Hi all, The problem can be fixed following these steps:
1. Revert the commit ff8928540e0d720b8a08ee4227c1bbadc2c1e733 (now, that is the last commit). 2. Apply this patch: >--- a/Makefile >+++ b/Makefile >@@ -118,8 +118,8 @@ endif ># > 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)) >+ OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.cpp)) >+ OBJECTS+=$(patsubst %.c,%.o,$(wildcard source/*.c)) > > mothur : $(OBJECTS) uchime > $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) In fact, the ff8928540e0d720b8a08ee4227c1bbadc2c1e733 was applied toward a wrong Makefile, not the top one. Regards, Hamid On Mon, Nov 8, 2021 at 4:25 PM Andreas Tille <ti...@debian.org> wrote: > > Am Mon, Oct 25, 2021 at 09:16:30PM -0400 schrieb Aaron M. Ucko: > > Andreas Tille <ti...@debian.org> writes: > > > > > I'm wondering why the makefile stopped working just because a new compiler > > > version is used. :-( > > > > Along the way, you pulled in a new upstream version, whose makefile > > evidently wasn't quite right. > > I think I've found the reason for the failure: It is the overlong line: > > > g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -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/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/kimura.o source/calculators/kmerdist.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 sg++ > -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -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/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/kimura.o source/calculators/kmerdist.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/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 > sour/usr/bin/ld: source/commands/unifracweightedcommand.o: warning: > relocation against `_ZTV10ColumnFile' in read-only section `.text.unlikely' > > > (Just mind the end > > ...source/commands/summarycommand.o sour/usr/bin/ld: > source/commands/unifracweightedcommand.o: warning: relocation against > `_ZTV10ColumnFile' in read-only section `.text.unlikely' > > which has an incomplete number of arguments that is interrupted > by '/usr/bin/ld') > > Any idea how to specify the number of object files more sensibly > to not explode the command line arguments too much? > > Kind regards > > Andreas. > > -- > http://fam-tille.de >
