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INSTALL report for RnBeads on tokay2

This page was generated on 2018-10-17 08:40:30 -0400 (Wed, 17 Oct 2018).

Package 1263/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 1.12.1
Fabian Mueller
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RnBeads
Branch: RELEASE_3_7
Last Commit: f662e69
Last Changed Date: 2018-05-07 19:50:22 -0400 (Mon, 07 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RnBeads
Version: 1.12.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RnBeads_1.12.1.tar.gz && rm -rf RnBeads.buildbin-libdir && mkdir RnBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.buildbin-libdir RnBeads_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RnBeads_1.12.1.zip && rm RnBeads_1.12.1.tar.gz RnBeads_1.12.1.zip
StartedAt: 2018-10-16 20:24:29 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:29:44 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 315.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RnBeads_1.12.1.tar.gz && rm -rf RnBeads.buildbin-libdir && mkdir RnBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.buildbin-libdir RnBeads_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RnBeads_1.12.1.zip && rm RnBeads_1.12.1.tar.gz RnBeads_1.12.1.zip
###
##############################################################################
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install for i386

* installing *source* package 'RnBeads' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RnBeads'
    finding HTML links ... done
    BMIQ                                    html  
    ClusterArchitecture-class               html  
    ClusterArchitectureSGE-class            html  
    M-methods                               html  
    Report-class                            html  
    ReportGgPlot-class                      html  
    ReportPlot-class                        html  
    RnBClusterRun-class                     html  
    RnBDiffMeth-class                       html  
    RnBSet-class                            html  
    RnBeadClustering-class                  html  
    RnBeadRawSet-class                      html  
    RnBeadSet-class                         html  
    RnBeads                                 html  
    RnBeads.data                            html  
    RnBiseqSet-class                        html  
    U-methods                               html  
    accepted                                html  
    addDiffMethTable-RnBDiffMeth-methods    html  
    addPheno-RnBSet-methods                 html  
    addRegionSubsegments                    html  
    annotation-methods                      html  
    apply.iEVORA                            html  
    as.RnBeadRawSet                         html  
    assembly-methods                        html  
    auto.select.rank.cut                    html  
    coercion-methods                        html  
    finding level-2 HTML links ... done

    cols.to.rank                            html  
    combine-methods                         html  
    combine.diffMeth.objs                   html  
    combineTestPvalsMeth                    html  
    computeDiffTab.region                   html  
    computeDiffTab.site                     html  
    covg-methods                            html  
    create.densityScatter                   html  
    create.hex.summary.plot                 html  
    create.scatter.dens.points              html  
    createReport                            html  
    createReportGgPlot                      html  
    createReportPlot                        html  
    data.frame2GRanges                      html  
    densRanks                               html  
    destroy-RnBDiffMeth-methods             html  
    destroy-methods                         html  
    deviation.plot.beta                     html  
    diffVar                                 html  
    dim-BigFfMat-method                     html  
    downloadLolaDbs                         html  
    dpval-methods                           html  
    estimateProportionsCP                   html  
    exportDMRs2regionFile                   html  
    get.adjustment.variables                html  
    get.comparison.grouplabels-RnBDiffMeth-methods
                                            html  
    get.comparison.groupsizes-RnBDiffMeth-methods
                                            html  
    get.comparison.info                     html  
    get.comparisons-RnBDiffMeth-methods     html  
    get.covariates.ct                       html  
    get.covariates.sva                      html  
    get.covg.thres-RnBDiffMeth-methods      html  
    get.cpg.stats                           html  
    get.files                               html  
    get.region.types-RnBDiffMeth-methods    html  
    get.site.test.method-RnBDiffMeth-methods
                                            html  
    get.table-RnBDiffMeth-methods           html  
    get.table.ids                           html  
    get.variability.method-RnBDiffMeth-methods
                                            html  
    getCellTypesFromLolaDb                  html  
    getExecutable-ClusterArchitecture-methods
                                            html  
    getModuleNumCores-RnBClusterRun-methods
                                            html  
    getNamesFromLolaDb                      html  
    getNumNaMeth-methods                    html  
    getSubCmdStr-ClusterArchitecture-methods
                                            html  
    getSubCmdTokens-ClusterArchitecture-methods
                                            html  
    getSubCmdTokens-ClusterArchitectureSGE-methods
                                            html  
    getTargetFromLolaDb                     html  
    greedycut.filter.matrix                 html  
    greedycut.get.statistics                html  
    greedycut.get.submatrix                 html  
    has.covariates.ct                       html  
    has.covariates.sva                      html  
    hasCovg-methods                         html  
    includes.sites-RnBDiffMeth-methods      html  
    initialize-ClusterArchitecture-method   html  
    initialize-ClusterArchitectureSGE-method
                                            html  
    initialize-RnBClusterRun-method         html  
    initialize-RnBDiffMeth-method           html  
    intensities.by.color                    html  
    is.valid-RnBDiffMeth-methods            html  
    isImputed-RnBSet-method                 html  
    join.diffMeth-methods                   html  
    limmaP                                  html  
    load.region.subsegment.annotation       html  
    load.rnb.diffmeth                       html  
    load.rnb.set                            html  
    loadLolaDbs                             html  
    logger.argument                         html  
    logger.getfiles                         html  
    logger.isinitialized                    html  
    logger.machine.name                     html  
    logger.validate.file                    html  
    loggerManagement                        html  
    loggerMessages                          html  
    lolaBarPlot                             html  
    lolaBoxPlotPerTarget                    html  
    lolaVolcanoPlot                         html  
    lump.hg19                               html  
    mask.sites.meth-methods                 html  
    mergeSamples-methods                    html  
    meth-methods                            html  
    mval-methods                            html  
    nsites-methods                          html  
    off-methods                             html  
    parallel.getNumWorkers                  html  
    parallel.isEnabled                      html  
    parallel.setup                          html  
    parallel.teardown                       html  
    performGOEnrichment.diffVar             html  
    performGOenrichment.diffMeth.entrez     html  
    performGoEnrichment.diffMeth            html  
    performLolaEnrichment.diffMeth          html  
    performLolaEnrichment.diffVar           html  
    pheno-methods                           html  
    prepareSOFTfileForGEO                   html  
    qc-methods                              html  
    read.GS.report                          html  
    read.bed.files                          html  
    read.data.dir                           html  
    read.idat.files                         html  
    read.idat.files2                        html  
    read.sample.annotation                  html  
    read.single.bed                         html  
    refFreeEWASP                            html  
    regionMapping-methods                   html  
    regions-methods                         html  
    reload-RnBDiffMeth-methods              html  
    remove.regions-methods                  html  
    remove.samples-methods                  html  
    remove.sites-methods                    html  
    rnb.RnBSet.to.GRangesList               html  
    rnb.RnBSet.to.bed                       html  
    rnb.RnBSet.to.bedGraph                  html  
    rnb.add.figure                          html  
    rnb.add.list                            html  
    rnb.add.paragraph                       html  
    rnb.add.reference                       html  
    rnb.add.section                         html  
    rnb.add.table                           html  
    rnb.add.tables                          html  
    rnb.annotation.size                     html  
    rnb.annotation2data.frame               html  
    rnb.beta2mval                           html  
    rnb.build.index                         html  
    rnb.call.destructor                     html  
    rnb.color.legends                       html  
    rnb.combine.arrays                      html  
    rnb.execute.age.prediction              html  
    rnb.execute.batch.qc                    html  
    rnb.execute.batcheffects                html  
    rnb.execute.clustering                  html  
    rnb.execute.clustering.all              html  
    rnb.execute.computeDiffMeth             html  
    rnb.execute.context.removal             html  
    rnb.execute.cross.reactive.removal      html  
    rnb.execute.ct.estimation               html  
    rnb.execute.diffVar                     html  
    rnb.execute.dreduction                  html  
    rnb.execute.export.csv                  html  
    rnb.execute.filter.summary              html  
    rnb.execute.gender.prediction           html  
    rnb.execute.genomewide                  html  
    rnb.execute.greedycut                   html  
    rnb.execute.high.coverage.removal       html  
    rnb.execute.import                      html  
    rnb.execute.imputation                  html  
    rnb.execute.low.coverage.masking        html  
    rnb.execute.lump                        html  
    rnb.execute.na.removal                  html  
    rnb.execute.normalization               html  
    rnb.execute.quality                     html  
    rnb.execute.sex.removal                 html  
    rnb.execute.snp.removal                 html  
    rnb.execute.sva                         html  
    rnb.execute.tnt                         html  
    rnb.execute.training                    html  
    rnb.execute.variability.removal         html  
    rnb.export.all.annotation               html  
    rnb.export.annotation                   html  
    rnb.export.to.ewasher                   html  
    rnb.export.to.trackhub                  html  
    rnb.find.relative.site.coord            html  
    rnb.get.annotation                      html  
    rnb.get.assemblies                      html  
    rnb.get.chromosomes                     html  
    rnb.get.directory                       html  
    rnb.get.mapping                         html  
    rnb.get.reference                       html  
    rnb.get.reliability.matrix              html  
    rnb.infinium.control.targets            html  
    rnb.initialize.reports                  html  
    rnb.is.option                           html  
    rnb.load.annotation                     html  
    rnb.load.annotation.from.db             html  
    rnb.load.sitelist                       html  
    rnb.message.plot                        html  
    rnb.mval2beta                           html  
    rnb.options                             html  
    rnb.options2xml                         html  
    rnb.performance.profile                 html  
    rnb.plot.beta.comparison                html  
    rnb.plot.betadistribution.probeCategories
                                            html  
    rnb.plot.betadistribution.sampleGroups
                                            html  
    rnb.plot.biseq.coverage                 html  
    rnb.plot.biseq.coverage.hist            html  
    rnb.plot.biseq.coverage.violin          html  
    rnb.plot.control.barplot                html  
    rnb.plot.control.boxplot                html  
    rnb.plot.coverage.thresholds            html  
    rnb.plot.ct.heatmap                     html  
    rnb.plot.dreduction                     html  
    rnb.plot.locus.profile                  html  
    rnb.plot.marker.fstat                   html  
    rnb.plot.negative.boxplot               html  
    rnb.plot.num.sites.covg                 html  
    rnb.plot.pheno.categories               html  
    rnb.plot.region.profile.density         html  
    rnb.plot.region.profiles                html  
    rnb.plot.region.site.density            html  
    rnb.plot.sentrix.distribution           html  
    rnb.plot.sentrix.distributions          html  
    rnb.plot.snp.barplot                    html  
    rnb.plot.snp.boxplot                    html  
    rnb.plot.snp.heatmap                    html  
    rnb.read.geo                            html  
    rnb.region.types                        html  
    rnb.region.types.for.analysis           html  
    rnb.remove.annotation                   html  
    rnb.run.analysis                        html  
    rnb.run.dj                              html  
    rnb.run.example                         html  
    rnb.run.xml                             html  
    rnb.runs                                html  
    rnb.sample.groups                       html  
    rnb.sample.replicates                   html  
    rnb.sample.summary.table                html  
    rnb.save.annotation                     html  
    rnb.section.diffVar.region              html  
    rnb.set.annotation                      html  
    rnb.set.annotation.and.cpg.stats        html  
    rnb.show.report                         html  
    rnb.step.betadistribution               html  
    rnb.write.table                         html  
    rnb.xml2options                         html  
    rowOneSampleTP                          html  
    rowPairedTP                             html  
    rowWelchP                               html  
    run-RnBClusterRun-methods               html  
    run.cross.validation                    html  
    sampleCovgApply-methods                 html  
    sampleMethApply-methods                 html  
    samples-methods                         html  
    save.rnb.diffmeth                       html  
    save.rnb.set                            html  
    save.tables-RnBDiffMeth-methods         html  
    set.covariates.ct                       html  
    set.covariates.sva                      html  
    setExecutable-ClusterArchitecture-methods
                                            html  
    setModuleNumCores-RnBClusterRun-methods
                                            html  
    setModuleResourceRequirements-RnBClusterRun-methods
                                            html  
    sites-methods                           html  
    sub-BigFfMat-ANY-ANY-ANY-method         html  
    subset-BigFfMat-ANY-ANY-ANY-method      html  
    summarize.regions-methods               html  
    summarized.regions-methods              html  
    updateMethylationSites-methods          html  
    updateRegionSummaries                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RnBeads' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RnBeads' as RnBeads_1.12.1.zip
* DONE (RnBeads)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RnBeads' successfully unpacked and MD5 sums checked
In R CMD INSTALL