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This page was generated on 2019-04-13 11:26:52 -0400 (Sat, 13 Apr 2019).
Package 277/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
clusterExperiment 2.2.0 Elizabeth Purdom
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | OK | |||||||
merida1 | OS X 10.11.6 El Capitan / x86_64 | ERROR | ERROR | skipped | skipped |
Package: clusterExperiment |
Version: 2.2.0 |
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/clusterExperiment_2.2.0.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.2.0.zip && rm clusterExperiment_2.2.0.tar.gz clusterExperiment_2.2.0.zip |
StartedAt: 2019-04-12 20:31:39 -0400 (Fri, 12 Apr 2019) |
EndedAt: 2019-04-12 20:34:15 -0400 (Fri, 12 Apr 2019) |
EllapsedTime: 156.2 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/clusterExperiment_2.2.0.tar.gz && rm -rf clusterExperiment.buildbin-libdir && mkdir clusterExperiment.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=clusterExperiment.buildbin-libdir clusterExperiment_2.2.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL clusterExperiment_2.2.0.zip && rm clusterExperiment_2.2.0.tar.gz clusterExperiment_2.2.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1314k 100 1314k 0 0 26.9M 0 --:--:-- --:--:-- --:--:-- 29.1M install for i386 * installing *source* package 'clusterExperiment' ... ** libs C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/clusterExperiment.buildbin-libdir/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 ClusterExperiment-methods html ClusterFunction-class html ClusterFunction-methods html RSEC html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/RSEC.Rd:41: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/RSEC.Rd:154: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/clusterContrasts.Rd:41: file link 'MAST' in package 'MAST' does not exist and so has been treated as a topic clusterExperiment-deprecated html clusterMany html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/clusterSingle.Rd:61: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/getBestFeatures.Rd:65: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/getBestFeatures.Rd:66: file link 'limma' in package 'limma' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/getBestFeatures.Rd:71: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/getBestFeatures.Rd:110: file link 'topTableF' in package 'limma' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/getBestFeatures.Rd:223: file link 'glmLRT' in package 'edgeR' does not exist and so has been treated as a topic getClusterManyParams html mainClustering html makeConsensus html makeDendrogram html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/makeDendrogram.Rd:52: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/mergeClusters.Rd:155: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic plotBarplot html plotClusters html plotClustersTable html plotClustersWorkflow html plotContrastHeatmap html plotDendrogram html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/plotDendrogram.Rd:117: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/plotFeatureBoxplot.Rd:39: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/plotFeatureScatter.Rd:38: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/plotHeatmap.Rd:54: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/plotHeatmap.Rd:133: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/reduceFunctions.Rd:90: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/reduceFunctions.Rd:174: file link 'SummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/reduceFunctions.Rd:284: file link 'reducedDim' in package 'SingleCellExperiment' does not exist and so has been treated as a topic rsecFluidigm html Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/rsecFluidigm.Rd:56: 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-3.8-bioc/tmpdir/RtmpYZqZiE/R.INSTALL22f439963f91/clusterExperiment/man/transformData.Rd:39: file link 'assay' in package 'SummarizedExperiment' does not exist and so has been treated as a topic updateObject html workflowClusters html ** building package indices ** installing vignettes ** testing if installed package can be loaded In R CMD INSTALL install for x64 * installing *source* package 'clusterExperiment' ... ** libs C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-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˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/clusterExperiment.buildbin-libdir/clusterExperiment/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'clusterExperiment' as clusterExperiment_2.2.0.zip * DONE (clusterExperiment) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library' package 'clusterExperiment' successfully unpacked and MD5 sums checked In R CMD INSTALL