############################################################################## ############################################################################## ### ### Running command: ### ### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library' * installing *source* package 'psichomics' ... ** using staged installation ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c progressBar.cpp -o progressBar.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c psiFastCalc.cpp -o psiFastCalc.o "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c vastToolsParser.cpp -o vastToolsParser.o C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-psichomics/00new/psichomics/libs/x64 ** R ** inst ** byte-compile and prepare package for lazy loading Creating a generic function for 'colSums' from package 'base' in package 'psichomics' ** help *** installing help indices converting help for package 'psichomics' finding HTML links ... done HTMLfast html addObjectAttrs html addTCGAdata html analysesTableSet html appServer html appUI html appendNewGroups html areSplicingEvents html articleUI html assignColours html assignValuePerSubject html basicStats html blendColours html browseDownloadFolderInput html browserHistory html calculateInclusionLevels html calculateLoadingsContribution html checkFileFormat html checkFirebrowse html checkGroupType html checkIntegrity html checkSurvivalInput html clusterICAset html clusterSet html colSums-EList-method html finding level-2 HTML links ... done colourInputMod html convertGeneIdentifiers html correlateGEandAS html createDataTab html createDensitySparklines html createEventPlotting html createGroup html createGroupByAttribute html createGroupById html createGroupFromInput html createJunctionsTemplate html createOptimalSurvData html createSparklines html customRowMeans html diagramSplicingEvent html diffAnalyses html diffExpressionSet html diffSplicingSet html disableTab html discardLowCoveragePSIvalues html discardOutsideSamplesFromGroups html display html dot-onAttach html downloadFiles html ensemblToUniprot html escape html eventPlotOptions html exportGroupsToFile html export_highcharts html fileBrowser html fileBrowserInput html filterGeneExpr html filterGroups html filterPSI html findASeventsFromGene html findEventData html geNormalisationFilteringInterface html geneExprFileInput html geneExprSurvSet html getAttributesTime html getClinicalDataForSurvival html getClinicalMatchFrom html getData html getDataRows html getDifferentialExpression html getDifferentialSplicing html getDownloadsFolder html getFirebrowseDateFormat html getGeneList html getGlobal html getGroups html getGtexDataTypes html getGtexDataURL html getGtexTissues html getHidden html getHighlightedPoints html getNumerics html getSampleFromSubject html getSelectedDataPanel html getServerFunctions html getSplicingEventCoordinates html getSplicingEventData html getSplicingEventFromGenes html getSplicingEventTypes html getSubjectFromSample html getTCGAdataTypes html getUiFunctions html getValidEvents html ggplotServer html ggplotTooltip html ggplotUI html globalSelectize html groupByAttribute html groupManipulation html groupManipulationInput html groupPerElem html groupsServerOnce html hc_scatter html hchart.survfit html importGroupsFrom html inclusionLevelsFilterInterface html inclusionLevelsInterface html inlineDialog html insideFile html is.whole html isFile html isFirebrowseUp html isRStudioServer html joinEventsPerType html junctionString html labelBasedOnCutoff html leveneTest html linkToArticles html linkToRunJS html listAllAnnotations html listSplicingAnnotations html loadAnnotation html loadAnnotationHub html loadBy html loadCustomSplicingAnnotationSet html loadFile html loadFileFormats html loadFirebrowseFolders html loadGeneExpressionSet html loadGtexData html loadGtexDataShiny html loadGtexFile html loadLocalFiles html loadSRAproject html loadSplicingQuantificationSet html loadTCGAdata html loadTCGAsampleMetadata html loadedDataModal html matchGroupASeventsAndGenes html matchGroupSubjectsAndSamples html matchSplicingEventsWithGenes html missingDataModal html modTabPanel html navSelectize html normaliseGeneExpression html operateOnGroups html optimSurvDiffSet html optimalSurvivalCutoff html parseCategoricalGroups html parseDateResponse html parseFile html parseFirebrowseMetadata html parseMatsEvent html parseMatsGeneric html parseMisoAnnotation html parseMisoEvent html parseMisoEventID html parseMisoGeneric html parseMisoId html parseSplicingEvent html parseSuppaEvent html parseSuppaGeneric html parseTcgaSampleInfo html REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-psichomics/00new/psichomics/help/parseTcgaSampleInfo.html parseUniprotXML html parseUrlsFromFirebrowseResponse html parseVastToolsEvent html parseVastToolsSE html performICA html performPCA html plot.GEandAScorrelation html plotClusters html plotDistribution html plotGeneExprPerSample html plotGroupIndependence html plotICA html plotLibrarySize html plotPCA html plotPCAvariance html plotPointsStyle html plotProtein html plotRowStats html plotSingleICA html plotSplicingEvent html plotSurvivalCurves html plotSurvivalPvaluesByCutoff html plotTranscripts html plottableXranges html prepareAnnotationFromEvents html prepareEventPlotOptions html prepareFileBrowser html prepareFirebrowseArchives html prepareGenePresentation html prepareJunctionQuantSTAR html preparePreMadeGroupForSelection html prepareSRAmetadata html prepareWordBreak html preserveAttributes html processButton html processDatasetNames html processSRAdata html processSurvData html processSurvTerms html processSurvival html psichomics html pubmedUI html quantifySplicing html quantifySplicingSet html queryEnsembl html queryEnsemblByGene html queryFirebrowseData html queryPubMed html queryUniprot html readAnnot html readFile html reduceDimensionality html renameDuplicated html renameGroups html renderBoxplot html renderDataTableSparklines html renderGeneticInfo html renderGroupInterface html renderProteinInfo html replaceStrInList html rm.null html roundDigits html roundMinDown html saveProcessedSRAdata html selectGroupsUI html selectPreMadeGroup html selectizeGeneInput html setFirebrowseData html setLocalData html setOperation html setOperationIcon html showAlert html showGroupsTable html sidebar html signifDigits html singleDiffAnalyses html sortCoordinates html startProcess html startProgress html styleModal html subjectMultiMatchWarning html subsetGeneExpressionFromMatchingGenes html survdiffTerms html survfit.survTerms html t.sticky html tabDataset html table2html html tableRow html testGroupIndependence html testSingleIndependence html testSurvival html testSurvivalCutoff html textSuggestions html toJSarray html traceInList html transformData html transformOptions html transformValues html trimWhitespace html uniqueBy html updateClinicalParams html updateFileBrowserInput html vennEvents html wilcox html *** copying figures ** 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 * DONE (psichomics) Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") : DESCRIPTION file of package 'EWCE' is missing or broken done