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This page was generated on 2021-10-22 12:04:39 -0400 (Fri, 22 Oct 2021).

BUILD BIN results for psichomics on riesling1

To the developers/maintainers of the psichomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psichomics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
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raw results

Package 1475/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.19.7  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: master
git_last_commit: 68bbd6b
git_last_commit_date: 2021-10-19 12:30:37 -0400 (Tue, 19 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: psichomics
Version: 1.19.7
Command: rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.19.7.tar.gz
StartedAt: 2021-10-22 07:05:59 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 07:10:50 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 291.4 seconds
RetCode: 0
Status:   OK  
PackageFile: psichomics_1.19.7.zip
PackageFileSize: 5.589 MiB

Command output

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###
### Running command:
###
###   rm -rf psichomics.buildbin-libdir && mkdir psichomics.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=psichomics.buildbin-libdir psichomics_1.19.7.tar.gz
###
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install for i386

* installing *source* package 'psichomics' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progressBar.cpp -o progressBar.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c psiFastCalc.cpp -o psiFastCalc.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vastToolsParser.cpp -o vastToolsParser.o
C:/rtools40/mingw32/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/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/psichomics.buildbin-libdir/00LOCK-psichomics/00new/psichomics/libs/i386
** 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-3.14-bioc/meat/psichomics.buildbin-libdir/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

install for x64

* installing *source* package 'psichomics' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-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"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progressBar.cpp -o progressBar.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c psiFastCalc.cpp -o psiFastCalc.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/psichomics.buildbin-libdir/psichomics/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'psichomics' as psichomics_1.19.7.zip
* DONE (psichomics)