{"action":"created","issue":{"url":"https://api.github.com/repos/mothur/mothur/issues/86","repository_url":"https://api.github.com/repos/mothur/mothur","labels_url":"https://api.github.com/repos/mothur/mothur/issues/86/labels{/name}","comments_url":"https://api.github.com/repos/mothur/mothur/issues/86/comments","events_url":"https://api.github.com/repos/mothur/mothur/issues/86/events","html_url":"https://github.com/mothur/mothur/issues/86","id":78327683,"number":86,"title":"Installation on Mac","user":{"login":"shalabhsuman","id":4998368,"avatar_url":"https://avatars.githubusercontent.com/u/4998368?v=3","gravatar_id":"","url":"https://api.github.com/users/shalabhsuman","html_url":"https://github.com/shalabhsuman","followers_url":"https://api.github.com/users/shalabhsuman/followers","following_url":"https://api.github.com/users/shalabhsuman/following{/other_user}","gists_url":"https://api.github.com/users/shalabhsuman/gists{/gist_id}","starred_url":"https://api.github.com/users/shalabhsuman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shalabhsuman/subscriptions","organizations_url":"https://api.github.com/users/shalabhsuman/orgs","repos_url":"https://api.github.com/users/shalabhsuman/repos","events_url":"https://api.github.com/users/shalabhsuman/events{/privacy}","received_events_url":"https://api.github.com/users/shalabhsuman/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2015-05-20T01:50:09Z","updated_at":"2017-01-16T18:15:16Z","closed_at":"2015-05-26T13:27:58Z","body":"**_Hello,**_\n\n**_I am trying to compile Mothur on a Mac machine and after running the \"make\" command inside the \"source\" directory, I get the following log (attached). But I am unable to run mothur in interactive-mode, after the compilation is finished. Does anyone have an idea what I am missing here??**_\n\n**_Thanks,**_\n**_Shalabh**_\n\n***_LOG Attached**_*\n\n```\nc++ -O3 -DBIT_VERSION -DRELEASE_DATE=\"\\\"3/23/2014\\\"\" -DVERSION=\"\\\"1.35.0\\\"\" -DUSE_READLINE -I.  -I calculators/  -I chimera/  -I classifier/  -I clearcut/  -I commands/  -I communitytype/  -I datastructures/  -I metastats/  -I randomforest/  -I read/  -I svm/  -arch x86_64 -c -o weightedlinkage.o weightedlinkage.cpp\nc++ -O3 -DBIT_VERSION -DRELEASE_DATE=\"\\\"3/23/2014\\\"\" -DVERSION=\"\\\"1.35.0\\\"\" -DUSE_READLINE -I.  -I calculators/  -I chimera/  -I classifier/  -I clearcut/  -I commands/  -I communitytype/  -I datastructures/  -I metastats/  -I randomforest/  -I read/  -I svm/  -arch x86_64 -c -o wilcox.o wilcox.cpp\ncd uchime_src && ./mk && mv uchime .. && cd ..\naddtargets2\nalignchime\nalignchimel\nalnparams\nalpha\nalpha2\nfractid\nfractid.cpp:182:28: warning: '&&' within '||' [-Wlogical-op-parentheses]\n                if (c == 'D' || c == 'I' && (p == Path || p[-1] == 'M'))\n                             ~~ ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\nfractid.cpp:182:28: note: place parentheses around the '&&' expression to silence this warning\n                if (c == 'D' || c == 'I' && (p == Path || p[-1] == 'M'))\n                                         ^\n                                (                                      )\n1 warning generated.\ngetparents\nglobalalign2\nmake3way\nmx\nmyutils\npath\nsearchchime\nseqdb\nsetnucmx\nsfasta\ntracebackbit\nuchime_main\nusort\nviterbifast\nwritechhit\n-rwxr-xr-x  1 sumans  NIH\\Domain Users   273K May 19 21:13 uchime\n65265 274 uchime\nc++  -Lcalculators/  -Lchimera/  -Lclassifier/  -Lclearcut/  -Lcommands/  -Lcommunitytype/  -Ldatastructures/  -Lmetastats/  -Lrandomforest/  -Lread/  -Lsvm/ -arch x86_64 -o mothur calculators/ace.o calculators/bergerparker.o calculators/boneh.o calculators/bootstrap.o calculators/bstick.o calculators/calculator.o calculators/canberra.o calculators/chao1.o calculators/coverage.o calculators/efron.o calculators/geom.o calculators/goodscoverage.o calculators/gower.o calculators/hamming.o calculators/heip.o calculators/hellinger.o calculators/invsimpson.o calculators/jackknife.o calculators/logsd.o calculators/manhattan.o calculators/memchi2.o calculators/memchord.o calculators/memeuclidean.o calculators/mempearson.o calculators/npshannon.o calculators/odum.o calculators/parsimony.o calculators/prng.o calculators/qstat.o calculators/shannon.o calculators/shannoneven.o calculators/shannonrange.o calculators/sharedace.o calculators/sharedanderbergs.o calculators/sharedbraycurtis.o calculators/sharedchao1.o calculators/sharedjabund.o calculators/sharedjackknife.o calculators/sharedjclass.o calculators/sharedjest.o calculators/sharedjsd.o calculators/sharedkstest.o calculators/sharedkulczynski.o calculators/sharedkulczynskicody.o calculators/sharedlennon.o calculators/sharedmarczewski.o calculators/sharedmorisitahorn.o calculators/sharedochiai.o calculators/sharedrjsd.o calculators/sharedsobs.o calculators/sharedsobscollectsummary.o calculators/sharedsorabund.o calculators/sharedsorclass.o calculators/sharedsorest.o calculators/sharedthetan.o calculators/sharedthetayc.o calculators/shen.o calculators/simpson.o calculators/simpsoneven.o calculators/smithwilson.o calculators/soergel.o calculators/solow.o calculators/spearman.o calculators/speciesprofile.o calculators/structchi2.o calculators/structchord.o calculators/structeuclidean.o calculators/structkulczynski.o calculators/structpearson.o calculators/unweighted.o calculators/uvest.o calculators/weighted.o calculators/whittaker.o chimera/bellerophon.o chimera/ccode.o chimera/chimera.o chimera/chimeracheckrdp.o chimera/chimerarealigner.o chimera/chimeraslayer.o chimera/decalc.o chimera/maligner.o chimera/myPerseus.o chimera/pintail.o chimera/slayer.o classifier/alignnode.o classifier/aligntree.o classifier/bayesian.o classifier/classify.o classifier/kmernode.o classifier/kmertree.o classifier/knn.o classifier/phylosummary.o classifier/phylotree.o classifier/taxonomyequalizer.o classifier/taxonomynode.o clearcut/clearcut.o clearcut/cmdargs.o clearcut/distclearcut.o clearcut/dmat.o clearcut/fasta.o clearcut/getopt_long.o commands/aligncommand.o commands/amovacommand.o commands/anosimcommand.o commands/binsequencecommand.o commands/catchallcommand.o commands/chimerabellerophoncommand.o commands/chimeraccodecommand.o commands/chimeracheckcommand.o commands/chimeraperseuscommand.o commands/chimerapintailcommand.o commands/chimeraslayercommand.o commands/chimerauchimecommand.o commands/chopseqscommand.o commands/classifyotucommand.o commands/classifyrfsharedcommand.o commands/classifyseqscommand.o commands/classifysvmsharedcommand.o commands/classifytreecommand.o commands/clearcutcommand.o commands/clearmemorycommand.o commands/clustercommand.o commands/clusterdoturcommand.o commands/clusterfragmentscommand.o commands/clustersplitcommand.o commands/collectcommand.o commands/collectsharedcommand.o commands/consensusseqscommand.o commands/cooccurrencecommand.o commands/corraxescommand.o commands/countgroupscommand.o commands/countseqscommand.o commands/createdatabasecommand.o commands/deconvolutecommand.o commands/degapseqscommand.o commands/deuniqueseqscommand.o commands/deuniquetreecommand.o commands/distancecommand.o commands/filterseqscommand.o commands/filtersharedcommand.o commands/getcommandinfocommand.o commands/getcoremicrobiomecommand.o commands/getcurrentcommand.o commands/getdistscommand.o commands/getgroupcommand.o commands/getgroupscommand.o commands/getlabelcommand.o commands/getlineagecommand.o commands/getlistcountcommand.o commands/getmetacommunitycommand.o commands/getmimarkspackagecommand.o commands/getotulabelscommand.o commands/getoturepcommand.o commands/getotuscommand.o commands/getrabundcommand.o commands/getrelabundcommand.o commands/getsabundcommand.o commands/getseqscommand.o commands/getsharedotucommand.o commands/hclustercommand.o commands/heatmapcommand.o commands/heatmapsimcommand.o commands/helpcommand.o commands/homovacommand.o commands/indicatorcommand.o commands/kruskalwalliscommand.o commands/lefsecommand.o commands/libshuffcommand.o commands/listotulabelscommand.o commands/listseqscommand.o commands/loadlogfilecommand.o commands/makebiomcommand.o commands/makecontigscommand.o commands/makefastqcommand.o commands/makegroupcommand.o commands/makelefsecommand.o commands/makelookupcommand.o commands/mantelcommand.o commands/matrixoutputcommand.o commands/mergefilecommand.o commands/mergegroupscommand.o commands/mergesfffilecommand.o commands/mergetaxsummarycommand.o commands/metastatscommand.o commands/mgclustercommand.o commands/mimarksattributescommand.o commands/newcommandtemplate.o commands/nmdscommand.o commands/nocommands.o commands/normalizesharedcommand.o commands/otuassociationcommand.o commands/otuhierarchycommand.o commands/pairwiseseqscommand.o commands/parsefastaqcommand.o commands/parselistscommand.o commands/parsimonycommand.o commands/pcacommand.o commands/pcoacommand.o commands/phylodiversitycommand.o commands/phylotypecommand.o commands/pipelinepdscommand.o commands/prcseqscommand.o commands/preclustercommand.o commands/primerdesigncommand.o commands/quitcommand.o commands/rarefactcommand.o commands/rarefactsharedcommand.o commands/removedistscommand.o commands/removegroupscommand.o commands/removelineagecommand.o commands/removeotulabelscommand.o commands/removeotuscommand.o commands/removerarecommand.o commands/removeseqscommand.o commands/renameseqscommand.o commands/reversecommand.o commands/screenseqscommand.o commands/secondarystructurecommand.o commands/sensspeccommand.o commands/seqerrorcommand.o commands/seqsummarycommand.o commands/setcurrentcommand.o commands/setdircommand.o commands/setlogfilecommand.o commands/sffinfocommand.o commands/sffmultiplecommand.o commands/sharedcommand.o commands/shhhercommand.o commands/shhhseqscommand.o commands/sortseqscommand.o commands/sparcccommand.o commands/splitabundcommand.o commands/splitgroupscommand.o commands/sracommand.o commands/subsamplecommand.o commands/summarycommand.o commands/summaryqualcommand.o commands/summarysharedcommand.o commands/summarytaxcommand.o commands/systemcommand.o commands/treegroupscommand.o commands/trimflowscommand.o commands/trimseqscommand.o commands/unifracunweightedcommand.o commands/unifracweightedcommand.o commands/venncommand.o communitytype/communitytype.o communitytype/kmeans.o communitytype/pam.o communitytype/qFinderDMM.o datastructures/alignment.o datastructures/alignmentcell.o datastructures/alignmentdb.o datastructures/blastalign.o datastructures/blastdb.o datastructures/counttable.o datastructures/database.o datastructures/designmap.o datastructures/distancedb.o datastructures/fastamap.o datastructures/fastqread.o datastructures/flowdata.o datastructures/fullmatrix.o datastructures/groupmap.o datastructures/kmer.o datastructures/kmeralign.o datastructures/kmerdb.o datastructures/listvector.o datastructures/nameassignment.o datastructures/oligos.o datastructures/ordervector.o datastructures/qualityscores.o datastructures/rabundvector.o datastructures/referencedb.o datastructures/reportfile.o datastructures/sabundvector.o datastructures/sequence.o datastructures/sequencecountparser.o datastructures/sequencedb.o datastructures/sequenceparser.o datastructures/sharedlistvector.o datastructures/sharedordervector.o datastructures/sharedrabundfloatvector.o datastructures/sharedrabundvector.o datastructures/sharedsabundvector.o datastructures/sparsedistancematrix.o datastructures/sparsematrix.o datastructures/suffixdb.o datastructures/suffixnodes.o datastructures/suffixtree.o datastructures/tree.o datastructures/treemap.o datastructures/treenode.o metastats/mothurfisher.o metastats/mothurmetastats.o metastats/spline.o randomforest/abstractdecisiontree.o randomforest/abstractrandomforest.o randomforest/decisiontree.o randomforest/forest.o randomforest/randomforest.o randomforest/regularizeddecisiontree.o randomforest/regularizedrandomforest.o randomforest/rftreenode.o read/formatcolumn.o read/formatphylip.o read/readblast.o read/readcluster.o read/readcolumn.o read/readphylip.o read/readphylipvector.o read/readtree.o read/splitmatrix.o read/treereader.o svm/svm.o  averagelinkage.o calcsparcc.o cluster.o clusterclassic.o collect.o commandfactory.o commandoptionparser.o completelinkage.o consensus.o dlibshuff.o engine.o fileoutput.o gotohoverlap.o hcluster.o heatmap.o heatmapsim.o inputdata.o libshuff.o linearalgebra.o mothur.o mothurout.o myseqdist.o nast.o nastreport.o needlemanoverlap.o noalign.o optionparser.o overlap.o progress.o randomnumber.o rarecalc.o raredisplay.o rarefact.o refchimeratest.o seqnoise.o sharedutilities.o singlelinkage.o slibshuff.o subsample.o trialSwap2.o trimoligos.o validcalculator.o validparameter.o venn.o weightedlinkage.o wilcox.o  bsplvb.o bsplvd.o bvalue.o daxpy.o ddot.o dpbfa.o dpbsl.o interv.o intrv.o sgram.o sinerp.o sslvrg.o stxwx.o -lreadline -lncurses\nstrip mothur\n```\n"},"comment":{"url":"https://api.github.com/repos/mothur/mothur/issues/comments/272930732","html_url":"https://github.com/mothur/mothur/issues/86#issuecomment-272930732","issue_url":"https://api.github.com/repos/mothur/mothur/issues/86","id":272930732,"user":{"login":"ramiro-caso","id":18744967,"avatar_url":"https://avatars.githubusercontent.com/u/18744967?v=3","gravatar_id":"","url":"https://api.github.com/users/ramiro-caso","html_url":"https://github.com/ramiro-caso","followers_url":"https://api.github.com/users/ramiro-caso/followers","following_url":"https://api.github.com/users/ramiro-caso/following{/other_user}","gists_url":"https://api.github.com/users/ramiro-caso/gists{/gist_id}","starred_url":"https://api.github.com/users/ramiro-caso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramiro-caso/subscriptions","organizations_url":"https://api.github.com/users/ramiro-caso/orgs","repos_url":"https://api.github.com/users/ramiro-caso/repos","events_url":"https://api.github.com/users/ramiro-caso/events{/privacy}","received_events_url":"https://api.github.com/users/ramiro-caso/received_events","type":"User","site_admin":false},"created_at":"2017-01-16T18:15:16Z","updated_at":"2017-01-16T18:15:16Z","body":"Hi!\r\nI tried to build mothur in a macbook pro with macOS Sierra 10.12.2. All goes well until this error happen:\r\n`c++ -DBIT_VERSION -O3 -DRELEASE_DATE=\"\\\"8/9/2016\\\"\" -DVERSION=\"\\\"1.38.1\\\"\" -O3 -DMOTHUR_FILES= -DUSE_READLINE -DUSE_BOOST -I /opt/local+quartz/include/ -I.  -I source/  -I source/calculators/  -I source/chimera/  -I source/classifier/  -I source/clearcut/  -I source/commands/  -I source/communitytype/  -I source/datastructures/  -I source/metastats/  -I source/randomforest/  -I source/read/  -I source/svm/   -c -o source/mothur.o source/mothur.cpp\r\nsource/mothur.cpp:52:30: error: expected expression\r\n                        string temp = MOTHUR_FILES; \r\n                                                  ^\r\n1 error generated.\r\nmake: *** [source/mothur.o] Error 1`\r\n\r\nIn my Makefile I have:\r\n`64BIT_VERSION ?= yes\r\nOPTIMIZE ?= yes\r\nUSEREADLINE ?= yes\r\nUSEBOOST ?= yes\r\nBOOST_LIBRARY_DIR=/opt/local+quartz/lib/\r\nBOOST_INCLUDE_DIR=/opt/local+quartz/include/\r\nMOTHUR_FILES=\r\nRELEASE_DATE = \"\\\"8/9/2016\\\"\"\r\nVERSION = \"\\\"1.38.1\\\"\"`\r\n\r\nCan someone help me please?"}}
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