printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild mothur 2>&1 The package 'mothur' will be built without being installed. Reading build dependency for mothur-1.33.3-2... Reading dependency for mothur-1.33.3-2... Reading build conflict for mothur-1.33.3-2... The package 'gcc49-compiler' will be installed. Reading dependency for gcc49-compiler-4.9.1-1000... Reading runtime dependency for gcc49-compiler-4.9.1-1000... The package 'libncurses5' will be installed. Reading dependency for libncurses5-5.9-20110507-1... Reading runtime dependency for libncurses5-5.9-20110507-1... The package 'openmpi' will be installed. Reading dependency for openmpi-1.8.1-3... Reading runtime dependency for openmpi-1.8.1-3... The package 'readline6' will be installed. Reading dependency for readline6-6.3.6-1... Reading runtime dependency for readline6-6.3.6-1... The package 'gcc49-shlibs' will be installed. Reading dependency for gcc49-shlibs-4.9.1-1000... Reading runtime dependency for gcc49-shlibs-4.9.1-1000... The package 'openmpi-shlibs' will be installed. Reading dependency for openmpi-shlibs-1.8.1-3... Reading runtime dependency for openmpi-shlibs-1.8.1-3... The package 'readline6-shlibs' will be installed. Reading dependency for readline6-shlibs-6.3.6-1... Reading runtime dependency for readline6-shlibs-6.3.6-1... The package 'gmp5-shlibs' will be installed. Reading dependency for gmp5-shlibs-6.0.0a-1... Reading runtime dependency for gmp5-shlibs-6.0.0a-1... The package 'libgmpxx5-shlibs' will be installed. Reading dependency for libgmpxx5-shlibs-6.0.0a-1... Reading runtime dependency for libgmpxx5-shlibs-6.0.0a-1... The package 'libmpfr4-shlibs' will be installed. Reading dependency for libmpfr4-shlibs-3.1.2-1... Reading runtime dependency for libmpfr4-shlibs-3.1.2-1... The package 'cloog-org2-shlibs' will be installed. Reading dependency for cloog-org2-shlibs-0.18.2-1... Reading runtime dependency for cloog-org2-shlibs-0.18.2-1... The package 'isl-shlibs' will be installed. Reading dependency for isl-shlibs-0.12.2-2... Reading runtime dependency for isl-shlibs-0.12.2-2... The package 'libmpc3-shlibs' will be installed. Reading dependency for libmpc3-shlibs-1.0.2-1... Reading runtime dependency for libmpc3-shlibs-1.0.2-1... The package 'hwloc' will be installed. Reading dependency for hwloc-1.9-1... Reading runtime dependency for hwloc-1.9-1... The package 'hwloc-shlibs' will be installed. Reading dependency for hwloc-shlibs-1.9-1... Reading runtime dependency for hwloc-shlibs-1.9-1... The following package will be rebuilt: mothur The following 15 additional packages will be installed: cloog-org2-shlibs gcc49-compiler gcc49-shlibs gmp5-shlibs hwloc hwloc-shlibs isl-shlibs libgmpxx5-shlibs libmpc3-shlibs libmpfr4-shlibs libncurses5 openmpi openmpi-shlibs readline6 readline6-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/Mothur.1.33.3.zip % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 1 2134k 1 41750 0 0 98650 0 0:00:22 --:--:-- 0:00:22 98466 24 2134k 24 518k 0 0 283k 0 0:00:07 0:00:01 0:00:06 282k 39 2134k 39 832k 0 0 344k 0 0:00:06 0:00:02 0:00:04 344k 79 2134k 79 1695k 0 0 496k 0 0:00:04 0:00:03 0:00:01 495k 100 2134k 100 2134k 0 0 563k 0 0:00:03 0:00:03 --:--:-- 563k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/hwloc_1.9-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/hwloc-shlibs_1.9-1_darwin-x86_64.deb Selecting previously deselected package hwloc. (Reading database ... 4740 files and directories currently installed.) Unpacking hwloc (from .../hwloc_1.9-1_darwin-x86_64.deb) ... Selecting previously deselected package hwloc-shlibs. Unpacking hwloc-shlibs (from .../hwloc-shlibs_1.9-1_darwin-x86_64.deb) ... Setting up hwloc-shlibs (1.9-1) ... Setting up hwloc (1.9-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb Selecting previously deselected package libgmpxx5-shlibs. (Reading database ... 4787 files and directories currently installed.) Unpacking libgmpxx5-shlibs (from .../libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Selecting previously deselected package gmp5-shlibs. Unpacking gmp5-shlibs (from .../gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Setting up gmp5-shlibs (6.0.0a-1) ... Setting up libgmpxx5-shlibs (6.0.0a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb Selecting previously deselected package libmpfr4-shlibs. (Reading database ... 4816 files and directories currently installed.) Unpacking libmpfr4-shlibs (from .../libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb) ... Setting up libmpfr4-shlibs (3.1.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/libncurses5_5.9-20110507-1_darwin-x86_64.deb Selecting previously deselected package libncurses5. (Reading database ... 4829 files and directories currently installed.) Unpacking libncurses5 (from .../libncurses5_5.9-20110507-1_darwin-x86_64.deb) ... Setting up libncurses5 (5.9-20110507-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/readline6_6.3.6-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/readline6-shlibs_6.3.6-1_darwin-x86_64.deb Selecting previously deselected package readline6. (Reading database ... 4878 files and directories currently installed.) Unpacking readline6 (from .../readline6_6.3.6-1_darwin-x86_64.deb) ... Selecting previously deselected package readline6-shlibs. Unpacking readline6-shlibs (from .../readline6-shlibs_6.3.6-1_darwin-x86_64.deb) ... Setting up readline6-shlibs (6.3.6-1) ... Setting up readline6 (6.3.6-1) ... * History: (history). The GNU history library API. install-info(/sw/share/info/history.info): creating new section `Libraries' * Readline: (readline). The GNU readline library API. * RLuserman: (rluserman). The GNU readline library User's Manual. Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/isl-shlibs_0.12.2-2_darwin-x86_64.deb Selecting previously deselected package isl-shlibs. (Reading database ... 4933 files and directories currently installed.) Unpacking isl-shlibs (from .../isl-shlibs_0.12.2-2_darwin-x86_64.deb) ... Setting up isl-shlibs (0.12.2-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpc3-shlibs_1.0.2-1_darwin-x86_64.deb Selecting previously deselected package libmpc3-shlibs. (Reading database ... 4934 files and directories currently installed.) Unpacking libmpc3-shlibs (from .../libmpc3-shlibs_1.0.2-1_darwin-x86_64.deb) ... Setting up libmpc3-shlibs (1.0.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/cloog-org2-shlibs_0.18.2-1_darwin-x86_64.deb Selecting previously deselected package cloog-org2-shlibs. (Reading database ... 4937 files and directories currently installed.) Unpacking cloog-org2-shlibs (from .../cloog-org2-shlibs_0.18.2-1_darwin-x86_64.deb) ... Setting up cloog-org2-shlibs (0.18.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc49-compiler_4.9.1-1000_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb Selecting previously deselected package gcc49-compiler. (Reading database ... 4938 files and directories currently installed.) Unpacking gcc49-compiler (from .../gcc49-compiler_4.9.1-1000_darwin-x86_64.deb) ... Selecting previously deselected package gcc49-shlibs. Unpacking gcc49-shlibs (from .../gcc49-shlibs_4.9.1-1000_darwin-x86_64.deb) ... Setting up gcc49-shlibs (4.9.1-1000) ... Clearing dependency_libs of .la files being installed Setting up gcc49-compiler (4.9.1-1000) ... Clearing dependency_libs of .la files being installed Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/openmpi_1.8.1-3_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.8.1-3_darwin-x86_64.deb Selecting previously deselected package openmpi. (Reading database ... 10475 files and directories currently installed.) Unpacking openmpi (from .../openmpi_1.8.1-3_darwin-x86_64.deb) ... Selecting previously deselected package openmpi-shlibs. Unpacking openmpi-shlibs (from .../openmpi-shlibs_1.8.1-3_darwin-x86_64.deb) ... Setting up openmpi-shlibs (1.8.1-3) ... Setting up openmpi (1.8.1-3) ... Clearing dependency_libs of .la files being installed Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-mothur-1.33.3-2 /sw/build.build dpkg-deb: building package `fink-buildlock-mothur-1.33.3-2' in `/sw/build.build/fink-buildlock-mothur-1.33.3-2_2014.08.05-06.15.44_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-mothur-1.33.3-2_2014.08.05-06.15.44_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-mothur-1.33.3-2. (Reading database ... 11859 files and directories currently installed.) Unpacking fink-buildlock-mothur-1.33.3-2 (from .../fink-buildlock-mothur-1.33.3-2_2014.08.05-06.15.44_darwin-x86_64.deb) ... Setting up fink-buildlock-mothur-1.33.3-2 (2014.08.05-06.15.44) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.CXs82 unzip -o /sw/src/Mothur.1.33.3.zip Archive: /sw/src/Mothur.1.33.3.zip creating: Mothur.source/ inflating: Mothur.source/.DS_Store creating: __MACOSX/ creating: __MACOSX/Mothur.source/ inflating: __MACOSX/Mothur.source/._.DS_Store inflating: Mothur.source/abstractdecisiontree.cpp inflating: __MACOSX/Mothur.source/._abstractdecisiontree.cpp inflating: Mothur.source/abstractdecisiontree.hpp inflating: __MACOSX/Mothur.source/._abstractdecisiontree.hpp inflating: Mothur.source/abstractrandomforest.cpp inflating: Mothur.source/abstractrandomforest.hpp inflating: Mothur.source/ace.cpp inflating: Mothur.source/ace.h inflating: Mothur.source/aligncommand.cpp inflating: __MACOSX/Mothur.source/._aligncommand.cpp inflating: Mothur.source/aligncommand.h inflating: __MACOSX/Mothur.source/._aligncommand.h inflating: Mothur.source/alignment.cpp inflating: Mothur.source/alignment.hpp inflating: Mothur.source/alignmentcell.cpp inflating: Mothur.source/alignmentcell.hpp inflating: Mothur.source/alignmentdb.cpp inflating: Mothur.source/alignmentdb.h inflating: Mothur.source/alignnode.cpp inflating: Mothur.source/alignnode.h inflating: Mothur.source/aligntree.cpp inflating: Mothur.source/aligntree.h inflating: Mothur.source/amovacommand.cpp inflating: Mothur.source/amovacommand.h inflating: Mothur.source/anosimcommand.cpp inflating: Mothur.source/anosimcommand.h inflating: Mothur.source/averagelinkage.cpp inflating: Mothur.source/bayesian.cpp inflating: Mothur.source/bayesian.h inflating: Mothur.source/bellerophon.cpp inflating: Mothur.source/bellerophon.h inflating: Mothur.source/bergerparker.cpp inflating: Mothur.source/bergerparker.h inflating: Mothur.source/binsequencecommand.cpp inflating: Mothur.source/binsequencecommand.h inflating: Mothur.source/blastalign.cpp inflating: Mothur.source/blastalign.hpp inflating: Mothur.source/blastdb.cpp inflating: __MACOSX/Mothur.source/._blastdb.cpp inflating: Mothur.source/blastdb.hpp inflating: Mothur.source/boneh.cpp inflating: Mothur.source/boneh.h inflating: Mothur.source/bootstrap.cpp inflating: Mothur.source/bootstrap.h inflating: Mothur.source/bsplvb.f inflating: Mothur.source/bsplvd.f inflating: Mothur.source/bstick.cpp inflating: Mothur.source/bstick.h inflating: Mothur.source/bvalue.f inflating: Mothur.source/calcsparcc.cpp inflating: Mothur.source/calcsparcc.h inflating: Mothur.source/calculator.cpp inflating: Mothur.source/calculator.h inflating: Mothur.source/canberra.cpp inflating: Mothur.source/canberra.h inflating: Mothur.source/catchallcommand.cpp inflating: Mothur.source/catchallcommand.h inflating: Mothur.source/ccode.cpp inflating: Mothur.source/ccode.h inflating: Mothur.source/chao1.cpp inflating: Mothur.source/chao1.h inflating: Mothur.source/chimera.cpp inflating: Mothur.source/chimera.h inflating: Mothur.source/chimerabellerophoncommand.cpp inflating: Mothur.source/chimerabellerophoncommand.h inflating: Mothur.source/chimeraccodecommand.cpp inflating: Mothur.source/chimeraccodecommand.h inflating: Mothur.source/chimeracheckcommand.cpp inflating: Mothur.source/chimeracheckcommand.h inflating: Mothur.source/chimeracheckrdp.cpp inflating: Mothur.source/chimeracheckrdp.h inflating: Mothur.source/chimeraperseuscommand.cpp inflating: __MACOSX/Mothur.source/._chimeraperseuscommand.cpp inflating: Mothur.source/chimeraperseuscommand.h inflating: Mothur.source/chimerapintailcommand.cpp inflating: Mothur.source/chimerapintailcommand.h inflating: Mothur.source/chimerarealigner.cpp inflating: Mothur.source/chimerarealigner.h inflating: Mothur.source/chimeraslayer.cpp inflating: Mothur.source/chimeraslayer.h inflating: Mothur.source/chimeraslayercommand.cpp inflating: __MACOSX/Mothur.source/._chimeraslayercommand.cpp inflating: Mothur.source/chimeraslayercommand.h inflating: Mothur.source/chimerauchimecommand.cpp inflating: __MACOSX/Mothur.source/._chimerauchimecommand.cpp inflating: Mothur.source/chimerauchimecommand.h inflating: Mothur.source/chopseqscommand.cpp inflating: Mothur.source/chopseqscommand.h inflating: Mothur.source/classify.cpp inflating: Mothur.source/classify.h inflating: Mothur.source/classifyotucommand.cpp inflating: __MACOSX/Mothur.source/._classifyotucommand.cpp inflating: Mothur.source/classifyotucommand.h inflating: Mothur.source/classifyrfsharedcommand.cpp inflating: Mothur.source/classifyrfsharedcommand.h inflating: Mothur.source/classifyseqscommand.cpp inflating: __MACOSX/Mothur.source/._classifyseqscommand.cpp inflating: Mothur.source/classifyseqscommand.h inflating: __MACOSX/Mothur.source/._classifyseqscommand.h inflating: Mothur.source/classifysharedcommand.cpp inflating: __MACOSX/Mothur.source/._classifysharedcommand.cpp inflating: Mothur.source/classifysharedcommand.h inflating: __MACOSX/Mothur.source/._classifysharedcommand.h inflating: Mothur.source/classifytreecommand.cpp inflating: Mothur.source/classifytreecommand.h inflating: Mothur.source/clearcut.cpp inflating: Mothur.source/clearcut.h inflating: Mothur.source/clearcutcommand.cpp inflating: Mothur.source/clearcutcommand.h inflating: Mothur.source/clearmemorycommand.cpp inflating: Mothur.source/clearmemorycommand.h inflating: Mothur.source/cluster.cpp inflating: Mothur.source/cluster.hpp inflating: Mothur.source/clusterclassic.cpp inflating: Mothur.source/clusterclassic.h inflating: Mothur.source/clustercommand.cpp inflating: Mothur.source/clustercommand.h inflating: Mothur.source/clusterdoturcommand.cpp inflating: Mothur.source/clusterdoturcommand.h inflating: Mothur.source/clusterfragmentscommand.cpp inflating: Mothur.source/clusterfragmentscommand.h inflating: Mothur.source/clustersplitcommand.cpp inflating: Mothur.source/clustersplitcommand.h inflating: Mothur.source/cmdargs.cpp inflating: Mothur.source/cmdargs.h inflating: Mothur.source/collect.cpp inflating: Mothur.source/collect.h inflating: Mothur.source/collectcommand.cpp inflating: Mothur.source/collectcommand.h inflating: Mothur.source/collectdisplay.h inflating: Mothur.source/collectorscurvedata.h inflating: Mothur.source/collectsharedcommand.cpp inflating: __MACOSX/Mothur.source/._collectsharedcommand.cpp inflating: Mothur.source/collectsharedcommand.h inflating: Mothur.source/command.hpp inflating: Mothur.source/commandfactory.cpp inflating: __MACOSX/Mothur.source/._commandfactory.cpp inflating: Mothur.source/commandfactory.hpp inflating: __MACOSX/Mothur.source/._commandfactory.hpp inflating: Mothur.source/commandoptionparser.cpp inflating: Mothur.source/commandoptionparser.hpp inflating: Mothur.source/commandparameter.h inflating: Mothur.source/common.h inflating: Mothur.source/communitytype.cpp inflating: __MACOSX/Mothur.source/._communitytype.cpp inflating: Mothur.source/communitytype.h inflating: __MACOSX/Mothur.source/._communitytype.h inflating: Mothur.source/completelinkage.cpp inflating: Mothur.source/consensus.cpp inflating: Mothur.source/consensus.h inflating: Mothur.source/consensusseqscommand.cpp inflating: Mothur.source/consensusseqscommand.h inflating: Mothur.source/cooccurrencecommand.cpp inflating: Mothur.source/cooccurrencecommand.h inflating: Mothur.source/corraxescommand.cpp inflating: Mothur.source/corraxescommand.h inflating: Mothur.source/countgroupscommand.cpp inflating: Mothur.source/countgroupscommand.h inflating: Mothur.source/countseqscommand.cpp inflating: Mothur.source/countseqscommand.h inflating: Mothur.source/counttable.cpp inflating: Mothur.source/counttable.h inflating: Mothur.source/coverage.cpp inflating: Mothur.source/coverage.h inflating: Mothur.source/createdatabasecommand.cpp inflating: __MACOSX/Mothur.source/._createdatabasecommand.cpp inflating: Mothur.source/createdatabasecommand.h inflating: Mothur.source/currentfile.h inflating: Mothur.source/database.cpp inflating: Mothur.source/database.hpp inflating: Mothur.source/datavector.hpp inflating: Mothur.source/daxpy.f inflating: Mothur.source/dayhoff.h inflating: Mothur.source/ddot.f inflating: Mothur.source/decalc.cpp inflating: Mothur.source/decalc.h inflating: Mothur.source/decisiontree.cpp inflating: Mothur.source/decisiontree.hpp inflating: Mothur.source/deconvolutecommand.cpp inflating: Mothur.source/deconvolutecommand.h inflating: Mothur.source/degapseqscommand.cpp inflating: Mothur.source/degapseqscommand.h inflating: Mothur.source/designmap.cpp inflating: Mothur.source/designmap.h inflating: Mothur.source/deuniqueseqscommand.cpp inflating: __MACOSX/Mothur.source/._deuniqueseqscommand.cpp inflating: Mothur.source/deuniqueseqscommand.h inflating: Mothur.source/deuniquetreecommand.cpp inflating: Mothur.source/deuniquetreecommand.h inflating: Mothur.source/display.h inflating: Mothur.source/dist.h inflating: Mothur.source/distancecommand.cpp inflating: Mothur.source/distancecommand.h inflating: Mothur.source/distancedb.cpp inflating: Mothur.source/distancedb.hpp inflating: Mothur.source/distclearcut.cpp inflating: Mothur.source/distclearcut.h inflating: Mothur.source/dlibshuff.cpp inflating: Mothur.source/dlibshuff.h inflating: Mothur.source/dmat.cpp inflating: Mothur.source/dmat.h inflating: Mothur.source/dpbfa.f inflating: Mothur.source/dpbsl.f inflating: Mothur.source/eachgapdist.h inflating: Mothur.source/eachgapdistignorens.h inflating: Mothur.source/eachgapignore.h inflating: Mothur.source/efron.cpp inflating: Mothur.source/efron.h inflating: Mothur.source/endiannessmacros.h inflating: Mothur.source/engine.cpp inflating: Mothur.source/engine.hpp inflating: Mothur.source/fasta.cpp inflating: Mothur.source/fasta.h inflating: Mothur.source/fastamap.cpp inflating: Mothur.source/fastamap.h inflating: Mothur.source/fileoutput.cpp inflating: Mothur.source/fileoutput.h inflating: Mothur.source/filters.h inflating: Mothur.source/filterseqscommand.cpp inflating: Mothur.source/filterseqscommand.h inflating: Mothur.source/filtersharedcommand.cpp inflating: Mothur.source/filtersharedcommand.h inflating: Mothur.source/flowdata.cpp inflating: Mothur.source/flowdata.h inflating: Mothur.source/forest.cpp inflating: Mothur.source/forest.h inflating: Mothur.source/formatcolumn.cpp inflating: Mothur.source/formatcolumn.h inflating: Mothur.source/formatmatrix.h inflating: Mothur.source/formatphylip.cpp inflating: Mothur.source/formatphylip.h inflating: Mothur.source/fullmatrix.cpp inflating: Mothur.source/fullmatrix.h inflating: Mothur.source/geom.cpp inflating: Mothur.source/geom.h inflating: Mothur.source/getcommandinfocommand.cpp inflating: Mothur.source/getcommandinfocommand.h inflating: Mothur.source/getcoremicrobiomecommand.cpp inflating: Mothur.source/getcoremicrobiomecommand.h inflating: Mothur.source/getcurrentcommand.cpp inflating: __MACOSX/Mothur.source/._getcurrentcommand.cpp inflating: Mothur.source/getcurrentcommand.h inflating: 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Mothur.source/summarytaxcommand.h inflating: __MACOSX/Mothur.source/._summarytaxcommand.h inflating: Mothur.source/systemcommand.cpp inflating: Mothur.source/systemcommand.h inflating: Mothur.source/taxonomyequalizer.cpp inflating: Mothur.source/taxonomyequalizer.h inflating: Mothur.source/taxonomynode.cpp inflating: Mothur.source/taxonomynode.h inflating: Mothur.source/tree.cpp inflating: Mothur.source/tree.h inflating: Mothur.source/treecalculator.h inflating: Mothur.source/treegroupscommand.cpp inflating: Mothur.source/treegroupscommand.h inflating: Mothur.source/treemap.cpp inflating: Mothur.source/treemap.h inflating: Mothur.source/treenode.cpp inflating: Mothur.source/treenode.h inflating: Mothur.source/treereader.cpp inflating: Mothur.source/treereader.h inflating: Mothur.source/trialSwap2.cpp inflating: Mothur.source/trialswap2.h inflating: Mothur.source/trimflowscommand.cpp inflating: Mothur.source/trimflowscommand.h inflating: Mothur.source/trimoligos.cpp inflating: Mothur.source/trimoligos.h inflating: Mothur.source/trimseqscommand.cpp inflating: Mothur.source/trimseqscommand.h creating: Mothur.source/uchime_src/ inflating: Mothur.source/uchime_src/addtargets2.cpp creating: __MACOSX/Mothur.source/uchime_src/ inflating: __MACOSX/Mothur.source/uchime_src/._addtargets2.cpp inflating: Mothur.source/uchime_src/addtargets2.o inflating: Mothur.source/uchime_src/alignchime.cpp inflating: __MACOSX/Mothur.source/uchime_src/._alignchime.cpp inflating: Mothur.source/uchime_src/alignchime.o inflating: Mothur.source/uchime_src/alignchimel.cpp inflating: __MACOSX/Mothur.source/uchime_src/._alignchimel.cpp inflating: Mothur.source/uchime_src/alignchimel.o inflating: Mothur.source/uchime_src/allocs.h inflating: __MACOSX/Mothur.source/uchime_src/._allocs.h inflating: Mothur.source/uchime_src/alnheuristics.h inflating: __MACOSX/Mothur.source/uchime_src/._alnheuristics.h inflating: Mothur.source/uchime_src/alnparams.cpp inflating: __MACOSX/Mothur.source/uchime_src/._alnparams.cpp inflating: Mothur.source/uchime_src/alnparams.h inflating: __MACOSX/Mothur.source/uchime_src/._alnparams.h inflating: Mothur.source/uchime_src/alnparams.o inflating: Mothur.source/uchime_src/alpha.cpp inflating: __MACOSX/Mothur.source/uchime_src/._alpha.cpp inflating: Mothur.source/uchime_src/alpha.h inflating: __MACOSX/Mothur.source/uchime_src/._alpha.h inflating: Mothur.source/uchime_src/alpha.o inflating: Mothur.source/uchime_src/alpha2.cpp inflating: __MACOSX/Mothur.source/uchime_src/._alpha2.cpp inflating: Mothur.source/uchime_src/alpha2.o inflating: Mothur.source/uchime_src/chainer.h inflating: __MACOSX/Mothur.source/uchime_src/._chainer.h inflating: Mothur.source/uchime_src/chime.h inflating: __MACOSX/Mothur.source/uchime_src/._chime.h inflating: Mothur.source/uchime_src/counters.h inflating: __MACOSX/Mothur.source/uchime_src/._counters.h inflating: Mothur.source/uchime_src/diagbox.h inflating: __MACOSX/Mothur.source/uchime_src/._diagbox.h inflating: Mothur.source/uchime_src/dp.h inflating: __MACOSX/Mothur.source/uchime_src/._dp.h inflating: Mothur.source/uchime_src/evalue.h inflating: __MACOSX/Mothur.source/uchime_src/._evalue.h inflating: Mothur.source/uchime_src/fractid.cpp inflating: __MACOSX/Mothur.source/uchime_src/._fractid.cpp inflating: Mothur.source/uchime_src/fractid.o inflating: Mothur.source/uchime_src/getparents.cpp inflating: __MACOSX/Mothur.source/uchime_src/._getparents.cpp inflating: Mothur.source/uchime_src/getparents.o inflating: Mothur.source/uchime_src/globalalign2.cpp inflating: __MACOSX/Mothur.source/uchime_src/._globalalign2.cpp inflating: Mothur.source/uchime_src/globalalign2.o inflating: Mothur.source/uchime_src/help.h inflating: __MACOSX/Mothur.source/uchime_src/._help.h inflating: Mothur.source/uchime_src/hsp.h inflating: __MACOSX/Mothur.source/uchime_src/._hsp.h inflating: Mothur.source/uchime_src/hspfinder.h inflating: __MACOSX/Mothur.source/uchime_src/._hspfinder.h inflating: Mothur.source/uchime_src/make3way.cpp inflating: __MACOSX/Mothur.source/uchime_src/._make3way.cpp inflating: Mothur.source/uchime_src/make3way.o inflating: Mothur.source/uchime_src/mk inflating: __MACOSX/Mothur.source/uchime_src/._mk inflating: Mothur.source/uchime_src/mk.stderr extracting: Mothur.source/uchime_src/mk.stdout inflating: Mothur.source/uchime_src/mx.cpp inflating: __MACOSX/Mothur.source/uchime_src/._mx.cpp inflating: Mothur.source/uchime_src/mx.h inflating: __MACOSX/Mothur.source/uchime_src/._mx.h inflating: Mothur.source/uchime_src/mx.o inflating: Mothur.source/uchime_src/myopts.h inflating: __MACOSX/Mothur.source/uchime_src/._myopts.h inflating: Mothur.source/uchime_src/myutils.cpp inflating: __MACOSX/Mothur.source/uchime_src/._myutils.cpp inflating: Mothur.source/uchime_src/myutils.h inflating: __MACOSX/Mothur.source/uchime_src/._myutils.h inflating: Mothur.source/uchime_src/myutils.o inflating: Mothur.source/uchime_src/orf.h inflating: __MACOSX/Mothur.source/uchime_src/._orf.h inflating: Mothur.source/uchime_src/out.h inflating: __MACOSX/Mothur.source/uchime_src/._out.h inflating: Mothur.source/uchime_src/path.cpp inflating: __MACOSX/Mothur.source/uchime_src/._path.cpp inflating: Mothur.source/uchime_src/path.h inflating: __MACOSX/Mothur.source/uchime_src/._path.h inflating: Mothur.source/uchime_src/path.o inflating: Mothur.source/uchime_src/searchchime.cpp inflating: __MACOSX/Mothur.source/uchime_src/._searchchime.cpp inflating: Mothur.source/uchime_src/searchchime.o inflating: Mothur.source/uchime_src/seq.h inflating: __MACOSX/Mothur.source/uchime_src/._seq.h inflating: Mothur.source/uchime_src/seqdb.cpp inflating: __MACOSX/Mothur.source/uchime_src/._seqdb.cpp inflating: Mothur.source/uchime_src/seqdb.h inflating: __MACOSX/Mothur.source/uchime_src/._seqdb.h inflating: Mothur.source/uchime_src/seqdb.o inflating: Mothur.source/uchime_src/setnucmx.cpp inflating: __MACOSX/Mothur.source/uchime_src/._setnucmx.cpp inflating: Mothur.source/uchime_src/setnucmx.o inflating: Mothur.source/uchime_src/sfasta.cpp inflating: __MACOSX/Mothur.source/uchime_src/._sfasta.cpp inflating: Mothur.source/uchime_src/sfasta.h inflating: __MACOSX/Mothur.source/uchime_src/._sfasta.h inflating: Mothur.source/uchime_src/sfasta.o inflating: Mothur.source/uchime_src/svnmods.h inflating: __MACOSX/Mothur.source/uchime_src/._svnmods.h inflating: Mothur.source/uchime_src/svnversion.h inflating: __MACOSX/Mothur.source/uchime_src/._svnversion.h inflating: Mothur.source/uchime_src/timers.h inflating: __MACOSX/Mothur.source/uchime_src/._timers.h inflating: Mothur.source/uchime_src/timing.h inflating: __MACOSX/Mothur.source/uchime_src/._timing.h inflating: Mothur.source/uchime_src/tracebackbit.cpp inflating: __MACOSX/Mothur.source/uchime_src/._tracebackbit.cpp inflating: Mothur.source/uchime_src/tracebackbit.o inflating: Mothur.source/uchime_src/uc.h inflating: __MACOSX/Mothur.source/uchime_src/._uc.h inflating: Mothur.source/uchime_src/uchime_main.cpp inflating: __MACOSX/Mothur.source/uchime_src/._uchime_main.cpp inflating: Mothur.source/uchime_src/uchime_main.o inflating: Mothur.source/uchime_src/ultra.h inflating: __MACOSX/Mothur.source/uchime_src/._ultra.h inflating: Mothur.source/uchime_src/usort.cpp inflating: __MACOSX/Mothur.source/uchime_src/._usort.cpp inflating: Mothur.source/uchime_src/usort.o inflating: Mothur.source/uchime_src/viterbifast.cpp inflating: __MACOSX/Mothur.source/uchime_src/._viterbifast.cpp inflating: Mothur.source/uchime_src/viterbifast.o inflating: Mothur.source/uchime_src/windex.h inflating: __MACOSX/Mothur.source/uchime_src/._windex.h inflating: Mothur.source/uchime_src/writechhit.cpp inflating: __MACOSX/Mothur.source/uchime_src/._writechhit.cpp inflating: Mothur.source/uchime_src/writechhit.o inflating: __MACOSX/Mothur.source/._uchime_src inflating: Mothur.source/unifracunweightedcommand.cpp inflating: Mothur.source/unifracunweightedcommand.h inflating: Mothur.source/unifracweightedcommand.cpp inflating: __MACOSX/Mothur.source/._unifracweightedcommand.cpp inflating: Mothur.source/unifracweightedcommand.h inflating: Mothur.source/unweighted.cpp inflating: __MACOSX/Mothur.source/._unweighted.cpp inflating: Mothur.source/unweighted.h inflating: Mothur.source/uvest.cpp inflating: Mothur.source/uvest.h inflating: Mothur.source/validcalculator.cpp inflating: __MACOSX/Mothur.source/._validcalculator.cpp inflating: Mothur.source/validcalculator.h inflating: Mothur.source/validparameter.cpp inflating: Mothur.source/validparameter.h inflating: Mothur.source/venn.cpp inflating: Mothur.source/venn.h inflating: Mothur.source/venncommand.cpp inflating: __MACOSX/Mothur.source/._venncommand.cpp inflating: Mothur.source/venncommand.h inflating: Mothur.source/weighted.cpp inflating: __MACOSX/Mothur.source/._weighted.cpp inflating: Mothur.source/weighted.h inflating: Mothur.source/weightedlinkage.cpp inflating: Mothur.source/whittaker.cpp inflating: Mothur.source/whittaker.h inflating: Mothur.source/wilcox.cpp inflating: Mothur.source/wilcox.h inflating: __MACOSX/._Mothur.source sudo -u fink-bld [ENV] sh -c /tmp/fink.v4k2n /tmp/fink.wzE5n #!/bin/sh -ev make \ USEMPI=yes \ FORTAN_COMPILER=gfortran-fsf-4.9 \ USECOMPRESSION=yes gfortran-fsf-4.9 -c -m64 *.f mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o abstractdecisiontree.o abstractdecisiontree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o abstractrandomforest.o abstractrandomforest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o ace.o ace.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o aligncommand.o aligncommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o alignment.o alignment.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o alignmentcell.o alignmentcell.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o alignmentdb.o alignmentdb.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o alignnode.o alignnode.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o aligntree.o aligntree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o amovacommand.o amovacommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o anosimcommand.o anosimcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o averagelinkage.o averagelinkage.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o bayesian.o bayesian.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o bellerophon.o bellerophon.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o bergerparker.o bergerparker.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o binsequencecommand.o binsequencecommand.cpp amovacommand.cpp:256:9: warning: expression result unused [-Wunused-value] for(itB;itB!=origGroupSampleMap.end();itB++){ ^~~ amovacommand.cpp:324:7: warning: expression result unused [-Wunused-value] for(it;it!=groupSampleMap.end();it++){ ^~ anosimcommand.cpp:225:9: warning: expression result unused [-Wunused-value] for(itB;itB!=origGroupSampleMap.end();itB++){ ^~~ anosimcommand.cpp:306:7: warning: expression result unused [-Wunused-value] for(it;it!=groupSampleMap.end();it++){ ^~ anosimcommand.cpp:367:9: warning: expression result unused [-Wunused-value] for(itB;itB!=groupSampleMap.end();itB++){ ^~~ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o blastalign.o blastalign.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o blastdb.o blastdb.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o boneh.o boneh.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o bootstrap.o bootstrap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o bstick.o bstick.cpp 3 warnings generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o calcsparcc.o calcsparcc.cpp 2 warnings generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o calculator.o calculator.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o canberra.o canberra.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o catchallcommand.o catchallcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o ccode.o ccode.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chao1.o chao1.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimera.o chimera.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimerabellerophoncommand.o chimerabellerophoncommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimeraccodecommand.o chimeraccodecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimeracheckcommand.o chimeracheckcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimeracheckrdp.o chimeracheckrdp.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimeraperseuscommand.o chimeraperseuscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimerapintailcommand.o chimerapintailcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimerarealigner.o chimerarealigner.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimeraslayer.o chimeraslayer.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimeraslayercommand.o chimeraslayercommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chimerauchimecommand.o chimerauchimecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o chopseqscommand.o chopseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o classify.o classify.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o classifyotucommand.o classifyotucommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o classifyrfsharedcommand.o classifyrfsharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o classifyseqscommand.o classifyseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o classifysharedcommand.o classifysharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o classifytreecommand.o classifytreecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clearcut.o clearcut.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clearcutcommand.o clearcutcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clearmemorycommand.o clearmemorycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o cluster.o cluster.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clusterclassic.o clusterclassic.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clustercommand.o clustercommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clusterdoturcommand.o clusterdoturcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clusterfragmentscommand.o clusterfragmentscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o clustersplitcommand.o clustersplitcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o cmdargs.o cmdargs.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o collect.o collect.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o collectcommand.o collectcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o collectsharedcommand.o collectsharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o commandfactory.o commandfactory.cpp In file included from clustersplitcommand.cpp:10: ./clustersplitcommand.h:110:1: warning: '/*' within block comment [-Wcomment] /************************************************************************************************** ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o commandoptionparser.o commandoptionparser.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o communitytype.o communitytype.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o completelinkage.o completelinkage.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o consensus.o consensus.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o consensusseqscommand.o consensusseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o cooccurrencecommand.o cooccurrencecommand.cpp In file included from commandfactory.cpp:75: ./clustersplitcommand.h:110:1: warning: '/*' within block comment [-Wcomment] /************************************************************************************************** ^ In file included from commandfactory.cpp:102: ./shhhercommand.h:206:1: warning: '/*' within block comment [-Wcomment] /************************************************************************************************** ^ ./shhhercommand.h:237:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:282:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:288:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:367:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:377:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:393:21: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:416:21: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:442:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:449:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:463:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:470:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:505:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:519:4: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:599:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:646:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:660:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:666:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:711:33: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:724:33: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:746:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:751:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:771:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:776:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:807:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:812:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:840:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:845:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:863:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:876:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:920:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:934:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:948:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:953:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:996:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1010:13: warning: '/*' within block comment [-Wcomment] /*****************************************************************************************************/ ^ ./shhhercommand.h:1020:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1065:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1078:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1101:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1107:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1203:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1207:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1246:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1250:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1278:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1282:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1331:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1335:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1349:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o corraxescommand.o corraxescommand.cpp 1 warning generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o countgroupscommand.o countgroupscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o countseqscommand.o countseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o counttable.o counttable.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o coverage.o coverage.cpp 51 warnings generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o createdatabasecommand.o createdatabasecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o database.o database.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o decalc.o decalc.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o decisiontree.o decisiontree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o deconvolutecommand.o deconvolutecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o degapseqscommand.o degapseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o designmap.o designmap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o deuniqueseqscommand.o deuniqueseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o deuniquetreecommand.o deuniquetreecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o distancecommand.o distancecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o distancedb.o distancedb.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o distclearcut.o distclearcut.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o dlibshuff.o dlibshuff.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o dmat.o dmat.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o efron.o efron.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o engine.o engine.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o fasta.o fasta.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o fastamap.o fastamap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o fileoutput.o fileoutput.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o filterseqscommand.o filterseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o filtersharedcommand.o filtersharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o flowdata.o flowdata.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o forest.o forest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o formatcolumn.o formatcolumn.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o formatphylip.o formatphylip.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o fullmatrix.o fullmatrix.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o geom.o geom.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getcommandinfocommand.o getcommandinfocommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getcoremicrobiomecommand.o getcoremicrobiomecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getcurrentcommand.o getcurrentcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getdistscommand.o getdistscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getgroupcommand.o getgroupcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getgroupscommand.o getgroupscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getlabelcommand.o getlabelcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getlineagecommand.o getlineagecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getlistcountcommand.o getlistcountcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getmetacommunitycommand.o getmetacommunitycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getopt_long.o getopt_long.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getotulabelscommand.o getotulabelscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getoturepcommand.o getoturepcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getotuscommand.o getotuscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getrabundcommand.o getrabundcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getrelabundcommand.o getrelabundcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getsabundcommand.o getsabundcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getseqscommand.o getseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o getsharedotucommand.o getsharedotucommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o goodscoverage.o goodscoverage.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o gotohoverlap.o gotohoverlap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o gower.o gower.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o groupmap.o groupmap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o hamming.o hamming.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o hcluster.o hcluster.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o hclustercommand.o hclustercommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o heatmap.o heatmap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o heatmapcommand.o heatmapcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o heatmapsim.o heatmapsim.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o heatmapsimcommand.o heatmapsimcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o heip.o heip.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o hellinger.o hellinger.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o helpcommand.o helpcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o homovacommand.o homovacommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o indicatorcommand.o indicatorcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o inputdata.o inputdata.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o invsimpson.o invsimpson.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o jackknife.o jackknife.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o kmeans.o kmeans.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o kmer.o kmer.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o kmerdb.o kmerdb.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o kmernode.o kmernode.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o kmertree.o kmertree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o knn.o knn.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o kruskalwalliscommand.o kruskalwalliscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o lefsecommand.o lefsecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o libshuff.o libshuff.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o libshuffcommand.o libshuffcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o linearalgebra.o linearalgebra.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o listotulabelscommand.o listotulabelscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o listseqscommand.o listseqscommand.cpp lefsecommand.cpp:560:17: warning: expression result unused [-Wunused-value] for(itB;itB!=class2SubClasses.end();itB++){ ^~~ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o listvector.o listvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o loadlogfilecommand.o loadlogfilecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o logsd.o logsd.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o makebiomcommand.o makebiomcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o makecontigscommand.o makecontigscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o makefastqcommand.o makefastqcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o makegroupcommand.o makegroupcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o makelefsecommand.o makelefsecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o makelookupcommand.o makelookupcommand.cpp 1 warning generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o maligner.o maligner.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o manhattan.o manhattan.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mantelcommand.o mantelcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o matrixoutputcommand.o matrixoutputcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o memchi2.o memchi2.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o memchord.o memchord.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o memeuclidean.o memeuclidean.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mempearson.o mempearson.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mergefilecommand.o mergefilecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mergegroupscommand.o mergegroupscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mergesfffilecommand.o mergesfffilecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mergetaxsummarycommand.o mergetaxsummarycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o metastatscommand.o metastatscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mgclustercommand.o mgclustercommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mothur.o mothur.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mothurfisher.o mothurfisher.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mothurmetastats.o mothurmetastats.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o mothurout.o mothurout.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o myPerseus.o myPerseus.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o myseqdist.o myseqdist.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o nameassignment.o nameassignment.cpp mothurout.cpp:1060:34: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] string tempName = string(tmpnam(0)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ mothurout.cpp:1106:30: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] string tempName = string(tmpnam(0)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ mothurout.cpp:1155:38: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] string tempName = string(tmpnam(0)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ mothurout.cpp:1204:38: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] string tempName = string(tmpnam(0)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ mothurout.cpp:1286:32: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] string tempName = string(tmpnam(0)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ mothurout.cpp:1328:38: warning: 'tmpnam' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of tmpnam(3), it is highly recommended that you use mkstemp(3) instead. [-Wdeprecated-declarations] string tempName = string(tmpnam(0)); ^ /usr/include/stdio.h:274:7: note: 'tmpnam' declared here char *tmpnam(char *); ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o nast.o nast.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o nastreport.o nastreport.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o needlemanoverlap.o needlemanoverlap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o newcommandtemplate.o newcommandtemplate.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o nmdscommand.o nmdscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o noalign.o noalign.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o nocommands.o nocommands.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o normalizesharedcommand.o normalizesharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o npshannon.o npshannon.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o odum.o odum.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o optionparser.o optionparser.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o ordervector.o ordervector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o otuassociationcommand.o otuassociationcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o otuhierarchycommand.o otuhierarchycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o overlap.o overlap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o pairwiseseqscommand.o pairwiseseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o pam.o pam.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o parsefastaqcommand.o parsefastaqcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o parselistscommand.o parselistscommand.cpp 6 warnings generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o parsimony.o parsimony.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o parsimonycommand.o parsimonycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o pcacommand.o pcacommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o pcoacommand.o pcoacommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o phylodiversitycommand.o phylodiversitycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o phylosummary.o phylosummary.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o phylotree.o phylotree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o phylotypecommand.o phylotypecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o pintail.o pintail.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o pipelinepdscommand.o pipelinepdscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o prcseqscommand.o prcseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o preclustercommand.o preclustercommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o primerdesigncommand.o primerdesigncommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o prng.o prng.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o progress.o progress.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o qFinderDMM.o qFinderDMM.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o qstat.o qstat.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o qualityscores.o qualityscores.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o quitcommand.o quitcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o rabundvector.o rabundvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o randomforest.o randomforest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o randomnumber.o randomnumber.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o rarecalc.o rarecalc.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o raredisplay.o raredisplay.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o rarefact.o rarefact.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o rarefactcommand.o rarefactcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o rarefactsharedcommand.o rarefactsharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o readblast.o readblast.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o readcluster.o readcluster.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o readcolumn.o readcolumn.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o readphylip.o readphylip.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o readphylipvector.o readphylipvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o readtree.o readtree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o refchimeratest.o refchimeratest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o referencedb.o referencedb.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o regularizeddecisiontree.o regularizeddecisiontree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o regularizedrandomforest.o regularizedrandomforest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removedistscommand.o removedistscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removegroupscommand.o removegroupscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removelineagecommand.o removelineagecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removeotulabelscommand.o removeotulabelscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removeotuscommand.o removeotuscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removerarecommand.o removerarecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o removeseqscommand.o removeseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o renameseqscommand.o renameseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o reportfile.o reportfile.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o reversecommand.o reversecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o rftreenode.o rftreenode.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sabundvector.o sabundvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o screenseqscommand.o screenseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o secondarystructurecommand.o secondarystructurecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sensspeccommand.o sensspeccommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o seqerrorcommand.o seqerrorcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o seqnoise.o seqnoise.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o seqsummarycommand.o seqsummarycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sequence.o sequence.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sequencecountparser.o sequencecountparser.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sequencedb.o sequencedb.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sequenceparser.o sequenceparser.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o setcurrentcommand.o setcurrentcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o setdircommand.o setdircommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o setlogfilecommand.o setlogfilecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sffinfocommand.o sffinfocommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sffmultiplecommand.o sffmultiplecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o shannon.o shannon.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o shannoneven.o shannoneven.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o shannonrange.o shannonrange.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedace.o sharedace.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedanderbergs.o sharedanderbergs.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedbraycurtis.o sharedbraycurtis.cpp In file included from sffmultiplecommand.cpp:9: In file included from ./sffmultiplecommand.h:16: ./shhhercommand.h:206:1: warning: '/*' within block comment [-Wcomment] /************************************************************************************************** ^ ./shhhercommand.h:237:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:282:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:288:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:367:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:377:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:393:21: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:416:21: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:442:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:449:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:463:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:470:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:505:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:519:4: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:599:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:646:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:660:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:666:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:711:33: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:724:33: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:746:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:751:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:771:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:776:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:807:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:812:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:840:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:845:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:863:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:876:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:920:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:934:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:948:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:953:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:996:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1010:13: warning: '/*' within block comment [-Wcomment] /*****************************************************************************************************/ ^ ./shhhercommand.h:1020:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1065:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1078:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1101:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1107:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1203:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1207:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1246:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1250:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1278:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1282:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1331:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1335:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1349:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedchao1.o sharedchao1.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedcommand.o sharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedjabund.o sharedjabund.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedjackknife.o sharedjackknife.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedjclass.o sharedjclass.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedjest.o sharedjest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedjsd.o sharedjsd.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedkstest.o sharedkstest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedkulczynski.o sharedkulczynski.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedkulczynskicody.o sharedkulczynskicody.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedlennon.o sharedlennon.cpp 50 warnings generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedlistvector.o sharedlistvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedmarczewski.o sharedmarczewski.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedmorisitahorn.o sharedmorisitahorn.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedochiai.o sharedochiai.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedordervector.o sharedordervector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedrabundfloatvector.o sharedrabundfloatvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedrabundvector.o sharedrabundvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedrjsd.o sharedrjsd.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedsabundvector.o sharedsabundvector.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedsobs.o sharedsobs.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedsobscollectsummary.o sharedsobscollectsummary.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedsorabund.o sharedsorabund.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedsorclass.o sharedsorclass.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedsorest.o sharedsorest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedthetan.o sharedthetan.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedthetayc.o sharedthetayc.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sharedutilities.o sharedutilities.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o shen.o shen.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o shhhercommand.o shhhercommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o shhhseqscommand.o shhhseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o simpson.o simpson.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o simpsoneven.o simpsoneven.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o singlelinkage.o singlelinkage.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o slayer.o slayer.cpp In file included from shhhercommand.cpp:10: ./shhhercommand.h:206:1: warning: '/*' within block comment [-Wcomment] /************************************************************************************************** ^ ./shhhercommand.h:237:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:282:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:288:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:367:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:377:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:393:21: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:416:21: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:442:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:449:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:463:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:470:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:505:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:519:4: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:599:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:646:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:660:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:666:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:711:33: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:724:33: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:746:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:751:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:771:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:776:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:807:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:812:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:840:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:845:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:863:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:876:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:920:17: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:934:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:948:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:953:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:996:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1010:13: warning: '/*' within block comment [-Wcomment] /*****************************************************************************************************/ ^ ./shhhercommand.h:1020:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1065:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1078:29: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1101:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1107:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1203:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1207:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1246:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1250:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1278:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1282:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1331:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1335:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ ./shhhercommand.h:1349:13: warning: '/*' within block comment [-Wcomment] /***************************************************************************************************** ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o slibshuff.o slibshuff.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o smithwilson.o smithwilson.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o soergel.o soergel.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o solow.o solow.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sortseqscommand.o sortseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sparcccommand.o sparcccommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sparsedistancematrix.o sparsedistancematrix.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sparsematrix.o sparsematrix.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o spearman.o spearman.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o speciesprofile.o speciesprofile.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o spline.o spline.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o splitabundcommand.o splitabundcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o splitgroupscommand.o splitgroupscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o splitmatrix.o splitmatrix.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o sracommand.o sracommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o structchi2.o structchi2.cpp 50 warnings generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o structchord.o structchord.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o structeuclidean.o structeuclidean.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o structkulczynski.o structkulczynski.cpp sracommand.cpp:22:66: warning: trigraph ignored [-Wtrigraphs] CommandParameter pplatform("platform", "Multiple", "454-???-???", "454", "", "", "","",false,false); parameters.push_back(pplatform); ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o structpearson.o structpearson.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o subsample.o subsample.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o subsamplecommand.o subsamplecommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o suffixdb.o suffixdb.cpp 1 warning generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o suffixnodes.o suffixnodes.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o suffixtree.o suffixtree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o summarycommand.o summarycommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o summaryqualcommand.o summaryqualcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o summarysharedcommand.o summarysharedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o summarytaxcommand.o summarytaxcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o systemcommand.o systemcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o taxonomyequalizer.o taxonomyequalizer.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o taxonomynode.o taxonomynode.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o tree.o tree.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o treegroupscommand.o treegroupscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o treemap.o treemap.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o treenode.o treenode.cpp tree.cpp:590:1: warning: '/*' within block comment [-Wcomment] /*****************************************************************/ ^ mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o treereader.o treereader.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o trialSwap2.o trialSwap2.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o trimflowscommand.o trimflowscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o trimoligos.o trimoligos.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o trimseqscommand.o trimseqscommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o unifracunweightedcommand.o unifracunweightedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o unifracweightedcommand.o unifracweightedcommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o unweighted.o unweighted.cpp 1 warning generated. mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o uvest.o uvest.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o validcalculator.o validcalculator.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o validparameter.o validparameter.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o venn.o venn.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o venncommand.o venncommand.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o weighted.o weighted.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o weightedlinkage.o weightedlinkage.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o whittaker.o whittaker.cpp mpic++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"3/20/2014\"" -DVERSION="\"1.33.3\"" -DUSE_READLINE -DUSE_MPI -DUSE_COMPRESSION -I. -I/sw/include -arch x86_64 -c -o wilcox.o wilcox.cpp cd uchime_src && ./mk && mv uchime .. && cd .. ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured fractid.cpp:182:28: warning: '&&' within '||' [-Wlogical-op-parentheses] if (c == 'D' || c == 'I' && (p == Path || p[-1] == 'M')) ~~ ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fractid.cpp:182:28: note: place parentheses around the '&&' expression to silence this warning if (c == 'D' || c == 'I' && (p == Path || p[-1] == 'M')) ^ ( ) 1 warning generated. ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured ./mk: line 9: /dev/tty: Device not configured -rwxr-xr-x 1 fink-bld fink-bld 241K Aug 5 06:19 uchime 22844 241 uchime mpic++ -L/sw/lib -arch x86_64 -o mothur abstractdecisiontree.o abstractrandomforest.o ace.o aligncommand.o alignment.o alignmentcell.o alignmentdb.o alignnode.o aligntree.o amovacommand.o anosimcommand.o averagelinkage.o bayesian.o bellerophon.o bergerparker.o binsequencecommand.o blastalign.o blastdb.o boneh.o bootstrap.o bstick.o calcsparcc.o calculator.o canberra.o catchallcommand.o ccode.o chao1.o chimera.o chimerabellerophoncommand.o chimeraccodecommand.o chimeracheckcommand.o chimeracheckrdp.o chimeraperseuscommand.o chimerapintailcommand.o chimerarealigner.o chimeraslayer.o chimeraslayercommand.o chimerauchimecommand.o chopseqscommand.o classify.o classifyotucommand.o classifyrfsharedcommand.o classifyseqscommand.o classifysharedcommand.o classifytreecommand.o clearcut.o clearcutcommand.o clearmemorycommand.o cluster.o clusterclassic.o clustercommand.o clusterdoturcommand.o clusterfragmentscommand.o clustersplitcommand.o cmdargs.o collect.o collectcommand.o collectsharedcommand.o commandfactory.o commandoptionparser.o communitytype.o completelinkage.o consensus.o consensusseqscommand.o cooccurrencecommand.o corraxescommand.o countgroupscommand.o countseqscommand.o counttable.o coverage.o createdatabasecommand.o database.o decalc.o decisiontree.o deconvolutecommand.o degapseqscommand.o designmap.o deuniqueseqscommand.o deuniquetreecommand.o distancecommand.o distancedb.o distclearcut.o dlibshuff.o dmat.o efron.o engine.o fasta.o fastamap.o fileoutput.o filterseqscommand.o filtersharedcommand.o flowdata.o forest.o formatcolumn.o formatphylip.o fullmatrix.o geom.o getcommandinfocommand.o getcoremicrobiomecommand.o getcurrentcommand.o getdistscommand.o getgroupcommand.o getgroupscommand.o getlabelcommand.o getlineagecommand.o getlistcountcommand.o getmetacommunitycommand.o getopt_long.o getotulabelscommand.o getoturepcommand.o getotuscommand.o getrabundcommand.o getrelabundcommand.o getsabundcommand.o getseqscommand.o getsharedotucommand.o goodscoverage.o gotohoverlap.o gower.o groupmap.o hamming.o hcluster.o hclustercommand.o heatmap.o heatmapcommand.o heatmapsim.o heatmapsimcommand.o heip.o hellinger.o helpcommand.o homovacommand.o indicatorcommand.o inputdata.o invsimpson.o jackknife.o kmeans.o kmer.o kmerdb.o kmernode.o kmertree.o knn.o kruskalwalliscommand.o lefsecommand.o libshuff.o libshuffcommand.o linearalgebra.o listotulabelscommand.o listseqscommand.o listvector.o loadlogfilecommand.o logsd.o makebiomcommand.o makecontigscommand.o makefastqcommand.o makegroupcommand.o makelefsecommand.o makelookupcommand.o maligner.o manhattan.o mantelcommand.o matrixoutputcommand.o memchi2.o memchord.o memeuclidean.o mempearson.o mergefilecommand.o mergegroupscommand.o mergesfffilecommand.o mergetaxsummarycommand.o metastatscommand.o mgclustercommand.o mothur.o mothurfisher.o mothurmetastats.o mothurout.o myPerseus.o myseqdist.o nameassignment.o nast.o nastreport.o needlemanoverlap.o newcommandtemplate.o nmdscommand.o noalign.o nocommands.o normalizesharedcommand.o npshannon.o odum.o optionparser.o ordervector.o otuassociationcommand.o otuhierarchycommand.o overlap.o pairwiseseqscommand.o pam.o parsefastaqcommand.o parselistscommand.o parsimony.o parsimonycommand.o pcacommand.o pcoacommand.o phylodiversitycommand.o phylosummary.o phylotree.o phylotypecommand.o pintail.o pipelinepdscommand.o prcseqscommand.o preclustercommand.o primerdesigncommand.o prng.o progress.o qFinderDMM.o qstat.o qualityscores.o quitcommand.o rabundvector.o randomforest.o randomnumber.o rarecalc.o raredisplay.o rarefact.o rarefactcommand.o rarefactsharedcommand.o readblast.o readcluster.o readcolumn.o readphylip.o readphylipvector.o readtree.o refchimeratest.o referencedb.o regularizeddecisiontree.o regularizedrandomforest.o removedistscommand.o removegroupscommand.o removelineagecommand.o removeotulabelscommand.o removeotuscommand.o removerarecommand.o removeseqscommand.o renameseqscommand.o reportfile.o reversecommand.o rftreenode.o sabundvector.o screenseqscommand.o secondarystructurecommand.o sensspeccommand.o seqerrorcommand.o seqnoise.o seqsummarycommand.o sequence.o sequencecountparser.o sequencedb.o sequenceparser.o setcurrentcommand.o setdircommand.o setlogfilecommand.o sffinfocommand.o sffmultiplecommand.o shannon.o shannoneven.o shannonrange.o sharedace.o sharedanderbergs.o sharedbraycurtis.o sharedchao1.o sharedcommand.o sharedjabund.o sharedjackknife.o sharedjclass.o sharedjest.o sharedjsd.o sharedkstest.o sharedkulczynski.o sharedkulczynskicody.o sharedlennon.o sharedlistvector.o sharedmarczewski.o sharedmorisitahorn.o sharedochiai.o sharedordervector.o sharedrabundfloatvector.o sharedrabundvector.o sharedrjsd.o sharedsabundvector.o sharedsobs.o sharedsobscollectsummary.o sharedsorabund.o sharedsorclass.o sharedsorest.o sharedthetan.o sharedthetayc.o sharedutilities.o shen.o shhhercommand.o shhhseqscommand.o simpson.o simpsoneven.o singlelinkage.o slayer.o slibshuff.o smithwilson.o soergel.o solow.o sortseqscommand.o sparcccommand.o sparsedistancematrix.o sparsematrix.o spearman.o speciesprofile.o spline.o splitabundcommand.o splitgroupscommand.o splitmatrix.o sracommand.o structchi2.o structchord.o structeuclidean.o structkulczynski.o structpearson.o subsample.o subsamplecommand.o suffixdb.o suffixnodes.o suffixtree.o summarycommand.o summaryqualcommand.o summarysharedcommand.o summarytaxcommand.o systemcommand.o taxonomyequalizer.o taxonomynode.o tree.o treegroupscommand.o treemap.o treenode.o treereader.o trialSwap2.o trimflowscommand.o trimoligos.o trimseqscommand.o unifracunweightedcommand.o unifracweightedcommand.o unweighted.o uvest.o validcalculator.o validparameter.o venn.o venncommand.o weighted.o weightedlinkage.o whittaker.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 strip mothur /bin/rm -rf /sw/build.build/root-mothur-1.33.3-2 /bin/mkdir -p /sw/build.build/root-mothur-1.33.3-2/sw /bin/mkdir -p /sw/build.build/root-mothur-1.33.3-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-mothur-1.33.3-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.AK7Om mkdir -p /sw/build.build/root-mothur-1.33.3-2/sw/bin && cp -p mothur /sw/build.build/root-mothur-1.33.3-2/sw/bin/ sudo -u fink-bld [ENV] sh -c /tmp/fink.cvQzq /bin/rm -f /sw/build.build/root-mothur-1.33.3-2/sw/info/dir /sw/build.build/root-mothur-1.33.3-2/sw/info/dir.old /sw/build.build/root-mothur-1.33.3-2/sw/share/info/dir /sw/build.build/root-mothur-1.33.3-2/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-mothur-1.33.3-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `mothur' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/mothur_1.33.3-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-mothur-1.33.3-2 (Reading database ... 11860 files and directories currently installed.) Removing fink-buildlock-mothur-1.33.3-2 ...