Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:07:15 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1639/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RnBeads 2.12.2 (landing page) Fabian Mueller
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 2.12.2 |
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RnBeads_2.12.2.tar.gz |
StartedAt: 2022-04-13 01:54:22 -0400 (Wed, 13 Apr 2022) |
EndedAt: 2022-04-13 02:14:46 -0400 (Wed, 13 Apr 2022) |
EllapsedTime: 1224.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: RnBeads.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RnBeads_2.12.2.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RnBeads.Rcheck' * using R version 4.1.3 (2022-03-10) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'RnBeads/DESCRIPTION' ... OK * this is package 'RnBeads' version '2.12.2' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster', 'ff', 'fields', 'ggplot2', 'gplots', 'grid', '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 whether package 'RnBeads' can be installed ... OK * checking installed package size ... NOTE installed size is 7.6Mb sub-directories of 1Mb or more: R 3.1Mb help 1.4Mb html 1.5Mb * 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 Package in Depends field not imported from: 'grid' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. 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' 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 'SigDF' rnb.execute.pOOBAH: no visible global function definition for 'pOOBAH' rnb.execute.pOOBAH: no visible binding for global variable 'sigset.l' rnb.execute.pOOBAH: no visible binding for global variable 'pIG' rnb.execute.pOOBAH: no visible binding for global variable 'pII' rnb.execute.pOOBAH: no visible binding for global variable 'pIR' 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 ChrNumeric DataTrack Density Deviance Difference DoISVA Error GenomeAxisTrack Group Hsapiens ID IdeogramTrack IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity Measure Mmusculus Predicted Probe RGChannelSet Rd2HTML SNP Sample Segment SigDF 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 p.vals.t.na.adj pData pIG pII pIR pOOBAH 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 sigset.l 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 ... ** running examples for arch 'i386' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed rnb.execute.pOOBAH 21.53 2.44 24.43 ** running examples for arch 'x64' ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed rnb.execute.pOOBAH 20.44 0.5 20.97 * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'runTests.R' OK ** running tests for arch 'x64' ... 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: 8 NOTEs See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RnBeads.Rcheck/00check.log' for details.
RnBeads.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RnBeads_2.12.2.tar.gz && rm -rf RnBeads.buildbin-libdir && mkdir RnBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.buildbin-libdir RnBeads_2.12.2.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RnBeads_2.12.2.zip && rm RnBeads_2.12.2.tar.gz RnBeads_2.12.2.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 26 3935k 26 1059k 0 0 1663k 0 0:00:02 --:--:-- 0:00:02 1663k 100 3935k 100 3935k 0 0 2443k 0 0:00:01 0:00:01 --:--:-- 2444k install for i386 * installing *source* package 'RnBeads' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'RnBeads' finding HTML links ... done BMIQ html ClusterArchitecture-class html ClusterArchitectureSGE-class html ClusterArchitectureSLURM-class html M-methods html Report-class html ReportGgPlot-class html ReportPlot-class html RnBClusterRun-class html RnBDiffMeth-class html RnBSet-class html RnBeadClustering-class html RnBeadRawSet-class html RnBeadSet-class html RnBeads html RnBeads.data html RnBiseqSet-class html U-methods html accepted html addDiffMethTable-RnBDiffMeth-methods html addPheno-RnBSet-methods html addRegionSubsegments html annotation-methods html apply.iEVORA html as.RnBeadRawSet html assembly-methods html auto.select.rank.cut html coercion-methods html finding level-2 HTML links ... done cols.to.rank html combine.diffMeth.objs html combine.rnb.sets-methods html combineTestPvalsMeth html computeDiffTab.region html computeDiffTab.site html covg-methods html create.densityScatter html create.hex.summary.plot html create.scatter.dens.points html createReport html createReportGgPlot html createReportPlot html data.frame2GRanges html densRanks html destroy-RnBDiffMeth-methods html destroy-methods html deviation.plot.beta html diffVar html dim-BigFfMat-method html downloadLolaDbs html dpval-methods html estimateProportionsCP html exportDMRs2regionFile html get.adjustment.variables html get.comparison.grouplabels-RnBDiffMeth-methods html get.comparison.groupsizes-RnBDiffMeth-methods html get.comparison.info html get.comparisons-RnBDiffMeth-methods html get.covariates.ct html get.covariates.sva html get.covg.thres-RnBDiffMeth-methods html get.cpg.stats html get.files html get.region.types-RnBDiffMeth-methods html get.site.test.method-RnBDiffMeth-methods html get.table-RnBDiffMeth-methods html get.table.ids html get.variability.method-RnBDiffMeth-methods html getCellTypesFromLolaDb html getExecutable-ClusterArchitecture-methods html getModuleNumCores-RnBClusterRun-methods html getNamesFromLolaDb html getNumNaMeth-methods html getSubCmdStr-ClusterArchitecture-methods html getSubCmdTokens-ClusterArchitecture-methods html getSubCmdTokens-ClusterArchitectureSGE-methods html getSubCmdTokens-ClusterArchitectureSLURM-methods html getTargetFromLolaDb html greedycut.filter.matrix html greedycut.get.statistics html greedycut.get.submatrix html has.covariates.ct html has.covariates.sva html hasCovg-methods html includes.sites-RnBDiffMeth-methods html initialize-ClusterArchitecture-method html initialize-ClusterArchitectureSGE-method html initialize-ClusterArchitectureSLURM-method html initialize-RnBClusterRun-method html initialize-RnBDiffMeth-method html intensities.by.color html is.valid-RnBDiffMeth-methods html isImputed-RnBSet-method html join.diffMeth-methods html limmaP html load.region.subsegment.annotation html load.rnb.diffmeth html load.rnb.set html loadLolaDbs html logger.argument html logger.getfiles html logger.isinitialized html logger.machine.name html logger.validate.file html loggerManagement html loggerMessages html lolaBarPlot html lolaBoxPlotPerTarget html lolaVolcanoPlot html lump.hg19 html lump.hg38 html mask.sites.meth-methods html mergeSamples-methods html meth-methods html mval-methods html nsites-methods html off-methods html parallel.getNumWorkers html parallel.isEnabled html parallel.setup html parallel.teardown html performGOEnrichment.diffVar html performGOenrichment.diffMeth.entrez html performGoEnrichment.diffMeth html performLolaEnrichment.diffMeth html performLolaEnrichment.diffVar html pheno-methods html prepareSOFTfileForGEO html qc-methods html read.GS.report html read.bed.files html read.data.dir html read.idat.files html read.idat.files2 html read.sample.annotation html read.single.bed html refFreeEWASP html regionMapping-methods html regions-methods html reload-RnBDiffMeth-methods html remove.regions-methods html remove.samples-methods html remove.sites-methods html rnb.RnBSet.to.GRangesList html rnb.RnBSet.to.bed html rnb.RnBSet.to.bedGraph html rnb.add.figure html rnb.add.list html rnb.add.paragraph html rnb.add.reference html rnb.add.section html rnb.add.table html rnb.add.tables html rnb.annotation.size html rnb.annotation2data.frame html rnb.bed.from.segmentation html rnb.beta2mval html rnb.boxplot.from.segmentation html rnb.build.index html rnb.call.destructor html rnb.color.legends html rnb.combine.arrays html rnb.combine.seq html rnb.execute.age.prediction html rnb.execute.batch.qc html rnb.execute.batcheffects html rnb.execute.clustering html rnb.execute.clustering.all html rnb.execute.computeDiffMeth html rnb.execute.context.removal html rnb.execute.cross.reactive.removal html rnb.execute.ct.estimation html rnb.execute.diffVar html rnb.execute.dreduction html rnb.execute.export.csv html rnb.execute.filter.summary html rnb.execute.gender.prediction html rnb.execute.genomewide html rnb.execute.greedycut html rnb.execute.high.coverage.removal html rnb.execute.high.dpval.masking html rnb.execute.import html rnb.execute.imputation html rnb.execute.low.coverage.masking html rnb.execute.lump html rnb.execute.na.removal html rnb.execute.normalization html rnb.execute.pOOBAH html rnb.execute.quality html rnb.execute.segmentation html rnb.execute.sex.prediction html rnb.execute.sex.removal html rnb.execute.snp.removal html rnb.execute.sva html rnb.execute.tnt html rnb.execute.training html rnb.execute.variability.removal html rnb.export.all.annotation html rnb.export.annotation html rnb.export.to.ewasher html rnb.export.to.trackhub html rnb.find.relative.site.coord html rnb.get.annotation html rnb.get.assemblies html rnb.get.chromosomes html rnb.get.directory html rnb.get.mapping html rnb.get.reference html rnb.get.reliability.matrix html rnb.infinium.control.targets html rnb.initialize.reports html rnb.is.option html rnb.load.annotation html rnb.load.annotation.from.db html rnb.load.sitelist html rnb.message.plot html rnb.mval2beta html rnb.options html rnb.options2xml html rnb.performance.profile html rnb.plot.beta.comparison html rnb.plot.betadistribution.probeCategories html rnb.plot.betadistribution.sampleGroups html rnb.plot.biseq.coverage html rnb.plot.biseq.coverage.hist html rnb.plot.biseq.coverage.violin html rnb.plot.control.barplot html rnb.plot.control.boxplot html rnb.plot.coverage.thresholds html rnb.plot.ct.heatmap html rnb.plot.dreduction html rnb.plot.locus.profile html rnb.plot.marker.fstat html rnb.plot.negative.boxplot html rnb.plot.num.sites.covg html rnb.plot.pheno.categories html rnb.plot.region.profile.density html rnb.plot.region.profiles html rnb.plot.region.site.density html rnb.plot.sentrix.distribution html rnb.plot.sentrix.distributions html rnb.plot.snp.barplot html rnb.plot.snp.boxplot html rnb.plot.snp.heatmap html rnb.read.geo html rnb.region.types html rnb.region.types.for.analysis html rnb.remove.annotation html rnb.run.analysis html rnb.run.dj html rnb.run.example html rnb.run.xml html rnb.runs html rnb.sample.groups html rnb.sample.replicates html rnb.sample.summary.table html rnb.save.annotation html rnb.section.diffVar.region html rnb.set.annotation html rnb.set.annotation.and.cpg.stats html rnb.show.report html rnb.step.betadistribution html rnb.step.cnv html rnb.write.table html rnb.xml2options html rowOneSampleTP html rowPairedTP html rowWelchP html run-RnBClusterRun-methods html run.cross.validation html sampleCovgApply-methods html sampleMethApply-methods html samples-methods html save.rnb.diffmeth html save.rnb.set html save.tables-RnBDiffMeth-methods html set.covariates.ct html set.covariates.sva html setExecutable-ClusterArchitecture-methods html setModuleNumCores-RnBClusterRun-methods html setModuleResourceRequirements-RnBClusterRun-methods html sites-methods html sub-BigFfMat-ANY-ANY-ANY-method html subset-BigFfMat-ANY-ANY-ANY-method html summarize.regions-methods html summarized.regions-methods html updateMethylationSites-methods html updateRegionSummaries html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'RnBeads' ... ** testing if installed package can be loaded * MD5 sums packaged installation of 'RnBeads' as RnBeads_2.12.2.zip * DONE (RnBeads) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'RnBeads' successfully unpacked and MD5 sums checked
RnBeads.Rcheck/tests_i386/runTests.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: i386-w64-mingw32/i386 (32-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: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: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp29VXtk/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 Spam version 2.8-0 (2022-01-05) 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 Try help(fields) to get started. 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: 'grid' The following object is masked from 'package:ff': pattern 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 1.5-9.5 2022-03-01 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 2022-04-13 02:03:39 0.4 STATUS STARTED Unit testing: differential 2022-04-13 02:03:39 0.4 STATUS STARTED Testing function: rowWelchP Loading required package: RnBeads.hg19 2022-04-13 02:03:39 0.4 STATUS COMPLETED Testing function: rowWelchP 2022-04-13 02:03:39 0.4 STATUS STARTED Testing function: limmaP 2022-04-13 02:03:39 0.4 STATUS COMPLETED Testing function: limmaP 2022-04-13 02:03:39 0.4 STATUS STARTED Testing function: computeDiffTab.extended.site 2022-04-13 02:03:40 0.5 INFO Conducting differential analysis using limma 2022-04-13 02:03:40 0.5 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2022-04-13 02:03:40 0.5 STATUS STARTED Testing function: computeDiffTab.default.region 2022-04-13 02:03:40 0.5 INFO Conducting differential analysis using limma 2022-04-13 02:03:48 0.7 STATUS COMPLETED Testing function: computeDiffTab.default.region 2022-04-13 02:03:48 0.7 STATUS STARTED Testing function: combineTestPvalsMeth 2022-04-13 02:03:48 0.7 STATUS COMPLETED Testing function: combineTestPvalsMeth 2022-04-13 02:03:48 0.7 STATUS STARTED Testing function: get.adjustment.variables 2022-04-13 02:03:48 0.7 STATUS COMPLETED Testing function: get.adjustment.variables 2022-04-13 02:03:48 0.7 STATUS STARTED Testing function: get.comparison.info 2022-04-13 02:03:48 0.7 STATUS COMPLETED Testing function: get.comparison.info 2022-04-13 02:03:48 0.7 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:03:48 0.7 STATUS STARTED Retrieving comparison info 2022-04-13 02:03:48 0.7 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:03:49 0.7 STATUS STARTED Computing differential methylation tables 2022-04-13 02:03:49 0.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:03:49 0.7 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:03:49 0.7 INFO Conducting differential analysis using limma 2022-04-13 02:03:49 0.7 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:03:49 0.7 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:03:49 0.7 STATUS Computed table for tiling 2022-04-13 02:03:50 0.7 STATUS Computed table for genes 2022-04-13 02:03:50 0.7 STATUS Computed table for promoters 2022-04-13 02:03:50 0.7 STATUS Computed table for cpgislands 2022-04-13 02:03:50 0.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:03:51 0.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:03:51 0.7 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:03:51 0.7 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:03:51 0.7 INFO Conducting differential analysis using limma 2022-04-13 02:03:51 0.7 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:03:51 0.7 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:03:51 0.7 STATUS Computed table for tiling 2022-04-13 02:03:53 0.7 STATUS Computed table for genes 2022-04-13 02:03:53 0.7 STATUS Computed table for promoters 2022-04-13 02:03:53 0.7 STATUS Computed table for cpgislands 2022-04-13 02:03:53 0.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:03:53 0.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:03:53 0.7 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:03:53 0.7 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:03:53 0.7 STATUS STARTED Testing function: diffVar 2022-04-13 02:03:53 0.7 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:04:52 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:04:52 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:04:52 2.8 WARNING Could not compute p-values with diffVar, returning NA 2022-04-13 02:04:52 2.8 INFO diffVar from missMethyl package not properly running 2022-04-13 02:04:52 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:04:52 2.8 STATUS STARTED Testing function: apply.iEVORA 2022-04-13 02:04:52 2.8 STATUS STARTED iEVORA method 2022-04-13 02:04:53 2.9 INFO No DVCs detected. All p-values set to 1. 2022-04-13 02:04:53 2.9 STATUS COMPLETED iEVORA method 2022-04-13 02:04:53 2.9 STATUS STARTED Testing function: rnb.execute.diffVar 2022-04-13 02:04:54 2.9 STATUS STARTED Differential Variability 2022-04-13 02:04:54 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:04:54 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:04:54 2.9 INFO No imputation method selected, 'knn' method used. 2022-04-13 02:04:54 2.9 STATUS STARTED Imputation procedure knn 2022-04-13 02:04:54 2.9 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:04:54 2.9 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:04:54 2.9 INFO Conducting differential variability using diffVar 2022-04-13 02:04:54 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:04:54 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:04:55 2.9 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:04:56 3.0 STATUS Computed table for tiling 2022-04-13 02:04:56 3.0 STATUS Computed table for genes 2022-04-13 02:04:57 3.0 STATUS Computed table for promoters 2022-04-13 02:04:57 3.1 STATUS Computed table for cpgislands 2022-04-13 02:04:58 3.1 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:04:58 3.1 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:04:58 3.1 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:04:58 3.1 INFO Conducting differential variability using diffVar 2022-04-13 02:04:58 3.1 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:04:58 3.1 STATUS COMPLETED diffVar method 2022-04-13 02:04:58 3.1 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:05:00 2.8 STATUS Computed table for tiling 2022-04-13 02:05:00 2.8 STATUS Computed table for genes 2022-04-13 02:05:01 2.8 STATUS Computed table for promoters 2022-04-13 02:05:01 2.8 STATUS Computed table for cpgislands 2022-04-13 02:05:01 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:05:01 2.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:01 2.8 STATUS COMPLETED Differential Variability 2022-04-13 02:05:01 2.8 STATUS COMPLETED Testing function: rnb.execute.diffVar 2022-04-13 02:05:01 2.8 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:05:01 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:02 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:02 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:02 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:02 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:02 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:02 2.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:05:02 2.8 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:05:02 2.8 INFO Conducting differential variability using diffVar 2022-04-13 02:05:02 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:05:02 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:05:03 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:03 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:03 2.9 STATUS Computed table for tiling 2022-04-13 02:05:04 2.9 STATUS Computed table for genes 2022-04-13 02:05:04 2.9 STATUS Computed table for promoters 2022-04-13 02:05:05 2.8 STATUS Computed table for cpgislands 2022-04-13 02:05:05 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:05 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:05 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:06 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:06 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:06 2.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:05:06 2.8 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:05:06 2.8 INFO Conducting differential variability using diffVar 2022-04-13 02:05:06 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:05:06 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:05:06 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:06 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:07 2.8 STATUS Computed table for tiling 2022-04-13 02:05:07 2.9 STATUS Computed table for genes 2022-04-13 02:05:08 2.9 STATUS Computed table for promoters 2022-04-13 02:05:08 2.9 STATUS Computed table for cpgislands 2022-04-13 02:05:08 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:08 2.9 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:08 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:08 2.9 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:05:09 2.9 STATUS STARTED Testing class: RnBDiffMeth 2022-04-13 02:05:09 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:09 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:09 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:09 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:09 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:09 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:09 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:09 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:10 2.8 STATUS Computed table for tiling 2022-04-13 02:05:11 2.8 STATUS Computed table for genes 2022-04-13 02:05:11 2.8 STATUS Computed table for promoters 2022-04-13 02:05:11 2.8 STATUS Computed table for cpgislands 2022-04-13 02:05:11 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:11 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:11 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:11 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:12 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:12 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:12 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:12 2.9 STATUS Computed table for tiling 2022-04-13 02:05:13 2.9 STATUS Computed table for genes 2022-04-13 02:05:13 2.9 STATUS Computed table for promoters 2022-04-13 02:05:14 2.8 STATUS Computed table for cpgislands 2022-04-13 02:05:14 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:14 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:14 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:14 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:14 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:14 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:14 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:14 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:14 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:15 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:15 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:15 2.8 STATUS Computed table for genes 2022-04-13 02:05:15 2.8 STATUS Computed table for tiling 2022-04-13 02:05:15 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:15 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:16 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:16 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:16 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:16 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:16 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:16 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:16 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:16 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:16 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:17 2.9 STATUS Computed table for genes 2022-04-13 02:05:17 2.9 STATUS Computed table for tiling 2022-04-13 02:05:17 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:17 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:17 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:17 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:17 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:18 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:18 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:18 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:18 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:18 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:18 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:18 2.9 STATUS Computed table for promoters 2022-04-13 02:05:19 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:19 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:19 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:19 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:19 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:19 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:20 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:20 2.9 STATUS Computed table for promoters 2022-04-13 02:05:20 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:20 2.9 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:20 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:21 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:21 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:21 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:21 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:21 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:21 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:21 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:21 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:22 2.8 STATUS Computed table for genes 2022-04-13 02:05:23 2.8 STATUS Computed table for tiling 2022-04-13 02:05:23 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:26 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:26 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:26 2.8 STATUS STARTED Testing function: get.region.types 2022-04-13 02:05:26 2.8 STATUS COMPLETED Testing function: get.region.types 2022-04-13 02:05:26 2.8 STATUS STARTED Testing function: get.comparisons 2022-04-13 02:05:26 2.8 STATUS COMPLETED Testing function: get.comparisons 2022-04-13 02:05:26 2.8 STATUS STARTED Testing function: get.comparison.grouplabels 2022-04-13 02:05:27 2.8 STATUS COMPLETED Testing function: get.comparison.grouplabels 2022-04-13 02:05:27 2.8 STATUS STARTED Testing function: get.site.test.method 2022-04-13 02:05:27 2.8 STATUS COMPLETED Testing function: get.site.test.method 2022-04-13 02:05:27 2.8 STATUS STARTED Testing function: get.table 2022-04-13 02:05:27 2.8 STATUS COMPLETED Testing function: get.table 2022-04-13 02:05:27 2.8 STATUS STARTED Testing function: addDiffMethTable 2022-04-13 02:05:27 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:27 2.8 STATUS COMPLETED Testing function: addDiffMethTable 2022-04-13 02:05:28 2.8 STATUS STARTED Testing functions: join.diffMeth, is.valid 2022-04-13 02:05:28 2.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2022-04-13 02:05:28 2.8 STATUS STARTED Destructor 2022-04-13 02:05:28 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:28 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:28 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:28 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:28 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:28 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:29 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:29 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:29 2.8 STATUS COMPLETED Destructor 2022-04-13 02:05:29 2.8 STATUS COMPLETED Testing class: RnBDiffMeth 2022-04-13 02:05:29 2.8 STATUS COMPLETED Testing function: apply.iEVORA 2022-04-13 02:05:29 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:29 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:29 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:29 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:30 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:30 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:30 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:30 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:30 2.9 STATUS Computed table for tiling 2022-04-13 02:05:31 2.9 STATUS Computed table for genes 2022-04-13 02:05:31 2.9 STATUS Computed table for promoters 2022-04-13 02:05:32 2.8 STATUS Computed table for cpgislands 2022-04-13 02:05:32 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:34 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:34 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:34 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:34 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:34 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:34 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:35 2.8 STATUS Computed table for tiling 2022-04-13 02:05:35 2.9 STATUS Computed table for genes 2022-04-13 02:05:35 2.9 STATUS Computed table for promoters 2022-04-13 02:05:36 2.9 STATUS Computed table for cpgislands 2022-04-13 02:05:36 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:36 2.9 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:36 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:36 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:36 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:36 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:36 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:36 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:37 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:37 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:37 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:37 2.9 STATUS Computed table for genes 2022-04-13 02:05:38 2.9 STATUS Computed table for tiling 2022-04-13 02:05:38 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:41 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:41 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:41 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:41 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:41 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:42 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:42 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:42 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:42 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:42 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:42 2.9 STATUS Computed table for genes 2022-04-13 02:05:43 2.8 STATUS Computed table for tiling 2022-04-13 02:05:43 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:45 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:45 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:45 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:45 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:45 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:45 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:46 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:46 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:46 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:46 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:46 2.8 STATUS Computed table for promoters 2022-04-13 02:05:46 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:46 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:46 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:46 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:47 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:05:47 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:48 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:49 2.9 STATUS Computed table for promoters 2022-04-13 02:05:49 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:49 2.9 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:49 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:49 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:49 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:49 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:49 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:49 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:49 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:50 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:50 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:50 2.9 STATUS Computed table for genes 2022-04-13 02:05:50 2.9 STATUS Computed table for tiling 2022-04-13 02:05:51 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:51 2.9 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:05:51 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:05:51 2.9 STATUS STARTED Testing function: get.region.types 2022-04-13 02:05:51 2.9 STATUS COMPLETED Testing function: get.region.types 2022-04-13 02:05:51 2.9 STATUS STARTED Testing function: get.comparisons 2022-04-13 02:05:51 2.9 STATUS COMPLETED Testing function: get.comparisons 2022-04-13 02:05:51 2.9 STATUS STARTED Testing function: get.comparison.grouplabels 2022-04-13 02:05:51 2.9 STATUS COMPLETED Testing function: get.comparison.grouplabels 2022-04-13 02:05:51 2.9 STATUS STARTED Testing function: get.site.test.method 2022-04-13 02:05:52 2.9 STATUS COMPLETED Testing function: get.site.test.method 2022-04-13 02:05:52 2.9 STATUS STARTED Testing function: get.table 2022-04-13 02:05:52 2.9 STATUS COMPLETED Testing function: get.table 2022-04-13 02:05:52 2.9 STATUS STARTED Testing function: addDiffMethTable 2022-04-13 02:05:52 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:52 2.9 STATUS COMPLETED Testing function: addDiffMethTable 2022-04-13 02:05:52 2.9 STATUS STARTED Testing functions: join.diffMeth, is.valid 2022-04-13 02:05:52 2.9 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2022-04-13 02:05:52 2.9 STATUS STARTED Destructor 2022-04-13 02:05:53 2.9 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:05:53 2.9 STATUS COMPLETED Destructor 2022-04-13 02:05:53 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:54 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:54 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:05:54 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:05:54 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:05:54 2.9 WARNING Could not compute p-values with diffVar, returning NA 2022-04-13 02:05:55 2.9 INFO diffVar from missMethyl package not properly running 2022-04-13 02:05:55 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:05:55 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:05:56 2.8 STATUS STARTED Unit testing: differential 2022-04-13 02:05:56 2.8 STATUS STARTED Testing function: rowWelchP 2022-04-13 02:05:56 2.8 STATUS COMPLETED Testing function: rowWelchP 2022-04-13 02:05:56 2.8 STATUS STARTED Testing function: limmaP 2022-04-13 02:05:56 2.9 STATUS COMPLETED Testing function: limmaP 2022-04-13 02:05:56 2.9 STATUS STARTED Testing function: computeDiffTab.extended.site 2022-04-13 02:05:56 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:56 2.9 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2022-04-13 02:05:57 2.9 STATUS STARTED Testing function: computeDiffTab.default.region 2022-04-13 02:05:57 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:57 2.9 STATUS COMPLETED Testing function: computeDiffTab.default.region 2022-04-13 02:05:57 2.9 STATUS STARTED Testing function: combineTestPvalsMeth 2022-04-13 02:05:57 2.9 STATUS COMPLETED Testing function: combineTestPvalsMeth 2022-04-13 02:05:57 2.9 STATUS STARTED Testing function: get.adjustment.variables 2022-04-13 02:05:57 2.9 STATUS COMPLETED Testing function: get.adjustment.variables 2022-04-13 02:05:57 2.9 STATUS STARTED Testing function: get.comparison.info 2022-04-13 02:05:58 2.9 STATUS COMPLETED Testing function: get.comparison.info 2022-04-13 02:05:58 2.9 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:05:58 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:05:58 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:05:58 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:05:58 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:05:58 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:05:58 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:05:58 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:05:59 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:05:59 2.9 STATUS Computed table for tiling 2022-04-13 02:05:59 2.9 STATUS Computed table for genes 2022-04-13 02:06:00 2.9 STATUS Computed table for promoters 2022-04-13 02:06:00 2.9 STATUS Computed table for cpgislands 2022-04-13 02:06:00 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:00 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:00 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:00 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:00 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:01 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:01 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:01 2.9 STATUS Computed table for tiling 2022-04-13 02:06:02 2.8 STATUS Computed table for genes 2022-04-13 02:06:03 2.8 STATUS Computed table for promoters 2022-04-13 02:06:03 2.8 STATUS Computed table for cpgislands 2022-04-13 02:06:03 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:03 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:03 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:03 2.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:06:03 2.8 STATUS STARTED Testing function: diffVar 2022-04-13 02:06:03 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:06:03 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:06:04 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:06:04 2.9 WARNING Could not compute p-values with diffVar, returning NA 2022-04-13 02:06:04 2.9 INFO diffVar from missMethyl package not properly running 2022-04-13 02:06:04 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:06:04 2.9 STATUS STARTED Testing function: apply.iEVORA 2022-04-13 02:06:04 2.9 STATUS STARTED iEVORA method 2022-04-13 02:06:05 2.9 INFO No DVCs detected. All p-values set to 1. 2022-04-13 02:06:05 2.9 STATUS COMPLETED iEVORA method 2022-04-13 02:06:05 2.9 STATUS STARTED Testing function: rnb.execute.diffVar 2022-04-13 02:06:05 2.9 STATUS STARTED Differential Variability 2022-04-13 02:06:05 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:05 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:06 2.9 STATUS STARTED Imputation procedure knn 2022-04-13 02:06:06 2.9 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:06:06 2.9 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:06 2.9 INFO Conducting differential variability using diffVar 2022-04-13 02:06:06 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:06:06 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:06:06 2.9 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:06:06 2.9 STATUS Computed table for tiling 2022-04-13 02:06:07 2.9 STATUS Computed table for genes 2022-04-13 02:06:07 2.9 STATUS Computed table for promoters 2022-04-13 02:06:08 2.8 STATUS Computed table for cpgislands 2022-04-13 02:06:08 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:06:08 2.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:08 2.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:08 2.8 INFO Conducting differential variability using diffVar 2022-04-13 02:06:08 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:06:08 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:06:09 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:06:09 2.9 STATUS Computed table for tiling 2022-04-13 02:06:09 2.9 STATUS Computed table for genes 2022-04-13 02:06:10 2.9 STATUS Computed table for promoters 2022-04-13 02:06:10 2.9 STATUS Computed table for cpgislands 2022-04-13 02:06:10 2.9 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:06:10 2.9 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:10 2.9 STATUS COMPLETED Differential Variability 2022-04-13 02:06:10 2.9 STATUS COMPLETED Testing function: rnb.execute.diffVar 2022-04-13 02:06:10 2.9 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:06:11 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:11 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:11 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:11 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:11 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:11 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:11 2.9 STATUS STARTED Imputation procedure knn 2022-04-13 02:06:11 2.9 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:06:11 2.9 INFO Conducting differential variability using diffVar 2022-04-13 02:06:11 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:06:12 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:06:12 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:12 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:12 2.9 STATUS Computed table for tiling 2022-04-13 02:06:13 2.8 STATUS Computed table for genes 2022-04-13 02:06:14 2.8 STATUS Computed table for promoters 2022-04-13 02:06:14 2.8 STATUS Computed table for cpgislands 2022-04-13 02:06:14 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:14 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:14 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:15 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:15 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:06:15 2.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:06:15 2.9 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:06:15 2.9 INFO Conducting differential variability using diffVar 2022-04-13 02:06:15 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:06:15 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:06:15 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:15 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:16 2.9 STATUS Computed table for tiling 2022-04-13 02:06:16 2.9 STATUS Computed table for genes 2022-04-13 02:06:17 2.8 STATUS Computed table for promoters 2022-04-13 02:06:18 2.8 STATUS Computed table for cpgislands 2022-04-13 02:06:18 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:18 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:18 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:18 2.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:06:18 2.8 STATUS STARTED Testing class: RnBDiffMeth 2022-04-13 02:06:18 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:18 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:18 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:19 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:19 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:19 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:06:19 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:19 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:19 2.9 STATUS Computed table for tiling 2022-04-13 02:06:20 2.9 STATUS Computed table for genes 2022-04-13 02:06:20 2.9 STATUS Computed table for promoters 2022-04-13 02:06:20 2.9 STATUS Computed table for cpgislands 2022-04-13 02:06:20 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:23 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:23 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:23 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:23 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:23 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:23 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:24 2.9 STATUS Computed table for tiling 2022-04-13 02:06:25 2.8 STATUS Computed table for genes 2022-04-13 02:06:25 2.8 STATUS Computed table for promoters 2022-04-13 02:06:25 2.8 STATUS Computed table for cpgislands 2022-04-13 02:06:25 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:25 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:26 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:26 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:26 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:26 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:26 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:26 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:26 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:06:26 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:26 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:27 2.9 STATUS Computed table for genes 2022-04-13 02:06:27 2.9 STATUS Computed table for tiling 2022-04-13 02:06:27 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:30 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:30 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:30 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:30 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:30 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:30 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:30 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:30 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:31 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:31 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:31 2.9 STATUS Computed table for genes 2022-04-13 02:06:31 2.9 STATUS Computed table for tiling 2022-04-13 02:06:32 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:36 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:36 2.9 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:36 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:36 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:36 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:41 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:41 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:41 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:41 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:41 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:41 2.9 STATUS Computed table for promoters 2022-04-13 02:06:42 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:42 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:42 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:42 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:42 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:44 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:44 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:44 2.8 STATUS Computed table for promoters 2022-04-13 02:06:44 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:44 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:45 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:45 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:45 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:45 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:45 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:45 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:45 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:06:45 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:45 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:46 2.8 STATUS Computed table for genes 2022-04-13 02:06:46 2.8 STATUS Computed table for tiling 2022-04-13 02:06:46 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:46 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:06:46 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:06:46 2.8 STATUS STARTED Testing function: get.region.types 2022-04-13 02:06:47 2.8 STATUS COMPLETED Testing function: get.region.types 2022-04-13 02:06:47 2.8 STATUS STARTED Testing function: get.comparisons 2022-04-13 02:06:47 2.8 STATUS COMPLETED Testing function: get.comparisons 2022-04-13 02:06:47 2.8 STATUS STARTED Testing function: get.comparison.grouplabels 2022-04-13 02:06:47 2.8 STATUS COMPLETED Testing function: get.comparison.grouplabels 2022-04-13 02:06:47 2.8 STATUS STARTED Testing function: get.site.test.method 2022-04-13 02:06:47 2.8 STATUS COMPLETED Testing function: get.site.test.method 2022-04-13 02:06:47 2.8 STATUS STARTED Testing function: get.table 2022-04-13 02:06:47 2.8 STATUS COMPLETED Testing function: get.table 2022-04-13 02:06:47 2.8 STATUS STARTED Testing function: addDiffMethTable 2022-04-13 02:06:48 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:06:48 2.8 STATUS COMPLETED Testing function: addDiffMethTable 2022-04-13 02:06:48 2.8 STATUS STARTED Testing functions: join.diffMeth, is.valid 2022-04-13 02:06:48 2.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2022-04-13 02:06:48 2.8 STATUS STARTED Destructor 2022-04-13 02:06:48 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:48 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:48 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:49 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:49 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:49 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:49 2.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:49 2.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:06:49 2.8 STATUS COMPLETED Destructor 2022-04-13 02:06:49 2.8 STATUS COMPLETED Testing class: RnBDiffMeth 2022-04-13 02:06:49 2.8 STATUS COMPLETED Testing function: apply.iEVORA 2022-04-13 02:06:49 2.8 STATUS STARTED iEVORA method 2022-04-13 02:06:50 2.8 INFO No DVCs detected. All p-values set to 1. Coefficients not estimable: x2x2 2022-04-13 02:06:51 2.9 STATUS STARTED Retrieving comparison info 2022-04-13 02:06:51 2.9 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:06:51 2.9 STATUS STARTED Computing differential methylation tables 2022-04-13 02:06:51 2.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:06:51 2.9 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:06:51 2.9 INFO Conducting differential analysis using limma 2022-04-13 02:06:51 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:06:51 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:06:52 2.8 STATUS Computed table for tiling 2022-04-13 02:06:53 2.8 STATUS Computed table for genes 2022-04-13 02:06:53 2.8 STATUS Computed table for promoters 2022-04-13 02:06:53 2.8 STATUS Computed table for cpgislands 2022-04-13 02:06:53 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:16 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:07:16 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:07:17 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:07:17 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:07:17 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:07:17 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:17 2.8 STATUS Computed table for tiling 2022-04-13 02:07:18 2.8 STATUS Computed table for genes 2022-04-13 02:07:18 2.8 STATUS Computed table for promoters 2022-04-13 02:07:18 2.8 STATUS Computed table for cpgislands 2022-04-13 02:07:18 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:19 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:07:19 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:07:19 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:07:19 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:07:19 2.8 STATUS STARTED Computing differential methylation tables 2022-04-13 02:07:19 2.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:07:19 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:07:19 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:07:20 2.9 STATUS STARTED Imputation procedure knn 2022-04-13 02:07:20 2.9 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:07:20 2.9 INFO Conducting differential variability using diffVar 2022-04-13 02:07:20 2.9 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:07:20 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:07:21 2.8 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:07:21 2.8 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:21 2.8 STATUS Computed table for tiling 2022-04-13 02:07:22 2.8 STATUS Computed table for genes 2022-04-13 02:07:22 2.8 STATUS Computed table for promoters 2022-04-13 02:07:22 2.8 STATUS Computed table for cpgislands 2022-04-13 02:07:22 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:25 2.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:07:25 2.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:07:25 2.8 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:07:25 2.8 INFO Conducting differential analysis using limma 2022-04-13 02:07:25 2.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:07:25 2.8 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:07:25 2.8 INFO Conducting differential variability using diffVar 2022-04-13 02:07:25 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:07:26 2.9 STATUS COMPLETED diffVar method 2022-04-13 02:07:26 2.9 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:07:26 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:27 2.8 STATUS Computed table for tiling 2022-04-13 02:07:27 2.8 STATUS Computed table for genes 2022-04-13 02:07:28 2.8 STATUS Computed table for promoters 2022-04-13 02:07:28 2.8 STATUS Computed table for cpgislands 2022-04-13 02:07:28 2.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:07:28 2.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:07:28 2.8 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:07:28 2.8 STATUS STARTED Differential Variability 2022-04-13 02:07:28 2.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:07:29 2.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:07:29 2.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:07:29 2.8 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:07:29 2.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:07:29 2.8 INFO Conducting differential variability using diffVar 2022-04-13 02:07:29 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:07:29 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:07:29 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:07:30 2.9 STATUS Computed table for tiling 2022-04-13 02:07:30 2.9 STATUS Computed table for genes 2022-04-13 02:07:31 2.8 STATUS Computed table for promoters 2022-04-13 02:07:31 2.8 STATUS Computed table for cpgislands 2022-04-13 02:07:31 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:07:38 2.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:07:38 2.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:07:38 2.8 INFO Conducting differential variability using diffVar 2022-04-13 02:07:38 2.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:07:38 2.8 STATUS COMPLETED diffVar method 2022-04-13 02:07:39 2.8 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:07:39 2.8 STATUS Computed table for tiling 2022-04-13 02:07:39 2.8 STATUS Computed table for genes 2022-04-13 02:07:40 2.8 STATUS Computed table for promoters 2022-04-13 02:07:40 2.8 STATUS Computed table for cpgislands 2022-04-13 02:07:40 2.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:07:40 2.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:07:40 2.8 STATUS COMPLETED Differential Variability 2022-04-13 02:07:40 2.8 STATUS STARTED Analysis 2022-04-13 02:07:40 2.8 INFO Loaded information from data.RData 2022-04-13 02:07:40 2.8 STATUS STARTED Processing Detection P-values 2022-04-13 02:07:41 2.8 INFO Removed 3979 probes that overlap with SNPs 2022-04-13 02:07:41 2.8 INFO Completed Greedycut on 510 samples 2022-04-13 02:07:41 2.8 STATUS COMPLETED Processing Detection P-values 2022-04-13 02:07:41 2.8 WARNING File not found: data2.RData 2022-04-13 02:07:41 2.8 STATUS COMPLETED Analysis 2022-04-13 02:07:41 2.8 STATUS STARTED Testing imputation 2022-04-13 02:07:41 2.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:07:42 2.9 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:07:42 2.9 STATUS STARTED Imputation procedure mean.samples 2022-04-13 02:07:43 2.8 STATUS COMPLETED Imputation procedure mean.samples 2022-04-13 02:07:43 2.8 STATUS STARTED Imputation procedure mean.cpgs 2022-04-13 02:07:43 2.8 STATUS COMPLETED Imputation procedure mean.cpgs 2022-04-13 02:07:43 2.8 STATUS STARTED Imputation procedure random 2022-04-13 02:07:44 2.9 STATUS COMPLETED Imputation procedure random 2022-04-13 02:07:44 2.9 STATUS COMPLETED Testing imputation 2022-04-13 02:07:44 2.9 STATUS STARTED Testing age prediction 2022-04-13 02:07:44 2.9 STATUS STARTED Performing Age Prediction 2022-04-13 02:07:57 3.0 STATUS COMPLETED Performing Age Prediction 2022-04-13 02:07:57 3.0 STATUS COMPLETED Testing age prediction 2022-04-13 02:07:58 3.0 STATUS STARTED Performing Age Prediction 2022-04-13 02:08:02 3.0 STATUS COMPLETED Performing Age Prediction 2022-04-13 02:08:02 3.0 STATUS STARTED Imputation procedure knn 2022-04-13 02:08:02 3.0 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:08:02 3.0 STATUS STARTED Imputation procedure mean.samples 2022-04-13 02:08:03 3.0 STATUS COMPLETED Imputation procedure mean.samples 2022-04-13 02:08:03 3.0 STATUS STARTED Imputation procedure mean.cpgs 2022-04-13 02:08:04 3.0 STATUS COMPLETED Imputation procedure mean.cpgs 2022-04-13 02:08:04 3.0 STATUS STARTED Imputation procedure random 2022-04-13 02:08:05 2.6 STATUS COMPLETED Imputation procedure random 2022-04-13 02:08:05 2.6 STATUS STARTED Testing imputation 2022-04-13 02:08:05 2.6 STATUS STARTED Imputation procedure knn 2022-04-13 02:08:05 2.7 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:08:05 2.7 STATUS STARTED Imputation procedure mean.samples 2022-04-13 02:08:06 2.8 STATUS COMPLETED Imputation procedure mean.samples 2022-04-13 02:08:06 2.8 STATUS STARTED Imputation procedure mean.cpgs 2022-04-13 02:08:06 2.9 STATUS COMPLETED Imputation procedure mean.cpgs 2022-04-13 02:08:07 2.9 STATUS STARTED Imputation procedure random 2022-04-13 02:08:08 2.8 STATUS COMPLETED Imputation procedure random 2022-04-13 02:08:08 2.8 STATUS COMPLETED Testing imputation 2022-04-13 02:08:08 2.8 STATUS STARTED Testing age prediction 2022-04-13 02:08:08 2.8 STATUS STARTED Performing Age Prediction 2022-04-13 02:08:10 3.0 STATUS COMPLETED Performing Age Prediction 2022-04-13 02:08:10 3.0 STATUS COMPLETED Testing age prediction RUNIT TEST PROTOCOL -- Wed Apr 13 02:10:44 2022 *********************************************** 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 209.56 16.14 441.34 |
RnBeads.Rcheck/tests_x64/runTests.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 (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: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: 'IRanges' The following object is masked from 'package:grDevices': windows Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/Rtmp4oF84a/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 Spam version 2.8-0 (2022-01-05) 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 Try help(fields) to get started. 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: 'grid' The following object is masked from 'package:ff': pattern 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 1.5-9.5 2022-03-01 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 2022-04-13 02:11:02 0.7 STATUS STARTED Unit testing: differential 2022-04-13 02:11:02 0.7 STATUS STARTED Testing function: rowWelchP Loading required package: RnBeads.hg19 2022-04-13 02:11:02 0.7 STATUS COMPLETED Testing function: rowWelchP 2022-04-13 02:11:02 0.7 STATUS STARTED Testing function: limmaP 2022-04-13 02:11:02 0.8 STATUS COMPLETED Testing function: limmaP 2022-04-13 02:11:02 0.8 STATUS STARTED Testing function: computeDiffTab.extended.site 2022-04-13 02:11:02 0.8 INFO Conducting differential analysis using limma 2022-04-13 02:11:02 0.8 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2022-04-13 02:11:02 0.8 STATUS STARTED Testing function: computeDiffTab.default.region 2022-04-13 02:11:02 0.8 INFO Conducting differential analysis using limma 2022-04-13 02:11:10 1.1 STATUS COMPLETED Testing function: computeDiffTab.default.region 2022-04-13 02:11:10 1.1 STATUS STARTED Testing function: combineTestPvalsMeth 2022-04-13 02:11:10 1.1 STATUS COMPLETED Testing function: combineTestPvalsMeth 2022-04-13 02:11:10 1.1 STATUS STARTED Testing function: get.adjustment.variables 2022-04-13 02:11:10 1.1 STATUS COMPLETED Testing function: get.adjustment.variables 2022-04-13 02:11:10 1.1 STATUS STARTED Testing function: get.comparison.info 2022-04-13 02:11:10 1.1 STATUS COMPLETED Testing function: get.comparison.info 2022-04-13 02:11:10 1.1 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:11:10 1.1 STATUS STARTED Retrieving comparison info 2022-04-13 02:11:10 1.1 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:11:10 1.1 STATUS STARTED Computing differential methylation tables 2022-04-13 02:11:10 1.1 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:11:10 1.1 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:11:10 1.1 INFO Conducting differential analysis using limma 2022-04-13 02:11:10 1.1 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:11:11 1.1 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:11:11 1.1 STATUS Computed table for tiling 2022-04-13 02:11:12 1.1 STATUS Computed table for genes 2022-04-13 02:11:12 1.1 STATUS Computed table for promoters 2022-04-13 02:11:13 1.0 STATUS Computed table for cpgislands 2022-04-13 02:11:13 1.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:11:14 1.0 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:11:14 1.0 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:11:14 1.0 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:11:14 1.0 INFO Conducting differential analysis using limma 2022-04-13 02:11:14 1.0 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:11:14 1.0 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:11:14 1.0 STATUS Computed table for tiling 2022-04-13 02:11:15 1.1 STATUS Computed table for genes 2022-04-13 02:11:15 1.1 STATUS Computed table for promoters 2022-04-13 02:11:15 1.2 STATUS Computed table for cpgislands 2022-04-13 02:11:15 1.2 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:11:15 1.2 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:11:15 1.2 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:11:15 1.2 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:11:15 1.2 STATUS STARTED Testing function: diffVar 2022-04-13 02:11:15 1.2 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:13 3.8 STATUS COMPLETED diffVar method 2022-04-13 02:12:13 3.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:13 3.8 WARNING Could not compute p-values with diffVar, returning NA 2022-04-13 02:12:13 3.8 INFO diffVar from missMethyl package not properly running 2022-04-13 02:12:13 3.8 STATUS COMPLETED diffVar method 2022-04-13 02:12:14 3.8 STATUS STARTED Testing function: apply.iEVORA 2022-04-13 02:12:14 3.8 STATUS STARTED iEVORA method 2022-04-13 02:12:14 3.8 INFO No DVCs detected. All p-values set to 1. 2022-04-13 02:12:14 3.8 STATUS COMPLETED iEVORA method 2022-04-13 02:12:15 3.8 STATUS STARTED Testing function: rnb.execute.diffVar 2022-04-13 02:12:15 3.8 STATUS STARTED Differential Variability 2022-04-13 02:12:15 3.8 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:15 3.8 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:15 3.8 INFO No imputation method selected, 'knn' method used. 2022-04-13 02:12:15 3.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:12:15 3.8 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:12:15 3.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:15 3.8 INFO Conducting differential variability using diffVar 2022-04-13 02:12:15 3.8 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:15 3.8 STATUS COMPLETED diffVar method 2022-04-13 02:12:15 3.9 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:12:16 4.0 STATUS Computed table for tiling 2022-04-13 02:12:17 3.7 STATUS Computed table for genes 2022-04-13 02:12:17 3.7 STATUS Computed table for promoters 2022-04-13 02:12:17 3.7 STATUS Computed table for cpgislands 2022-04-13 02:12:17 3.7 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:12:17 3.7 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:17 3.7 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:17 3.7 INFO Conducting differential variability using diffVar 2022-04-13 02:12:17 3.7 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:18 3.7 STATUS COMPLETED diffVar method 2022-04-13 02:12:18 3.7 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:12:18 3.7 STATUS Computed table for tiling 2022-04-13 02:12:18 3.7 STATUS Computed table for genes 2022-04-13 02:12:18 3.7 STATUS Computed table for promoters 2022-04-13 02:12:21 3.5 STATUS Computed table for cpgislands 2022-04-13 02:12:21 3.5 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:12:21 3.5 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:21 3.5 STATUS COMPLETED Differential Variability 2022-04-13 02:12:21 3.5 STATUS COMPLETED Testing function: rnb.execute.diffVar 2022-04-13 02:12:21 3.5 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:12:21 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:21 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:21 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:21 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:21 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:21 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:21 3.5 STATUS STARTED Imputation procedure knn 2022-04-13 02:12:21 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:12:21 3.5 INFO Conducting differential variability using diffVar 2022-04-13 02:12:21 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:22 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:12:22 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:22 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:22 3.6 STATUS Computed table for tiling 2022-04-13 02:12:27 3.0 STATUS Computed table for genes 2022-04-13 02:12:27 3.0 STATUS Computed table for promoters 2022-04-13 02:12:28 3.0 STATUS Computed table for cpgislands 2022-04-13 02:12:28 3.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:28 3.0 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:28 3.0 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:28 3.0 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:28 3.0 INFO Conducting differential analysis using limma 2022-04-13 02:12:28 3.0 STATUS STARTED Imputation procedure knn 2022-04-13 02:12:28 3.0 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:12:28 3.0 INFO Conducting differential variability using diffVar 2022-04-13 02:12:28 3.0 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:28 3.0 STATUS COMPLETED diffVar method 2022-04-13 02:12:28 3.0 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:28 3.0 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:29 3.0 STATUS Computed table for tiling 2022-04-13 02:12:29 3.2 STATUS Computed table for genes 2022-04-13 02:12:30 3.3 STATUS Computed table for promoters 2022-04-13 02:12:30 3.3 STATUS Computed table for cpgislands 2022-04-13 02:12:30 3.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:30 3.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:30 3.3 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:31 3.3 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:12:31 3.3 STATUS STARTED Testing class: RnBDiffMeth 2022-04-13 02:12:31 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:31 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:31 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:31 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:31 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:31 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:31 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:31 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:32 3.4 STATUS Computed table for tiling 2022-04-13 02:12:32 3.4 STATUS Computed table for genes 2022-04-13 02:12:33 3.4 STATUS Computed table for promoters 2022-04-13 02:12:33 3.4 STATUS Computed table for cpgislands 2022-04-13 02:12:33 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:33 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:33 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:33 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:33 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:33 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:33 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:34 3.4 STATUS Computed table for tiling 2022-04-13 02:12:34 3.4 STATUS Computed table for genes 2022-04-13 02:12:34 3.4 STATUS Computed table for promoters 2022-04-13 02:12:35 3.4 STATUS Computed table for cpgislands 2022-04-13 02:12:35 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:35 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:35 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:35 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:35 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:35 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:35 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:35 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:35 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:35 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:35 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:36 3.4 STATUS Computed table for genes 2022-04-13 02:12:36 3.5 STATUS Computed table for tiling 2022-04-13 02:12:36 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:36 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:36 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:36 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:37 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:37 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:37 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:37 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:37 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:37 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:37 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:38 3.4 STATUS Computed table for genes 2022-04-13 02:12:39 3.4 STATUS Computed table for tiling 2022-04-13 02:12:39 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:39 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:39 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:39 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:39 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:39 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:39 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:39 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:39 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:39 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:39 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:39 3.4 STATUS Computed table for promoters 2022-04-13 02:12:40 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:40 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:40 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:40 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:40 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:40 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:40 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:40 3.4 STATUS Computed table for promoters 2022-04-13 02:12:40 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:40 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:40 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:40 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:40 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:41 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:41 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:41 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:41 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:41 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:41 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:41 3.4 STATUS Computed table for genes 2022-04-13 02:12:42 3.4 STATUS Computed table for tiling 2022-04-13 02:12:42 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:42 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:42 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:42 3.4 STATUS STARTED Testing function: get.region.types 2022-04-13 02:12:42 3.4 STATUS COMPLETED Testing function: get.region.types 2022-04-13 02:12:42 3.4 STATUS STARTED Testing function: get.comparisons 2022-04-13 02:12:42 3.4 STATUS COMPLETED Testing function: get.comparisons 2022-04-13 02:12:42 3.4 STATUS STARTED Testing function: get.comparison.grouplabels 2022-04-13 02:12:42 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels 2022-04-13 02:12:42 3.4 STATUS STARTED Testing function: get.site.test.method 2022-04-13 02:12:42 3.4 STATUS COMPLETED Testing function: get.site.test.method 2022-04-13 02:12:42 3.4 STATUS STARTED Testing function: get.table 2022-04-13 02:12:42 3.4 STATUS COMPLETED Testing function: get.table 2022-04-13 02:12:42 3.4 STATUS STARTED Testing function: addDiffMethTable 2022-04-13 02:12:42 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:43 3.5 STATUS COMPLETED Testing function: addDiffMethTable 2022-04-13 02:12:43 3.5 STATUS STARTED Testing functions: join.diffMeth, is.valid 2022-04-13 02:12:43 3.5 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2022-04-13 02:12:43 3.5 STATUS STARTED Destructor 2022-04-13 02:12:43 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:43 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:43 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:43 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:43 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:43 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:43 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:44 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:44 3.5 STATUS COMPLETED Destructor 2022-04-13 02:12:44 3.5 STATUS COMPLETED Testing class: RnBDiffMeth 2022-04-13 02:12:44 3.5 STATUS COMPLETED Testing function: apply.iEVORA 2022-04-13 02:12:44 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:44 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:44 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:44 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:44 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:44 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:44 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:44 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:45 3.5 STATUS Computed table for tiling 2022-04-13 02:12:46 3.4 STATUS Computed table for genes 2022-04-13 02:12:46 3.4 STATUS Computed table for promoters 2022-04-13 02:12:46 3.4 STATUS Computed table for cpgislands 2022-04-13 02:12:46 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:46 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:46 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:46 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:46 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:46 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:47 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:47 3.4 STATUS Computed table for tiling 2022-04-13 02:12:47 3.4 STATUS Computed table for genes 2022-04-13 02:12:47 3.4 STATUS Computed table for promoters 2022-04-13 02:12:48 3.4 STATUS Computed table for cpgislands 2022-04-13 02:12:48 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:48 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:48 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:48 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:48 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:48 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:48 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:48 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:48 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:48 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:48 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:49 3.5 STATUS Computed table for genes 2022-04-13 02:12:49 3.5 STATUS Computed table for tiling 2022-04-13 02:12:49 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:49 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:49 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:49 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:49 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:49 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:49 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:49 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:50 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:50 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:50 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:50 3.5 STATUS Computed table for genes 2022-04-13 02:12:51 3.4 STATUS Computed table for tiling 2022-04-13 02:12:51 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:51 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:51 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:51 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:51 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:51 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:51 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:52 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:52 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:52 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:52 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:52 3.4 STATUS Computed table for promoters 2022-04-13 02:12:52 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:52 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:52 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:52 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:52 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:52 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:52 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:53 3.4 STATUS Computed table for promoters 2022-04-13 02:12:53 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:53 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:53 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:53 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:53 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:53 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:53 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:53 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:53 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:53 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:53 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:54 3.4 STATUS Computed table for genes 2022-04-13 02:12:54 3.4 STATUS Computed table for tiling 2022-04-13 02:12:54 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:12:54 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:12:54 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:12:54 3.4 STATUS STARTED Testing function: get.region.types 2022-04-13 02:12:54 3.4 STATUS COMPLETED Testing function: get.region.types 2022-04-13 02:12:54 3.4 STATUS STARTED Testing function: get.comparisons 2022-04-13 02:12:54 3.4 STATUS COMPLETED Testing function: get.comparisons 2022-04-13 02:12:55 3.4 STATUS STARTED Testing function: get.comparison.grouplabels 2022-04-13 02:12:55 3.4 STATUS COMPLETED Testing function: get.comparison.grouplabels 2022-04-13 02:12:55 3.4 STATUS STARTED Testing function: get.site.test.method 2022-04-13 02:12:55 3.4 STATUS COMPLETED Testing function: get.site.test.method 2022-04-13 02:12:55 3.4 STATUS STARTED Testing function: get.table 2022-04-13 02:12:55 3.4 STATUS COMPLETED Testing function: get.table 2022-04-13 02:12:55 3.4 STATUS STARTED Testing function: addDiffMethTable 2022-04-13 02:12:55 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:12:55 3.4 STATUS COMPLETED Testing function: addDiffMethTable 2022-04-13 02:12:55 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid 2022-04-13 02:12:55 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2022-04-13 02:12:55 3.4 STATUS STARTED Destructor 2022-04-13 02:12:55 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:12:56 3.4 STATUS COMPLETED Destructor 2022-04-13 02:12:56 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:56 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:57 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:57 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:12:57 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:57 3.5 WARNING Could not compute p-values with diffVar, returning NA 2022-04-13 02:12:57 3.5 INFO diffVar from missMethyl package not properly running 2022-04-13 02:12:57 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:12:57 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:12:57 3.5 STATUS STARTED Unit testing: differential 2022-04-13 02:12:57 3.5 STATUS STARTED Testing function: rowWelchP 2022-04-13 02:12:57 3.5 STATUS COMPLETED Testing function: rowWelchP 2022-04-13 02:12:57 3.5 STATUS STARTED Testing function: limmaP 2022-04-13 02:12:58 3.5 STATUS COMPLETED Testing function: limmaP 2022-04-13 02:12:58 3.5 STATUS STARTED Testing function: computeDiffTab.extended.site 2022-04-13 02:12:58 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:58 3.5 STATUS COMPLETED Testing function: computeDiffTab.extended.site 2022-04-13 02:12:58 3.5 STATUS STARTED Testing function: computeDiffTab.default.region 2022-04-13 02:12:58 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:58 3.5 STATUS COMPLETED Testing function: computeDiffTab.default.region 2022-04-13 02:12:58 3.5 STATUS STARTED Testing function: combineTestPvalsMeth 2022-04-13 02:12:58 3.5 STATUS COMPLETED Testing function: combineTestPvalsMeth 2022-04-13 02:12:58 3.5 STATUS STARTED Testing function: get.adjustment.variables 2022-04-13 02:12:59 3.5 STATUS COMPLETED Testing function: get.adjustment.variables 2022-04-13 02:12:59 3.5 STATUS STARTED Testing function: get.comparison.info 2022-04-13 02:12:59 3.5 STATUS COMPLETED Testing function: get.comparison.info 2022-04-13 02:12:59 3.5 STATUS STARTED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:12:59 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:12:59 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:12:59 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:12:59 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:12:59 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:12:59 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:12:59 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:12:59 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:00 3.4 STATUS Computed table for tiling 2022-04-13 02:13:01 3.4 STATUS Computed table for genes 2022-04-13 02:13:01 3.4 STATUS Computed table for promoters 2022-04-13 02:13:01 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:01 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:01 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:01 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:01 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:02 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:02 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:02 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:02 3.4 STATUS Computed table for tiling 2022-04-13 02:13:02 3.4 STATUS Computed table for genes 2022-04-13 02:13:03 3.4 STATUS Computed table for promoters 2022-04-13 02:13:03 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:03 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:03 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:03 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:03 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth 2022-04-13 02:13:03 3.4 STATUS STARTED Testing function: diffVar 2022-04-13 02:13:03 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:03 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:04 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:04 3.5 WARNING Could not compute p-values with diffVar, returning NA 2022-04-13 02:13:04 3.5 INFO diffVar from missMethyl package not properly running 2022-04-13 02:13:04 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:04 3.5 STATUS STARTED Testing function: apply.iEVORA 2022-04-13 02:13:04 3.5 STATUS STARTED iEVORA method 2022-04-13 02:13:05 3.5 INFO No DVCs detected. All p-values set to 1. 2022-04-13 02:13:05 3.5 STATUS COMPLETED iEVORA method 2022-04-13 02:13:05 3.5 STATUS STARTED Testing function: rnb.execute.diffVar 2022-04-13 02:13:05 3.5 STATUS STARTED Differential Variability 2022-04-13 02:13:05 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:05 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:05 3.5 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:05 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:05 3.5 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:05 3.5 INFO Conducting differential variability using diffVar 2022-04-13 02:13:05 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:06 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:06 3.5 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:07 3.4 STATUS Computed table for tiling 2022-04-13 02:13:07 3.4 STATUS Computed table for genes 2022-04-13 02:13:07 3.4 STATUS Computed table for promoters 2022-04-13 02:13:07 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:07 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:07 3.4 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:07 3.4 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:07 3.4 INFO Conducting differential variability using diffVar 2022-04-13 02:13:08 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:08 3.4 STATUS COMPLETED diffVar method 2022-04-13 02:13:08 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:08 3.4 STATUS Computed table for tiling 2022-04-13 02:13:08 3.5 STATUS Computed table for genes 2022-04-13 02:13:09 3.5 STATUS Computed table for promoters 2022-04-13 02:13:09 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:09 3.5 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:09 3.5 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:09 3.5 STATUS COMPLETED Differential Variability 2022-04-13 02:13:09 3.5 STATUS COMPLETED Testing function: rnb.execute.diffVar 2022-04-13 02:13:09 3.5 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:13:09 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:09 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:09 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:09 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:09 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:09 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:09 3.5 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:10 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:10 3.5 INFO Conducting differential variability using diffVar 2022-04-13 02:13:10 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:10 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:10 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:10 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:10 3.5 STATUS Computed table for tiling 2022-04-13 02:13:11 3.4 STATUS Computed table for genes 2022-04-13 02:13:12 3.4 STATUS Computed table for promoters 2022-04-13 02:13:12 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:12 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:12 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:12 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:12 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:12 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:12 3.4 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:13 3.4 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:13 3.4 INFO Conducting differential variability using diffVar 2022-04-13 02:13:13 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:13 3.4 STATUS COMPLETED diffVar method 2022-04-13 02:13:13 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:13 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:13 3.4 STATUS Computed table for tiling 2022-04-13 02:13:14 3.5 STATUS Computed table for genes 2022-04-13 02:13:14 3.5 STATUS Computed table for promoters 2022-04-13 02:13:15 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:15 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:15 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:15 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:15 3.5 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability 2022-04-13 02:13:15 3.5 STATUS STARTED Testing class: RnBDiffMeth 2022-04-13 02:13:15 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:15 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:15 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:15 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:15 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:15 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:15 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:15 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:17 3.4 STATUS Computed table for tiling 2022-04-13 02:13:17 3.4 STATUS Computed table for genes 2022-04-13 02:13:17 3.4 STATUS Computed table for promoters 2022-04-13 02:13:17 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:17 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:17 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:18 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:18 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:18 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:18 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:18 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:18 3.4 STATUS Computed table for tiling 2022-04-13 02:13:19 3.5 STATUS Computed table for genes 2022-04-13 02:13:19 3.5 STATUS Computed table for promoters 2022-04-13 02:13:19 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:19 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:19 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:19 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:19 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:19 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:20 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:20 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:20 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:20 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:20 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:20 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:20 3.5 STATUS Computed table for genes 2022-04-13 02:13:21 3.4 STATUS Computed table for tiling 2022-04-13 02:13:21 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:21 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:21 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:21 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:21 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:21 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:22 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:22 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:22 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:22 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:22 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:22 3.4 STATUS Computed table for genes 2022-04-13 02:13:22 3.4 STATUS Computed table for tiling 2022-04-13 02:13:23 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:23 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:23 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:23 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:23 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:23 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:23 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:23 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:23 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:23 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:23 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:23 3.5 STATUS Computed table for promoters 2022-04-13 02:13:23 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:24 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:24 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:24 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:24 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:24 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:24 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:24 3.5 STATUS Computed table for promoters 2022-04-13 02:13:24 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:24 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:24 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:24 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:24 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:25 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:25 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:25 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:25 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:25 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:25 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:25 3.5 STATUS Computed table for genes 2022-04-13 02:13:26 3.5 STATUS Computed table for tiling 2022-04-13 02:13:26 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:26 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:26 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:26 3.5 STATUS STARTED Testing function: get.region.types 2022-04-13 02:13:26 3.5 STATUS COMPLETED Testing function: get.region.types 2022-04-13 02:13:26 3.5 STATUS STARTED Testing function: get.comparisons 2022-04-13 02:13:26 3.5 STATUS COMPLETED Testing function: get.comparisons 2022-04-13 02:13:26 3.5 STATUS STARTED Testing function: get.comparison.grouplabels 2022-04-13 02:13:26 3.5 STATUS COMPLETED Testing function: get.comparison.grouplabels 2022-04-13 02:13:26 3.5 STATUS STARTED Testing function: get.site.test.method 2022-04-13 02:13:26 3.5 STATUS COMPLETED Testing function: get.site.test.method 2022-04-13 02:13:26 3.5 STATUS STARTED Testing function: get.table 2022-04-13 02:13:26 3.5 STATUS COMPLETED Testing function: get.table 2022-04-13 02:13:26 3.5 STATUS STARTED Testing function: addDiffMethTable 2022-04-13 02:13:26 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:27 3.5 STATUS COMPLETED Testing function: addDiffMethTable 2022-04-13 02:13:27 3.5 STATUS STARTED Testing functions: join.diffMeth, is.valid 2022-04-13 02:13:27 3.5 STATUS COMPLETED Testing functions: join.diffMeth, is.valid 2022-04-13 02:13:27 3.5 STATUS STARTED Destructor 2022-04-13 02:13:27 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:27 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk 2022-04-13 02:13:28 3.5 STATUS COMPLETED Destructor 2022-04-13 02:13:28 3.5 STATUS COMPLETED Testing class: RnBDiffMeth 2022-04-13 02:13:28 3.5 STATUS COMPLETED Testing function: apply.iEVORA 2022-04-13 02:13:28 3.5 STATUS STARTED iEVORA method 2022-04-13 02:13:29 3.4 INFO No DVCs detected. All p-values set to 1. Coefficients not estimable: x2x2 2022-04-13 02:13:29 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:30 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:30 3.4 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:30 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:30 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:30 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:30 3.4 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:30 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:30 3.4 STATUS Computed table for tiling 2022-04-13 02:13:31 3.5 STATUS Computed table for genes 2022-04-13 02:13:31 3.5 STATUS Computed table for promoters 2022-04-13 02:13:31 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:31 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:31 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:31 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:31 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:31 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:31 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:32 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:32 3.5 STATUS Computed table for tiling 2022-04-13 02:13:32 3.5 STATUS Computed table for genes 2022-04-13 02:13:32 3.5 STATUS Computed table for promoters 2022-04-13 02:13:33 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:33 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:33 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:33 3.5 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:33 3.5 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:33 3.5 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:33 3.5 STATUS STARTED Computing differential methylation tables 2022-04-13 02:13:33 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:33 3.5 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:33 3.5 INFO Conducting differential analysis using limma 2022-04-13 02:13:33 3.5 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:33 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:33 3.5 INFO Conducting differential variability using diffVar 2022-04-13 02:13:34 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:34 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:34 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:34 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:35 3.4 STATUS Computed table for tiling 2022-04-13 02:13:35 3.4 STATUS Computed table for genes 2022-04-13 02:13:36 3.4 STATUS Computed table for promoters 2022-04-13 02:13:36 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:36 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:36 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:36 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:36 3.4 STATUS STARTED Computing Differential Methylation Table 2022-04-13 02:13:36 3.4 INFO Conducting differential analysis using limma 2022-04-13 02:13:36 3.4 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:36 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:36 3.5 INFO Conducting differential variability using diffVar 2022-04-13 02:13:36 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:37 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:37 3.5 STATUS COMPLETED Computing Differential Methylation Table 2022-04-13 02:13:37 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:37 3.5 STATUS Computed table for tiling 2022-04-13 02:13:38 3.5 STATUS Computed table for genes 2022-04-13 02:13:39 3.4 STATUS Computed table for promoters 2022-04-13 02:13:39 3.4 STATUS Computed table for cpgislands 2022-04-13 02:13:39 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level) 2022-04-13 02:13:39 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:39 3.4 STATUS COMPLETED Computing differential methylation tables 2022-04-13 02:13:39 3.4 STATUS STARTED Differential Variability 2022-04-13 02:13:39 3.4 STATUS STARTED Retrieving comparison info 2022-04-13 02:13:39 3.4 STATUS COMPLETED Retrieving comparison info 2022-04-13 02:13:40 3.4 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:40 3.4 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:40 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:40 3.4 INFO Conducting differential variability using diffVar 2022-04-13 02:13:40 3.4 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:40 3.4 STATUS COMPLETED diffVar method 2022-04-13 02:13:40 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:40 3.4 STATUS Computed table for tiling 2022-04-13 02:13:41 3.5 STATUS Computed table for genes 2022-04-13 02:13:41 3.5 STATUS Computed table for promoters 2022-04-13 02:13:41 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:41 3.5 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:41 3.5 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group) 2022-04-13 02:13:41 3.5 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:41 3.5 INFO Conducting differential variability using diffVar 2022-04-13 02:13:41 3.5 STATUS STARTED diffVar method coef not specified. Using all columns of design matrix. 2022-04-13 02:13:42 3.5 STATUS COMPLETED diffVar method 2022-04-13 02:13:42 3.5 STATUS STARTED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:42 3.5 STATUS Computed table for tiling 2022-04-13 02:13:42 3.5 STATUS Computed table for genes 2022-04-13 02:13:43 3.5 STATUS Computed table for promoters 2022-04-13 02:13:43 3.5 STATUS Computed table for cpgislands 2022-04-13 02:13:43 3.5 STATUS COMPLETED Computing Differential Variability Tables (Region Level) 2022-04-13 02:13:43 3.5 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment) 2022-04-13 02:13:43 3.5 STATUS COMPLETED Differential Variability 2022-04-13 02:13:43 3.5 STATUS STARTED Analysis 2022-04-13 02:13:43 3.5 INFO Loaded information from data.RData 2022-04-13 02:13:43 3.5 STATUS STARTED Processing Detection P-values 2022-04-13 02:13:43 3.5 INFO Removed 3979 probes that overlap with SNPs 2022-04-13 02:13:43 3.5 INFO Completed Greedycut on 510 samples 2022-04-13 02:13:43 3.5 STATUS COMPLETED Processing Detection P-values 2022-04-13 02:13:43 3.5 WARNING File not found: data2.RData 2022-04-13 02:13:44 3.5 STATUS COMPLETED Analysis 2022-04-13 02:13:44 3.5 STATUS STARTED Testing imputation 2022-04-13 02:13:44 3.5 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:45 3.4 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:45 3.4 STATUS STARTED Imputation procedure mean.samples 2022-04-13 02:13:46 3.4 STATUS COMPLETED Imputation procedure mean.samples 2022-04-13 02:13:46 3.4 STATUS STARTED Imputation procedure mean.cpgs 2022-04-13 02:13:46 3.5 STATUS COMPLETED Imputation procedure mean.cpgs 2022-04-13 02:13:46 3.5 STATUS STARTED Imputation procedure random 2022-04-13 02:13:47 3.5 STATUS COMPLETED Imputation procedure random 2022-04-13 02:13:47 3.5 STATUS COMPLETED Testing imputation 2022-04-13 02:13:47 3.5 STATUS STARTED Testing age prediction 2022-04-13 02:13:47 3.5 STATUS STARTED Performing Age Prediction 2022-04-13 02:13:51 3.2 STATUS COMPLETED Performing Age Prediction 2022-04-13 02:13:51 3.2 STATUS COMPLETED Testing age prediction 2022-04-13 02:13:51 3.2 STATUS STARTED Performing Age Prediction 2022-04-13 02:13:53 3.8 STATUS COMPLETED Performing Age Prediction 2022-04-13 02:13:54 3.8 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:55 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:55 3.5 STATUS STARTED Imputation procedure mean.samples 2022-04-13 02:13:55 3.5 STATUS COMPLETED Imputation procedure mean.samples 2022-04-13 02:13:56 3.5 STATUS STARTED Imputation procedure mean.cpgs 2022-04-13 02:13:56 3.5 STATUS COMPLETED Imputation procedure mean.cpgs 2022-04-13 02:13:56 3.5 STATUS STARTED Imputation procedure random 2022-04-13 02:13:57 3.5 STATUS COMPLETED Imputation procedure random 2022-04-13 02:13:57 3.5 STATUS STARTED Testing imputation 2022-04-13 02:13:57 3.5 STATUS STARTED Imputation procedure knn 2022-04-13 02:13:57 3.5 STATUS COMPLETED Imputation procedure knn 2022-04-13 02:13:57 3.5 STATUS STARTED Imputation procedure mean.samples 2022-04-13 02:13:59 3.5 STATUS COMPLETED Imputation procedure mean.samples 2022-04-13 02:13:59 3.5 STATUS STARTED Imputation procedure mean.cpgs 2022-04-13 02:13:59 3.5 STATUS COMPLETED Imputation procedure mean.cpgs 2022-04-13 02:13:59 3.5 STATUS STARTED Imputation procedure random 2022-04-13 02:14:00 3.5 STATUS COMPLETED Imputation procedure random 2022-04-13 02:14:00 3.5 STATUS COMPLETED Testing imputation 2022-04-13 02:14:00 3.5 STATUS STARTED Testing age prediction 2022-04-13 02:14:00 3.5 STATUS STARTED Performing Age Prediction 2022-04-13 02:14:02 3.8 STATUS COMPLETED Performing Age Prediction 2022-04-13 02:14:02 3.8 STATUS COMPLETED Testing age prediction RUNIT TEST PROTOCOL -- Wed Apr 13 02:14:25 2022 *********************************************** 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 195.04 5.51 219.79 |
RnBeads.Rcheck/examples_i386/RnBeads-Ex.timings
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RnBeads.Rcheck/examples_x64/RnBeads-Ex.timings
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