Package: clusterExperiment

Version: 2.3.1

Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/clusterExperiment_2.3.1.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.3.1.zip && rm clusterExperiment_2.3.1.tar.gz clusterExperiment_2.3.1.zip

StartedAt: 2019-04-08 20:39:24 -0400 (Mon, 08 Apr 2019)

EndedAt: 2019-04-08 20:41:50 -0400 (Mon, 08 Apr 2019)

EllapsedTime: 146.0 seconds

RetCode: 0

Status:  OK

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### Running command:
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###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/clusterExperiment_2.3.1.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.3.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.3.1.zip && rm clusterExperiment_2.3.1.tar.gz clusterExperiment_2.3.1.zip
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install for i386

* installing *source* package 'clusterExperiment' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c search_pairs.cpp -o search_pairs.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subsampleLoop.cpp -o subsampleLoop.o
subsampleLoop.cpp: In function 'Rcpp::IntegerMatrix subsampleLoop(Rcpp::List, int)':
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterj = j <= indexClusterEnds & j >= indexClusterStarts;
                                ^
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterk = k <= indexClusterEnds & k >= indexClusterStarts;
                                ^
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if((it->second).first>0 | (it->second).second==NA_INTEGER){
                         ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.buildbin-libdir/00LOCK-clusterExperiment/00new/clusterExperiment/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
Found more than one class "Annotated" in cache; using the first, from namespace 'S4Vectors'
Also defined by 'RNeXML'
** help
*** installing help indices
  converting help for package 'clusterExperiment'
    finding HTML links ... done
    ClusterExperiment-class                 html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:198: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:202: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/ClusterExperiment-class.Rd:235: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
    ClusterExperiment-methods               html  
    ClusterFunction-class                   html  
    ClusterFunction-methods                 html  
    RSEC                                    html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/RSEC.Rd:40: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/RSEC.Rd:155: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    addClusterings                          html  
    assignUnassigned                        html  
    builtInClusteringFunctions              html  
    clusterContrasts                        html  
    finding level-2 HTML links ... done

Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterContrasts.Rd:41: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterContrasts.Rd:41: file link 'MAST' in package 'MAST' does not exist and so has been treated as a topic
    clusterDendrogram                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:114: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:117: file link 'tdata' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterDendrogram.Rd:200: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
    clusterExperiment-deprecated            html  
    clusterMany                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterMany.Rd:38: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterMany.Rd:134: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    clusterSingle                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterSingle.Rd:36: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/clusterSingle.Rd:56: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    getBestFeatures                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:67: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:68: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:76: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:124: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/getBestFeatures.Rd:237: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    getClusterIndex                         html  
    getClusterManyParams                    html  
    mainClustering                          html  
    makeConsensus                           html  
    makeDendrogram                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/makeDendrogram.Rd:54: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    mergeClusters                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/mergeClusters.Rd:156: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    numericalAsCharacter                    html  
    plotBarplot                             html  
    plotClusters                            html  
    plotClustersTable                       html  
    plotClustersWorkflow                    html  
    plotContrastHeatmap                     html  
    plotDendrogram                          html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotDendrogram.Rd:113: file link 'tiplabels' in package 'ape' does not exist and so has been treated as a topic
    plotFeatureBoxplot                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotFeatureBoxplot.Rd:40: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotFeatureScatter                      html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotFeatureScatter.Rd:39: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotHeatmap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotHeatmap.Rd:56: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/plotHeatmap.Rd:127: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    plotReducedDims                         html  
    plottingFunctions                       html  
    reduceFunctions                         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:94: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:178: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/reduceFunctions.Rd:289: file link 'reducedDim' in package 'SingleCellExperiment' does not exist and so has been treated as a topic
    renameClusters                          html  
    rsecFluidigm                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/rsecFluidigm.Rd:66: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
    search_pairs                            html  
    seqCluster                              html  
    simData                                 html  
    subsampleClustering                     html  
    subset                                  html  
    transformData                           html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/transformData.Rd:40: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    updateObject                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/updateObject.Rd:57: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpwr2fa6/R.INSTALL1ca43f7e68e7/clusterExperiment/man/updateObject.Rd:63: file link 'nodeLabels' in package 'phylobase' does not exist and so has been treated as a topic
    workflowClusters                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'clusterExperiment' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c search_pairs.cpp -o search_pairs.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c subsampleLoop.cpp -o subsampleLoop.o
subsampleLoop.cpp: In function 'Rcpp::IntegerMatrix subsampleLoop(Rcpp::List, int)':
subsampleLoop.cpp:89:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterj = j <= indexClusterEnds & j >= indexClusterStarts;
                                ^
subsampleLoop.cpp:90:32: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
     LogicalVector clusterk = k <= indexClusterEnds & k >= indexClusterStarts;
                                ^
subsampleLoop.cpp:122:25: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
    if((it->second).first>0 | (it->second).second==NA_INTEGER){
                         ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_2.3.1.zip
* DONE (clusterExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'clusterExperiment' successfully unpacked and MD5 sums checked