############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf RnBeads.buildbin-libdir && mkdir RnBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.buildbin-libdir RnBeads_2.12.2.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'RnBeads' ... ** using staged installation ** 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 ClusterArchitectureSLURM-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.diffMeth.objs html combine.rnb.sets-methods 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 getSubCmdTokens-ClusterArchitectureSLURM-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-ClusterArchitectureSLURM-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 lump.hg38 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.bed.from.segmentation html rnb.beta2mval html rnb.boxplot.from.segmentation html rnb.build.index html rnb.call.destructor html rnb.color.legends html rnb.combine.arrays html rnb.combine.seq 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.high.dpval.masking 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.pOOBAH html rnb.execute.quality html rnb.execute.segmentation html rnb.execute.sex.prediction 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.step.cnv 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 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 'RnBeads' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'RnBeads' as RnBeads_2.12.2.zip * DONE (RnBeads)