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CHECK report for RnBeads on malbec1

This page was generated on 2021-05-06 12:28:53 -0400 (Thu, 06 May 2021).

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 1560/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 2.8.1  (landing page)
Fabian Mueller
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/RnBeads
Branch: RELEASE_3_12
Last Commit: b87f536
Last Changed Date: 2021-03-01 06:26:56 -0400 (Mon, 01 Mar 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: RnBeads
Version: 2.8.1
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RnBeads_2.8.1.tar.gz
StartedAt: 2021-05-06 05:25:35 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:36:58 -0400 (Thu, 06 May 2021)
EllapsedTime: 683.8 seconds
RetCode: 0
Status:   OK  
CheckDir: RnBeads.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings RnBeads_2.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/RnBeads.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘2.8.1’
* 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’
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.example: no visible global function definition for ‘install’
rnb.run.preprocessing : logger.completed.filtering: no visible global
  function definition for ‘samples’
rnb.sample.summary.table: no visible global function definition for
  ‘samples’
rnb.section.ageprediction: no visible global function definition for
  ‘samples’
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
  function definition for ‘samples’
rnb.section.clustering: no visible global function definition for
  ‘samples’
rnb.section.diffMeth.region: no visible global function definition for
  ‘%dopar%’
rnb.section.diffMeth.region: no visible global function definition for
  ‘foreach’
rnb.section.diffMeth.region: no visible binding for global variable ‘k’
rnb.section.diffMeth.region : do.enrichment.table: no visible global
  function definition for ‘sigCategories’
rnb.section.diffMeth.region : do.enrichment.table.var: no visible
  global function definition for ‘sigCategories’
rnb.section.diffMeth.site: no visible global function definition for
  ‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
  ‘foreach’
rnb.section.diffVar: no visible global function definition for
  ‘%dopar%’
rnb.section.diffVar: no visible global function definition for
  ‘foreach’
rnb.section.diffVar.region: no visible global function definition for
  ‘%dopar%’
rnb.section.diffVar.region: no visible global function definition for
  ‘foreach’
rnb.section.diffVar.region: no visible binding for global variable ‘k’
rnb.section.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
  ‘phenoData’
rnb.section.imputation: no visible global function definition for
  ‘melt’
rnb.section.locus.profiles: no visible global function definition for
  ‘samples’
rnb.section.locus.profiles : do.plots: no visible global function
  definition for ‘plotTracks’
rnb.section.locus.profiles: no visible global function definition for
  ‘%dopar%’
rnb.section.locus.profiles: no visible global function definition for
  ‘foreach’
rnb.section.na.removal: no visible global function definition for
  ‘samples’
rnb.section.normalization: no visible global function definition for
  ‘samples’
rnb.section.region.description: no visible binding for global variable
  ‘size’
rnb.section.region.description: no visible binding for global variable
  ‘n.sites’
rnb.section.region.profiles: no visible global function definition for
  ‘samples’
rnb.section.region.subsegmentation : get.summary.df.from.list: no
  visible global function definition for ‘melt’
rnb.section.region.subsegmentation: no visible binding for global
  variable ‘region.size’
rnb.section.region.subsegmentation: no visible binding for global
  variable ‘is.subsegmentation’
rnb.section.region.subsegmentation: no visible binding for global
  variable ‘num.sites’
rnb.section.sex.prediction: no visible global function definition for
  ‘muted’
rnb.step.betadistribution.internal: no visible global function
  definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
  definition for ‘foreach’
rnb.step.cell.types: no visible global function definition for
  ‘samples’
rnb.step.clustering.internal: no visible global function definition for
  ‘samples’
rnb.step.dreduction: no visible global function definition for
  ‘%dopar%’
rnb.step.dreduction: no visible global function definition for
  ‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
  for ‘percent_format’
rnb.step.filter.summary.internal: no visible global function definition
  for ‘samples’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.na.removal: no visible binding for global variable
  ‘sites2ignore’
rnb.step.na.removal.internal: no visible global function definition for
  ‘samples’
rnb.step.normalization: no visible global function definition for
  ‘phenoData’
robustHyperGResultSummary: no visible global function definition for
  ‘sigCategories’
robustHyperGResultSummary: no visible global function definition for
  ‘pvalues’
robustHyperGResultSummary: no visible global function definition for
  ‘oddsRatios’
robustHyperGResultSummary: no visible global function definition for
  ‘expectedCounts’
robustHyperGResultSummary: no visible global function definition for
  ‘geneCounts’
robustHyperGResultSummary: no visible global function definition for
  ‘universeCounts’
robustHyperGResultSummary: no visible binding for global variable
  ‘Term’
run.cross.validation: no visible global function definition for
  ‘samples’
run.cross.validation: no visible global function definition for ‘melt’
run.cross.validation: no visible binding for global variable ‘Measure’
run.cross.validation: no visible binding for global variable ‘Error’
sampleCovgApply: no visible global function definition for ‘samples’
set.covariates.ct: no visible global function definition for ‘samples’
simpleGlmnet: no visible global function definition for ‘impute.knn’
simpleGlmnet: no visible global function definition for ‘cv.glmnet’
simpleGlmnet: no visible global function definition for ‘glmnet’
simpleGlmnetBiseq: no visible global function definition for
  ‘cv.glmnet’
simpleGlmnetBiseq: no visible global function definition for ‘glmnet’
simpleGlmnetEvaluate: no visible global function definition for
  ‘cv.glmnet’
simpleGlmnetEvaluate: no visible global function definition for
  ‘glmnet’
symmetric.melt: no visible global function definition for ‘melt’
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
  ‘reg.type’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘getManifest’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘getGreen’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘getRed’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘pData’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for ‘featureData<-’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for ‘featureNames<-’
coerce,RnBeadRawSet-RGChannelSet: no visible global function definition
  for ‘RGChannelSet’
join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function
  definition for ‘clone’
mask.sites.meth,RnBSet: no visible global function definition for
  ‘samples’
remove.samples,RnBSet: no visible global function definition for
  ‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
  ‘samples’
remove.samples,RnBeadSet: no visible global function definition for
  ‘samples’
remove.sites,RnBSet: no visible global function definition for
  ‘samples’
sampleCovgApply,RnBSet: no visible global function definition for
  ‘samples’
sampleMethApply,RnBSet: no visible global function definition for
  ‘samples’
summarize.regions,RnBSet: no visible global function definition for
  ‘samples’
summarize.regions,RnBSet: multiple local function definitions for
  ‘aggr.f’ with different formal arguments
updateMethylationSites,RnBSet: no visible global function definition
  for ‘samples’
Undefined global functions or variables:
  %dopar% ..count.. ..density.. .inds.g2 Address Age Annotated AvgMeth
  BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
  Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack
  Group Hsapiens ID 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 combinedRank combinedRank.var comma covgMedian covgPercLow
  covgPercUp cv.glmnet daglad diffmeth diffmeth.p.adj.fdr
  diffmeth.p.val dinucleotideFrequency eps expectedCounts featureData
  featureData<- featureNames featureNames<- foreach geneCounts genome<-
  getCN getDoParWorkers getGreen getManifest getMeth getRed getSex
  getTable getUnmeth getVarCov glmnet grid.draw grid.newpage group
  group1 group2 i impute.knn install is.subsegmentation k
  letterFrequency lme loadRegionDB log10FDR log10P mapToGenome mclapply
  mean.diff mean.quot.log2 melt mergeRegionDBs muted n.sites num.sites
  numSites numeric.names oddsRatios p.vals.t.na.adj pData
  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-3.12-bioc/meat/RnBeads.Rcheck/00check.log’
for details.

Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL RnBeads
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

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

> BiocGenerics:::testPackage("RnBeads")

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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


Attaching package: 'S4Vectors'

The following 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/Rtmp4Ljhm4/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 2.6-0 (2020-12-14) 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: 'MatrixGenerics'

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

    rowMedians

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'Biostrings'

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

    mismatch, pattern

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

    strsplit

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

Attaching package: 'plyr'

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

    compact

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

    count

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

    desc

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

    rename

2021-05-06 05:33:26     1.4  STATUS STARTED Unit testing: differential
2021-05-06 05:33:26     1.4  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2021-05-06 05:33:26     1.4  STATUS     COMPLETED Testing function: rowWelchP
2021-05-06 05:33:26     1.4  STATUS     STARTED Testing function: limmaP
2021-05-06 05:33:26     1.4  STATUS     COMPLETED Testing function: limmaP
2021-05-06 05:33:26     1.4  STATUS     STARTED Testing function: computeDiffTab.extended.site
2021-05-06 05:33:26     1.4    INFO         Conducting differential analysis using limma
2021-05-06 05:33:26     1.4  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2021-05-06 05:33:26     1.4  STATUS     STARTED Testing function: computeDiffTab.default.region
2021-05-06 05:33:26     1.4    INFO         Conducting differential analysis using limma
2021-05-06 05:33:34     1.6  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2021-05-06 05:33:34     1.6  STATUS     STARTED Testing function: combineTestPvalsMeth
2021-05-06 05:33:34     1.6  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2021-05-06 05:33:34     1.6  STATUS     STARTED Testing function: get.adjustment.variables
2021-05-06 05:33:34     1.6  STATUS     COMPLETED Testing function: get.adjustment.variables
2021-05-06 05:33:34     1.6  STATUS     STARTED Testing function: get.comparison.info
2021-05-06 05:33:34     1.6  STATUS     COMPLETED Testing function: get.comparison.info
2021-05-06 05:33:34     1.6  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2021-05-06 05:33:34     1.6  STATUS         STARTED Retrieving comparison info
2021-05-06 05:33:34     1.6  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:33:34     1.6  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:33:34     1.6  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:33:34     1.6  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:33:34     1.6    INFO                     Conducting differential analysis using limma
2021-05-06 05:33:34     1.6  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:33:34     1.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:33:35     1.6  STATUS                     Computed table for tiling
2021-05-06 05:33:36     1.6  STATUS                     Computed table for genes
2021-05-06 05:33:36     1.7  STATUS                     Computed table for promoters
2021-05-06 05:33:36     1.7  STATUS                     Computed table for cpgislands
2021-05-06 05:33:36     1.7  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:33:36     1.8  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:33:36     1.8  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:33:36     1.8  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:33:36     1.8    INFO                     Conducting differential analysis using limma
2021-05-06 05:33:36     1.8  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:33:36     1.8  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:33:38     1.8  STATUS                     Computed table for tiling
2021-05-06 05:33:38     1.8  STATUS                     Computed table for genes
2021-05-06 05:33:38     1.8  STATUS                     Computed table for promoters
2021-05-06 05:33:39     1.8  STATUS                     Computed table for cpgislands
2021-05-06 05:33:39     1.8  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:33:39     1.8  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:33:39     1.8  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:33:39     1.8  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-05-06 05:33:39     1.8  STATUS     STARTED Testing function: diffVar
2021-05-06 05:33:39     1.8  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:34:53     4.4  STATUS         COMPLETED diffVar method
2021-05-06 05:34:53     4.4  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:34:53     4.4 WARNING             Could not compute p-values with diffVar, returning NA
2021-05-06 05:34:53     4.4    INFO             diffVar from missMethyl package not properly running
2021-05-06 05:34:53     4.4  STATUS         COMPLETED diffVar method
2021-05-06 05:34:53     4.4  STATUS         STARTED Testing function: apply.iEVORA
2021-05-06 05:34:53     4.4  STATUS             STARTED iEVORA method
2021-05-06 05:34:54     4.4    INFO                 No DVCs detected. All p-values set to 1.
2021-05-06 05:34:54     4.4  STATUS             COMPLETED iEVORA method
2021-05-06 05:34:54     4.4  STATUS             STARTED Testing function: rnb.execute.diffVar
2021-05-06 05:34:54     4.4  STATUS                 STARTED Differential Variability
2021-05-06 05:34:54     4.4  STATUS                     STARTED Retrieving comparison info
2021-05-06 05:34:54     4.4  STATUS                     COMPLETED Retrieving comparison info
2021-05-06 05:34:54     4.4    INFO                     No imputation method selected, 'knn' method used.
2021-05-06 05:34:54     4.4  STATUS                     STARTED Imputation procedure knn 
2021-05-06 05:34:54     4.4  STATUS                     COMPLETED Imputation procedure knn 
2021-05-06 05:34:54     4.4  STATUS                     STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:34:54     4.4    INFO                         Conducting differential variability using diffVar
2021-05-06 05:34:54     4.4  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:34:54     4.4  STATUS                         COMPLETED diffVar method
2021-05-06 05:34:54     4.5  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 05:34:56     4.3  STATUS                             Computed table for tiling
2021-05-06 05:34:57     4.3  STATUS                             Computed table for genes
2021-05-06 05:34:57     4.3  STATUS                             Computed table for promoters
2021-05-06 05:34:57     4.3  STATUS                             Computed table for cpgislands
2021-05-06 05:34:57     4.3  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 05:34:57     4.3  STATUS                     COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:34:57     4.3  STATUS                     STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2021-05-06 05:34:57     4.3    INFO                         Conducting differential variability using diffVar
2021-05-06 05:34:57     4.3  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:34:57     4.3  STATUS                         COMPLETED diffVar method
2021-05-06 05:34:57     4.3  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 05:34:58     4.3  STATUS                             Computed table for tiling
2021-05-06 05:35:01     4.2  STATUS                             Computed table for genes
2021-05-06 05:35:01     4.2  STATUS                             Computed table for promoters
2021-05-06 05:35:01     4.2  STATUS                             Computed table for cpgislands
2021-05-06 05:35:01     4.2  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 05:35:01     4.2  STATUS                     COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:01     4.2  STATUS                 COMPLETED Differential Variability
2021-05-06 05:35:01     4.2  STATUS             COMPLETED Testing function: rnb.execute.diffVar
2021-05-06 05:35:01     4.2  STATUS             STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 05:35:01     4.2  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:01     4.2  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:01     4.2  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:01     4.2  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:01     4.2  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:01     4.2    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:01     4.2  STATUS                             STARTED Imputation procedure knn 
2021-05-06 05:35:01     4.2  STATUS                             COMPLETED Imputation procedure knn 
2021-05-06 05:35:01     4.2    INFO                             Conducting differential variability using diffVar
2021-05-06 05:35:01     4.2  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:01     4.2  STATUS                             COMPLETED diffVar method
2021-05-06 05:35:01     4.2  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:01     4.2  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:02     4.2  STATUS                             Computed table for tiling
2021-05-06 05:35:08     3.6  STATUS                             Computed table for genes
2021-05-06 05:35:08     3.6  STATUS                             Computed table for promoters
2021-05-06 05:35:08     3.6  STATUS                             Computed table for cpgislands
2021-05-06 05:35:08     3.6  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:08     3.6  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:08     3.6  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:08     3.6  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:08     3.6    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:08     3.6  STATUS                             STARTED Imputation procedure knn 
2021-05-06 05:35:08     3.6  STATUS                             COMPLETED Imputation procedure knn 
2021-05-06 05:35:08     3.6    INFO                             Conducting differential variability using diffVar
2021-05-06 05:35:08     3.6  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:08     3.6  STATUS                             COMPLETED diffVar method
2021-05-06 05:35:08     3.6  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:08     3.6  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:09     3.8  STATUS                             Computed table for tiling
2021-05-06 05:35:09     3.9  STATUS                             Computed table for genes
2021-05-06 05:35:10     4.0  STATUS                             Computed table for promoters
2021-05-06 05:35:11     4.0  STATUS                             Computed table for cpgislands
2021-05-06 05:35:11     4.0  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:11     4.0  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:11     4.0  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:11     4.0  STATUS             COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 05:35:11     4.0  STATUS             STARTED Testing class: RnBDiffMeth
2021-05-06 05:35:11     4.0  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:11     4.0  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:11     4.0  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:11     4.0  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:11     4.0  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:11     4.0    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:11     4.0  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:11     4.0  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:12     4.0  STATUS                             Computed table for tiling
2021-05-06 05:35:12     4.0  STATUS                             Computed table for genes
2021-05-06 05:35:12     4.0  STATUS                             Computed table for promoters
2021-05-06 05:35:13     4.0  STATUS                             Computed table for cpgislands
2021-05-06 05:35:13     4.0  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:13     4.0  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:13     4.0  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:13     4.0  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:13     4.0    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:13     4.0  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:13     4.0  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:14     4.0  STATUS                             Computed table for tiling
2021-05-06 05:35:14     4.0  STATUS                             Computed table for genes
2021-05-06 05:35:14     4.0  STATUS                             Computed table for promoters
2021-05-06 05:35:15     4.0  STATUS                             Computed table for cpgislands
2021-05-06 05:35:15     4.0  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:15     4.0  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:15     4.0  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:15     4.0  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:15     4.0  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:15     4.0  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:15     4.0  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:15     4.0  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:15     4.0    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:15     4.0  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:15     4.0  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:15     4.0  STATUS                             Computed table for genes
2021-05-06 05:35:16     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:16     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:16     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:16     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:16     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:16     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:16     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:16     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:16     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:16     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:16     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:16     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:16     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:17     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:17     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:17     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:17     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:17     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:17     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:17     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:17     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:17     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:17     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:17     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:17     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:17     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:17     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:17     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:17     4.1  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:17     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:17     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:17     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:17     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:17     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:17     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:17     4.1  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:17     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:17     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:17     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:17     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:17     4.1  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:17     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:17     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:17     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:17     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:18     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:18     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:18     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:18     4.1  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing function: get.region.types
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Testing function: get.region.types
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing function: get.comparisons
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Testing function: get.comparisons
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing function: get.comparison.grouplabels
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing function: get.site.test.method
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Testing function: get.site.test.method
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing function: get.table
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Testing function: get.table
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing function: addDiffMethTable
2021-05-06 05:35:18     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:18     4.1  STATUS                 COMPLETED Testing function: addDiffMethTable
2021-05-06 05:35:18     4.1  STATUS                 STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 05:35:19     4.1  STATUS                 COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 05:35:19     4.1  STATUS                 STARTED Destructor
2021-05-06 05:35:19     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:19     4.1  STATUS                 COMPLETED Destructor
2021-05-06 05:35:19     4.1  STATUS             COMPLETED Testing class: RnBDiffMeth
2021-05-06 05:35:19     4.1  STATUS         COMPLETED Testing function: apply.iEVORA
2021-05-06 05:35:20     4.1  STATUS         STARTED Retrieving comparison info
2021-05-06 05:35:20     4.1  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:35:20     4.1  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:35:20     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:20     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:20     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:20     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:20     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:20     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:20     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:21     4.1  STATUS                     Computed table for promoters
2021-05-06 05:35:21     4.1  STATUS                     Computed table for cpgislands
2021-05-06 05:35:21     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:21     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:21     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:21     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:21     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:21     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:21     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:22     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:22     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:22     4.1  STATUS                     Computed table for promoters
2021-05-06 05:35:23     4.1  STATUS                     Computed table for cpgislands
2021-05-06 05:35:23     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:23     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:23     4.1  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:35:23     4.1  STATUS         STARTED Retrieving comparison info
2021-05-06 05:35:23     4.1  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:35:23     4.1  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:35:23     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:23     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:23     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:23     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:23     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:23     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:24     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:24     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:24     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:24     4.1  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:35:25     4.1  STATUS         STARTED Retrieving comparison info
2021-05-06 05:35:25     4.1  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:35:25     4.1  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:35:25     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:25     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:25     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:25     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:25     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:25     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:26     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:26     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:26     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:26     4.1  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:35:26     4.1  STATUS         STARTED Retrieving comparison info
2021-05-06 05:35:26     4.1  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:35:26     4.1  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:35:26     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:26     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:26     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:26     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:26     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:26     4.1  STATUS                     Computed table for promoters
2021-05-06 05:35:26     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:26     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:26     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:26     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:26     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:26     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:26     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:27     4.1  STATUS                     Computed table for promoters
2021-05-06 05:35:27     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:27     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:27     4.1  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:35:27     4.1  STATUS         STARTED Retrieving comparison info
2021-05-06 05:35:27     4.1  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:35:27     4.1  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:35:27     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:27     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:27     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:27     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:27     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:27     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:28     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:28     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:28     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing function: get.region.types
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing function: get.region.types
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing function: get.comparisons
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing function: get.comparisons
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing function: get.comparison.grouplabels
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing function: get.site.test.method
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing function: get.site.test.method
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing function: get.table
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing function: get.table
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing function: addDiffMethTable
2021-05-06 05:35:28     4.1    INFO             Conducting differential analysis using limma
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing function: addDiffMethTable
2021-05-06 05:35:28     4.1  STATUS         STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 05:35:28     4.1  STATUS         STARTED Destructor
2021-05-06 05:35:28     4.1  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:28     4.1  STATUS         COMPLETED Destructor
2021-05-06 05:35:28     4.1    INFO         Conducting differential analysis using limma
2021-05-06 05:35:29     4.1    INFO         Conducting differential analysis using limma
2021-05-06 05:35:29     4.1  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:29     4.1  STATUS         COMPLETED diffVar method
2021-05-06 05:35:29     4.1  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:29     4.1 WARNING             Could not compute p-values with diffVar, returning NA
2021-05-06 05:35:29     4.1    INFO             diffVar from missMethyl package not properly running
2021-05-06 05:35:29     4.1  STATUS             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:29     4.1  STATUS             COMPLETED diffVar method
2021-05-06 05:35:29     4.1  STATUS STARTED Unit testing: differential
2021-05-06 05:35:29     4.1  STATUS     STARTED Testing function: rowWelchP
2021-05-06 05:35:29     4.1  STATUS     COMPLETED Testing function: rowWelchP
2021-05-06 05:35:29     4.1  STATUS     STARTED Testing function: limmaP
2021-05-06 05:35:29     4.1  STATUS     COMPLETED Testing function: limmaP
2021-05-06 05:35:29     4.1  STATUS     STARTED Testing function: computeDiffTab.extended.site
2021-05-06 05:35:30     4.1    INFO         Conducting differential analysis using limma
2021-05-06 05:35:30     4.1  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2021-05-06 05:35:30     4.1  STATUS     STARTED Testing function: computeDiffTab.default.region
2021-05-06 05:35:30     4.1    INFO         Conducting differential analysis using limma
2021-05-06 05:35:30     4.1  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2021-05-06 05:35:30     4.1  STATUS     STARTED Testing function: combineTestPvalsMeth
2021-05-06 05:35:30     4.1  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2021-05-06 05:35:30     4.1  STATUS     STARTED Testing function: get.adjustment.variables
2021-05-06 05:35:30     4.1  STATUS     COMPLETED Testing function: get.adjustment.variables
2021-05-06 05:35:30     4.1  STATUS     STARTED Testing function: get.comparison.info
2021-05-06 05:35:30     4.1  STATUS     COMPLETED Testing function: get.comparison.info
2021-05-06 05:35:30     4.1  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2021-05-06 05:35:30     4.1  STATUS         STARTED Retrieving comparison info
2021-05-06 05:35:30     4.1  STATUS         COMPLETED Retrieving comparison info
2021-05-06 05:35:30     4.1  STATUS         STARTED Computing differential methylation tables
2021-05-06 05:35:30     4.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:30     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:30     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:30     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:30     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:30     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:31     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:31     4.1  STATUS                     Computed table for promoters
2021-05-06 05:35:31     4.1  STATUS                     Computed table for cpgislands
2021-05-06 05:35:31     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:31     4.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:31     4.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:31     4.1  STATUS                 STARTED Computing Differential Methylation Table
2021-05-06 05:35:31     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:31     4.1  STATUS                 COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:31     4.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:32     4.1  STATUS                     Computed table for tiling
2021-05-06 05:35:32     4.1  STATUS                     Computed table for genes
2021-05-06 05:35:32     4.1  STATUS                     Computed table for promoters
2021-05-06 05:35:33     4.1  STATUS                     Computed table for cpgislands
2021-05-06 05:35:33     4.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:33     4.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:33     4.1  STATUS         COMPLETED Computing differential methylation tables
2021-05-06 05:35:33     4.1  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-05-06 05:35:33     4.1  STATUS     STARTED Testing function: diffVar
2021-05-06 05:35:33     4.1  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:33     4.1  STATUS         COMPLETED diffVar method
2021-05-06 05:35:33     4.1  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:33     4.1 WARNING             Could not compute p-values with diffVar, returning NA
2021-05-06 05:35:33     4.1    INFO             diffVar from missMethyl package not properly running
2021-05-06 05:35:33     4.1  STATUS         COMPLETED diffVar method
2021-05-06 05:35:33     4.1  STATUS         STARTED Testing function: apply.iEVORA
2021-05-06 05:35:33     4.1  STATUS             STARTED iEVORA method
2021-05-06 05:35:34     4.1    INFO                 No DVCs detected. All p-values set to 1.
2021-05-06 05:35:34     4.1  STATUS             COMPLETED iEVORA method
2021-05-06 05:35:34     4.1  STATUS             STARTED Testing function: rnb.execute.diffVar
2021-05-06 05:35:34     4.1  STATUS                 STARTED Differential Variability
2021-05-06 05:35:34     4.1  STATUS                     STARTED Retrieving comparison info
2021-05-06 05:35:34     4.1  STATUS                     COMPLETED Retrieving comparison info
2021-05-06 05:35:34     4.1  STATUS                     STARTED Imputation procedure knn 
2021-05-06 05:35:34     4.1  STATUS                     COMPLETED Imputation procedure knn 
2021-05-06 05:35:34     4.1  STATUS                     STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:34     4.1    INFO                         Conducting differential variability using diffVar
2021-05-06 05:35:34     4.1  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:34     4.1  STATUS                         COMPLETED diffVar method
2021-05-06 05:35:34     4.1  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 05:35:34     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:35     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:35     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:35     4.1  STATUS                             Computed table for cpgislands
2021-05-06 05:35:35     4.1  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 05:35:35     4.1  STATUS                     COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:35     4.1  STATUS                     STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:35     4.1    INFO                         Conducting differential variability using diffVar
2021-05-06 05:35:35     4.1  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:35     4.1  STATUS                         COMPLETED diffVar method
2021-05-06 05:35:35     4.1  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 05:35:35     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:36     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:36     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:37     4.1  STATUS                             Computed table for cpgislands
2021-05-06 05:35:37     4.1  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 05:35:37     4.1  STATUS                     COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:37     4.1  STATUS                 COMPLETED Differential Variability
2021-05-06 05:35:37     4.1  STATUS             COMPLETED Testing function: rnb.execute.diffVar
2021-05-06 05:35:37     4.1  STATUS             STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 05:35:37     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:37     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:37     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:37     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:37     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:37     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:37     4.1  STATUS                             STARTED Imputation procedure knn 
2021-05-06 05:35:37     4.1  STATUS                             COMPLETED Imputation procedure knn 
2021-05-06 05:35:37     4.1    INFO                             Conducting differential variability using diffVar
2021-05-06 05:35:37     4.1  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:37     4.1  STATUS                             COMPLETED diffVar method
2021-05-06 05:35:37     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:37     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:38     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:39     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:39     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:39     4.1  STATUS                             Computed table for cpgislands
2021-05-06 05:35:39     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:39     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:39     4.1  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:39     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:39     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:39     4.1  STATUS                             STARTED Imputation procedure knn 
2021-05-06 05:35:39     4.1  STATUS                             COMPLETED Imputation procedure knn 
2021-05-06 05:35:39     4.1    INFO                             Conducting differential variability using diffVar
2021-05-06 05:35:39     4.1  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:39     4.1  STATUS                             COMPLETED diffVar method
2021-05-06 05:35:39     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:39     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:40     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:41     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:42     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:42     4.1  STATUS                             Computed table for cpgislands
2021-05-06 05:35:42     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:42     4.1  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:42     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:42     4.1  STATUS             COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-05-06 05:35:42     4.1  STATUS             STARTED Testing class: RnBDiffMeth
2021-05-06 05:35:42     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:42     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:42     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:42     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:42     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:42     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:42     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:42     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:43     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:43     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:43     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:43     4.1  STATUS                             Computed table for cpgislands
2021-05-06 05:35:43     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:43     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:43     4.1  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:43     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:43     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:43     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:43     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:44     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:45     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:46     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:46     4.1  STATUS                             Computed table for cpgislands
2021-05-06 05:35:46     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:46     4.1  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:46     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:46     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:46     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:46     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:46     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:46     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:46     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:46     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:46     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:46     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:46     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:46     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:46     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:46     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:46     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:46     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:46     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:46     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:46     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:46     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:47     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:47     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:47     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:47     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:47     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:47     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:47     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:47     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:47     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:47     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:47     4.1  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:47     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:47     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:47     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:47     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:48     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:48     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:48     4.1  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:48     4.1  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:48     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:48     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:48     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:48     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:48     4.1  STATUS                             Computed table for promoters
2021-05-06 05:35:48     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:48     4.1  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:48     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:48     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:35:48     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:35:48     4.1  STATUS                 STARTED Computing differential methylation tables
2021-05-06 05:35:48     4.1  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:48     4.1  STATUS                         STARTED Computing Differential Methylation Table
2021-05-06 05:35:48     4.1    INFO                             Conducting differential analysis using limma
2021-05-06 05:35:48     4.1  STATUS                         COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:48     4.1  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:49     4.1  STATUS                             Computed table for genes
2021-05-06 05:35:49     4.1  STATUS                             Computed table for tiling
2021-05-06 05:35:49     4.1  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:49     4.1  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:49     4.1  STATUS                 COMPLETED Computing differential methylation tables
2021-05-06 05:35:49     4.1  STATUS                 STARTED Testing function: get.region.types
2021-05-06 05:35:49     4.1  STATUS                 COMPLETED Testing function: get.region.types
2021-05-06 05:35:49     4.1  STATUS                 STARTED Testing function: get.comparisons
2021-05-06 05:35:49     4.1  STATUS                 COMPLETED Testing function: get.comparisons
2021-05-06 05:35:49     4.1  STATUS                 STARTED Testing function: get.comparison.grouplabels
2021-05-06 05:35:49     4.1  STATUS                 COMPLETED Testing function: get.comparison.grouplabels
2021-05-06 05:35:49     4.1  STATUS                 STARTED Testing function: get.site.test.method
2021-05-06 05:35:49     4.1  STATUS                 COMPLETED Testing function: get.site.test.method
2021-05-06 05:35:49     4.1  STATUS                 STARTED Testing function: get.table
2021-05-06 05:35:49     4.1  STATUS                 COMPLETED Testing function: get.table
2021-05-06 05:35:49     4.1  STATUS                 STARTED Testing function: addDiffMethTable
2021-05-06 05:35:49     4.1    INFO                     Conducting differential analysis using limma
2021-05-06 05:35:50     4.1  STATUS                 COMPLETED Testing function: addDiffMethTable
2021-05-06 05:35:50     4.1  STATUS                 STARTED Testing functions: join.diffMeth, is.valid
2021-05-06 05:35:50     4.1  STATUS                 COMPLETED Testing functions: join.diffMeth, is.valid
2021-05-06 05:35:50     4.1  STATUS                 STARTED Destructor
2021-05-06 05:35:50     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-05-06 05:35:50     4.1  STATUS                 COMPLETED Destructor
2021-05-06 05:35:50     4.1  STATUS             COMPLETED Testing class: RnBDiffMeth
2021-05-06 05:35:50     4.1  STATUS         COMPLETED Testing function: apply.iEVORA
2021-05-06 05:35:50     4.1  STATUS         STARTED iEVORA method
2021-05-06 05:35:51     4.1    INFO             No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2021-05-06 05:35:51     4.1  STATUS             STARTED Retrieving comparison info
2021-05-06 05:35:51     4.1  STATUS             COMPLETED Retrieving comparison info
2021-05-06 05:35:51     4.1  STATUS             STARTED Computing differential methylation tables
2021-05-06 05:35:51     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:51     4.1  STATUS                     STARTED Computing Differential Methylation Table
2021-05-06 05:35:51     4.1    INFO                         Conducting differential analysis using limma
2021-05-06 05:35:51     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:51     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:52     4.1  STATUS                         Computed table for tiling
2021-05-06 05:35:52     4.1  STATUS                         Computed table for genes
2021-05-06 05:35:53     4.1  STATUS                         Computed table for promoters
2021-05-06 05:35:53     4.1  STATUS                         Computed table for cpgislands
2021-05-06 05:35:53     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:53     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:53     4.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:53     4.1  STATUS                     STARTED Computing Differential Methylation Table
2021-05-06 05:35:53     4.1    INFO                         Conducting differential analysis using limma
2021-05-06 05:35:53     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:53     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:54     4.1  STATUS                         Computed table for tiling
2021-05-06 05:35:54     4.1  STATUS                         Computed table for genes
2021-05-06 05:35:55     4.1  STATUS                         Computed table for promoters
2021-05-06 05:35:55     4.1  STATUS                         Computed table for cpgislands
2021-05-06 05:35:55     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:55     4.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:55     4.1  STATUS             COMPLETED Computing differential methylation tables
2021-05-06 05:35:55     4.1  STATUS             STARTED Retrieving comparison info
2021-05-06 05:35:55     4.1  STATUS             COMPLETED Retrieving comparison info
2021-05-06 05:35:55     4.1  STATUS             STARTED Computing differential methylation tables
2021-05-06 05:35:55     4.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:55     4.1  STATUS                     STARTED Computing Differential Methylation Table
2021-05-06 05:35:55     4.1    INFO                         Conducting differential analysis using limma
2021-05-06 05:35:55     4.1  STATUS                         STARTED Imputation procedure knn 
2021-05-06 05:35:55     4.1  STATUS                         COMPLETED Imputation procedure knn 
2021-05-06 05:35:55     4.1    INFO                         Conducting differential variability using diffVar
2021-05-06 05:35:55     4.1  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:55     4.1  STATUS                         COMPLETED diffVar method
2021-05-06 05:35:55     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:55     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:56     4.1  STATUS                         Computed table for tiling
2021-05-06 05:35:56     4.1  STATUS                         Computed table for genes
2021-05-06 05:35:57     4.1  STATUS                         Computed table for promoters
2021-05-06 05:35:58     4.1  STATUS                         Computed table for cpgislands
2021-05-06 05:35:58     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:58     4.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:35:58     4.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:35:58     4.1  STATUS                     STARTED Computing Differential Methylation Table
2021-05-06 05:35:58     4.1    INFO                         Conducting differential analysis using limma
2021-05-06 05:35:58     4.1  STATUS                         STARTED Imputation procedure knn 
2021-05-06 05:35:58     4.1  STATUS                         COMPLETED Imputation procedure knn 
2021-05-06 05:35:58     4.1    INFO                         Conducting differential variability using diffVar
2021-05-06 05:35:58     4.1  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:35:58     4.1  STATUS                         COMPLETED diffVar method
2021-05-06 05:35:58     4.1  STATUS                     COMPLETED Computing Differential Methylation Table
2021-05-06 05:35:58     4.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:35:59     4.1  STATUS                         Computed table for tiling
2021-05-06 05:35:59     4.1  STATUS                         Computed table for genes
2021-05-06 05:35:59     4.1  STATUS                         Computed table for promoters
2021-05-06 05:36:00     4.1  STATUS                         Computed table for cpgislands
2021-05-06 05:36:00     4.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2021-05-06 05:36:00     4.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-05-06 05:36:00     4.1  STATUS             COMPLETED Computing differential methylation tables
2021-05-06 05:36:00     4.1  STATUS             STARTED Differential Variability
2021-05-06 05:36:00     4.1  STATUS                 STARTED Retrieving comparison info
2021-05-06 05:36:00     4.1  STATUS                 COMPLETED Retrieving comparison info
2021-05-06 05:36:00     4.1  STATUS                 STARTED Imputation procedure knn 
2021-05-06 05:36:00     4.1  STATUS                 COMPLETED Imputation procedure knn 
2021-05-06 05:36:00     4.1  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:36:00     4.1    INFO                     Conducting differential variability using diffVar
2021-05-06 05:36:00     4.1  STATUS                     STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:36:00     4.1  STATUS                     COMPLETED diffVar method
2021-05-06 05:36:00     4.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 05:36:00     4.1  STATUS                         Computed table for tiling
2021-05-06 05:36:01     4.1  STATUS                         Computed table for genes
2021-05-06 05:36:02     4.1  STATUS                         Computed table for promoters
2021-05-06 05:36:02     4.1  STATUS                         Computed table for cpgislands
2021-05-06 05:36:02     4.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 05:36:02     4.1  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2021-05-06 05:36:02     4.1  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2021-05-06 05:36:02     4.1    INFO                     Conducting differential variability using diffVar
2021-05-06 05:36:02     4.1  STATUS                     STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-05-06 05:36:02     4.1  STATUS                     COMPLETED diffVar method
2021-05-06 05:36:02     4.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2021-05-06 05:36:02     4.1  STATUS                         Computed table for tiling
2021-05-06 05:36:03     4.1  STATUS                         Computed table for genes
2021-05-06 05:36:03     4.1  STATUS                         Computed table for promoters
2021-05-06 05:36:03     4.1  STATUS                         Computed table for cpgislands
2021-05-06 05:36:03     4.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2021-05-06 05:36:03     4.1  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2021-05-06 05:36:03     4.1  STATUS             COMPLETED Differential Variability
2021-05-06 05:36:03     4.1  STATUS STARTED Analysis
2021-05-06 05:36:03     4.1    INFO     Loaded information from data.RData
2021-05-06 05:36:03     4.1  STATUS     STARTED Processing Detection P-values
2021-05-06 05:36:03     4.1    INFO         Removed 3979 probes that overlap with SNPs
2021-05-06 05:36:03     4.1    INFO         Completed Greedycut on 510 samples
2021-05-06 05:36:03     4.1  STATUS     COMPLETED Processing Detection P-values
2021-05-06 05:36:03     4.1 WARNING     File not found: data2.RData
2021-05-06 05:36:03     4.1  STATUS COMPLETED Analysis

2021-05-06 05:36:04     4.1  STATUS STARTED Testing imputation
2021-05-06 05:36:04     4.1  STATUS     STARTED Imputation procedure knn 
2021-05-06 05:36:05     4.1  STATUS     COMPLETED Imputation procedure knn 
2021-05-06 05:36:05     4.1  STATUS     STARTED Imputation procedure mean.samples 
2021-05-06 05:36:05     4.1  STATUS     COMPLETED Imputation procedure mean.samples 
2021-05-06 05:36:05     4.1  STATUS     STARTED Imputation procedure mean.cpgs 
2021-05-06 05:36:07     4.1  STATUS     COMPLETED Imputation procedure mean.cpgs 
2021-05-06 05:36:07     4.1  STATUS     STARTED Imputation procedure random 
2021-05-06 05:36:07     4.1  STATUS     COMPLETED Imputation procedure random 
2021-05-06 05:36:07     4.1  STATUS COMPLETED Testing imputation

2021-05-06 05:36:07     4.1  STATUS STARTED Testing age prediction
2021-05-06 05:36:07     4.1  STATUS     STARTED Performing Age Prediction
2021-05-06 05:36:09     4.3  STATUS     COMPLETED Performing Age Prediction
2021-05-06 05:36:09     4.3  STATUS COMPLETED Testing age prediction

2021-05-06 05:36:09     4.3  STATUS STARTED Performing Age Prediction
2021-05-06 05:36:13     4.4  STATUS COMPLETED Performing Age Prediction

2021-05-06 05:36:13     4.4  STATUS STARTED Imputation procedure knn 
2021-05-06 05:36:14     4.4  STATUS COMPLETED Imputation procedure knn 

2021-05-06 05:36:14     4.4  STATUS STARTED Imputation procedure mean.samples 
2021-05-06 05:36:14     4.4  STATUS COMPLETED Imputation procedure mean.samples 

2021-05-06 05:36:14     4.4  STATUS STARTED Imputation procedure mean.cpgs 
2021-05-06 05:36:15     4.4  STATUS COMPLETED Imputation procedure mean.cpgs 

2021-05-06 05:36:15     4.4  STATUS STARTED Imputation procedure random 
2021-05-06 05:36:15     4.4  STATUS COMPLETED Imputation procedure random 

2021-05-06 05:36:15     4.4  STATUS STARTED Testing imputation
2021-05-06 05:36:16     4.4  STATUS     STARTED Imputation procedure knn 
2021-05-06 05:36:17     4.4  STATUS     COMPLETED Imputation procedure knn 
2021-05-06 05:36:17     4.4  STATUS     STARTED Imputation procedure mean.samples 
2021-05-06 05:36:17     4.4  STATUS     COMPLETED Imputation procedure mean.samples 
2021-05-06 05:36:18     4.4  STATUS     STARTED Imputation procedure mean.cpgs 
2021-05-06 05:36:18     4.4  STATUS     COMPLETED Imputation procedure mean.cpgs 
2021-05-06 05:36:18     4.4  STATUS     STARTED Imputation procedure random 
2021-05-06 05:36:19     4.4  STATUS     COMPLETED Imputation procedure random 
2021-05-06 05:36:19     4.4  STATUS COMPLETED Testing imputation

2021-05-06 05:36:19     4.4  STATUS STARTED Testing age prediction
2021-05-06 05:36:19     4.4  STATUS     STARTED Performing Age Prediction
2021-05-06 05:36:22     4.4  STATUS     COMPLETED Performing Age Prediction
2021-05-06 05:36:22     4.4  STATUS COMPLETED Testing age prediction



RUNIT TEST PROTOCOL -- Thu May  6 05:36:45 2021 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RnBeads RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
There were 25 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
192.696  20.124 220.784

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
downloadLolaDbs0.0000.0040.000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods000
get.comparison.info000
get.comparisons-RnBDiffMeth-methods000
get.covariates.sva000
get.covg.thres-RnBDiffMeth-methods000
get.files000
get.region.types-RnBDiffMeth-methods000
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getSubCmdTokens-ClusterArchitectureSLURM-methods000
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.file000
loggerManagement000
loggerMessages0.0040.0000.000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot000
mergeSamples-methods000
meth-methods000
mval-methods000
nsites-methods000
parallel.getNumWorkers000
parallel.isEnabled000
parallel.setup000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth000
performLolaEnrichment.diffMeth000
performLolaEnrichment.diffVar000
pheno-methods000
qc-methods000
read.sample.annotation000
regionMapping-methods000
regions-methods000
reload-RnBDiffMeth-methods000
remove.regions-methods000
remove.samples-methods000
remove.sites-methods000
rnb.RnBSet.to.GRangesList0.0040.0000.000
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.beta2mval000
rnb.execute.batcheffects0.0000.0000.001
rnb.execute.clustering000
rnb.execute.computeDiffMeth000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal000
rnb.execute.dreduction000
rnb.execute.export.csv000
rnb.execute.greedycut000
rnb.execute.import000
rnb.execute.na.removal000
rnb.execute.normalization000
rnb.execute.sex.prediction000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
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.mapping000
rnb.get.reference000
rnb.get.reliability.matrix000
rnb.infinium.control.targets0.0000.0000.001
rnb.initialize.reports000
rnb.is.option000
rnb.load.annotation.from.db000
rnb.message.plot000
rnb.mval2beta0.0000.0000.001
rnb.options000
rnb.options2xml000
rnb.plot.betadistribution.probeCategories0.0000.0000.001
rnb.plot.betadistribution.sampleGroups000
rnb.plot.control.barplot000
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.distribution000
rnb.plot.snp.barplot000
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-methods0.0000.0040.000
samples-methods000
save.tables-RnBDiffMeth-methods000
set.covariates.sva000
sites-methods000
summarize.regions-methods000
summarized.regions-methods000