Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:51 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the RnBeads package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1614/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RnBeads 2.10.0 (landing page) Fabian Mueller
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: RnBeads |
Version: 2.10.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RnBeads_2.10.0.tar.gz |
StartedAt: 2021-10-14 11:23:07 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 11:32:22 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 555.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RnBeads.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings RnBeads_2.10.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/RnBeads.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RnBeads/DESCRIPTION’ ... OK * this is package ‘RnBeads’ version ‘2.10.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster', 'ff', 'fields', 'ggplot2', 'gplots', 'gridExtra', 'limma', 'matrixStats', 'illuminaio', 'methylumi', 'plyr' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .travis.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘RnBeads’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: ‘qvalue’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... NOTE Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’ A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: 'Gviz:::.getBMFeatureMap' 'doParallel:::.options' 'grDevices:::.smoothScatterCalcDensity' 'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k' 'minfi:::.normalizeFunnorm450k' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .stopImplicitCluster: no visible global function definition for ‘stopCluster’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘phenoData’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘assayDataElementNames’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘featureNames’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘varLabels’ MethyLumiSet2RnBeadSet: no visible global function definition for ‘featureData’ add.age.histogram: no visible binding for global variable ‘Age’ add.age.histogram: no visible binding for global variable ‘..count..’ add.age.histogram: no visible binding for global variable ‘..density..’ add.agecomparison.plot: no visible global function definition for ‘samples’ add.agecomparison.plot: no visible binding for global variable ‘Sample’ add.agecomparison.plot: no visible global function definition for ‘%dopar%’ add.agecomparison.plot: no visible global function definition for ‘foreach’ add.agecomparison.plot: no visible binding for global variable ‘i’ add.combination.plot: no visible global function definition for ‘samples’ add.combination.plot: no visible binding for global variable ‘Difference’ add.combination.plot: no visible binding for global variable ‘Density’ add.combination.plot: no visible binding for global variable ‘yint’ add.combination.plot: no visible binding for global variable ‘Measure’ add.error.plot: no visible binding for global variable ‘Value’ add.error.plot: no visible binding for global variable ‘Sample’ add.error.plot: no visible binding for global variable ‘Deviance’ add.error.plot: no visible binding for global variable ‘yint’ add.error.plot: no visible binding for global variable ‘Measure’ add.negative.control.boxplot: no visible global function definition for ‘samples’ add.profile.plots: no visible global function definition for ‘mclapply’ add.qc.barplots: no visible global function definition for ‘samples’ add.quantile.plot: no visible binding for global variable ‘Difference’ add.quantile.plot: no visible binding for global variable ‘..density..’ add.quantile.plot: no visible binding for global variable ‘Sample’ add.quantile.plot: no visible binding for global variable ‘Density’ add.seq.coverage.histograms: no visible global function definition for ‘samples’ add.seq.coverage.plot: no visible global function definition for ‘samples’ add.seq.coverage.violins: no visible global function definition for ‘samples’ add.stratification.plot: no visible global function definition for ‘%dopar%’ add.stratification.plot: no visible global function definition for ‘foreach’ add.stratification.plot: no visible binding for global variable ‘Group’ add.stratification.plot: no visible binding for global variable ‘Increase’ add.stratification.plot: no visible binding for global variable ‘Predicted’ add.stratification.plot: no visible binding for global variable ‘Annotated’ add.stratification.plot.immune: no visible global function definition for ‘%dopar%’ add.stratification.plot.immune: no visible global function definition for ‘foreach’ add.stratification.plot.immune: no visible binding for global variable ‘Group’ add.stratification.plot.immune: no visible binding for global variable ‘Immune’ addReportPlot.diffVar.volcano: no visible binding for global variable ‘var.diff’ addReportPlot.diffVar.volcano: no visible binding for global variable ‘log10P’ addReportPlot.diffVar.volcano: no visible binding for global variable ‘combinedRank.var’ addReportPlot.diffVar.volcano: no visible binding for global variable ‘log10FDR’ addReportPlots.diffMeth.bin.site.volcano: no visible binding for global variable ‘mean.diff’ addReportPlots.diffMeth.bin.site.volcano: no visible binding for global variable ‘diffmeth.p.val’ addReportPlots.diffMeth.bin.site.volcano: no visible binding for global variable ‘combinedRank’ addReportPlots.diffMeth.bin.site.volcano: no visible binding for global variable ‘mean.quot.log2’ addReportPlots.diffMeth.bin.site.volcano: no visible binding for global variable ‘diffmeth.p.adj.fdr’ agePredictorBiseq: no visible global function definition for ‘impute.knn’ agePredictorBiseq: no visible global function definition for ‘samples’ agePredictorChip: no visible global function definition for ‘impute.knn’ append.cpg.stats: no visible global function definition for ‘%dopar%’ append.cpg.stats: no visible global function definition for ‘foreach’ append.cpg.stats: no visible binding for global variable ‘chrom’ basic_combine: no visible global function definition for ‘samples’ computeDiffTab.default.region: no visible global function definition for ‘%dopar%’ computeDiffTab.default.region: no visible global function definition for ‘foreach’ computeDiffTab.default.region: no visible binding for global variable ‘i’ computeDiffTab.default.site: no visible binding for global variable ‘p.vals.t.na.adj’ computeDiffTab.default.site : <anonymous>: no visible binding for global variable ‘.inds.g2’ computeDiffVar.bin.site: no visible binding for global variable ‘p.vals.t.na.adj’ computeDiffVar.bin.site : <anonymous>: no visible binding for global variable ‘eps’ computeDiffVar.bin.site : <anonymous>: no visible binding for global variable ‘.inds.g2’ computeDiffVar.default.region: no visible global function definition for ‘%dopar%’ computeDiffVar.default.region: no visible global function definition for ‘foreach’ computeDiffVar.default.region: no visible binding for global variable ‘i’ create.densityScatter: no visible binding for global variable ‘..density..’ create.diffMeth.diffVar.subsample: no visible binding for global variable ‘..density..’ create.ucsc.track.hub: no visible global function definition for ‘samples’ createPredictor : ret: no visible global function definition for ‘impute.knn’ cv.array: no visible global function definition for ‘impute.knn’ data.frame2GRanges: no visible global function definition for ‘seqlevels<-’ data.frame2GRanges: no visible global function definition for ‘genome<-’ diffVar: no visible global function definition for ‘varFit’ diffVar: no visible binding for global variable ‘group1’ diffVar: no visible binding for global variable ‘group2’ estimateProportionsCP: no visible global function definition for ‘lme’ estimateProportionsCP: no visible global function definition for ‘getVarCov’ general.cv: no visible global function definition for ‘%dopar%’ general.cv: no visible global function definition for ‘foreach’ general.cv: no visible binding for global variable ‘i’ get.adjustment.variables: no visible global function definition for ‘samples’ get.comparison.info : rm.na.from.adj.tab: no visible global function definition for ‘samples’ get.components.isva: no visible global function definition for ‘DoISVA’ get.components.sva: no visible global function definition for ‘sva’ get.cpg.stats: no visible global function definition for ‘dinucleotideFrequency’ get.cpg.stats: no visible global function definition for ‘letterFrequency’ get.dataset.matrix: no visible global function definition for ‘samples’ get.diffmeth.tab.col.desc.list.txt: no visible binding for global variable ‘report’ get.diffmeth.tab.col.desc.list.txt: no visible binding for global variable ‘refText’ get.diffmeth.tab.col.desc.list.txt: no visible binding for global variable ‘diffmeth’ get.platform.tokens: no visible global function definition for ‘setNames’ getCGCounts: no visible global function definition for ‘seqlengths’ getCGCounts : <anonymous>: no visible global function definition for ‘ChrNumeric’ getGLADProfiles: no visible global function definition for ‘samples’ getGLADProfiles: no visible global function definition for ‘mclapply’ getGLADProfiles : <anonymous>: no visible global function definition for ‘as.profileCGH’ getGLADProfiles : <anonymous>: no visible global function definition for ‘daglad’ getMergeList: no visible global function definition for ‘samples’ groupPermutationP.site.parallel: no visible global function definition for ‘%dopar%’ groupPermutationP.site.parallel: no visible global function definition for ‘foreach’ iEVORA: no visible global function definition for ‘qvalue’ imputation.low.memory.cpgs: no visible global function definition for ‘samples’ inferWBCbyLme: no visible global function definition for ‘lme’ inferWBCbyLme: no visible global function definition for ‘getVarCov’ intensities.by.color: no visible binding for global variable ‘IlluminaHumanMethylationEPICmanifest’ intensities.by.color: no visible binding for global variable ‘IlluminaHumanMethylation450kmanifest’ intensities.by.color: no visible global function definition for ‘samples’ knn.imputation: no visible global function definition for ‘impute.knn’ limmaP: no visible binding for global variable ‘group1’ limmaP: no visible binding for global variable ‘group2’ loadLolaDbs: no visible global function definition for ‘loadRegionDB’ loadLolaDbs: no visible global function definition for ‘mergeRegionDBs’ locus.profile.get.base.tracks: no visible global function definition for ‘useMart’ locus.profile.get.base.tracks: no visible global function definition for ‘IdeogramTrack’ locus.profile.get.base.tracks: no visible global function definition for ‘GenomeAxisTrack’ locus.profile.get.base.tracks: no visible global function definition for ‘BiomartGeneRegionTrack’ locus.profile.get.base.tracks: no visible global function definition for ‘UcscTrack’ locus.profile.get.methylation.track.heatmap: no visible global function definition for ‘DataTrack’ locus.profile.get.methylation.track.smooth: no visible global function definition for ‘DataTrack’ methylumi.intensities.by.color: no visible global function definition for ‘featureNames’ methylumi.intensities.by.color: no visible binding for global variable ‘IlluminaHumanMethylation450kmanifest’ methylumi.intensities.by.color: no visible global function definition for ‘assayDataElement’ parallel.setup: no visible global function definition for ‘registerDoParallel’ parallel.setup: no visible global function definition for ‘getDoParWorkers’ performLolaEnrichment.diffMeth: no visible global function definition for ‘runLOLA’ performLolaEnrichment.diffVar: no visible global function definition for ‘runLOLA’ plot.heatmap.pc.correlations: no visible global function definition for ‘melt’ plot.heatmap.pc.correlations: no visible global function definition for ‘grid.newpage’ plot.heatmap.pc.correlations: no visible global function definition for ‘grid.draw’ plot.heatmap.pc.pvalues: no visible global function definition for ‘melt’ plot.heatmap.pc.pvalues: no visible global function definition for ‘grid.newpage’ plot.heatmap.pc.pvalues: no visible global function definition for ‘grid.draw’ plot.heatmap.rand: no visible global function definition for ‘melt’ plot.heatmap.symm: no visible global function definition for ‘melt’ plot.heatmap.symm: no visible global function definition for ‘grid.newpage’ plot.heatmap.symm: no visible global function definition for ‘grid.draw’ plotCGHProfile: no visible global function definition for ‘ChrNumeric’ prepareGEOSampleInfoTemplate: no visible global function definition for ‘samples’ projectWBC: no visible global function definition for ‘solve.QP’ read.GS.report: no visible global function definition for ‘featureNames’ read.idat.files: no visible binding for global variable ‘barcode’ refFreeEWASP: no visible global function definition for ‘EstDimRMT’ refFreeEWASP: no visible global function definition for ‘RefFreeEwasModel’ refFreeEWASP: no visible global function definition for ‘PairsBootRefFreeEwasModel’ refFreeEWASP: no visible global function definition for ‘BootRefFreeEwasModel’ rnb.RnBSet.to.GRangesList: no visible global function definition for ‘samples’ rnb.RnBSet.to.bed: no visible global function definition for ‘samples’ rnb.RnBSet.to.bedGraph: no visible global function definition for ‘samples’ rnb.bed.from.segmentation: no visible global function definition for ‘samples’ rnb.boxplot.from.segmentation: no visible global function definition for ‘samples’ rnb.boxplot.from.segmentation: no visible binding for global variable ‘Segment’ rnb.boxplot.from.segmentation: no visible binding for global variable ‘AvgMeth’ rnb.chromosome.lengths: no visible global function definition for ‘seqlengths’ rnb.combine.seq: no visible global function definition for ‘samples’ rnb.enmix.oob: no visible global function definition for ‘%dopar%’ rnb.enmix.oob: no visible global function definition for ‘foreach’ rnb.execute.dreduction: no visible global function definition for ‘samples’ rnb.execute.filter.summary.internal: no visible global function definition for ‘samples’ rnb.execute.high.coverage.removal.internal: no visible global function definition for ‘samples’ rnb.execute.high.dpval.masking.internal: no visible global function definition for ‘samples’ rnb.execute.imputation: no visible global function definition for ‘samples’ rnb.execute.low.coverage.masking.internal: no visible global function definition for ‘samples’ rnb.execute.na.removal.internal: no visible global function definition for ‘samples’ rnb.execute.normalization: no visible global function definition for ‘phenoData’ rnb.execute.normalization: no visible global function definition for ‘phenoData<-’ rnb.execute.normalization: no visible global function definition for ‘RGChannelSet’ rnb.execute.normalization: no visible global function definition for ‘preprocessSWAN’ rnb.execute.normalization: no visible global function definition for ‘getMeth’ rnb.execute.normalization: no visible global function definition for ‘getUnmeth’ rnb.execute.normalization: no visible global function definition for ‘featureNames’ rnb.execute.normalization: no visible global function definition for ‘samples’ rnb.execute.normalization: no visible global function definition for ‘mapToGenome’ rnb.execute.normalization: no visible global function definition for ‘addSex’ rnb.execute.normalization: no visible global function definition for ‘getSex’ rnb.execute.normalization: no visible global function definition for ‘getCN’ rnb.execute.normalization.bmiq: no visible global function definition for ‘%dopar%’ rnb.execute.normalization.bmiq: no visible global function definition for ‘foreach’ rnb.execute.pOOBAH: no visible global function definition for ‘samples’ rnb.execute.pOOBAH: no visible global function definition for ‘SigSet’ rnb.execute.pOOBAH: no visible global function definition for ‘IG<-’ rnb.execute.pOOBAH: no visible global function definition for ‘IR<-’ rnb.execute.pOOBAH: no visible global function definition for ‘II<-’ rnb.execute.pOOBAH: no visible global function definition for ‘oobG<-’ rnb.execute.pOOBAH: no visible global function definition for ‘oobR<-’ rnb.execute.pOOBAH: no visible global function definition for ‘oobG’ rnb.execute.pOOBAH: no visible global function definition for ‘oobR’ rnb.execute.pOOBAH: no visible global function definition for ‘IR’ rnb.execute.pOOBAH: no visible global function definition for ‘IG’ rnb.execute.pOOBAH: no visible global function definition for ‘II’ rnb.execute.quality: no visible global function definition for ‘samples’ rnb.execute.quality : <anonymous>: no visible global function definition for ‘samples’ rnb.execute.segmentation: no visible binding for global variable ‘Hsapiens’ rnb.execute.segmentation: no visible binding for global variable ‘Mmusculus’ rnb.execute.segmentation: no visible global function definition for ‘seqlengths’ rnb.execute.segmentation: no visible global function definition for ‘browserSession’ rnb.execute.segmentation: no visible global function definition for ‘genome<-’ rnb.execute.segmentation: no visible global function definition for ‘ucscTableQuery’ rnb.execute.segmentation: no visible global function definition for ‘getTable’ rnb.execute.segmentation: no visible global function definition for ‘samples’ rnb.execute.segmentation: no visible global function definition for ‘readMethylome’ rnb.execute.segmentation: no visible global function definition for ‘readSNPTable’ rnb.execute.segmentation: no visible global function definition for ‘removeSNPs’ rnb.execute.segmentation: no visible global function definition for ‘segmentPMDs’ rnb.execute.segmentation: no visible global function definition for ‘plotAlphaDistributionOneChr’ rnb.execute.segmentation: no visible global function definition for ‘calculateFDRs’ rnb.execute.segmentation: no visible global function definition for ‘segmentUMRsLMRs’ rnb.export.to.ewasher: no visible global function definition for ‘samples’ rnb.filter.dataset: no visible global function definition for ‘samples’ rnb.final.segmentation: no visible global function definition for ‘samples’ rnb.get.reliability.counts.per.sample: no visible global function definition for ‘samples’ rnb.options.description.table.fromRd: no visible global function definition for ‘Rd2HTML’ rnb.options.description.table.fromRd: no visible binding for global variable ‘xmlValue’ rnb.plot.beta.density.group: no visible binding for global variable ‘group’ rnb.plot.biseq.coverage: no visible global function definition for ‘samples’ rnb.plot.biseq.coverage.hist: no visible global function definition for ‘samples’ rnb.plot.control.barplot: no visible global function definition for ‘samples’ rnb.plot.control.barplot: no visible binding for global variable ‘Target’ rnb.plot.control.barplot: no visible binding for global variable ‘Index’ rnb.plot.control.barplot: no visible binding for global variable ‘ID’ rnb.plot.control.barplot: no visible binding for global variable ‘Address’ rnb.plot.control.barplot: no visible global function definition for ‘grid.newpage’ rnb.plot.control.barplot: no visible binding for global variable ‘Intensity’ rnb.plot.control.barplot: no visible global function definition for ‘grid.draw’ rnb.plot.control.boxplot: no visible global function definition for ‘grid.newpage’ rnb.plot.control.boxplot: no visible binding for global variable ‘Probe’ rnb.plot.control.boxplot: no visible binding for global variable ‘Intensity’ rnb.plot.control.boxplot: no visible global function definition for ‘grid.draw’ rnb.plot.ct.heatmap: no visible binding for global variable ‘x’ rnb.plot.ct.heatmap: no visible binding for global variable ‘y’ rnb.plot.ct.heatmap: no visible binding for global variable ‘v’ rnb.plot.ct.heatmap: no visible global function definition for ‘grid.newpage’ rnb.plot.ct.heatmap: no visible global function definition for ‘grid.draw’ rnb.plot.dreduction: no visible global function definition for ‘tsne’ rnb.plot.locus.profile: no visible global function definition for ‘plotTracks’ rnb.plot.marker.fstat: no visible binding for global variable ‘x’ rnb.plot.marker.fstat: no visible binding for global variable ‘y’ rnb.plot.marker.fstat: no visible global function definition for ‘muted’ rnb.plot.negative.boxplot: no visible global function definition for ‘samples’ rnb.plot.negative.boxplot: no visible binding for global variable ‘numeric.names’ rnb.plot.negative.boxplot: no visible binding for global variable ‘type’ rnb.plot.negative.boxplot: no visible binding for global variable ‘types’ rnb.plot.negative.boxplot: no visible global function definition for ‘grid.newpage’ rnb.plot.negative.boxplot: no visible binding for global variable ‘Sample’ rnb.plot.negative.boxplot: no visible binding for global variable ‘Intensity’ rnb.plot.negative.boxplot: no visible global function definition for ‘grid.draw’ rnb.plot.num.sites.covg: no visible global function definition for ‘samples’ rnb.plot.num.sites.covg : <anonymous>: no visible global function definition for ‘samples’ rnb.plot.num.sites.covg: no visible binding for global variable ‘numSites’ rnb.plot.num.sites.covg: no visible binding for global variable ‘covgMedian’ rnb.plot.num.sites.covg: no visible binding for global variable ‘covgPercLow’ rnb.plot.num.sites.covg: no visible binding for global variable ‘covgPercUp’ rnb.plot.num.sites.covg: no visible binding for global variable ‘comma’ rnb.plot.region.profile.density: no visible binding for global variable ‘relative.coord’ rnb.plot.region.profile.density: no visible binding for global variable ‘..density..’ rnb.plot.region.profiles : <anonymous>: no visible global function definition for ‘samples’ rnb.plot.region.profiles: no visible binding for global variable ‘relative.coord’ rnb.plot.region.profiles: no visible binding for global variable ‘group’ rnb.plot.region.site.density: no visible binding for global variable ‘relative.coord’ rnb.plot.segmentation.distributions: no visible binding for global variable ‘x2’ rnb.plot.segmentation.distributions: no visible binding for global variable ‘y2’ rnb.plot.segmentation.distributions: no visible binding for global variable ‘texthere’ rnb.plot.segmentation.final: no visible global function definition for ‘plotFinalSegmentation’ rnb.plot.sentrix.distributions: no visible global function definition for ‘samples’ rnb.plot.sentrix.distributions: no visible binding for global variable ‘Slide’ rnb.plot.snp.boxplot: no visible binding for global variable ‘SNP’ rnb.plot.snp.boxplot: no visible binding for global variable ‘bv’ rnb.run.example: no visible global function definition for ‘install’ rnb.run.preprocessing : logger.completed.filtering: no visible global function definition for ‘samples’ rnb.sample.summary.table: no visible global function definition for ‘samples’ rnb.section.ageprediction: no visible global function definition for ‘samples’ rnb.section.clustering : <anonymous> : <anonymous>: no visible global function definition for ‘samples’ rnb.section.clustering: no visible global function definition for ‘samples’ rnb.section.diffMeth.region: no visible global function definition for ‘%dopar%’ rnb.section.diffMeth.region: no visible global function definition for ‘foreach’ rnb.section.diffMeth.region: no visible binding for global variable ‘k’ rnb.section.diffMeth.region : do.enrichment.table: no visible global function definition for ‘sigCategories’ rnb.section.diffMeth.region : do.enrichment.table.var: no visible global function definition for ‘sigCategories’ rnb.section.diffMeth.site: no visible global function definition for ‘%dopar%’ rnb.section.diffMeth.site: no visible global function definition for ‘foreach’ rnb.section.diffVar: no visible global function definition for ‘%dopar%’ rnb.section.diffVar: no visible global function definition for ‘foreach’ rnb.section.diffVar.region: no visible global function definition for ‘%dopar%’ rnb.section.diffVar.region: no visible global function definition for ‘foreach’ rnb.section.diffVar.region: no visible binding for global variable ‘k’ rnb.section.import: no visible global function definition for ‘samples’ rnb.section.import: no visible global function definition for ‘phenoData’ rnb.section.imputation: no visible global function definition for ‘melt’ rnb.section.locus.profiles: no visible global function definition for ‘samples’ rnb.section.locus.profiles : do.plots: no visible global function definition for ‘plotTracks’ rnb.section.locus.profiles: no visible global function definition for ‘%dopar%’ rnb.section.locus.profiles: no visible global function definition for ‘foreach’ rnb.section.na.removal: no visible global function definition for ‘samples’ rnb.section.normalization: no visible global function definition for ‘samples’ rnb.section.region.description: no visible binding for global variable ‘size’ rnb.section.region.description: no visible binding for global variable ‘n.sites’ rnb.section.region.profiles: no visible global function definition for ‘samples’ rnb.section.region.subsegmentation : get.summary.df.from.list: no visible global function definition for ‘melt’ rnb.section.region.subsegmentation: no visible binding for global variable ‘region.size’ rnb.section.region.subsegmentation: no visible binding for global variable ‘is.subsegmentation’ rnb.section.region.subsegmentation: no visible binding for global variable ‘num.sites’ rnb.section.sex.prediction: no visible global function definition for ‘muted’ rnb.step.betadistribution.internal: no visible global function definition for ‘%dopar%’ rnb.step.betadistribution.internal: no visible global function definition for ‘foreach’ rnb.step.cell.types: no visible global function definition for ‘samples’ rnb.step.clustering.internal: no visible global function definition for ‘samples’ rnb.step.dreduction: no visible global function definition for ‘%dopar%’ rnb.step.dreduction: no visible global function definition for ‘foreach’ rnb.step.dreduction: no visible binding for global variable ‘target’ rnb.step.filter.summary.internal: no visible global function definition for ‘percent_format’ rnb.step.filter.summary.internal: no visible global function definition for ‘samples’ rnb.step.import: no visible global function definition for ‘samples’ rnb.step.import: no visible global function definition for ‘phenoData’ rnb.step.na.removal: no visible binding for global variable ‘sites2ignore’ rnb.step.na.removal.internal: no visible global function definition for ‘samples’ rnb.step.normalization: no visible global function definition for ‘phenoData’ robustHyperGResultSummary: no visible global function definition for ‘sigCategories’ robustHyperGResultSummary: no visible global function definition for ‘pvalues’ robustHyperGResultSummary: no visible global function definition for ‘oddsRatios’ robustHyperGResultSummary: no visible global function definition for ‘expectedCounts’ robustHyperGResultSummary: no visible global function definition for ‘geneCounts’ robustHyperGResultSummary: no visible global function definition for ‘universeCounts’ robustHyperGResultSummary: no visible binding for global variable ‘Term’ run.cross.validation: no visible global function definition for ‘samples’ run.cross.validation: no visible global function definition for ‘melt’ run.cross.validation: no visible binding for global variable ‘Measure’ run.cross.validation: no visible binding for global variable ‘Error’ sampleCovgApply: no visible global function definition for ‘samples’ set.covariates.ct: no visible global function definition for ‘samples’ simpleGlmnet: no visible global function definition for ‘impute.knn’ simpleGlmnet: no visible global function definition for ‘cv.glmnet’ simpleGlmnet: no visible global function definition for ‘glmnet’ simpleGlmnetBiseq: no visible global function definition for ‘cv.glmnet’ simpleGlmnetBiseq: no visible global function definition for ‘glmnet’ simpleGlmnetEvaluate: no visible global function definition for ‘cv.glmnet’ simpleGlmnetEvaluate: no visible global function definition for ‘glmnet’ symmetric.melt: no visible global function definition for ‘melt’ addDiffMethTable,RnBDiffMeth: no visible binding for global variable ‘reg.type’ coerce,RGChannelSet-RnBeadRawSet: no visible global function definition for ‘getManifest’ coerce,RGChannelSet-RnBeadRawSet: no visible global function definition for ‘getGreen’ coerce,RGChannelSet-RnBeadRawSet: no visible global function definition for ‘getRed’ coerce,RGChannelSet-RnBeadRawSet: no visible global function definition for ‘pData’ coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition for ‘featureData<-’ coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition for ‘featureNames<-’ coerce,RnBeadRawSet-RGChannelSet: no visible global function definition for ‘RGChannelSet’ join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function definition for ‘clone’ mask.sites.meth,RnBSet: no visible global function definition for ‘samples’ remove.samples,RnBSet: no visible global function definition for ‘samples’ remove.samples,RnBeadRawSet: no visible global function definition for ‘samples’ remove.samples,RnBeadSet: no visible global function definition for ‘samples’ remove.sites,RnBSet: no visible global function definition for ‘samples’ sampleCovgApply,RnBSet: no visible global function definition for ‘samples’ sampleMethApply,RnBSet: no visible global function definition for ‘samples’ summarize.regions,RnBSet: no visible global function definition for ‘samples’ summarize.regions,RnBSet: multiple local function definitions for ‘aggr.f’ with different formal arguments updateMethylationSites,RnBSet: no visible global function definition for ‘samples’ Undefined global functions or variables: %dopar% ..count.. ..density.. .inds.g2 Address Age Annotated AvgMeth BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack Group Hsapiens ID IG IG<- II II<- IR IR<- IdeogramTrack IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity Measure Mmusculus PairsBootRefFreeEwasModel Predicted Probe RGChannelSet Rd2HTML RefFreeEwasModel SNP Sample Segment SigSet Slide Target Term UcscTrack Value addSex as.profileCGH assayDataElement assayDataElementNames barcode browserSession bv calculateFDRs chrom clone combinedRank combinedRank.var comma covgMedian covgPercLow covgPercUp cv.glmnet daglad diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency eps expectedCounts featureData featureData<- featureNames featureNames<- foreach geneCounts genome<- getCN getDoParWorkers getGreen getManifest getMeth getRed getSex getTable getUnmeth getVarCov glmnet grid.draw grid.newpage group group1 group2 i impute.knn install is.subsegmentation k letterFrequency lme loadRegionDB log10FDR log10P mapToGenome mclapply mean.diff mean.quot.log2 melt mergeRegionDBs muted n.sites num.sites numSites numeric.names oddsRatios oobG oobG<- oobR oobR<- p.vals.t.na.adj pData percent_format phenoData phenoData<- plotAlphaDistributionOneChr plotFinalSegmentation plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable refText reg.type region.size registerDoParallel relative.coord removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs seqlengths seqlevels<- setNames sigCategories sites2ignore size solve.QP stopCluster sva target texthere tsne type types ucscTableQuery universeCounts useMart v var.diff varFit varLabels x x2 xmlValue y y2 yint Consider adding importFrom("stats", "setNames") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed rnb.execute.pOOBAH 22.115 0.767 22.904 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 6 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/RnBeads.Rcheck/00check.log’ for details.
RnBeads.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL RnBeads ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘RnBeads’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** 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 (RnBeads)
RnBeads.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BiocGenerics:::testPackage("RnBeads") Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="/tmp/RtmpdR7C0u/ff" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system Attaching package: 'ff' The following objects are masked from 'package:utils': write.csv, write.csv2 The following objects are masked from 'package:base': is.factor, is.ordered Attaching package: 'grid' The following object is masked from 'package:ff': pattern Spam version 2.7-0 (2021-06-25) is loaded. Type 'help( Spam)' or 'demo( spam)' for a short introduction and overview of this package. Help for individual functions is also obtained by adding the suffix '.spam' to the function name, e.g. 'help( chol.spam)'. Attaching package: 'spam' The following object is masked from 'package:stats4': mle The following objects are masked from 'package:base': backsolve, forwardsolve See https://github.com/NCAR/Fields for an extensive vignette, other supplements and source code Attaching package: 'gplots' The following object is masked from 'package:IRanges': space The following object is masked from 'package:S4Vectors': space The following object is masked from 'package:stats': lowess Attaching package: 'gridExtra' The following object is masked from 'package:BiocGenerics': combine Attaching package: 'limma' The following object is masked from 'package:BiocGenerics': plotMA Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'scales' The following object is masked from 'package:viridis': viridis_pal Attaching package: 'AnnotationDbi' The following object is masked from 'package:MASS': select Attaching package: 'MatrixGenerics' The following object is masked from 'package:Biobase': rowMedians The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Attaching package: 'Biostrings' The following object is masked from 'package:grid': pattern The following objects are masked from 'package:ff': mismatch, pattern The following object is masked from 'package:base': strsplit locfit 1.5-9.4 2020-03-24 Setting options('download.file.method.GEOquery'='auto') Setting options('GEOquery.inmemory.gpl'=FALSE) Attaching package: 'plyr' The following object is masked from 'package:XVector': compact The following object is masked from 'package:matrixStats': count The following object is masked from 'package:IRanges': desc The following object is masked from 'package:S4Vectors': rename 2021-10-14 11:29:35 1.0 STATUS STARTED Unit testing: differential 2021-10-14 11:29:35 1.0 STATUS STARTED Testing function: rowWelchP Loading required package: RnBeads.hg19 2021-10-14 11:29:35 1.0 STATUS COMPLETED Testing function: rowWelchP 2021-10-14 11:29:35 1.0 STATUS STARTED Testing function: limmaP 2021-10-14 11:29:35 1.0 STATUS COMPLETED Testing function: limmaP 2021-10-14 11:29:35 1.0 STATUS STARTED Testing function: computeDiffTab.extended.site 2021-10-14 11:29:35 1.0 INFO Conducting differential analysis using limma 2021-10-14 11:29:35 1.0 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2021-10-14 11:29:35 1.0 STATUS STARTED Testing function: computeDiffTab.default.region 2021-10-14 11:29:35 1.0 INFO Conducting differential analysis using limma 2021-10-14 11:29:42 1.4 STATUS COMPLETED Testing function: computeDiffTab.default.region 2021-10-14 11:29:42 1.4 STATUS STARTED Testing function: combineTestPvalsMeth 2021-10-14 11:29:42 1.4 STATUS COMPLETED Testing function: combineTestPvalsMeth 2021-10-14 11:29:42 1.4 STATUS STARTED Testing function: get.adjustment.variables 2021-10-14 11:29:42 1.4 STATUS COMPLETED Testing function: get.adjustment.variables 2021-10-14 11:29:42 1.4 STATUS STARTED Testing function: get.comparison.info 2021-10-14 11:29:42 1.4 STATUS COMPLETED Testing function: get.comparison.info 2021-10-14 11:29:42 1.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2021-10-14 11:29:42 1.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:29:42 1.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:29:42 1.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:29:42 1.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:29:42 1.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:29:42 1.4 INFO Conducting differential analysis using limma 2021-10-14 11:29:43 1.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:29:43 1.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:29:43 1.4 STATUS Computed table for tiling 2021-10-14 11:29:43 1.4 STATUS Computed table for genes 2021-10-14 11:29:43 1.4 STATUS Computed table for promoters 2021-10-14 11:29:44 1.4 STATUS Computed table for cpgislands 2021-10-14 11:29:44 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:29:44 1.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:29:44 1.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:29:44 1.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:29:44 1.4 INFO Conducting differential analysis using limma 2021-10-14 11:29:44 1.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:29:44 1.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:29:44 1.4 STATUS Computed table for tiling 2021-10-14 11:29:44 1.4 STATUS Computed table for genes 2021-10-14 11:29:44 1.4 STATUS Computed table for promoters 2021-10-14 11:29:45 1.4 STATUS Computed table for cpgislands 2021-10-14 11:29:45 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:29:45 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:29:45 1.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:29:45 1.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2021-10-14 11:29:45 1.4 STATUS STARTED Testing function: diffVar 2021-10-14 11:29:45 1.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:30:50 4.0 STATUS COMPLETED diffVar method 2021-10-14 11:30:50 4.0 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:30:50 4.0 WARNING Could not compute p-values with diffVar, returning NA 2021-10-14 11:30:50 4.0 INFO diffVar from missMethyl package not properly running 2021-10-14 11:30:50 4.0 STATUS COMPLETED diffVar method 2021-10-14 11:30:50 4.0 STATUS STARTED Testing function: apply.iEVORA 2021-10-14 11:30:51 4.0 STATUS STARTED iEVORA method 2021-10-14 11:30:51 4.1 INFO No DVCs detected. All p-values set to 1. 2021-10-14 11:30:51 4.1 STATUS COMPLETED iEVORA method 2021-10-14 11:30:51 4.1 STATUS STARTED Testing function: rnb.execute.diffVar 2021-10-14 11:30:51 4.1 STATUS STARTED Differential Variability 2021-10-14 11:30:51 4.1 STATUS STARTED Retrieving comparison info 2021-10-14 11:30:51 4.1 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:30:51 4.1 INFO No imputation method selected, 'knn' method used. 2021-10-14 11:30:51 4.1 STATUS STARTED Imputation procedure knn 2021-10-14 11:30:51 4.1 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:30:51 4.1 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:30:51 4.1 INFO Conducting differential variability using diffVar 2021-10-14 11:30:51 4.1 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:30:51 4.1 STATUS COMPLETED diffVar method 2021-10-14 11:30:51 4.1 STATUS STARTED Computing Differential Variability Tables (Region Level) 2021-10-14 11:30:52 4.2 STATUS Computed table for tiling 2021-10-14 11:30:52 4.3 STATUS Computed table for genes 2021-10-14 11:30:52 4.3 STATUS Computed table for promoters 2021-10-14 11:30:53 4.1 STATUS Computed table for cpgislands 2021-10-14 11:30:53 4.1 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2021-10-14 11:30:53 4.1 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:30:53 4.1 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2021-10-14 11:30:53 4.1 INFO Conducting differential variability using diffVar 2021-10-14 11:30:53 4.1 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:30:53 4.1 STATUS COMPLETED diffVar method 2021-10-14 11:30:53 4.1 STATUS STARTED Computing Differential Variability Tables (Region Level) 2021-10-14 11:30:54 4.1 STATUS Computed table for tiling 2021-10-14 11:30:54 4.1 STATUS Computed table for genes 2021-10-14 11:30:54 4.1 STATUS Computed table for promoters 2021-10-14 11:30:54 4.1 STATUS Computed table for cpgislands 2021-10-14 11:30:54 4.1 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2021-10-14 11:30:54 4.1 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2021-10-14 11:30:54 4.1 STATUS COMPLETED Differential Variability 2021-10-14 11:30:54 4.1 STATUS COMPLETED Testing function: rnb.execute.diffVar 2021-10-14 11:30:54 4.1 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability 2021-10-14 11:30:54 4.1 STATUS STARTED Retrieving comparison info 2021-10-14 11:30:54 4.1 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:30:54 4.1 STATUS STARTED Computing differential methylation tables 2021-10-14 11:30:54 4.1 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:30:54 4.1 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:30:54 4.1 INFO Conducting differential analysis using limma 2021-10-14 11:30:54 4.1 STATUS STARTED Imputation procedure knn 2021-10-14 11:30:54 4.1 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:30:54 4.1 INFO Conducting differential variability using diffVar 2021-10-14 11:30:54 4.1 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:30:54 4.1 STATUS COMPLETED diffVar method 2021-10-14 11:30:54 4.1 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:30:54 4.1 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:30:57 4.0 STATUS Computed table for tiling 2021-10-14 11:30:58 4.0 STATUS Computed table for genes 2021-10-14 11:30:58 4.0 STATUS Computed table for promoters 2021-10-14 11:30:58 4.0 STATUS Computed table for cpgislands 2021-10-14 11:30:58 4.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:30:58 4.0 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:30:58 4.0 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:30:58 4.0 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:30:58 4.0 INFO Conducting differential analysis using limma 2021-10-14 11:30:58 4.0 STATUS STARTED Imputation procedure knn 2021-10-14 11:30:58 4.0 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:30:58 4.0 INFO Conducting differential variability using diffVar 2021-10-14 11:30:58 4.0 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:30:58 4.0 STATUS COMPLETED diffVar method 2021-10-14 11:30:58 4.0 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:30:58 4.0 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:03 3.4 STATUS Computed table for tiling 2021-10-14 11:31:03 3.4 STATUS Computed table for genes 2021-10-14 11:31:04 3.4 STATUS Computed table for promoters 2021-10-14 11:31:04 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:04 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:04 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:04 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:04 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability 2021-10-14 11:31:04 3.4 STATUS STARTED Testing class: RnBDiffMeth 2021-10-14 11:31:04 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:04 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:04 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:04 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:04 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:04 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:04 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:04 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:05 3.4 STATUS Computed table for tiling 2021-10-14 11:31:05 3.4 STATUS Computed table for genes 2021-10-14 11:31:06 3.4 STATUS Computed table for promoters 2021-10-14 11:31:06 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:06 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:06 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:06 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:06 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:06 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:06 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:06 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:06 3.4 STATUS Computed table for tiling 2021-10-14 11:31:07 3.4 STATUS Computed table for genes 2021-10-14 11:31:07 3.4 STATUS Computed table for promoters 2021-10-14 11:31:07 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:07 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:07 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:07 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:07 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:07 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:07 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:07 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:07 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:07 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:07 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:07 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:07 3.4 STATUS Computed table for genes 2021-10-14 11:31:08 3.4 STATUS Computed table for tiling 2021-10-14 11:31:08 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:08 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:08 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:08 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:08 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:08 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:08 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:08 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:08 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:08 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:08 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:08 3.4 STATUS Computed table for genes 2021-10-14 11:31:09 3.4 STATUS Computed table for tiling 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:09 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:09 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:09 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:09 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:09 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:09 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:09 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:09 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:09 3.4 STATUS Computed table for promoters 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:09 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:09 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:09 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:09 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:09 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:09 3.4 STATUS Computed table for promoters 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:09 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:09 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:09 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:09 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:09 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:09 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:09 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:09 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:09 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:10 3.4 STATUS Computed table for genes 2021-10-14 11:31:10 3.4 STATUS Computed table for tiling 2021-10-14 11:31:10 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:10 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:10 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:10 3.4 STATUS STARTED Testing function: get.region.types 2021-10-14 11:31:10 3.4 STATUS COMPLETED Testing function: get.region.types 2021-10-14 11:31:10 3.4 STATUS STARTED Testing function: get.comparisons 2021-10-14 11:31:10 3.4 STATUS COMPLETED Testing function: get.comparisons 2021-10-14 11:31:10 3.4 STATUS STARTED Testing function: get.comparison.grouplabels 2021-10-14 11:31:10 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels 2021-10-14 11:31:10 3.4 STATUS STARTED Testing function: get.site.test.method 2021-10-14 11:31:10 3.4 STATUS COMPLETED Testing function: get.site.test.method 2021-10-14 11:31:10 3.4 STATUS STARTED Testing function: get.table 2021-10-14 11:31:10 3.4 STATUS COMPLETED Testing function: get.table 2021-10-14 11:31:10 3.4 STATUS STARTED Testing function: addDiffMethTable 2021-10-14 11:31:10 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:11 3.4 STATUS COMPLETED Testing function: addDiffMethTable 2021-10-14 11:31:11 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid 2021-10-14 11:31:11 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2021-10-14 11:31:11 3.4 STATUS STARTED Destructor 2021-10-14 11:31:11 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:11 3.4 STATUS COMPLETED Destructor 2021-10-14 11:31:11 3.4 STATUS COMPLETED Testing class: RnBDiffMeth 2021-10-14 11:31:11 3.4 STATUS COMPLETED Testing function: apply.iEVORA 2021-10-14 11:31:11 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:11 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:11 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:11 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:11 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:11 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:11 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:11 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:11 3.4 STATUS Computed table for tiling 2021-10-14 11:31:12 3.4 STATUS Computed table for genes 2021-10-14 11:31:12 3.4 STATUS Computed table for promoters 2021-10-14 11:31:12 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:12 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:12 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:12 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:12 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:12 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:13 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:13 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:13 3.4 STATUS Computed table for tiling 2021-10-14 11:31:13 3.4 STATUS Computed table for genes 2021-10-14 11:31:13 3.4 STATUS Computed table for promoters 2021-10-14 11:31:14 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:14 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:14 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:14 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:14 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:14 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:14 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:14 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:14 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:14 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:14 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:14 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:14 3.4 STATUS Computed table for genes 2021-10-14 11:31:15 3.4 STATUS Computed table for tiling 2021-10-14 11:31:15 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:15 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:15 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:15 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:15 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:15 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:15 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:15 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:15 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:15 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:15 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:15 3.4 STATUS Computed table for genes 2021-10-14 11:31:16 3.4 STATUS Computed table for tiling 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:16 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:16 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:16 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:16 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:16 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:16 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:16 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:16 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:16 3.4 STATUS Computed table for promoters 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:16 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:16 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:16 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:16 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:16 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:16 3.4 STATUS Computed table for promoters 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:16 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:16 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:16 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:16 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:16 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:16 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:16 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:16 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:16 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:17 3.4 STATUS Computed table for genes 2021-10-14 11:31:17 3.4 STATUS Computed table for tiling 2021-10-14 11:31:17 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:17 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:17 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:17 3.4 STATUS STARTED Testing function: get.region.types 2021-10-14 11:31:17 3.4 STATUS COMPLETED Testing function: get.region.types 2021-10-14 11:31:17 3.4 STATUS STARTED Testing function: get.comparisons 2021-10-14 11:31:17 3.4 STATUS COMPLETED Testing function: get.comparisons 2021-10-14 11:31:17 3.4 STATUS STARTED Testing function: get.comparison.grouplabels 2021-10-14 11:31:17 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels 2021-10-14 11:31:17 3.4 STATUS STARTED Testing function: get.site.test.method 2021-10-14 11:31:17 3.4 STATUS COMPLETED Testing function: get.site.test.method 2021-10-14 11:31:17 3.4 STATUS STARTED Testing function: get.table 2021-10-14 11:31:17 3.4 STATUS COMPLETED Testing function: get.table 2021-10-14 11:31:17 3.4 STATUS STARTED Testing function: addDiffMethTable 2021-10-14 11:31:17 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:18 3.4 STATUS COMPLETED Testing function: addDiffMethTable 2021-10-14 11:31:18 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid 2021-10-14 11:31:18 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2021-10-14 11:31:18 3.4 STATUS STARTED Destructor 2021-10-14 11:31:18 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:18 3.4 STATUS COMPLETED Destructor 2021-10-14 11:31:18 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:18 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:18 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:18 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:18 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:18 3.4 WARNING Could not compute p-values with diffVar, returning NA 2021-10-14 11:31:18 3.4 INFO diffVar from missMethyl package not properly running 2021-10-14 11:31:18 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:18 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:18 3.4 STATUS STARTED Unit testing: differential 2021-10-14 11:31:18 3.4 STATUS STARTED Testing function: rowWelchP 2021-10-14 11:31:18 3.4 STATUS COMPLETED Testing function: rowWelchP 2021-10-14 11:31:18 3.4 STATUS STARTED Testing function: limmaP 2021-10-14 11:31:18 3.4 STATUS COMPLETED Testing function: limmaP 2021-10-14 11:31:18 3.4 STATUS STARTED Testing function: computeDiffTab.extended.site 2021-10-14 11:31:18 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:18 3.4 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2021-10-14 11:31:18 3.4 STATUS STARTED Testing function: computeDiffTab.default.region 2021-10-14 11:31:18 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:19 3.4 STATUS COMPLETED Testing function: computeDiffTab.default.region 2021-10-14 11:31:19 3.4 STATUS STARTED Testing function: combineTestPvalsMeth 2021-10-14 11:31:19 3.4 STATUS COMPLETED Testing function: combineTestPvalsMeth 2021-10-14 11:31:19 3.4 STATUS STARTED Testing function: get.adjustment.variables 2021-10-14 11:31:19 3.4 STATUS COMPLETED Testing function: get.adjustment.variables 2021-10-14 11:31:19 3.4 STATUS STARTED Testing function: get.comparison.info 2021-10-14 11:31:19 3.4 STATUS COMPLETED Testing function: get.comparison.info 2021-10-14 11:31:19 3.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2021-10-14 11:31:19 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:19 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:19 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:19 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:19 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:19 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:19 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:19 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:20 3.4 STATUS Computed table for tiling 2021-10-14 11:31:20 3.4 STATUS Computed table for genes 2021-10-14 11:31:21 3.4 STATUS Computed table for promoters 2021-10-14 11:31:21 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:21 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:21 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:21 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:21 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:21 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:21 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:21 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:21 3.4 STATUS Computed table for tiling 2021-10-14 11:31:22 3.4 STATUS Computed table for genes 2021-10-14 11:31:23 3.4 STATUS Computed table for promoters 2021-10-14 11:31:23 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:23 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:23 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:23 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:23 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2021-10-14 11:31:23 3.4 STATUS STARTED Testing function: diffVar 2021-10-14 11:31:23 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:23 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:23 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:23 3.4 WARNING Could not compute p-values with diffVar, returning NA 2021-10-14 11:31:23 3.4 INFO diffVar from missMethyl package not properly running 2021-10-14 11:31:23 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:23 3.4 STATUS STARTED Testing function: apply.iEVORA 2021-10-14 11:31:23 3.4 STATUS STARTED iEVORA method 2021-10-14 11:31:24 3.4 INFO No DVCs detected. All p-values set to 1. 2021-10-14 11:31:24 3.4 STATUS COMPLETED iEVORA method 2021-10-14 11:31:24 3.4 STATUS STARTED Testing function: rnb.execute.diffVar 2021-10-14 11:31:24 3.4 STATUS STARTED Differential Variability 2021-10-14 11:31:24 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:24 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:24 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:24 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:24 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:24 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:24 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:24 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:24 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:25 3.4 STATUS Computed table for tiling 2021-10-14 11:31:25 3.4 STATUS Computed table for genes 2021-10-14 11:31:25 3.4 STATUS Computed table for promoters 2021-10-14 11:31:26 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:26 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:26 3.4 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:26 3.4 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:26 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:26 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:26 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:26 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:26 3.4 STATUS Computed table for tiling 2021-10-14 11:31:26 3.4 STATUS Computed table for genes 2021-10-14 11:31:26 3.4 STATUS Computed table for promoters 2021-10-14 11:31:26 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:26 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:26 3.4 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:26 3.4 STATUS COMPLETED Differential Variability 2021-10-14 11:31:26 3.4 STATUS COMPLETED Testing function: rnb.execute.diffVar 2021-10-14 11:31:26 3.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability 2021-10-14 11:31:27 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:27 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:27 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:27 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:27 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:27 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:27 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:27 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:27 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:27 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:27 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:27 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:28 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:28 3.4 STATUS Computed table for tiling 2021-10-14 11:31:28 3.4 STATUS Computed table for genes 2021-10-14 11:31:29 3.4 STATUS Computed table for promoters 2021-10-14 11:31:29 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:29 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:29 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:29 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:29 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:29 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:29 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:29 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:29 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:29 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:29 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:30 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:30 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:30 3.4 STATUS Computed table for tiling 2021-10-14 11:31:30 3.4 STATUS Computed table for genes 2021-10-14 11:31:31 3.4 STATUS Computed table for promoters 2021-10-14 11:31:31 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:31 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:31 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:31 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:31 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability 2021-10-14 11:31:31 3.4 STATUS STARTED Testing class: RnBDiffMeth 2021-10-14 11:31:32 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:32 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:32 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:32 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:32 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:32 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:32 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:32 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:32 3.4 STATUS Computed table for tiling 2021-10-14 11:31:32 3.4 STATUS Computed table for genes 2021-10-14 11:31:32 3.4 STATUS Computed table for promoters 2021-10-14 11:31:32 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:32 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:32 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:32 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:32 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:32 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:32 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:32 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:34 3.4 STATUS Computed table for tiling 2021-10-14 11:31:34 3.4 STATUS Computed table for genes 2021-10-14 11:31:34 3.4 STATUS Computed table for promoters 2021-10-14 11:31:34 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:34 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:34 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:34 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:34 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:34 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:34 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:34 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:34 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:34 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:34 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:34 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:35 3.4 STATUS Computed table for genes 2021-10-14 11:31:36 3.4 STATUS Computed table for tiling 2021-10-14 11:31:36 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:36 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:36 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:36 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:36 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:36 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:36 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:36 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:36 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:36 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:36 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:36 3.4 STATUS Computed table for genes 2021-10-14 11:31:36 3.4 STATUS Computed table for tiling 2021-10-14 11:31:36 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:36 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:36 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:36 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:36 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:36 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:36 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:36 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:36 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:36 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:36 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:37 3.4 STATUS Computed table for promoters 2021-10-14 11:31:37 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:37 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:37 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:37 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:37 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:37 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:37 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:37 3.4 STATUS Computed table for promoters 2021-10-14 11:31:37 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:37 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:37 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:37 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:37 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:37 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:37 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:37 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:37 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:37 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:37 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:37 3.4 STATUS Computed table for genes 2021-10-14 11:31:38 3.4 STATUS Computed table for tiling 2021-10-14 11:31:38 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:38 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:38 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:38 3.4 STATUS STARTED Testing function: get.region.types 2021-10-14 11:31:38 3.4 STATUS COMPLETED Testing function: get.region.types 2021-10-14 11:31:38 3.4 STATUS STARTED Testing function: get.comparisons 2021-10-14 11:31:38 3.4 STATUS COMPLETED Testing function: get.comparisons 2021-10-14 11:31:38 3.4 STATUS STARTED Testing function: get.comparison.grouplabels 2021-10-14 11:31:38 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels 2021-10-14 11:31:38 3.4 STATUS STARTED Testing function: get.site.test.method 2021-10-14 11:31:38 3.4 STATUS COMPLETED Testing function: get.site.test.method 2021-10-14 11:31:38 3.4 STATUS STARTED Testing function: get.table 2021-10-14 11:31:38 3.4 STATUS COMPLETED Testing function: get.table 2021-10-14 11:31:38 3.4 STATUS STARTED Testing function: addDiffMethTable 2021-10-14 11:31:38 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:39 3.4 STATUS COMPLETED Testing function: addDiffMethTable 2021-10-14 11:31:39 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid 2021-10-14 11:31:39 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2021-10-14 11:31:39 3.4 STATUS STARTED Destructor 2021-10-14 11:31:39 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2021-10-14 11:31:39 3.4 STATUS COMPLETED Destructor 2021-10-14 11:31:39 3.4 STATUS COMPLETED Testing class: RnBDiffMeth 2021-10-14 11:31:39 3.4 STATUS COMPLETED Testing function: apply.iEVORA 2021-10-14 11:31:39 3.4 STATUS STARTED iEVORA method 2021-10-14 11:31:40 3.4 INFO No DVCs detected. All p-values set to 1. Coefficients not estimable: x2x2 2021-10-14 11:31:40 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:40 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:40 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:40 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:40 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:40 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:40 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:40 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:41 3.4 STATUS Computed table for tiling 2021-10-14 11:31:41 3.4 STATUS Computed table for genes 2021-10-14 11:31:41 3.4 STATUS Computed table for promoters 2021-10-14 11:31:41 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:41 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:41 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:41 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:41 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:41 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:41 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:41 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:42 3.4 STATUS Computed table for tiling 2021-10-14 11:31:43 3.4 STATUS Computed table for genes 2021-10-14 11:31:43 3.4 STATUS Computed table for promoters 2021-10-14 11:31:43 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:43 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:43 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:43 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:43 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:43 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:43 3.4 STATUS STARTED Computing differential methylation tables 2021-10-14 11:31:43 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:43 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:43 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:43 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:43 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:43 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:43 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:43 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:43 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:43 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:44 3.4 STATUS Computed table for tiling 2021-10-14 11:31:45 3.4 STATUS Computed table for genes 2021-10-14 11:31:45 3.4 STATUS Computed table for promoters 2021-10-14 11:31:45 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:45 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:45 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:45 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:45 3.4 STATUS STARTED Computing Differential Methylation Table 2021-10-14 11:31:45 3.4 INFO Conducting differential analysis using limma 2021-10-14 11:31:45 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:45 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:45 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:45 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:45 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:45 3.4 STATUS COMPLETED Computing Differential Methylation Table 2021-10-14 11:31:45 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:46 3.4 STATUS Computed table for tiling 2021-10-14 11:31:47 3.4 STATUS Computed table for genes 2021-10-14 11:31:47 3.4 STATUS Computed table for promoters 2021-10-14 11:31:47 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:47 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2021-10-14 11:31:47 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:47 3.4 STATUS COMPLETED Computing differential methylation tables 2021-10-14 11:31:47 3.4 STATUS STARTED Differential Variability 2021-10-14 11:31:47 3.4 STATUS STARTED Retrieving comparison info 2021-10-14 11:31:47 3.4 STATUS COMPLETED Retrieving comparison info 2021-10-14 11:31:47 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:47 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:47 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:47 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:47 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:47 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:47 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:48 3.4 STATUS Computed table for tiling 2021-10-14 11:31:48 3.4 STATUS Computed table for genes 2021-10-14 11:31:48 3.4 STATUS Computed table for promoters 2021-10-14 11:31:49 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:49 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:49 3.4 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2021-10-14 11:31:49 3.4 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:49 3.4 INFO Conducting differential variability using diffVar 2021-10-14 11:31:49 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2021-10-14 11:31:49 3.4 STATUS COMPLETED diffVar method 2021-10-14 11:31:49 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:49 3.4 STATUS Computed table for tiling 2021-10-14 11:31:49 3.4 STATUS Computed table for genes 2021-10-14 11:31:49 3.4 STATUS Computed table for promoters 2021-10-14 11:31:49 3.4 STATUS Computed table for cpgislands 2021-10-14 11:31:49 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2021-10-14 11:31:49 3.4 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2021-10-14 11:31:49 3.4 STATUS COMPLETED Differential Variability 2021-10-14 11:31:50 3.4 STATUS STARTED Analysis 2021-10-14 11:31:50 3.4 INFO Loaded information from data.RData 2021-10-14 11:31:50 3.4 STATUS STARTED Processing Detection P-values 2021-10-14 11:31:50 3.4 INFO Removed 3979 probes that overlap with SNPs 2021-10-14 11:31:50 3.4 INFO Completed Greedycut on 510 samples 2021-10-14 11:31:50 3.4 STATUS COMPLETED Processing Detection P-values 2021-10-14 11:31:50 3.4 WARNING File not found: data2.RData 2021-10-14 11:31:50 3.4 STATUS COMPLETED Analysis 2021-10-14 11:31:50 3.4 STATUS STARTED Testing imputation 2021-10-14 11:31:50 3.4 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:51 3.4 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:51 3.4 STATUS STARTED Imputation procedure mean.samples 2021-10-14 11:31:51 3.4 STATUS COMPLETED Imputation procedure mean.samples 2021-10-14 11:31:51 3.4 STATUS STARTED Imputation procedure mean.cpgs 2021-10-14 11:31:52 3.4 STATUS COMPLETED Imputation procedure mean.cpgs 2021-10-14 11:31:52 3.4 STATUS STARTED Imputation procedure random 2021-10-14 11:31:53 3.4 STATUS COMPLETED Imputation procedure random 2021-10-14 11:31:53 3.4 STATUS COMPLETED Testing imputation 2021-10-14 11:31:53 3.4 STATUS STARTED Testing age prediction 2021-10-14 11:31:53 3.4 STATUS STARTED Performing Age Prediction 2021-10-14 11:31:56 3.5 STATUS COMPLETED Performing Age Prediction 2021-10-14 11:31:56 3.5 STATUS COMPLETED Testing age prediction 2021-10-14 11:31:56 3.5 STATUS STARTED Performing Age Prediction 2021-10-14 11:31:59 3.6 STATUS COMPLETED Performing Age Prediction 2021-10-14 11:31:59 3.6 STATUS STARTED Imputation procedure knn 2021-10-14 11:31:59 3.6 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:31:59 3.6 STATUS STARTED Imputation procedure mean.samples 2021-10-14 11:32:01 3.6 STATUS COMPLETED Imputation procedure mean.samples 2021-10-14 11:32:01 3.6 STATUS STARTED Imputation procedure mean.cpgs 2021-10-14 11:32:01 3.6 STATUS COMPLETED Imputation procedure mean.cpgs 2021-10-14 11:32:01 3.6 STATUS STARTED Imputation procedure random 2021-10-14 11:32:01 3.6 STATUS COMPLETED Imputation procedure random 2021-10-14 11:32:01 3.6 STATUS STARTED Testing imputation 2021-10-14 11:32:01 3.6 STATUS STARTED Imputation procedure knn 2021-10-14 11:32:02 3.6 STATUS COMPLETED Imputation procedure knn 2021-10-14 11:32:02 3.6 STATUS STARTED Imputation procedure mean.samples 2021-10-14 11:32:03 3.6 STATUS COMPLETED Imputation procedure mean.samples 2021-10-14 11:32:03 3.6 STATUS STARTED Imputation procedure mean.cpgs 2021-10-14 11:32:04 3.6 STATUS COMPLETED Imputation procedure mean.cpgs 2021-10-14 11:32:04 3.6 STATUS STARTED Imputation procedure random 2021-10-14 11:32:04 3.6 STATUS COMPLETED Imputation procedure random 2021-10-14 11:32:04 3.6 STATUS COMPLETED Testing imputation 2021-10-14 11:32:04 3.6 STATUS STARTED Testing age prediction 2021-10-14 11:32:04 3.6 STATUS STARTED Performing Age Prediction 2021-10-14 11:32:07 3.6 STATUS COMPLETED Performing Age Prediction 2021-10-14 11:32:07 3.6 STATUS COMPLETED Testing age prediction RUNIT TEST PROTOCOL -- Thu Oct 14 11:32:13 2021 *********************************************** Number of test functions: 24 Number of errors: 0 Number of failures: 0 1 Test Suite : RnBeads RUnit Tests - 24 test functions, 0 errors, 0 failures Number of test functions: 24 Number of errors: 0 Number of failures: 0 There were 25 warnings (use warnings() to see them) > > proc.time() user system elapsed 169.451 5.279 174.754
RnBeads.Rcheck/RnBeads-Ex.timings
name | user | system | elapsed | |
M-methods | 0 | 0 | 0 | |
U-methods | 0.000 | 0.000 | 0.001 | |
addDiffMethTable-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
addPheno-RnBSet-methods | 0.000 | 0.000 | 0.001 | |
addRegionSubsegments | 0 | 0 | 0 | |
annotation-methods | 0 | 0 | 0 | |
assembly-methods | 0 | 0 | 0 | |
combine.rnb.sets-methods | 0 | 0 | 0 | |
combineTestPvalsMeth | 0 | 0 | 0 | |
computeDiffTab.region | 0.000 | 0.001 | 0.000 | |
computeDiffTab.site | 0 | 0 | 0 | |
covg-methods | 0 | 0 | 0 | |
create.densityScatter | 0 | 0 | 0 | |
create.scatter.dens.points | 0.000 | 0.000 | 0.001 | |
createReport | 0 | 0 | 0 | |
createReportPlot | 0 | 0 | 0 | |
downloadLolaDbs | 0 | 0 | 0 | |
dpval-methods | 0.000 | 0.000 | 0.001 | |
exportDMRs2regionFile | 0 | 0 | 0 | |
get.adjustment.variables | 0 | 0 | 0 | |
get.comparison.grouplabels-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.comparison.groupsizes-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.comparison.info | 0.001 | 0.000 | 0.000 | |
get.comparisons-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.covariates.sva | 0 | 0 | 0 | |
get.covg.thres-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
get.files | 0 | 0 | 0 | |
get.region.types-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.site.test.method-RnBDiffMeth-methods | 0 | 0 | 0 | |
get.table-RnBDiffMeth-methods | 0 | 0 | 0 | |
getCellTypesFromLolaDb | 0 | 0 | 0 | |
getNamesFromLolaDb | 0 | 0 | 0 | |
getSubCmdTokens-ClusterArchitectureSGE-methods | 0 | 0 | 0 | |
getSubCmdTokens-ClusterArchitectureSLURM-methods | 0 | 0 | 0 | |
getTargetFromLolaDb | 0 | 0 | 0 | |
has.covariates.sva | 0 | 0 | 0 | |
hasCovg-methods | 0.000 | 0.000 | 0.001 | |
includes.sites-RnBDiffMeth-methods | 0 | 0 | 0 | |
is.valid-RnBDiffMeth-methods | 0 | 0 | 0 | |
join.diffMeth-methods | 0 | 0 | 0 | |
limmaP | 0.000 | 0.000 | 0.001 | |
loadLolaDbs | 0.000 | 0.001 | 0.000 | |
logger.argument | 0 | 0 | 0 | |
logger.getfiles | 0 | 0 | 0 | |
logger.isinitialized | 0.001 | 0.000 | 0.000 | |
logger.validate.file | 0 | 0 | 0 | |
loggerManagement | 0 | 0 | 0 | |
loggerMessages | 0.000 | 0.000 | 0.001 | |
lolaBarPlot | 0 | 0 | 0 | |
lolaBoxPlotPerTarget | 0.000 | 0.001 | 0.000 | |
lolaVolcanoPlot | 0 | 0 | 0 | |
mergeSamples-methods | 0.000 | 0.000 | 0.001 | |
meth-methods | 0 | 0 | 0 | |
mval-methods | 0 | 0 | 0 | |
nsites-methods | 0 | 0 | 0 | |
parallel.getNumWorkers | 0.000 | 0.000 | 0.001 | |
parallel.isEnabled | 0 | 0 | 0 | |
parallel.setup | 0 | 0 | 0 | |
parallel.teardown | 0 | 0 | 0 | |
performGOEnrichment.diffVar | 0.000 | 0.000 | 0.001 | |
performGOenrichment.diffMeth.entrez | 0.000 | 0.001 | 0.000 | |
performGoEnrichment.diffMeth | 0 | 0 | 0 | |
performLolaEnrichment.diffMeth | 0 | 0 | 0 | |
performLolaEnrichment.diffVar | 0.000 | 0.000 | 0.001 | |
pheno-methods | 0.000 | 0.001 | 0.000 | |
qc-methods | 0 | 0 | 0 | |
read.sample.annotation | 0 | 0 | 0 | |
regionMapping-methods | 0.000 | 0.000 | 0.001 | |
regions-methods | 0.000 | 0.001 | 0.000 | |
reload-RnBDiffMeth-methods | 0 | 0 | 0 | |
remove.regions-methods | 0 | 0 | 0 | |
remove.samples-methods | 0.000 | 0.000 | 0.001 | |
remove.sites-methods | 0 | 0 | 0 | |
rnb.RnBSet.to.GRangesList | 0 | 0 | 0 | |
rnb.RnBSet.to.bed | 0 | 0 | 0 | |
rnb.RnBSet.to.bedGraph | 0 | 0 | 0 | |
rnb.add.list | 0 | 0 | 0 | |
rnb.add.paragraph | 0 | 0 | 0 | |
rnb.add.reference | 0 | 0 | 0 | |
rnb.add.section | 0.000 | 0.001 | 0.000 | |
rnb.annotation.size | 0 | 0 | 0 | |
rnb.annotation2data.frame | 0 | 0 | 0 | |
rnb.beta2mval | 0 | 0 | 0 | |
rnb.execute.batcheffects | 0 | 0 | 0 | |
rnb.execute.clustering | 0 | 0 | 0 | |
rnb.execute.computeDiffMeth | 0 | 0 | 0 | |
rnb.execute.context.removal | 0 | 0 | 0 | |
rnb.execute.cross.reactive.removal | 0.001 | 0.000 | 0.000 | |
rnb.execute.dreduction | 0 | 0 | 0 | |
rnb.execute.export.csv | 0 | 0 | 0 | |
rnb.execute.greedycut | 0.000 | 0.000 | 0.001 | |
rnb.execute.import | 0 | 0 | 0 | |
rnb.execute.na.removal | 0 | 0 | 0 | |
rnb.execute.normalization | 0 | 0 | 0 | |
rnb.execute.pOOBAH | 22.115 | 0.767 | 22.904 | |
rnb.execute.sex.prediction | 0 | 0 | 0 | |
rnb.execute.sex.removal | 0 | 0 | 0 | |
rnb.execute.snp.removal | 0.001 | 0.000 | 0.000 | |
rnb.execute.sva | 0.000 | 0.000 | 0.001 | |
rnb.execute.tnt | 0 | 0 | 0 | |
rnb.execute.variability.removal | 0 | 0 | 0 | |
rnb.export.all.annotation | 0.001 | 0.000 | 0.000 | |
rnb.export.annotation | 0.000 | 0.000 | 0.001 | |
rnb.export.to.ewasher | 0 | 0 | 0 | |
rnb.export.to.trackhub | 0 | 0 | 0 | |
rnb.get.annotation | 0.001 | 0.000 | 0.000 | |
rnb.get.assemblies | 0.000 | 0.000 | 0.001 | |
rnb.get.chromosomes | 0.000 | 0.001 | 0.000 | |
rnb.get.directory | 0 | 0 | 0 | |
rnb.get.mapping | 0 | 0 | 0 | |
rnb.get.reference | 0.000 | 0.000 | 0.001 | |
rnb.get.reliability.matrix | 0 | 0 | 0 | |
rnb.infinium.control.targets | 0 | 0 | 0 | |
rnb.initialize.reports | 0.001 | 0.000 | 0.000 | |
rnb.is.option | 0.000 | 0.000 | 0.001 | |
rnb.load.annotation.from.db | 0 | 0 | 0 | |
rnb.message.plot | 0 | 0 | 0 | |
rnb.mval2beta | 0.001 | 0.000 | 0.000 | |
rnb.options | 0.000 | 0.000 | 0.001 | |
rnb.options2xml | 0 | 0 | 0 | |
rnb.plot.betadistribution.probeCategories | 0 | 0 | 0 | |
rnb.plot.betadistribution.sampleGroups | 0 | 0 | 0 | |
rnb.plot.control.barplot | 0.000 | 0.001 | 0.001 | |
rnb.plot.control.boxplot | 0 | 0 | 0 | |
rnb.plot.dreduction | 0 | 0 | 0 | |
rnb.plot.locus.profile | 0 | 0 | 0 | |
rnb.plot.negative.boxplot | 0.000 | 0.001 | 0.001 | |
rnb.plot.region.profile.density | 0 | 0 | 0 | |
rnb.plot.region.profiles | 0 | 0 | 0 | |
rnb.plot.region.site.density | 0 | 0 | 0 | |
rnb.plot.sentrix.distribution | 0.000 | 0.000 | 0.001 | |
rnb.plot.snp.barplot | 0 | 0 | 0 | |
rnb.plot.snp.boxplot | 0 | 0 | 0 | |
rnb.plot.snp.heatmap | 0 | 0 | 0 | |
rnb.region.types | 0.000 | 0.000 | 0.001 | |
rnb.region.types.for.analysis | 0.000 | 0.001 | 0.000 | |
rnb.remove.annotation | 0 | 0 | 0 | |
rnb.run.example | 0 | 0 | 0 | |
rnb.runs | 0 | 0 | 0 | |
rnb.sample.groups | 0.000 | 0.000 | 0.001 | |
rnb.sample.summary.table | 0 | 0 | 0 | |
rnb.set.annotation | 0.001 | 0.000 | 0.000 | |
rnb.write.table | 0 | 0 | 0 | |
rnb.xml2options | 0.000 | 0.001 | 0.000 | |
rowOneSampleTP | 0 | 0 | 0 | |
rowWelchP | 0 | 0 | 0 | |
run-RnBClusterRun-methods | 0 | 0 | 0 | |
samples-methods | 0.000 | 0.001 | 0.000 | |
save.tables-RnBDiffMeth-methods | 0 | 0 | 0 | |
set.covariates.sva | 0.001 | 0.000 | 0.000 | |
sites-methods | 0.000 | 0.000 | 0.001 | |
summarize.regions-methods | 0 | 0 | 0 | |
summarized.regions-methods | 0 | 0 | 0 | |