Elizabeth Purdom
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/clusterExperiment |
| Branch: RELEASE_3_9 |
| Last Commit: 7199648 |
| Last Changed Date: 2019-06-07 14:39:55 -0400 (Fri, 07 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:36:14 -0400 (Wed, 16 Oct 2019).
| Package 292/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| clusterExperiment 2.4.4 Elizabeth Purdom
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | [ OK ] | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: clusterExperiment |
| Version: 2.4.4 |
| Command: 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_2.4.4.tar.gz |
| StartedAt: 2019-10-16 08:55:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 08:57:31 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 120.2 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: clusterExperiment_2.4.4.zip |
| PackageFileSize: 5.786 MiB |
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### Running command:
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### 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_2.4.4.tar.gz
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install for i386
* installing *source* package 'clusterExperiment' ...
** using staged installation
** 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
** inst
** 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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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/RtmpEnG8Dc/R.INSTALL1d7458e07088/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_2.4.4.zip
* DONE (clusterExperiment)