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CHECK report for RnBeads on malbec2

This page was generated on 2020-10-17 11:55:36 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RnBeads PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1518/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 2.6.0
Fabian Mueller
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RnBeads
Branch: RELEASE_3_11
Last Commit: fd7f6e3
Last Changed Date: 2020-04-27 14:48:53 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RnBeads
Version: 2.6.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RnBeads_2.6.0.tar.gz
StartedAt: 2020-10-17 04:55:42 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:07:19 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 697.2 seconds
RetCode: 0
Status:  OK 
CheckDir: RnBeads.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RnBeads_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RnBeads.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘2.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
  'ff', 'fields', 'ggplot2', 'gplots', 'gridExtra', 'limma',
  'matrixStats', 'illuminaio', 'methylumi', 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    bin   1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qvalue’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
  'grDevices:::.smoothScatterCalcDensity'
  'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
  'minfi:::.normalizeFunnorm450k'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
  ‘stopCluster’
BigFfMat : <anonymous>: no visible global function definition for
  ‘close.ff’
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’
getCGCounts: no visible global function definition for ‘seqlengths’
getCGCounts : <anonymous>: no visible global function definition for
  ‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles: no visible global function definition for ‘mclapply’
getGLADProfiles : <anonymous>: no visible global function definition
  for ‘as.profileCGH’
getGLADProfiles : <anonymous>: no visible global function definition
  for ‘daglad’
getMergeList: no visible global function definition for ‘samples’
groupPermutationP.site.parallel: no visible global function definition
  for ‘%dopar%’
groupPermutationP.site.parallel: no visible global function definition
  for ‘foreach’
iEVORA: no visible global function definition for ‘qvalue’
imputation.low.memory.cpgs: no visible global function definition for
  ‘samples’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICmanifest’
intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
intensities.by.color: no visible global function definition for
  ‘samples’
knn.imputation: no visible global function definition for ‘impute.knn’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
loadLolaDbs: no visible global function definition for ‘loadRegionDB’
loadLolaDbs: no visible global function definition for ‘mergeRegionDBs’
locus.profile.get.base.tracks: no visible global function definition
  for ‘useMart’
locus.profile.get.base.tracks: no visible global function definition
  for ‘IdeogramTrack’
locus.profile.get.base.tracks: no visible global function definition
  for ‘GenomeAxisTrack’
locus.profile.get.base.tracks: no visible global function definition
  for ‘BiomartGeneRegionTrack’
locus.profile.get.base.tracks: no visible global function definition
  for ‘UcscTrack’
locus.profile.get.methylation.track.heatmap: no visible global function
  definition for ‘DataTrack’
locus.profile.get.methylation.track.smooth: no visible global function
  definition for ‘DataTrack’
methylumi.intensities.by.color: no visible global function definition
  for ‘featureNames’
methylumi.intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
methylumi.intensities.by.color: no visible global function definition
  for ‘assayDataElement’
parallel.setup: no visible global function definition for
  ‘registerDoParallel’
parallel.setup: no visible global function definition for
  ‘getDoParWorkers’
performLolaEnrichment.diffMeth: no visible global function definition
  for ‘runLOLA’
performLolaEnrichment.diffVar: no visible global function definition
  for ‘runLOLA’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘grid.newpage’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘grid.draw’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘melt’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘grid.newpage’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘grid.draw’
plot.heatmap.rand: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for
  ‘grid.newpage’
plot.heatmap.symm: no visible global function definition for
  ‘grid.draw’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
prepareGEOSampleInfoTemplate: no visible global function definition for
  ‘samples’
projectWBC: no visible global function definition for ‘solve.QP’
read.GS.report: no visible global function definition for
  ‘featureNames’
read.idat.files: no visible binding for global variable ‘barcode’
refFreeEWASP: no visible global function definition for ‘EstDimRMT’
refFreeEWASP: no visible global function definition for
  ‘RefFreeEwasModel’
refFreeEWASP: no visible global function definition for
  ‘PairsBootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for
  ‘BootRefFreeEwasModel’
rnb.RnBSet.to.GRangesList: no visible global function definition for
  ‘samples’
rnb.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
  ‘samples’
rnb.bed.from.segmentation: no visible global function definition for
  ‘samples’
rnb.boxplot.from.segmentation: no visible global function definition
  for ‘samples’
rnb.boxplot.from.segmentation: no visible binding for global variable
  ‘Segment’
rnb.boxplot.from.segmentation: no visible binding for global variable
  ‘AvgMeth’
rnb.chromosome.lengths: no visible global function definition for
  ‘seqlengths’
rnb.combine.seq: no visible global function definition for ‘samples’
rnb.enmix.oob: no visible global function definition for ‘%dopar%’
rnb.enmix.oob: no visible global function definition for ‘foreach’
rnb.execute.dreduction: no visible global function definition for
  ‘samples’
rnb.execute.filter.summary.internal: no visible global function
  definition for ‘samples’
rnb.execute.high.coverage.removal.internal: no visible global function
  definition for ‘samples’
rnb.execute.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.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.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’
[,BigFfMat-ANY-ANY-ANY : <anonymous>: no visible global function
  definition for ‘open.ff’
[,BigFfMat-ANY-ANY-ANY : <anonymous>: no visible global function
  definition for ‘close.ff’
[<-,BigFfMat-ANY-ANY-ANY: no visible global function definition for
  ‘open.ff’
[<-,BigFfMat-ANY-ANY-ANY: no visible global function definition for
  ‘close.ff’
[<-,BigFfMat-ANY-ANY-ANY : <anonymous>: no visible global function
  definition for ‘open.ff’
[<-,BigFfMat-ANY-ANY-ANY : <anonymous>: no visible global function
  definition for ‘close.ff’
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<-’
join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function
  definition for ‘clone’
mask.sites.meth,RnBSet: no visible global function definition for
  ‘samples’
remove.samples,RnBSet: no visible global function definition for
  ‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
  ‘samples’
remove.samples,RnBeadSet: no visible global function definition for
  ‘samples’
remove.sites,RnBSet: no visible global function definition for
  ‘samples’
sampleCovgApply,RnBSet: no visible global function definition for
  ‘samples’
sampleMethApply,RnBSet: no visible global function definition for
  ‘samples’
summarize.regions,RnBSet: no visible global function definition for
  ‘samples’
summarize.regions,RnBSet: multiple local function definitions for
  ‘aggr.f’ with different formal arguments
updateMethylationSites,RnBSet: no visible global function definition
  for ‘samples’
Undefined global functions or variables:
  %dopar% ..count.. ..density.. .inds.g2 Address Age Annotated AvgMeth
  BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
  Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack
  Group Hsapiens ID IdeogramTrack IlluminaHumanMethylation450kmanifest
  IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity
  Measure Mmusculus PairsBootRefFreeEwasModel Predicted Probe
  RGChannelSet Rd2HTML RefFreeEwasModel SNP Sample Segment Slide Target
  Term UcscTrack Value addSex as.profileCGH assayDataElement
  assayDataElementNames barcode browserSession bv calculateFDRs chrom
  clone close.ff 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 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 open.ff p.vals.t.na.adj pData percent_format
  phenoData phenoData<- plotAlphaDistributionOneChr
  plotFinalSegmentation plotTracks preprocessSWAN pvalues qvalue
  readMethylome readSNPTable refText reg.type region.size
  registerDoParallel relative.coord removeSNPs report runLOLA samples
  segmentPMDs segmentUMRsLMRs seqlengths seqlevels<- sigCategories
  sites2ignore size solve.QP stopCluster sva target texthere tsne type
  types ucscTableQuery universeCounts useMart v var.diff varFit
  varLabels x x2 xmlValue y y2 yint
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/RnBeads.Rcheck/00check.log’
for details.

Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RnBeads
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘RnBeads’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RnBeads)

Tests output

RnBeads.Rcheck/tests/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RnBeads")

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/RtmptPhTcM/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 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following object is masked from 'package:stats4':

    mle

The following objects are masked from 'package:base':

    backsolve, forwardsolve

See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess


Attaching package: 'gridExtra'

The following object is masked from 'package:BiocGenerics':

    combine


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:MASS':

    select



Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:ff':

    maxlength

The following objects are masked from 'package:base':

    aperm, apply, rowsum


Attaching package: 'Biostrings'

The following objects are masked from 'package:ff':

    mismatch, pattern

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.4 	 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:matrixStats':

    count

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

2020-10-17 05:03:52     1.3  STATUS STARTED Unit testing: differential
2020-10-17 05:03:52     1.3  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2020-10-17 05:03:52     1.3  STATUS     COMPLETED Testing function: rowWelchP
2020-10-17 05:03:52     1.3  STATUS     STARTED Testing function: limmaP
2020-10-17 05:03:52     1.3  STATUS     COMPLETED Testing function: limmaP
2020-10-17 05:03:52     1.3  STATUS     STARTED Testing function: computeDiffTab.extended.site
2020-10-17 05:03:53     1.4    INFO         Conducting differential analysis using limma
2020-10-17 05:03:53     1.4  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2020-10-17 05:03:53     1.4  STATUS     STARTED Testing function: computeDiffTab.default.region
2020-10-17 05:03:53     1.4    INFO         Conducting differential analysis using limma
2020-10-17 05:04:01     1.6  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2020-10-17 05:04:01     1.6  STATUS     STARTED Testing function: combineTestPvalsMeth
2020-10-17 05:04:01     1.6  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2020-10-17 05:04:01     1.6  STATUS     STARTED Testing function: get.adjustment.variables
2020-10-17 05:04:01     1.6  STATUS     COMPLETED Testing function: get.adjustment.variables
2020-10-17 05:04:01     1.6  STATUS     STARTED Testing function: get.comparison.info
2020-10-17 05:04:01     1.6  STATUS     COMPLETED Testing function: get.comparison.info
2020-10-17 05:04:01     1.6  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2020-10-17 05:04:01     1.6  STATUS         STARTED Retrieving comparison info
2020-10-17 05:04:01     1.6  STATUS         COMPLETED Retrieving comparison info
2020-10-17 05:04:01     1.6  STATUS         STARTED Computing differential methylation tables
2020-10-17 05:04:01     1.6  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:04:01     1.6  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:04:01     1.6    INFO                     Conducting differential analysis using limma
2020-10-17 05:04:01     1.6  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:04:01     1.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:04:02     1.6  STATUS                     Computed table for tiling
2020-10-17 05:04:02     1.6  STATUS                     Computed table for genes
2020-10-17 05:04:03     1.7  STATUS                     Computed table for promoters
2020-10-17 05:04:03     1.7  STATUS                     Computed table for cpgislands
2020-10-17 05:04:03     1.7  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:04:03     1.7  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:04:03     1.7  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:04:03     1.7  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:04:03     1.7    INFO                     Conducting differential analysis using limma
2020-10-17 05:04:03     1.7  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:04:03     1.7  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:04:05     1.7  STATUS                     Computed table for tiling
2020-10-17 05:04:05     1.7  STATUS                     Computed table for genes
2020-10-17 05:04:06     1.7  STATUS                     Computed table for promoters
2020-10-17 05:04:06     1.7  STATUS                     Computed table for cpgislands
2020-10-17 05:04:06     1.7  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:04:06     1.8  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:04:06     1.8  STATUS         COMPLETED Computing differential methylation tables
2020-10-17 05:04:06     1.8  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2020-10-17 05:04:06     1.8  STATUS     STARTED Testing function: diffVar
2020-10-17 05:04:06     1.8  STATUS         STARTED diffVar method
2020-10-17 05:05:14     4.3  STATUS         COMPLETED diffVar method
2020-10-17 05:05:14     4.3  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2020-10-17 05:05:14     4.4  STATUS         COMPLETED diffVar method
2020-10-17 05:05:14     4.4  STATUS     COMPLETED Testing function: diffVar
2020-10-17 05:05:14     4.4  STATUS     STARTED Testing function: apply.iEVORA
2020-10-17 05:05:14     4.4  STATUS         STARTED iEVORA method
2020-10-17 05:05:16     4.4    INFO             No DVCs detected. All p-values set to 1.
2020-10-17 05:05:16     4.4  STATUS         COMPLETED iEVORA method
2020-10-17 05:05:16     4.4  STATUS         STARTED Testing function: rnb.execute.diffVar
2020-10-17 05:05:16     4.4  STATUS             STARTED Differential Variability
2020-10-17 05:05:16     4.4  STATUS                 STARTED Retrieving comparison info
2020-10-17 05:05:16     4.4  STATUS                 COMPLETED Retrieving comparison info
2020-10-17 05:05:16     4.5    INFO                 No imputation method selected, 'knn' method used.
2020-10-17 05:05:16     4.5  STATUS                 STARTED Imputation procedure knn 
2020-10-17 05:05:16     4.5  STATUS                 COMPLETED Imputation procedure knn 
2020-10-17 05:05:16     4.5  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:16     4.5    INFO                     Conducting differential variability using diffVar
2020-10-17 05:05:16     4.5  STATUS                     STARTED diffVar method
2020-10-17 05:05:16     4.5  STATUS                     COMPLETED diffVar method
2020-10-17 05:05:17     4.3  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:18     4.3  STATUS                         Computed table for tiling
2020-10-17 05:05:18     4.3  STATUS                         Computed table for genes
2020-10-17 05:05:18     4.3  STATUS                         Computed table for promoters
2020-10-17 05:05:18     4.3  STATUS                         Computed table for cpgislands
2020-10-17 05:05:18     4.3  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:18     4.3  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:18     4.3  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:18     4.3    INFO                     Conducting differential variability using diffVar
2020-10-17 05:05:18     4.3  STATUS                     STARTED diffVar method
2020-10-17 05:05:19     4.3  STATUS                     COMPLETED diffVar method
2020-10-17 05:05:19     4.3  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:22     4.2  STATUS                         Computed table for tiling
2020-10-17 05:05:22     4.2  STATUS                         Computed table for genes
2020-10-17 05:05:22     4.2  STATUS                         Computed table for promoters
2020-10-17 05:05:22     4.2  STATUS                         Computed table for cpgislands
2020-10-17 05:05:22     4.2  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:22     4.2  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:22     4.2  STATUS             COMPLETED Differential Variability
2020-10-17 05:05:22     4.2  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2020-10-17 05:05:22     4.2  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2020-10-17 05:05:22     4.2  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:22     4.2  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:22     4.2  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:22     4.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:22     4.2  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:22     4.2    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:22     4.2  STATUS                         STARTED Imputation procedure knn 
2020-10-17 05:05:22     4.2  STATUS                         COMPLETED Imputation procedure knn 
2020-10-17 05:05:22     4.2    INFO                         Conducting differential variability using diffVar
2020-10-17 05:05:22     4.2  STATUS                         STARTED diffVar method
2020-10-17 05:05:23     4.2  STATUS                         COMPLETED diffVar method
2020-10-17 05:05:23     4.2  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:23     4.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:28     3.6  STATUS                         Computed table for tiling
2020-10-17 05:05:28     3.6  STATUS                         Computed table for genes
2020-10-17 05:05:28     3.6  STATUS                         Computed table for promoters
2020-10-17 05:05:29     3.6  STATUS                         Computed table for cpgislands
2020-10-17 05:05:29     3.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:29     3.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:29     3.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:29     3.6  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:29     3.6    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:29     3.6  STATUS                         STARTED Imputation procedure knn 
2020-10-17 05:05:29     3.6  STATUS                         COMPLETED Imputation procedure knn 
2020-10-17 05:05:29     3.6    INFO                         Conducting differential variability using diffVar
2020-10-17 05:05:29     3.6  STATUS                         STARTED diffVar method
2020-10-17 05:05:29     3.6  STATUS                         COMPLETED diffVar method
2020-10-17 05:05:29     3.6  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:29     3.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:30     3.8  STATUS                         Computed table for tiling
2020-10-17 05:05:30     3.9  STATUS                         Computed table for genes
2020-10-17 05:05:31     4.0  STATUS                         Computed table for promoters
2020-10-17 05:05:31     4.0  STATUS                         Computed table for cpgislands
2020-10-17 05:05:31     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:31     4.0  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:31     4.0  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:05:31     4.0  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2020-10-17 05:05:31     4.0  STATUS         STARTED Testing class: RnBDiffMeth
2020-10-17 05:05:31     4.0  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:31     4.0  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:31     4.0  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:31     4.0  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:31     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:31     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:31     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:31     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:32     4.0  STATUS                         Computed table for tiling
2020-10-17 05:05:32     4.0  STATUS                         Computed table for genes
2020-10-17 05:05:32     4.0  STATUS                         Computed table for promoters
2020-10-17 05:05:32     4.0  STATUS                         Computed table for cpgislands
2020-10-17 05:05:32     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:32     4.0  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:32     4.0  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:32     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:32     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:32     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:32     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:33     4.0  STATUS                         Computed table for tiling
2020-10-17 05:05:33     4.0  STATUS                         Computed table for genes
2020-10-17 05:05:33     4.0  STATUS                         Computed table for promoters
2020-10-17 05:05:34     4.0  STATUS                         Computed table for cpgislands
2020-10-17 05:05:34     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:34     4.0  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:34     4.0  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:05:34     4.0  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:34     4.0  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:34     4.0  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:34     4.0  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:34     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:34     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:34     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:34     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:35     4.0  STATUS                         Computed table for genes
2020-10-17 05:05:35     4.0  STATUS                         Computed table for tiling
2020-10-17 05:05:35     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:35     4.0  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:35     4.0  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:05:35     4.0  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:35     4.0  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:35     4.0  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:35     4.0  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:35     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:35     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:35     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:35     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:35     4.0  STATUS                         Computed table for genes
2020-10-17 05:05:36     4.0  STATUS                         Computed table for tiling
2020-10-17 05:05:36     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:36     4.0  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:36     4.0  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:05:36     4.0  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:36     4.0  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:36     4.0  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:36     4.0  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:36     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:36     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:36     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:36     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:36     4.0  STATUS                         Computed table for promoters
2020-10-17 05:05:36     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:36     4.0  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:36     4.0  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:36     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:36     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:36     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:36     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:37     4.0  STATUS                         Computed table for promoters
2020-10-17 05:05:37     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:37     4.0  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:37     4.0  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:05:37     4.0  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:37     4.0  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:37     4.0  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:37     4.0  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:37     4.0  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:37     4.0    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:37     4.0  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:37     4.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:37     4.0  STATUS                         Computed table for genes
2020-10-17 05:05:38     4.0  STATUS                         Computed table for tiling
2020-10-17 05:05:38     4.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:38     4.0  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:38     4.0  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:05:38     4.0  STATUS             STARTED Testing function: get.region.types
2020-10-17 05:05:38     4.0  STATUS             COMPLETED Testing function: get.region.types
2020-10-17 05:05:38     4.0  STATUS             STARTED Testing function: get.comparisons
2020-10-17 05:05:38     4.0  STATUS             COMPLETED Testing function: get.comparisons
2020-10-17 05:05:38     4.0  STATUS             STARTED Testing function: get.comparison.grouplabels
2020-10-17 05:05:38     4.0  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2020-10-17 05:05:38     4.0  STATUS             STARTED Testing function: get.site.test.method
2020-10-17 05:05:38     4.0  STATUS             COMPLETED Testing function: get.site.test.method
2020-10-17 05:05:38     4.0  STATUS             STARTED Testing function: get.table
2020-10-17 05:05:38     4.0  STATUS             COMPLETED Testing function: get.table
2020-10-17 05:05:38     4.0  STATUS             STARTED Testing function: addDiffMethTable
2020-10-17 05:05:38     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:39     4.0  STATUS             COMPLETED Testing function: addDiffMethTable
2020-10-17 05:05:39     4.0  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2020-10-17 05:05:40     4.0  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2020-10-17 05:05:40     4.0  STATUS             STARTED Destructor
2020-10-17 05:05:40     4.0  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:40     4.0  STATUS             COMPLETED Destructor
2020-10-17 05:05:40     4.0  STATUS         COMPLETED Testing class: RnBDiffMeth
2020-10-17 05:05:40     4.0  STATUS     COMPLETED Testing function: apply.iEVORA
2020-10-17 05:05:40     4.0  STATUS     STARTED Retrieving comparison info
2020-10-17 05:05:40     4.0  STATUS     COMPLETED Retrieving comparison info
2020-10-17 05:05:40     4.0  STATUS     STARTED Computing differential methylation tables
2020-10-17 05:05:40     4.0  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:40     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:40     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:40     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:40     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:40     4.0  STATUS                 Computed table for tiling
2020-10-17 05:05:41     4.0  STATUS                 Computed table for genes
2020-10-17 05:05:41     4.0  STATUS                 Computed table for promoters
2020-10-17 05:05:41     4.0  STATUS                 Computed table for cpgislands
2020-10-17 05:05:41     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:41     4.0  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:41     4.0  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:41     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:41     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:41     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:41     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:42     4.0  STATUS                 Computed table for tiling
2020-10-17 05:05:42     4.0  STATUS                 Computed table for genes
2020-10-17 05:05:42     4.0  STATUS                 Computed table for promoters
2020-10-17 05:05:42     4.0  STATUS                 Computed table for cpgislands
2020-10-17 05:05:42     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:43     4.0  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:43     4.0  STATUS     COMPLETED Computing differential methylation tables
2020-10-17 05:05:43     4.0  STATUS     STARTED Retrieving comparison info
2020-10-17 05:05:43     4.0  STATUS     COMPLETED Retrieving comparison info
2020-10-17 05:05:43     4.0  STATUS     STARTED Computing differential methylation tables
2020-10-17 05:05:43     4.0  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:43     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:43     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:43     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:43     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:43     4.0  STATUS                 Computed table for genes
2020-10-17 05:05:44     4.0  STATUS                 Computed table for tiling
2020-10-17 05:05:44     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:44     4.0  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:44     4.0  STATUS     COMPLETED Computing differential methylation tables
2020-10-17 05:05:44     4.0  STATUS     STARTED Retrieving comparison info
2020-10-17 05:05:44     4.0  STATUS     COMPLETED Retrieving comparison info
2020-10-17 05:05:44     4.0  STATUS     STARTED Computing differential methylation tables
2020-10-17 05:05:44     4.0  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:44     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:44     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:44     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:44     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:44     4.0  STATUS                 Computed table for genes
2020-10-17 05:05:44     4.0  STATUS                 Computed table for tiling
2020-10-17 05:05:44     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:44     4.0  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:44     4.0  STATUS     COMPLETED Computing differential methylation tables
2020-10-17 05:05:44     4.0  STATUS     STARTED Retrieving comparison info
2020-10-17 05:05:44     4.0  STATUS     COMPLETED Retrieving comparison info
2020-10-17 05:05:44     4.0  STATUS     STARTED Computing differential methylation tables
2020-10-17 05:05:44     4.0  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:44     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:44     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:44     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:44     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:45     4.0  STATUS                 Computed table for promoters
2020-10-17 05:05:45     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:45     4.0  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:45     4.0  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:45     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:45     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:45     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:45     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:45     4.0  STATUS                 Computed table for promoters
2020-10-17 05:05:45     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:45     4.0  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:45     4.0  STATUS     COMPLETED Computing differential methylation tables
2020-10-17 05:05:45     4.0  STATUS     STARTED Retrieving comparison info
2020-10-17 05:05:45     4.0  STATUS     COMPLETED Retrieving comparison info
2020-10-17 05:05:45     4.0  STATUS     STARTED Computing differential methylation tables
2020-10-17 05:05:45     4.0  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:45     4.0  STATUS             STARTED Computing Differential Methylation Table
2020-10-17 05:05:45     4.0    INFO                 Conducting differential analysis using limma
2020-10-17 05:05:45     4.0  STATUS             COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:45     4.0  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:45     4.0  STATUS                 Computed table for genes
2020-10-17 05:05:46     4.0  STATUS                 Computed table for tiling
2020-10-17 05:05:46     4.0  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:46     4.0  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:46     4.0  STATUS     COMPLETED Computing differential methylation tables
2020-10-17 05:05:46     4.0  STATUS     STARTED Testing function: get.region.types
2020-10-17 05:05:46     4.0  STATUS     COMPLETED Testing function: get.region.types
2020-10-17 05:05:46     4.0  STATUS     STARTED Testing function: get.comparisons
2020-10-17 05:05:46     4.0  STATUS     COMPLETED Testing function: get.comparisons
2020-10-17 05:05:46     4.0  STATUS     STARTED Testing function: get.comparison.grouplabels
2020-10-17 05:05:46     4.0  STATUS     COMPLETED Testing function: get.comparison.grouplabels
2020-10-17 05:05:46     4.0  STATUS     STARTED Testing function: get.site.test.method
2020-10-17 05:05:46     4.0  STATUS     COMPLETED Testing function: get.site.test.method
2020-10-17 05:05:46     4.0  STATUS     STARTED Testing function: get.table
2020-10-17 05:05:46     4.0  STATUS     COMPLETED Testing function: get.table
2020-10-17 05:05:46     4.0  STATUS     STARTED Testing function: addDiffMethTable
2020-10-17 05:05:46     4.0    INFO         Conducting differential analysis using limma
2020-10-17 05:05:47     4.0  STATUS     COMPLETED Testing function: addDiffMethTable
2020-10-17 05:05:47     4.0  STATUS     STARTED Testing functions: join.diffMeth, is.valid
2020-10-17 05:05:47     4.0  STATUS     COMPLETED Testing functions: join.diffMeth, is.valid
2020-10-17 05:05:47     4.0  STATUS     STARTED Destructor
2020-10-17 05:05:47     4.0  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:05:47     4.0  STATUS     COMPLETED Destructor
2020-10-17 05:05:47     4.0    INFO     Conducting differential analysis using limma
2020-10-17 05:05:47     4.0    INFO     Conducting differential analysis using limma
2020-10-17 05:05:47     4.0  STATUS     STARTED diffVar method
2020-10-17 05:05:47     4.0  STATUS     COMPLETED diffVar method
2020-10-17 05:05:47     4.0  STATUS     STARTED diffVar method
Coefficients not estimable: x2x2 
2020-10-17 05:05:47     4.0  STATUS     COMPLETED diffVar method
2020-10-17 05:05:47     4.0  STATUS     STARTED diffVar method
2020-10-17 05:05:47     4.0 WARNING         Could not compute p-values with diffVar, returning NA
2020-10-17 05:05:48     4.0  STATUS STARTED Unit testing: differential
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: rowWelchP
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: rowWelchP
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: limmaP
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: limmaP
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: computeDiffTab.extended.site
2020-10-17 05:05:48     4.0    INFO         Conducting differential analysis using limma
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: computeDiffTab.default.region
2020-10-17 05:05:48     4.0    INFO         Conducting differential analysis using limma
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: combineTestPvalsMeth
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: get.adjustment.variables
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: get.adjustment.variables
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: get.comparison.info
2020-10-17 05:05:48     4.0  STATUS     COMPLETED Testing function: get.comparison.info
2020-10-17 05:05:48     4.0  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2020-10-17 05:05:48     4.0  STATUS         STARTED Retrieving comparison info
2020-10-17 05:05:48     4.0  STATUS         COMPLETED Retrieving comparison info
2020-10-17 05:05:48     4.0  STATUS         STARTED Computing differential methylation tables
2020-10-17 05:05:48     4.0  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:48     4.0  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:05:48     4.0    INFO                     Conducting differential analysis using limma
2020-10-17 05:05:48     4.0  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:48     4.0  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:49     4.0  STATUS                     Computed table for tiling
2020-10-17 05:05:49     4.0  STATUS                     Computed table for genes
2020-10-17 05:05:49     4.1  STATUS                     Computed table for promoters
2020-10-17 05:05:49     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:05:49     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:49     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:49     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:49     4.1  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:05:49     4.1    INFO                     Conducting differential analysis using limma
2020-10-17 05:05:49     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:49     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:50     4.1  STATUS                     Computed table for tiling
2020-10-17 05:05:51     4.1  STATUS                     Computed table for genes
2020-10-17 05:05:51     4.1  STATUS                     Computed table for promoters
2020-10-17 05:05:51     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:05:51     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:51     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:51     4.1  STATUS         COMPLETED Computing differential methylation tables
2020-10-17 05:05:51     4.1  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2020-10-17 05:05:51     4.1  STATUS     STARTED Testing function: diffVar
2020-10-17 05:05:51     4.1  STATUS         STARTED diffVar method
2020-10-17 05:05:51     4.1  STATUS         COMPLETED diffVar method
2020-10-17 05:05:51     4.1  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2020-10-17 05:05:51     4.1  STATUS         COMPLETED diffVar method
2020-10-17 05:05:51     4.1  STATUS     COMPLETED Testing function: diffVar
2020-10-17 05:05:51     4.1  STATUS     STARTED Testing function: apply.iEVORA
2020-10-17 05:05:51     4.1  STATUS         STARTED iEVORA method
2020-10-17 05:05:52     4.1    INFO             No DVCs detected. All p-values set to 1.
2020-10-17 05:05:52     4.1  STATUS         COMPLETED iEVORA method
2020-10-17 05:05:52     4.1  STATUS         STARTED Testing function: rnb.execute.diffVar
2020-10-17 05:05:52     4.1  STATUS             STARTED Differential Variability
2020-10-17 05:05:52     4.1  STATUS                 STARTED Retrieving comparison info
2020-10-17 05:05:52     4.1  STATUS                 COMPLETED Retrieving comparison info
2020-10-17 05:05:52     4.1  STATUS                 STARTED Imputation procedure knn 
2020-10-17 05:05:52     4.1  STATUS                 COMPLETED Imputation procedure knn 
2020-10-17 05:05:52     4.1  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:52     4.1    INFO                     Conducting differential variability using diffVar
2020-10-17 05:05:52     4.1  STATUS                     STARTED diffVar method
2020-10-17 05:05:52     4.1  STATUS                     COMPLETED diffVar method
2020-10-17 05:05:53     4.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:53     4.1  STATUS                         Computed table for tiling
2020-10-17 05:05:53     4.1  STATUS                         Computed table for genes
2020-10-17 05:05:53     4.1  STATUS                         Computed table for promoters
2020-10-17 05:05:53     4.1  STATUS                         Computed table for cpgislands
2020-10-17 05:05:53     4.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:54     4.1  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:54     4.1  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:54     4.1    INFO                     Conducting differential variability using diffVar
2020-10-17 05:05:54     4.1  STATUS                     STARTED diffVar method
2020-10-17 05:05:54     4.1  STATUS                     COMPLETED diffVar method
2020-10-17 05:05:54     4.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:55     4.1  STATUS                         Computed table for tiling
2020-10-17 05:05:55     4.1  STATUS                         Computed table for genes
2020-10-17 05:05:55     4.1  STATUS                         Computed table for promoters
2020-10-17 05:05:55     4.1  STATUS                         Computed table for cpgislands
2020-10-17 05:05:55     4.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2020-10-17 05:05:55     4.1  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:55     4.1  STATUS             COMPLETED Differential Variability
2020-10-17 05:05:55     4.1  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2020-10-17 05:05:55     4.1  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2020-10-17 05:05:55     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:05:55     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:05:55     4.1  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:05:55     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:55     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:55     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:55     4.1  STATUS                         STARTED Imputation procedure knn 
2020-10-17 05:05:55     4.1  STATUS                         COMPLETED Imputation procedure knn 
2020-10-17 05:05:55     4.1    INFO                         Conducting differential variability using diffVar
2020-10-17 05:05:55     4.1  STATUS                         STARTED diffVar method
2020-10-17 05:05:55     4.1  STATUS                         COMPLETED diffVar method
2020-10-17 05:05:55     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:55     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:56     4.1  STATUS                         Computed table for tiling
2020-10-17 05:05:56     4.1  STATUS                         Computed table for genes
2020-10-17 05:05:57     4.1  STATUS                         Computed table for promoters
2020-10-17 05:05:57     4.1  STATUS                         Computed table for cpgislands
2020-10-17 05:05:57     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:57     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:05:57     4.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:05:57     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:05:57     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:05:57     4.1  STATUS                         STARTED Imputation procedure knn 
2020-10-17 05:05:57     4.1  STATUS                         COMPLETED Imputation procedure knn 
2020-10-17 05:05:57     4.1    INFO                         Conducting differential variability using diffVar
2020-10-17 05:05:57     4.1  STATUS                         STARTED diffVar method
2020-10-17 05:05:58     4.1  STATUS                         COMPLETED diffVar method
2020-10-17 05:05:58     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:05:58     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:05:59     4.1  STATUS                         Computed table for tiling
2020-10-17 05:06:00     4.1  STATUS                         Computed table for genes
2020-10-17 05:06:00     4.1  STATUS                         Computed table for promoters
2020-10-17 05:06:01     4.1  STATUS                         Computed table for cpgislands
2020-10-17 05:06:01     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:01     4.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:01     4.1  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:06:01     4.1  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2020-10-17 05:06:01     4.1  STATUS         STARTED Testing class: RnBDiffMeth
2020-10-17 05:06:01     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:06:01     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:06:01     4.1  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:06:01     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:01     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:01     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:01     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:01     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:02     4.1  STATUS                         Computed table for tiling
2020-10-17 05:06:02     4.1  STATUS                         Computed table for genes
2020-10-17 05:06:04     4.1  STATUS                         Computed table for promoters
2020-10-17 05:06:04     4.1  STATUS                         Computed table for cpgislands
2020-10-17 05:06:04     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:04     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:04     4.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:04     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:04     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:04     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:04     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:05     4.1  STATUS                         Computed table for tiling
2020-10-17 05:06:05     4.1  STATUS                         Computed table for genes
2020-10-17 05:06:05     4.1  STATUS                         Computed table for promoters
2020-10-17 05:06:06     4.1  STATUS                         Computed table for cpgislands
2020-10-17 05:06:06     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:06     4.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:06     4.1  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:06:06     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:06:06     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:06:06     4.1  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:06:06     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:06     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:06     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:06     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:06     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:06     4.1  STATUS                         Computed table for genes
2020-10-17 05:06:07     4.1  STATUS                         Computed table for tiling
2020-10-17 05:06:07     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:07     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:07     4.1  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:06:07     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:06:07     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:06:07     4.1  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:06:07     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:07     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:07     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:07     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:07     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:07     4.1  STATUS                         Computed table for genes
2020-10-17 05:06:08     4.1  STATUS                         Computed table for tiling
2020-10-17 05:06:08     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:08     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:08     4.1  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:06:08     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:06:08     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:06:08     4.1  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:06:08     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:08     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:08     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:08     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:08     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:09     4.1  STATUS                         Computed table for promoters
2020-10-17 05:06:09     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:09     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:09     4.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:09     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:09     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:09     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:09     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:09     4.1  STATUS                         Computed table for promoters
2020-10-17 05:06:09     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:09     4.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:09     4.1  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:06:09     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:06:09     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:06:09     4.1  STATUS             STARTED Computing differential methylation tables
2020-10-17 05:06:09     4.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:09     4.1  STATUS                     STARTED Computing Differential Methylation Table
2020-10-17 05:06:09     4.1    INFO                         Conducting differential analysis using limma
2020-10-17 05:06:09     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:09     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:09     4.1  STATUS                         Computed table for genes
2020-10-17 05:06:10     4.1  STATUS                         Computed table for tiling
2020-10-17 05:06:10     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:10     4.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Computing differential methylation tables
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing function: get.region.types
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing function: get.region.types
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing function: get.comparisons
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing function: get.comparisons
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing function: get.comparison.grouplabels
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing function: get.site.test.method
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing function: get.site.test.method
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing function: get.table
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing function: get.table
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing function: addDiffMethTable
2020-10-17 05:06:10     4.1    INFO                 Conducting differential analysis using limma
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing function: addDiffMethTable
2020-10-17 05:06:10     4.1  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2020-10-17 05:06:10     4.1  STATUS             STARTED Destructor
2020-10-17 05:06:10     4.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2020-10-17 05:06:10     4.1  STATUS             COMPLETED Destructor
2020-10-17 05:06:10     4.1  STATUS         COMPLETED Testing class: RnBDiffMeth
2020-10-17 05:06:10     4.1  STATUS     COMPLETED Testing function: apply.iEVORA
2020-10-17 05:06:10     4.1  STATUS     STARTED iEVORA method
2020-10-17 05:06:11     4.1    INFO         No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2020-10-17 05:06:11     4.1  STATUS         STARTED Retrieving comparison info
2020-10-17 05:06:11     4.1  STATUS         COMPLETED Retrieving comparison info
2020-10-17 05:06:11     4.1  STATUS         STARTED Computing differential methylation tables
2020-10-17 05:06:11     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:11     4.1  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:06:11     4.1    INFO                     Conducting differential analysis using limma
2020-10-17 05:06:11     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:11     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:13     4.1  STATUS                     Computed table for tiling
2020-10-17 05:06:13     4.1  STATUS                     Computed table for genes
2020-10-17 05:06:13     4.1  STATUS                     Computed table for promoters
2020-10-17 05:06:13     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:06:14     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:14     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:14     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:14     4.1  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:06:14     4.1    INFO                     Conducting differential analysis using limma
2020-10-17 05:06:14     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:14     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:14     4.1  STATUS                     Computed table for tiling
2020-10-17 05:06:14     4.1  STATUS                     Computed table for genes
2020-10-17 05:06:14     4.1  STATUS                     Computed table for promoters
2020-10-17 05:06:15     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:06:15     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:15     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:15     4.1  STATUS         COMPLETED Computing differential methylation tables
2020-10-17 05:06:15     4.1  STATUS         STARTED Retrieving comparison info
2020-10-17 05:06:15     4.1  STATUS         COMPLETED Retrieving comparison info
2020-10-17 05:06:15     4.1  STATUS         STARTED Computing differential methylation tables
2020-10-17 05:06:15     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:15     4.1  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:06:15     4.1    INFO                     Conducting differential analysis using limma
2020-10-17 05:06:15     4.1  STATUS                     STARTED Imputation procedure knn 
2020-10-17 05:06:15     4.1  STATUS                     COMPLETED Imputation procedure knn 
2020-10-17 05:06:15     4.1    INFO                     Conducting differential variability using diffVar
2020-10-17 05:06:15     4.1  STATUS                     STARTED diffVar method
2020-10-17 05:06:15     4.1  STATUS                     COMPLETED diffVar method
2020-10-17 05:06:15     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:15     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:16     4.1  STATUS                     Computed table for tiling
2020-10-17 05:06:16     4.1  STATUS                     Computed table for genes
2020-10-17 05:06:17     4.1  STATUS                     Computed table for promoters
2020-10-17 05:06:17     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:06:17     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:17     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:17     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:17     4.1  STATUS                 STARTED Computing Differential Methylation Table
2020-10-17 05:06:17     4.1    INFO                     Conducting differential analysis using limma
2020-10-17 05:06:17     4.1  STATUS                     STARTED Imputation procedure knn 
2020-10-17 05:06:17     4.1  STATUS                     COMPLETED Imputation procedure knn 
2020-10-17 05:06:17     4.1    INFO                     Conducting differential variability using diffVar
2020-10-17 05:06:17     4.1  STATUS                     STARTED diffVar method
2020-10-17 05:06:17     4.1  STATUS                     COMPLETED diffVar method
2020-10-17 05:06:17     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2020-10-17 05:06:17     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:18     4.1  STATUS                     Computed table for tiling
2020-10-17 05:06:19     4.1  STATUS                     Computed table for genes
2020-10-17 05:06:19     4.1  STATUS                     Computed table for promoters
2020-10-17 05:06:21     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:06:21     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2020-10-17 05:06:21     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:21     4.1  STATUS         COMPLETED Computing differential methylation tables
2020-10-17 05:06:21     4.1  STATUS         STARTED Differential Variability
2020-10-17 05:06:21     4.1  STATUS             STARTED Retrieving comparison info
2020-10-17 05:06:21     4.1  STATUS             COMPLETED Retrieving comparison info
2020-10-17 05:06:21     4.1  STATUS             STARTED Imputation procedure knn 
2020-10-17 05:06:21     4.1  STATUS             COMPLETED Imputation procedure knn 
2020-10-17 05:06:21     4.1  STATUS             STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:21     4.1    INFO                 Conducting differential variability using diffVar
2020-10-17 05:06:21     4.1  STATUS                 STARTED diffVar method
2020-10-17 05:06:21     4.1  STATUS                 COMPLETED diffVar method
2020-10-17 05:06:21     4.1  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2020-10-17 05:06:22     4.1  STATUS                     Computed table for tiling
2020-10-17 05:06:22     4.1  STATUS                     Computed table for genes
2020-10-17 05:06:22     4.1  STATUS                     Computed table for promoters
2020-10-17 05:06:23     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:06:23     4.1  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2020-10-17 05:06:23     4.1  STATUS             COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2020-10-17 05:06:23     4.1  STATUS             STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:23     4.1    INFO                 Conducting differential variability using diffVar
2020-10-17 05:06:23     4.1  STATUS                 STARTED diffVar method
2020-10-17 05:06:23     4.1  STATUS                 COMPLETED diffVar method
2020-10-17 05:06:23     4.1  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2020-10-17 05:06:23     4.1  STATUS                     Computed table for tiling
2020-10-17 05:06:23     4.1  STATUS                     Computed table for genes
2020-10-17 05:06:24     4.1  STATUS                     Computed table for promoters
2020-10-17 05:06:24     4.1  STATUS                     Computed table for cpgislands
2020-10-17 05:06:24     4.1  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2020-10-17 05:06:24     4.1  STATUS             COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2020-10-17 05:06:24     4.1  STATUS         COMPLETED Differential Variability
2020-10-17 05:06:24     4.1  STATUS STARTED Analysis
2020-10-17 05:06:24     4.1    INFO     Loaded information from data.RData
2020-10-17 05:06:24     4.1  STATUS     STARTED Processing Detection P-values
2020-10-17 05:06:24     4.1    INFO         Removed 3979 probes that overlap with SNPs
2020-10-17 05:06:24     4.1    INFO         Completed Greedycut on 510 samples
2020-10-17 05:06:24     4.1  STATUS     COMPLETED Processing Detection P-values
2020-10-17 05:06:24     4.1 WARNING     File not found: data2.RData
2020-10-17 05:06:24     4.1  STATUS COMPLETED Analysis

2020-10-17 05:06:24     4.1  STATUS STARTED Testing imputation
2020-10-17 05:06:24     4.1  STATUS     STARTED Imputation procedure knn 
2020-10-17 05:06:25     4.1  STATUS     COMPLETED Imputation procedure knn 
2020-10-17 05:06:25     4.1  STATUS     STARTED Imputation procedure mean.samples 
2020-10-17 05:06:26     4.1  STATUS     COMPLETED Imputation procedure mean.samples 
2020-10-17 05:06:26     4.1  STATUS     STARTED Imputation procedure mean.cpgs 
2020-10-17 05:06:27     4.1  STATUS     COMPLETED Imputation procedure mean.cpgs 
2020-10-17 05:06:27     4.1  STATUS     STARTED Imputation procedure random 
2020-10-17 05:06:27     4.1  STATUS     COMPLETED Imputation procedure random 
2020-10-17 05:06:27     4.1  STATUS COMPLETED Testing imputation

2020-10-17 05:06:27     4.1  STATUS STARTED Testing age prediction
2020-10-17 05:06:27     4.1  STATUS     STARTED Performing Age Prediction
2020-10-17 05:06:31     4.2  STATUS     COMPLETED Performing Age Prediction
2020-10-17 05:06:31     4.2  STATUS COMPLETED Testing age prediction

2020-10-17 05:06:31     4.2  STATUS STARTED Performing Age Prediction
2020-10-17 05:06:32     4.3  STATUS COMPLETED Performing Age Prediction

2020-10-17 05:06:32     4.3  STATUS STARTED Imputation procedure knn 
2020-10-17 05:06:33     4.3  STATUS COMPLETED Imputation procedure knn 

2020-10-17 05:06:33     4.3  STATUS STARTED Imputation procedure mean.samples 
2020-10-17 05:06:34     4.3  STATUS COMPLETED Imputation procedure mean.samples 

2020-10-17 05:06:34     4.3  STATUS STARTED Imputation procedure mean.cpgs 
2020-10-17 05:06:35     4.3  STATUS COMPLETED Imputation procedure mean.cpgs 

2020-10-17 05:06:35     4.3  STATUS STARTED Imputation procedure random 
2020-10-17 05:06:36     4.3  STATUS COMPLETED Imputation procedure random 

2020-10-17 05:06:36     4.3  STATUS STARTED Testing imputation
2020-10-17 05:06:36     4.3  STATUS     STARTED Imputation procedure knn 
2020-10-17 05:06:37     4.3  STATUS     COMPLETED Imputation procedure knn 
2020-10-17 05:06:37     4.3  STATUS     STARTED Imputation procedure mean.samples 
2020-10-17 05:06:38     4.3  STATUS     COMPLETED Imputation procedure mean.samples 
2020-10-17 05:06:38     4.3  STATUS     STARTED Imputation procedure mean.cpgs 
2020-10-17 05:06:38     4.3  STATUS     COMPLETED Imputation procedure mean.cpgs 
2020-10-17 05:06:38     4.3  STATUS     STARTED Imputation procedure random 
2020-10-17 05:06:39     4.3  STATUS     COMPLETED Imputation procedure random 
2020-10-17 05:06:39     4.3  STATUS COMPLETED Testing imputation

2020-10-17 05:06:39     4.3  STATUS STARTED Testing age prediction
2020-10-17 05:06:39     4.3  STATUS     STARTED Performing Age Prediction
2020-10-17 05:06:41     4.3  STATUS     COMPLETED Performing Age Prediction
2020-10-17 05:06:41     4.3  STATUS COMPLETED Testing age prediction



RUNIT TEST PROTOCOL -- Sat Oct 17 05:07:06 2020 
*********************************************** 
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 38 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
191.537  21.475 216.076

Example timings

RnBeads.Rcheck/RnBeads-Ex.timings

nameusersystemelapsed
M-methods000
U-methods000
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods000
addRegionSubsegments000
annotation-methods000
assembly-methods000
combine-methods000
combineTestPvalsMeth000
computeDiffTab.region000
computeDiffTab.site000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport000
createReportPlot000
downloadLolaDbs000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods0.0010.0000.000
get.comparison.info000
get.comparisons-RnBDiffMeth-methods000
get.covariates.sva000
get.covg.thres-RnBDiffMeth-methods0.0000.0000.001
get.files000
get.region.types-RnBDiffMeth-methods000
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getSubCmdTokens-ClusterArchitectureSLURM-methods0.0000.0000.001
getTargetFromLolaDb000
has.covariates.sva000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods000
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods000
limmaP000
loadLolaDbs000
logger.argument000
logger.getfiles000
logger.isinitialized000
logger.validate.file0.0010.0000.000
loggerManagement000
loggerMessages000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot000
mergeSamples-methods000
meth-methods000
mval-methods0.0010.0000.000
nsites-methods0.0000.0000.001
parallel.getNumWorkers000
parallel.isEnabled000
parallel.setup000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth0.0010.0000.000
performLolaEnrichment.diffMeth0.0000.0000.001
performLolaEnrichment.diffVar000
pheno-methods000
qc-methods000
read.sample.annotation000
regionMapping-methods000
regions-methods000
reload-RnBDiffMeth-methods0.0010.0000.000
remove.regions-methods0.0000.0000.001
remove.samples-methods000
remove.sites-methods000
rnb.RnBSet.to.GRangesList000
rnb.RnBSet.to.bed000
rnb.RnBSet.to.bedGraph000
rnb.add.list000
rnb.add.paragraph000
rnb.add.reference000
rnb.add.section000
rnb.annotation.size000
rnb.annotation2data.frame000
rnb.beta2mval0.0010.0000.000
rnb.execute.batcheffects0.0000.0000.001
rnb.execute.clustering000
rnb.execute.computeDiffMeth000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal0.0010.0000.000
rnb.execute.dreduction000
rnb.execute.export.csv000
rnb.execute.greedycut000
rnb.execute.import0.0000.0000.001
rnb.execute.na.removal000
rnb.execute.normalization000
rnb.execute.sex.prediction000
rnb.execute.sex.removal0.0010.0000.000
rnb.execute.snp.removal0.0000.0000.001
rnb.execute.sva000
rnb.execute.tnt000
rnb.execute.variability.removal000
rnb.export.all.annotation000
rnb.export.annotation000
rnb.export.to.ewasher000
rnb.export.to.trackhub000
rnb.get.annotation000
rnb.get.assemblies000
rnb.get.chromosomes000
rnb.get.directory000
rnb.get.mapping0.0010.0000.000
rnb.get.reference0.0000.0000.001
rnb.get.reliability.matrix000
rnb.infinium.control.targets000
rnb.initialize.reports000
rnb.is.option000
rnb.load.annotation.from.db000
rnb.message.plot000
rnb.mval2beta000
rnb.options0.0000.0000.001
rnb.options2xml000
rnb.plot.betadistribution.probeCategories000
rnb.plot.betadistribution.sampleGroups000
rnb.plot.control.barplot0.0010.0000.000
rnb.plot.control.boxplot000
rnb.plot.dreduction000
rnb.plot.locus.profile000
rnb.plot.negative.boxplot000
rnb.plot.region.profile.density000
rnb.plot.region.profiles000
rnb.plot.region.site.density000
rnb.plot.sentrix.distribution0.0010.0000.000
rnb.plot.snp.barplot0.0000.0000.001
rnb.plot.snp.boxplot000
rnb.plot.snp.heatmap000
rnb.region.types000
rnb.region.types.for.analysis000
rnb.remove.annotation000
rnb.run.example000
rnb.runs000
rnb.sample.groups000
rnb.sample.summary.table000
rnb.set.annotation000
rnb.write.table000
rnb.xml2options000
rowOneSampleTP000
rowWelchP000
run-RnBClusterRun-methods000
samples-methods000
save.tables-RnBDiffMeth-methods000
set.covariates.sva000
sites-methods000
summarize.regions-methods000
summarized.regions-methods000