/commands/degapseqscommand.o source/commands/deuniqueseqscommand.o source/commands/deuniquetreecommand.o source/commands/distancecommand.o source/commands/distsharedcommand.o source/commands/diversityestimatorcommand.o source/commands/filterseqscommand.o source/commands/filtersharedcommand.o source/commands/getcoremicrobiomecommand.o source/commands/getcurrentcommand.o source/commands/getdistscommand.o source/commands/getgroupcommand.o source/commands/getgroupscommand.o source/commands/getlabelcommand.o source/commands/getlineagecommand.o source/commands/getlistcountcommand.o source/commands/getmetacommunitycommand.o source/commands/getmimarkspackagecommand.o source/commands/getoturepcommand.o source/commands/getotuscommand.o source/commands/getrabundcommand.o source/commands/getrelabundcommand.o source/commands/getsabundcommand.o source/commands/getseqscommand.o source/commands/getsharedotucommand.o source/commands/heatmapcommand.o source/commands/heatmapsimcommand.o source/commands/helpcommand.o source/commands/homovacommand.o source/commands/indicatorcommand.o source/commands/kruskalwalliscommand.o source/commands/lefsecommand.o source/commands/libshuffcommand.o source/commands/listotuscommand.o source/commands/listseqscommand.o source/commands/makebiomcommand.o source/commands/makeclrcommand.o source/commands/makecontigscommand.o source/commands/makefastqcommand.o source/commands/makefilecommand.o source/commands/makegroupcommand.o source/commands/makelefsecommand.o source/commands/makelookupcommand.o source/commands/makesharedcommand.o source/commands/mantelcommand.o source/commands/mergecountcommand.o source/commands/mergefilecommand.o source/commands/mergegroupscommand.o source/commands/mergeotuscommand.o source/commands/mergesfffilecommand.o source/commands/mergetaxsummarycommand.o source/commands/metastatscommand.o source/commands/mgclustercommand.o source/commands/mimarksattributescommand.o source/commands/newcommandtemplate.o source/commands/nmdscommand.o source/commands/nocommands.o source/commands/normalizesharedcommand.o source/commands/otuassociationcommand.o source/commands/otuhierarchycommand.o source/commands/pairwiseseqscommand.o source/commands/parsefastaqcommand.o source/commands/parsimonycommand.o source/commands/pcacommand.o source/commands/pcoacommand.o source/commands/pcrseqscommand.o source/commands/phylodiversitycommand.o source/commands/phylotypecommand.o source/commands/preclustercommand.o source/commands/primerdesigncommand.o source/commands/quitcommand.o source/commands/rarefactcommand.o source/commands/rarefactsharedcommand.o source/commands/removedistscommand.o source/commands/removegroupscommand.o source/commands/removelineagecommand.o source/commands/removeotuscommand.o source/commands/removerarecommand.o source/commands/removeseqscommand.o source/commands/renamefilecommand.o source/commands/renameseqscommand.o source/commands/reversecommand.o source/commands/screenseqscommand.o source/commands/sensspeccommand.o source/commands/seqerrorcommand.o source/commands/seqsummarycommand.o source/commands/setcurrentcommand.o source/commands/setdircommand.o source/commands/setlogfilecommand.o source/commands/setseedcommand.o source/commands/sffinfocommand.o source/commands/sffmultiplecommand.o source/commands/shhhercommand.o source/commands/shhhseqscommand.o source/commands/sortseqscommand.o source/commands/sparcccommand.o source/commands/splitabundcommand.o source/commands/splitgroupscommand.o source/commands/sracommand.o source/commands/srainfocommand.o source/commands/subsamplecommand.o source/commands/summarycommand.o source/commands/summaryqualcommand.o source/commands/summarysharedcommand.o source/commands/summarytaxcommand.o source/commands/systemcommand.o source/commands/treesharedcommand.o source/commands/trimflowscommand.o source/commands/trimseqscommand.o source/commands/unifracunweightedcommand.o source/commands/unifracweightedcommand.o source/commands/venncommand.o source/communitytype/communitytype.o source/communitytype/kmeans.o source/communitytype/pam.o source/communitytype/qFinderDMM.o source/datastructures/alignment.o source/datastructures/alignmentcell.o source/datastructures/alignmentdb.o source/datastructures/blastalign.o source/datastructures/blastdb.o source/datastructures/counttable.o source/datastructures/designmap.o source/datastructures/distancedb.o source/datastructures/fastamap.o source/datastructures/fastqread.o source/datastructures/filefile.o source/datastructures/flowdata.o source/datastructures/fullmatrix.o source/datastructures/groupmap.o source/datastructures/kmer.o source/datastructures/kmeralign.o source/datastructures/kmerdb.o source/datastructures/listvector.o source/datastructures/nameassignment.o source/datastructures/oligos.o source/datastructures/optiblastmatrix.o source/datastructures/optidata.o source/datastructures/optidb.o source/datastructures/optimatrix.o source/datastructures/optirefmatrix.o source/datastructures/ordervector.o source/datastructures/qualityscores.o source/datastructures/rabundfloatvector.o source/datastructures/rabundvector.o source/datastructures/reportfile.o source/datastructures/sabundvector.o source/datastructures/sequence.o source/datastructures/sequencecountparser.o source/datastructures/sequencedb.o source/datastructures/sequenceparser.o source/datastructures/sffheader.o source/datastructures/sffread.o source/datastructures/sharedclrvector.o source/datastructures/sharedclrvectors.o source/datastructures/sharedlistvector.o source/datastructures/sharedordervector.o source/datastructures/sharedrabundfloatvector.o source/datastructures/sharedrabundfloatvectors.o source/datastructures/sharedrabundvector.o source/datastructures/sharedrabundvectors.o source/datastructures/sparsedistancematrix.o source/datastructures/sparsematrix.o source/datastructures/suffixdb.o source/datastructures/suffixnodes.o source/datastructures/suffixtree.o source/datastructures/taxonomy.o source/datastructures/tree.o source/datastructures/treemap.o source/datastructures/treenode.o source/engines/batchengine.o source/engines/interactengine.o source/engines/scriptengine.o source/metastats/mothurfisher.o source/metastats/mothurmetastats.o source/read/readblast.o source/read/readcluster.o source/read/readcolumn.o source/read/readphylip.o source/read/readphylipvector.o source/read/readtree.o source/read/splitmatrix.o source/read/treereader.o source/svm/svm.o  source/averagelinkage.o source/calcsparcc.o source/cluster.o source/clusterclassic.o source/collect.o source/commandfactory.o source/commandoptionparser.o source/completelinkage.o source/consensus.o source/currentfile.o source/dlibshuff.o source/fileoutput.o source/gotohoverlap.o source/heatmap.o source/heatmapsim.o source/inputdata.o source/libshuff.o source/linearalgebra.o source/mothur.o source/mothurout.o source/myseqdist.o source/nast.o source/nastreport.o source/needlemanoverlap.o source/noalign.o source/opticluster.o source/optifitcluster.o source/optionparser.o source/overlap.o source/raredisplay.o source/rarefact.o source/refchimeratest.o source/sensspeccalc.o source/seqnoise.o source/singlelinkage.o source/slibshuff.o source/subsample.o source/summary.o source/trialSwap2.o source/trimoligos.o source/utils.o source/validcalculator.o source/validparameter.o source/venn.o source/vsearchfileparser.o source/weightedlinkage.o source/wilcox.o  -L/usr/local/lib -lreadline

This is maybe tolerated by the linux gcc-based toolchain, but this isn't tolerated by the clang-based toolchain.

mothur-westcott commented 4 years ago

It looks like the source directory object files are getting added twice. Try changing this line in the make file:

subdirs := $(sort $(dir $(filter-out $(skipUchime), source/, $(wildcard source/*/))))

to

subdirs := $(sort $(dir $(filter-out $(skipUchime), $(wildcard source/*/))))

yurivict commented 3 years ago

This issue is closed bu the bug is still present.

mothur / mothur

duplicate symbol: AverageLinkage::updateDistance(PDistCell&, PDistCell&) #756