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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/clusterExperiment_2.10.1.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.10.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.10.1.zip && rm clusterExperiment_2.10.1.tar.gz clusterExperiment_2.10.1.zip
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install for i386

* installing *source* package 'clusterExperiment' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c search_pairs.cpp -o search_pairs.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c subsampleLoop.cpp -o subsampleLoop.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:206: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:210: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/ClusterExperiment-class.Rd:252: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/RSEC.Rd:61: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/RSEC.Rd:190: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterContrasts.Rd:46: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterContrasts.Rd:46: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:111: file link 'phylo' in package 'ape' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:114: file link 'tdata' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterDendrogram.Rd:217: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterMany.Rd:68: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterMany.Rd:167: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterSingle.Rd:45: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/clusterSingle.Rd:62: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    fluidigmData                            html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/fluidigmData.Rd:30: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
    getBestFeatures                         html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:78: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:79: file link 'limma' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:87: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:135: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/getBestFeatures.Rd:248: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic
    getClusterIndex                         html  
    getClusterManyParams                    html  
    mainClustering                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/mainClustering.Rd:44: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    makeConsensus                           html  
    makeDendrogram                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/makeDendrogram.Rd:66: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/mergeClusters.Rd:174: 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  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:66: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:152: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotClustersTable.Rd:229: file link 'prop.table' in package 'base' does not exist and so has been treated as a topic
    plotClustersWorkflow                    html  
    plotContrastHeatmap                     html  
    plotDendrogram                          html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotDendrogram.Rd:124: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureBoxplot.Rd:45: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureScatter.Rd:45: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotFeatureScatter.Rd:56: file link 'plot' in package 'graphics' does not exist and so has been treated as a topic
    plotHeatmap                             html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotHeatmap.Rd:74: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/plotHeatmap.Rd:145: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:121: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:205: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/reduceFunctions.Rd:316: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/rsecFluidigm.Rd:51: file link 'fluidigm' in package 'scRNAseq' does not exist and so has been treated as a topic
    search_pairs                            html  
    seqCluster                              html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/seqCluster.Rd:25: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    simData                                 html  
    subsampleClustering                     html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/subsampleClustering.Rd:37: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    subset                                  html  
    transformData                           html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/transformData.Rd:37: 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-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/updateObject.Rd:55: file link 'phylo4d' in package 'phylobase' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpOWqNMF/R.INSTALL28d046833c6b/clusterExperiment/man/updateObject.Rd:61: 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:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c search_pairs.cpp -o search_pairs.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c subsampleLoop.cpp -o subsampleLoop.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o clusterExperiment.dll tmp.def RcppExports.o search_pairs.o subsampleLoop.o -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'clusterExperiment' as clusterExperiment_2.10.1.zip
* DONE (clusterExperiment)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'clusterExperiment' successfully unpacked and MD5 sums checked