Hi,
I’m trying to install 1.11.0, and I’m getting several ‘undefined reference’ errors. What am I doing wrong?
thanks,
Bill
# make
g++ -lreadline -lncurses -L../readline-5.1 \
./sharedutilities.o\
./treegroupscommand.o\
./bootstrapsharedcommand.o\
./matrixoutputcommand.o\
./getoturepcommand.o\
./screenseqscommand.o\
./chimera.o\
./decalc.o\
./readotucommand.o\
./readdistcommand.o\
./commandfactory.o\
./alignment.o\
./alignmentcell.o\
./gotohoverlap.o\
./overlap.o\
./needlemanoverlap.o\
./blastalign.o\
./noalign.o\
./suffixdb.o\
./suffixnodes.o\
./suffixtree.o\
./blastdb.o\
./nast.o\
./nastreport.o\
./boneh.o\
./efron.o\
./solow.o\
./unifracweightedcommand.o\
./weighted.o\
./unweighted.o\
./unifracunweightedcommand.o\
./getsabundcommand.o\
./getrabundcommand.o\
./bellerophon.o\
./pintail.o\
./sharedanderbergs.o\
./venncommand.o\
./venn.o\
./fullmatrix.o\
./heatmap.o\
./heatmapcommand.o\
./libshuffcommand.o\
./nocommands.o\
./sharedbraycurtis.o\
./sharedkulczynski.o\
./sharedlennon.o\
./sharedkulczynskicody.o\
./sharedmorisitahorn.o\
./sharedochiai.o\
./readcolumn.o\
./readotu.o\
./readphylip.o\
./consensuscommand.o\
./heatmapsimcommand.o\
./heatmapsim.o\
./optionparser.o\
./filterseqscommand.o\
./goodscoverage.o\
./sequencedb.o\
./sharedjackknife.o\
./sharedmarczewski.o\
./aligncommand.o\
./treemap.o\
./parsimonycommand.o\
./parsimony.o\
./seqsummarycommand.o\
./chimeraccodecommand.o\
./chimerabellerophoncommand.o\
./chimeracheckcommand.o\
./chimeraslayercommand.o\
./chimerapintailcommand.o\
./chimeraseqscommand.o\
./sharedlistvector.o\
./tree.o\
./readtree.o\
./sharedsobscollectsummary.o\
./deconvolutecommand.o\
./listseqscommand.o\
./getseqscommand.o\
./removeseqscommand.o\
./systemcommand.o\
./binsequencecommand.o\
./distancecommand.o\
./ace.o\
./averagelinkage.o\
./bootstrap.o\
./calculator.o\
./chao1.o\
./cluster.o\
./clustercommand.o\
./collect.o\
./collectcommand.o\
./collectsharedcommand.o\
./commandoptionparser.o\
./completelinkage.o\
./database.o\
./engine.o\
./fastamap.o\
./fileoutput.o\
./globaldata.o\
./groupmap.o\
./helpcommand.o\
./makegroupcommand.o\
./chopseqscommand.o\
./clearcutcommand.o\
./catchallcommand.o\
./splitabundcommand.o\
./splitmatrix.o\
./clustersplitcommand.o\
./weightedlinkage.o\
./inputdata.o\
./jackknife.o\
./kmer.o\
./kmerdb.o\
./listvector.o\
./mothur.o\
./nameassignment.o\
./npshannon.o\
./ordervector.o\
./progress.o\
./quitcommand.o\
./rabundvector.o\
./rarecalc.o\
./raredisplay.o\
./rarefact.o\
./rarefactcommand.o\
./rarefactsharedcommand.o\
./sabundvector.o\
./sequence.o\
./shannon.o\
./sharedace.o\
./sharedchao1.o\
./sharedcommand.o\
./sharedjabund.o\
./sharedjclass.o\
./sharedjest.o\
./sharedordervector.o\
./sharedrabundvector.o\
./sharedsabundvector.o\
./sharedsobs.o\
./sharedsorabund.o\
./sharedsorclass.o\
./sharedsorest.o\
./sharedthetan.o\
./sharedthetayc.o\
./simpson.o\
./singlelinkage.o\
./sparsematrix.o\
./summarycommand.o\
./summarysharedcommand.o\
./uvest.o\
./validcalculator.o\
./validparameter.o\
./treenode.o\
./readtreecommand.o\
./reversecommand.o\
./trimseqscommand.o\
./slibshuff.o\
./libshuff.o\
./dlibshuff.o\
./mergefilecommand.o\
./coverage.o\
./whittaker.o\
./preclustercommand.o\
./otuhierarchycommand.o\
./setdircommand.o\
./getgroupcommand.o\
./getlabelcommand.o\
./secondarystructurecommand.o\
./mothurout.o\
./parselistscommand.o\
./readblast.o\
./chimeracheckrdp.o\
./hclustercommand.o\
./hcluster.o\
./getlistcountcommand.o\
./readcluster.o\
./ccode.o\
./taxonomyequalizer.o\
./phylotypecommand.o\
./classifyseqscommand.o\
./classifyotucommand.o\
./parsesffcommand.o\
./classify.o\
./phylotree.o\
./phylodiversity.o\
./phylodiversitycommand.o\
./bayesian.o\
./phylosummary.o\
./alignmentdb.o\
./knn.o\
./distancedb.o\
./chimeraslayer.o\
./slayer.o\
./pcacommand.o\
./formatcolumn.o\
./formatphylip.o\
./mgclustercommand.o\
./getsharedotucommand.o\
./maligner.o\
./chimerarealigner.o\
./bergerparker.o\
./bstick.o\
./sharedkstest.o\
./qstat.o\
./shen.o\
./logsd.o\
./geom.o\
./setlogfilecommand.o\
-o mothur
./averagelinkage.o: In function `AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float)':
averagelinkage.cpp:(.text+0x65): undefined reference to `Cluster::Cluster(RAbundVector*, ListVector*, SparseMatrix*, float)'
./averagelinkage.o: In function `AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float)':
averagelinkage.cpp:(.text+0x95): undefined reference to `Cluster::Cluster(RAbundVector*, ListVector*, SparseMatrix*, float)'
./averagelinkage.o:(.rodata._ZTV14AverageLinkage[vtable for AverageLinkage]+0x10): undefined reference to `Cluster::update()'
./clustercommand.o: In function `ClusterCommand::ClusterCommand(std::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
clustercommand.cpp:(.text+0x321a): undefined reference to `CompleteLinkage::CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
clustercommand.cpp:(.text+0x3da0): undefined reference to `AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
./clustercommand.o: In function `ClusterCommand::ClusterCommand(std::basic_string<char, std::char_traits<char>, std::allocator<char> >)':
clustercommand.cpp:(.text+0x5fba): undefined reference to `CompleteLinkage::CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
clustercommand.cpp:(.text+0x6b40): undefined reference to `AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
./completelinkage.o: In function `CompleteLinkage::CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float)':completelinkage.cpp:(.text+0x65): undefined reference to `Cluster::Cluster(RAbundVector*, ListVector*, SparseMatrix*, float)'
./completelinkage.o: In function `CompleteLinkage::CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float)':completelinkage.cpp:(.text+0x85): undefined reference to `Cluster::Cluster(RAbundVector*, ListVector*, SparseMatrix*, float)'
./completelinkage.o:(.rodata._ZTV15CompleteLinkage[vtable for CompleteLinkage]+0x10): undefined reference to `Cluster::update()'
./clustersplitcommand.o: In function `ClusterSplitCommand::cluster(std::vector<std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::allocator<std::map<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > > >, std::set<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&)':
clustersplitcommand.cpp:(.text+0x183f): undefined reference to `CompleteLinkage::CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
clustersplitcommand.cpp:(.text+0x255b): undefined reference to `AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
./chimeraslayer.o: In function `ChimeraSlayer::getChimeras(Sequence*)':
chimeraslayer.cpp:(.text+0x5a6c): undefined reference to `Slayer::Slayer(int, int, int, float, int, int)'
./mgclustercommand.o: In function `MGClusterCommand::execute()':
mgclustercommand.cpp:(.text+0xaef5): undefined reference to `CompleteLinkage::CompleteLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
mgclustercommand.cpp:(.text+0xb67b): undefined reference to `AverageLinkage::AverageLinkage(RAbundVector*, ListVector*, SparseMatrix*, float, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)'
collect2: ld returned 1 exit status
make: *** [mothur] Error 1