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CHECK report for RnBeads on merida2

This page was generated on 2018-10-17 08:54:47 -0400 (Wed, 17 Oct 2018).

Package 1263/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 1.12.1
Fabian Mueller
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/RnBeads
Branch: RELEASE_3_7
Last Commit: f662e69
Last Changed Date: 2018-05-07 19:50:22 -0400 (Mon, 07 May 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RnBeads
Version: 1.12.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RnBeads_1.12.1.tar.gz
StartedAt: 2018-10-16 23:46:44 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 23:57:52 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 668.3 seconds
RetCode: 0
Status:  OK 
CheckDir: RnBeads.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RnBeads_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RnBeads.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘1.12.1’
* 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  5.3Mb
  sub-directories of 1Mb or more:
    R   3.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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.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.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’
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 binding for global variable ‘ng.2’
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 : <anonymous>: no visible global function definition for
  ‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
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.add.snp.distances: no visible global function definition for
  ‘grid.newpage’
rnb.add.snp.distances: no visible global function definition for
  ‘grid.draw’
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.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.export.to.ewasher: no visible global function definition for
  ‘samples’
rnb.filter.dataset: 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.sentrix.distributions: no visible global function definition
  for ‘samples’
rnb.plot.sentrix.distributions: no visible binding for global variable
  ‘Slide’
rnb.plot.snp.boxplot: no visible binding for global variable ‘SNP’
rnb.plot.snp.boxplot: no visible binding for global variable ‘bv’
rnb.run.preprocessing : logger.completed.filtering: no visible global
  function definition for ‘samples’
rnb.sample.summary.table: no visible global function definition for
  ‘samples’
rnb.section.ageprediction: no visible global function definition for
  ‘samples’
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
  function definition for ‘samples’
rnb.section.clustering: no visible global function definition for
  ‘samples’
rnb.section.diffMeth.region: no visible global function definition for
  ‘%dopar%’
rnb.section.diffMeth.region: no visible global function definition for
  ‘foreach’
rnb.section.diffMeth.region: no visible binding for global variable ‘k’
rnb.section.diffMeth.region : do.enrichment.table: no visible global
  function definition for ‘sigCategories’
rnb.section.diffMeth.region : do.enrichment.table.var: no visible
  global function definition for ‘sigCategories’
rnb.section.diffMeth.site: no visible global function definition for
  ‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
  ‘foreach’
rnb.section.diffVar: no visible global function definition for
  ‘%dopar%’
rnb.section.diffVar: no visible global function definition for
  ‘foreach’
rnb.section.diffVar.region: no visible global function definition for
  ‘%dopar%’
rnb.section.diffVar.region: no visible global function definition for
  ‘foreach’
rnb.section.diffVar.region: no visible binding for global variable ‘k’
rnb.section.gender.prediction: no visible global function definition
  for ‘muted’
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.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.cnv: no visible binding for global variable ‘intensities’
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<-’
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
  BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
  Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack ID
  IdeogramTrack IlluminaHumanMethylation450kmanifest
  IlluminaHumanMethylationEPICmanifest Index Intensity Measure
  PairsBootRefFreeEwasModel Probe RGChannelSet Rd2HTML RefFreeEwasModel
  SNP Sample Slide Target Term UcscTrack Value addSex as.profileCGH
  assayDataElement assayDataElementNames barcode bv chrom 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 getUnmeth
  getVarCov glmnet grid.draw grid.newpage group group1 group2 i
  impute.knn intensities is.subsegmentation k letterFrequency lme
  loadRegionDB log10FDR log10P mapToGenome mean.diff mean.quot.log2
  melt mergeRegionDBs muted n.sites ng.2 num.sites numSites
  numeric.names oddsRatios p.vals.t.na.adj pData percent_format
  phenoData phenoData<- plotTracks preprocessSWAN pvalues qvalue
  refText reg.type region.size registerDoParallel relative.coord report
  runLOLA samples seqlengths seqlevels<- sigCategories sites2ignore
  size solve.QP stopCluster sva target tsne type types universeCounts
  useMart v var.diff varFit varLabels x xmlValue y 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 sizes of PDF files under ‘inst/doc’ ... 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/RnBeads.Rcheck/00check.log’
for details.

Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RnBeads
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘RnBeads’ ...
** 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
* DONE (RnBeads)

Tests output

RnBeads.Rcheck/tests/runTests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

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

    xor

Attaching package ff
- getOption("fftempdir")=="/tmp/RtmpwezBUC"

- 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:bit':

    clone, clone.default, clone.list

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 2.2-0 (2018-06-19) 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


Attaching package: 'maps'

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

    votes.repub

See www.image.ucar.edu/˜nychka/Fields for
 a vignette and other supplements. 

Attaching package: 'gplots'

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

    space

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

    space

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

    lowess


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'limma'

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

    plotMA

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    anyMissing, rowMedians


Attaching package: 'AnnotationDbi'

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

    select



Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply


Attaching package: 'Biostrings'

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

    type

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

    mismatch, pattern

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

    strsplit

locfit 1.5-9.1 	 2013-03-22
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:maps':

    ozone

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

    desc

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

    rename

2018-10-16 23:53:27     0.7  STATUS STARTED Unit testing: differential
2018-10-16 23:53:27     0.7  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2018-10-16 23:53:28     0.7  STATUS     COMPLETED Testing function: rowWelchP
2018-10-16 23:53:28     0.7  STATUS     STARTED Testing function: limmaP
2018-10-16 23:53:28     0.7  STATUS     COMPLETED Testing function: limmaP
2018-10-16 23:53:28     0.7  STATUS     STARTED Testing function: computeDiffTab.extended.site
2018-10-16 23:53:28     0.7    INFO         Conducting differential analysis using limma
2018-10-16 23:53:29     0.7  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2018-10-16 23:53:29     0.7  STATUS     STARTED Testing function: computeDiffTab.default.region
2018-10-16 23:53:29     0.7    INFO         Conducting differential analysis using limma
2018-10-16 23:53:33     0.8  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2018-10-16 23:53:33     0.8  STATUS     STARTED Testing function: combineTestPvalsMeth
2018-10-16 23:53:34     0.8  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2018-10-16 23:53:34     0.8  STATUS     STARTED Testing function: get.adjustment.variables
2018-10-16 23:53:34     0.8  STATUS     COMPLETED Testing function: get.adjustment.variables
2018-10-16 23:53:34     0.8  STATUS     STARTED Testing function: get.comparison.info
2018-10-16 23:53:35     0.8  STATUS     COMPLETED Testing function: get.comparison.info
2018-10-16 23:53:35     0.8  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2018-10-16 23:53:35     0.8  STATUS         STARTED Retrieving comparison info
2018-10-16 23:53:35     0.8  STATUS         COMPLETED Retrieving comparison info
2018-10-16 23:53:35     0.8  STATUS         STARTED Computing differential methylation tables
2018-10-16 23:53:36     0.8  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:53:36     0.8  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:53:36     0.8    INFO                     Conducting differential analysis using limma
2018-10-16 23:53:36     0.8  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:53:36     0.8  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:53:37     1.0  STATUS                     Computed table for tiling
2018-10-16 23:53:38     1.1  STATUS                     Computed table for genes
2018-10-16 23:53:38     1.1  STATUS                     Computed table for promoters
2018-10-16 23:53:39     1.1  STATUS                     Computed table for cpgislands
2018-10-16 23:53:39     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:53:39     1.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:53:39     1.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:53:40     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:53:40     1.1    INFO                     Conducting differential analysis using limma
2018-10-16 23:53:40     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:53:40     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:53:41     1.1  STATUS                     Computed table for tiling
2018-10-16 23:53:41     1.2  STATUS                     Computed table for genes
2018-10-16 23:53:42     1.2  STATUS                     Computed table for promoters
2018-10-16 23:53:42     1.2  STATUS                     Computed table for cpgislands
2018-10-16 23:53:42     1.2  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:53:43     1.2  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:53:43     1.2  STATUS         COMPLETED Computing differential methylation tables
2018-10-16 23:53:43     1.2  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2018-10-16 23:53:43     1.2  STATUS     STARTED Testing function: diffVar
2018-10-16 23:53:43     1.2  STATUS         STARTED diffVar method
2018-10-16 23:53:44     1.2  STATUS         COMPLETED diffVar method
2018-10-16 23:53:44     1.2  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-16 23:53:45     1.1  STATUS         COMPLETED diffVar method
2018-10-16 23:53:45     1.1  STATUS     COMPLETED Testing function: diffVar
2018-10-16 23:53:46     1.1  STATUS     STARTED Testing function: apply.iEVORA
2018-10-16 23:53:46     1.1  STATUS         STARTED iEVORA method
2018-10-16 23:53:47     1.2    INFO             No DVCs detected. All p-values set to 1.
2018-10-16 23:53:48     1.2  STATUS         COMPLETED iEVORA method
2018-10-16 23:53:48     1.2  STATUS         STARTED Testing function: rnb.execute.diffVar
2018-10-16 23:53:48     1.2  STATUS             STARTED Differential Variability
2018-10-16 23:53:48     1.2  STATUS                 STARTED Retrieving comparison info
2018-10-16 23:53:48     1.2  STATUS                 COMPLETED Retrieving comparison info
2018-10-16 23:53:48     1.2    INFO                 No imputation method selected, 'knn' method used.
2018-10-16 23:53:49     1.2  STATUS                 STARTED Imputation procedure knn 
2018-10-16 23:53:49     1.2  STATUS                 COMPLETED Imputation procedure knn 
2018-10-16 23:53:49     1.2  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:53:49     1.2    INFO                     Conducting differential variability using diffVar
2018-10-16 23:53:49     1.2  STATUS                     STARTED diffVar method
2018-10-16 23:53:50     1.2  STATUS                     COMPLETED diffVar method
2018-10-16 23:53:50     1.2  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-16 23:53:51     1.2  STATUS                         Computed table for tiling
2018-10-16 23:53:51     1.2  STATUS                         Computed table for genes
2018-10-16 23:53:52     1.2  STATUS                         Computed table for promoters
2018-10-16 23:53:52     1.2  STATUS                         Computed table for cpgislands
2018-10-16 23:53:52     1.2  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-16 23:53:52     1.2  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:53:52     1.2  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-16 23:53:53     1.2    INFO                     Conducting differential variability using diffVar
2018-10-16 23:53:53     1.2  STATUS                     STARTED diffVar method
2018-10-16 23:53:53     1.2  STATUS                     COMPLETED diffVar method
2018-10-16 23:53:54     1.2  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-16 23:53:54     1.2  STATUS                         Computed table for tiling
2018-10-16 23:53:55     1.2  STATUS                         Computed table for genes
2018-10-16 23:53:55     1.2  STATUS                         Computed table for promoters
2018-10-16 23:53:55     1.2  STATUS                         Computed table for cpgislands
2018-10-16 23:53:56     1.2  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-16 23:53:56     1.2  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-16 23:53:56     1.2  STATUS             COMPLETED Differential Variability
2018-10-16 23:53:56     1.2  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2018-10-16 23:53:56     1.2  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-16 23:53:57     1.2  STATUS             STARTED Retrieving comparison info
2018-10-16 23:53:57     1.2  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:53:57     1.2  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:53:57     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:53:57     1.2  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:53:58     1.2    INFO                         Conducting differential analysis using limma
2018-10-16 23:53:58     1.2  STATUS                         STARTED Imputation procedure knn 
2018-10-16 23:53:58     1.2  STATUS                         COMPLETED Imputation procedure knn 
2018-10-16 23:53:58     1.2    INFO                         Conducting differential variability using diffVar
2018-10-16 23:53:58     1.2  STATUS                         STARTED diffVar method
2018-10-16 23:53:59     1.2  STATUS                         COMPLETED diffVar method
2018-10-16 23:53:59     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:53:59     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:01     1.2  STATUS                         Computed table for tiling
2018-10-16 23:54:01     1.2  STATUS                         Computed table for genes
2018-10-16 23:54:02     1.2  STATUS                         Computed table for promoters
2018-10-16 23:54:03     1.2  STATUS                         Computed table for cpgislands
2018-10-16 23:54:03     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:03     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:03     1.2  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:04     1.2  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:04     1.2    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:04     1.2  STATUS                         STARTED Imputation procedure knn 
2018-10-16 23:54:04     1.2  STATUS                         COMPLETED Imputation procedure knn 
2018-10-16 23:54:04     1.2    INFO                         Conducting differential variability using diffVar
2018-10-16 23:54:05     1.2  STATUS                         STARTED diffVar method
2018-10-16 23:54:05     1.2  STATUS                         COMPLETED diffVar method
2018-10-16 23:54:06     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:06     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:08     1.2  STATUS                         Computed table for tiling
2018-10-16 23:54:08     1.2  STATUS                         Computed table for genes
2018-10-16 23:54:09     1.2  STATUS                         Computed table for promoters
2018-10-16 23:54:10     1.2  STATUS                         Computed table for cpgislands
2018-10-16 23:54:10     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:10     1.2  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:11     1.2  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:54:11     1.2  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-16 23:54:11     1.2  STATUS         STARTED Testing class: RnBDiffMeth
2018-10-16 23:54:11     1.2  STATUS             STARTED Retrieving comparison info
2018-10-16 23:54:11     1.2  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:54:12     1.2  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:54:12     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:12     1.2  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:12     1.2    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:12     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:13     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:14     1.2  STATUS                         Computed table for tiling
2018-10-16 23:54:14     1.2  STATUS                         Computed table for genes
2018-10-16 23:54:15     1.2  STATUS                         Computed table for promoters
2018-10-16 23:54:15     1.2  STATUS                         Computed table for cpgislands
2018-10-16 23:54:15     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:16     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:16     1.2  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:16     1.2  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:16     1.2    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:16     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:17     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:18     1.3  STATUS                         Computed table for tiling
2018-10-16 23:54:18     1.2  STATUS                         Computed table for genes
2018-10-16 23:54:19     1.2  STATUS                         Computed table for promoters
2018-10-16 23:54:19     1.2  STATUS                         Computed table for cpgislands
2018-10-16 23:54:20     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:20     1.2  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:20     1.2  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:54:20     1.2  STATUS             STARTED Retrieving comparison info
2018-10-16 23:54:20     1.2  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:54:21     1.2  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:54:21     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:21     1.2  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:21     1.2    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:21     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:22     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:22     1.3  STATUS                         Computed table for genes
2018-10-16 23:54:23     1.3  STATUS                         Computed table for tiling
2018-10-16 23:54:23     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:23     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:24     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:54:24     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:54:24     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:54:24     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:54:24     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:25     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:25     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:25     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:25     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:26     1.3  STATUS                         Computed table for genes
2018-10-16 23:54:27     1.3  STATUS                         Computed table for tiling
2018-10-16 23:54:27     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:27     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:27     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:54:27     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:54:28     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:54:28     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:54:28     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:28     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:28     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:29     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:29     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:29     1.3  STATUS                         Computed table for promoters
2018-10-16 23:54:30     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:30     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:30     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:30     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:30     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:31     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:31     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:31     1.3  STATUS                         Computed table for promoters
2018-10-16 23:54:32     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:32     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:32     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:54:32     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:54:32     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:54:33     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:54:33     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:33     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:54:33     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:54:33     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:34     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:34     1.3  STATUS                         Computed table for genes
2018-10-16 23:54:35     1.3  STATUS                         Computed table for tiling
2018-10-16 23:54:35     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:35     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:35     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:54:36     1.3  STATUS             STARTED Testing function: get.region.types
2018-10-16 23:54:36     1.3  STATUS             COMPLETED Testing function: get.region.types
2018-10-16 23:54:36     1.3  STATUS             STARTED Testing function: get.comparisons
2018-10-16 23:54:36     1.3  STATUS             COMPLETED Testing function: get.comparisons
2018-10-16 23:54:36     1.3  STATUS             STARTED Testing function: get.comparison.grouplabels
2018-10-16 23:54:37     1.3  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2018-10-16 23:54:37     1.3  STATUS             STARTED Testing function: get.site.test.method
2018-10-16 23:54:37     1.3  STATUS             COMPLETED Testing function: get.site.test.method
2018-10-16 23:54:37     1.3  STATUS             STARTED Testing function: get.table
2018-10-16 23:54:38     1.3  STATUS             COMPLETED Testing function: get.table
2018-10-16 23:54:38     1.3  STATUS             STARTED Testing function: addDiffMethTable
2018-10-16 23:54:38     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:54:38     1.3  STATUS             COMPLETED Testing function: addDiffMethTable
2018-10-16 23:54:39     1.3  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2018-10-16 23:54:39     1.3  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-16 23:54:39     1.3  STATUS             STARTED Destructor
2018-10-16 23:54:39     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:40     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:40     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:40     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:40     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:40     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:41     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:41     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:54:41     1.3  STATUS             COMPLETED Destructor
2018-10-16 23:54:41     1.3  STATUS         COMPLETED Testing class: RnBDiffMeth
2018-10-16 23:54:41     1.3  STATUS     COMPLETED Testing function: apply.iEVORA
2018-10-16 23:54:42     1.3  STATUS     STARTED Retrieving comparison info
2018-10-16 23:54:42     1.3  STATUS     COMPLETED Retrieving comparison info
2018-10-16 23:54:42     1.3  STATUS     STARTED Computing differential methylation tables
2018-10-16 23:54:42     1.3  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:43     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:54:43     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:54:43     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:43     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:44     1.3  STATUS                 Computed table for tiling
2018-10-16 23:54:45     1.3  STATUS                 Computed table for genes
2018-10-16 23:54:46     1.3  STATUS                 Computed table for promoters
2018-10-16 23:54:46     1.3  STATUS                 Computed table for cpgislands
2018-10-16 23:54:46     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:46     1.3  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:47     1.3  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:47     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:54:47     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:54:47     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:47     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:48     1.3  STATUS                 Computed table for tiling
2018-10-16 23:54:49     1.3  STATUS                 Computed table for genes
2018-10-16 23:54:49     1.3  STATUS                 Computed table for promoters
2018-10-16 23:54:50     1.3  STATUS                 Computed table for cpgislands
2018-10-16 23:54:50     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:50     1.3  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:54:50     1.3  STATUS     COMPLETED Computing differential methylation tables
2018-10-16 23:54:51     1.3  STATUS     STARTED Retrieving comparison info
2018-10-16 23:54:51     1.3  STATUS     COMPLETED Retrieving comparison info
2018-10-16 23:54:51     1.3  STATUS     STARTED Computing differential methylation tables
2018-10-16 23:54:51     1.3  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:51     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:54:52     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:54:52     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:52     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:53     1.3  STATUS                 Computed table for genes
2018-10-16 23:54:54     1.3  STATUS                 Computed table for tiling
2018-10-16 23:54:54     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:54     1.3  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:54     1.3  STATUS     COMPLETED Computing differential methylation tables
2018-10-16 23:54:54     1.3  STATUS     STARTED Retrieving comparison info
2018-10-16 23:54:54     1.3  STATUS     COMPLETED Retrieving comparison info
2018-10-16 23:54:55     1.3  STATUS     STARTED Computing differential methylation tables
2018-10-16 23:54:55     1.3  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:55     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:54:55     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:54:55     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:56     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:56     1.3  STATUS                 Computed table for genes
2018-10-16 23:54:57     1.3  STATUS                 Computed table for tiling
2018-10-16 23:54:57     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:57     1.3  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:58     1.3  STATUS     COMPLETED Computing differential methylation tables
2018-10-16 23:54:58     1.3  STATUS     STARTED Retrieving comparison info
2018-10-16 23:54:58     1.3  STATUS     COMPLETED Retrieving comparison info
2018-10-16 23:54:58     1.3  STATUS     STARTED Computing differential methylation tables
2018-10-16 23:54:58     1.3  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:54:58     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:54:59     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:54:59     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:54:59     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:54:59     1.3  STATUS                 Computed table for promoters
2018-10-16 23:55:00     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:00     1.3  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:00     1.3  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:00     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:55:00     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:55:00     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:01     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:01     1.3  STATUS                 Computed table for promoters
2018-10-16 23:55:01     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:01     1.3  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:02     1.3  STATUS     COMPLETED Computing differential methylation tables
2018-10-16 23:55:02     1.3  STATUS     STARTED Retrieving comparison info
2018-10-16 23:55:02     1.3  STATUS     COMPLETED Retrieving comparison info
2018-10-16 23:55:02     1.3  STATUS     STARTED Computing differential methylation tables
2018-10-16 23:55:02     1.3  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:03     1.3  STATUS             STARTED Computing Differential Methylation Table
2018-10-16 23:55:03     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:55:03     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:03     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:04     1.3  STATUS                 Computed table for genes
2018-10-16 23:55:05     1.3  STATUS                 Computed table for tiling
2018-10-16 23:55:05     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:05     1.3  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:05     1.3  STATUS     COMPLETED Computing differential methylation tables
2018-10-16 23:55:05     1.3  STATUS     STARTED Testing function: get.region.types
2018-10-16 23:55:06     1.3  STATUS     COMPLETED Testing function: get.region.types
2018-10-16 23:55:06     1.3  STATUS     STARTED Testing function: get.comparisons
2018-10-16 23:55:06     1.3  STATUS     COMPLETED Testing function: get.comparisons
2018-10-16 23:55:06     1.3  STATUS     STARTED Testing function: get.comparison.grouplabels
2018-10-16 23:55:06     1.3  STATUS     COMPLETED Testing function: get.comparison.grouplabels
2018-10-16 23:55:07     1.3  STATUS     STARTED Testing function: get.site.test.method
2018-10-16 23:55:07     1.3  STATUS     COMPLETED Testing function: get.site.test.method
2018-10-16 23:55:07     1.3  STATUS     STARTED Testing function: get.table
2018-10-16 23:55:07     1.3  STATUS     COMPLETED Testing function: get.table
2018-10-16 23:55:07     1.3  STATUS     STARTED Testing function: addDiffMethTable
2018-10-16 23:55:08     1.3    INFO         Conducting differential analysis using limma
2018-10-16 23:55:08     1.3  STATUS     COMPLETED Testing function: addDiffMethTable
2018-10-16 23:55:08     1.3  STATUS     STARTED Testing functions: join.diffMeth, is.valid
2018-10-16 23:55:08     1.3  STATUS     COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-16 23:55:09     1.3  STATUS     STARTED Destructor
2018-10-16 23:55:09     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:09     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:09     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:09     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:10     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:10     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:10     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:10     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:55:10     1.3  STATUS     COMPLETED Destructor
2018-10-16 23:55:11     1.3    INFO     Conducting differential analysis using limma
2018-10-16 23:55:11     1.3    INFO     Conducting differential analysis using limma
2018-10-16 23:55:11     1.3  STATUS     STARTED diffVar method
2018-10-16 23:55:11     1.3  STATUS     COMPLETED diffVar method
2018-10-16 23:55:12     1.3  STATUS     STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-16 23:55:12     1.3  STATUS     COMPLETED diffVar method
2018-10-16 23:55:12     1.3  STATUS STARTED Unit testing: differential
2018-10-16 23:55:12     1.3  STATUS     STARTED Testing function: rowWelchP
2018-10-16 23:55:13     1.3  STATUS     COMPLETED Testing function: rowWelchP
2018-10-16 23:55:13     1.3  STATUS     STARTED Testing function: limmaP
2018-10-16 23:55:13     1.3  STATUS     COMPLETED Testing function: limmaP
2018-10-16 23:55:13     1.3  STATUS     STARTED Testing function: computeDiffTab.extended.site
2018-10-16 23:55:13     1.3    INFO         Conducting differential analysis using limma
2018-10-16 23:55:14     1.3  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2018-10-16 23:55:14     1.3  STATUS     STARTED Testing function: computeDiffTab.default.region
2018-10-16 23:55:14     1.3    INFO         Conducting differential analysis using limma
2018-10-16 23:55:15     1.3  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2018-10-16 23:55:15     1.3  STATUS     STARTED Testing function: combineTestPvalsMeth
2018-10-16 23:55:15     1.3  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2018-10-16 23:55:15     1.3  STATUS     STARTED Testing function: get.adjustment.variables
2018-10-16 23:55:15     1.3  STATUS     COMPLETED Testing function: get.adjustment.variables
2018-10-16 23:55:16     1.3  STATUS     STARTED Testing function: get.comparison.info
2018-10-16 23:55:16     1.3  STATUS     COMPLETED Testing function: get.comparison.info
2018-10-16 23:55:16     1.3  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2018-10-16 23:55:16     1.3  STATUS         STARTED Retrieving comparison info
2018-10-16 23:55:16     1.3  STATUS         COMPLETED Retrieving comparison info
2018-10-16 23:55:16     1.3  STATUS         STARTED Computing differential methylation tables
2018-10-16 23:55:17     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:17     1.3  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:55:17     1.3    INFO                     Conducting differential analysis using limma
2018-10-16 23:55:17     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:17     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:18     1.3  STATUS                     Computed table for tiling
2018-10-16 23:55:19     1.3  STATUS                     Computed table for genes
2018-10-16 23:55:19     1.3  STATUS                     Computed table for promoters
2018-10-16 23:55:19     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:55:20     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:20     1.3  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:20     1.3  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:20     1.3  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:55:20     1.3    INFO                     Conducting differential analysis using limma
2018-10-16 23:55:21     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:21     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:21     1.3  STATUS                     Computed table for tiling
2018-10-16 23:55:22     1.3  STATUS                     Computed table for genes
2018-10-16 23:55:23     1.3  STATUS                     Computed table for promoters
2018-10-16 23:55:23     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:55:23     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:24     1.3  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:24     1.3  STATUS         COMPLETED Computing differential methylation tables
2018-10-16 23:55:24     1.3  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2018-10-16 23:55:24     1.3  STATUS     STARTED Testing function: diffVar
2018-10-16 23:55:24     1.3  STATUS         STARTED diffVar method
2018-10-16 23:55:25     1.3  STATUS         COMPLETED diffVar method
2018-10-16 23:55:25     1.3  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-16 23:55:25     1.3  STATUS         COMPLETED diffVar method
2018-10-16 23:55:25     1.3  STATUS     COMPLETED Testing function: diffVar
2018-10-16 23:55:26     1.3  STATUS     STARTED Testing function: apply.iEVORA
2018-10-16 23:55:26     1.3  STATUS         STARTED iEVORA method
2018-10-16 23:55:28     1.3    INFO             No DVCs detected. All p-values set to 1.
2018-10-16 23:55:28     1.3  STATUS         COMPLETED iEVORA method
2018-10-16 23:55:28     1.3  STATUS         STARTED Testing function: rnb.execute.diffVar
2018-10-16 23:55:28     1.3  STATUS             STARTED Differential Variability
2018-10-16 23:55:29     1.3  STATUS                 STARTED Retrieving comparison info
2018-10-16 23:55:29     1.3  STATUS                 COMPLETED Retrieving comparison info
2018-10-16 23:55:29     1.3  STATUS                 STARTED Imputation procedure knn 
2018-10-16 23:55:29     1.3  STATUS                 COMPLETED Imputation procedure knn 
2018-10-16 23:55:29     1.3  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:29     1.3    INFO                     Conducting differential variability using diffVar
2018-10-16 23:55:30     1.3  STATUS                     STARTED diffVar method
2018-10-16 23:55:30     1.3  STATUS                     COMPLETED diffVar method
2018-10-16 23:55:30     1.3  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-16 23:55:31     1.3  STATUS                         Computed table for tiling
2018-10-16 23:55:32     1.3  STATUS                         Computed table for genes
2018-10-16 23:55:32     1.3  STATUS                         Computed table for promoters
2018-10-16 23:55:32     1.3  STATUS                         Computed table for cpgislands
2018-10-16 23:55:33     1.3  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-16 23:55:33     1.3  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:33     1.3  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:33     1.3    INFO                     Conducting differential variability using diffVar
2018-10-16 23:55:34     1.3  STATUS                     STARTED diffVar method
2018-10-16 23:55:34     1.3  STATUS                     COMPLETED diffVar method
2018-10-16 23:55:34     1.3  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-16 23:55:35     1.3  STATUS                         Computed table for tiling
2018-10-16 23:55:36     1.3  STATUS                         Computed table for genes
2018-10-16 23:55:36     1.3  STATUS                         Computed table for promoters
2018-10-16 23:55:37     1.3  STATUS                         Computed table for cpgislands
2018-10-16 23:55:37     1.3  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-16 23:55:37     1.3  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:37     1.3  STATUS             COMPLETED Differential Variability
2018-10-16 23:55:38     1.3  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2018-10-16 23:55:38     1.3  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-16 23:55:38     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:55:38     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:55:39     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:55:39     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:39     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:55:39     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:55:39     1.3  STATUS                         STARTED Imputation procedure knn 
2018-10-16 23:55:40     1.3  STATUS                         COMPLETED Imputation procedure knn 
2018-10-16 23:55:40     1.3    INFO                         Conducting differential variability using diffVar
2018-10-16 23:55:40     1.3  STATUS                         STARTED diffVar method
2018-10-16 23:55:40     1.3  STATUS                         COMPLETED diffVar method
2018-10-16 23:55:41     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:41     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:43     1.3  STATUS                         Computed table for tiling
2018-10-16 23:55:43     1.3  STATUS                         Computed table for genes
2018-10-16 23:55:44     1.3  STATUS                         Computed table for promoters
2018-10-16 23:55:45     1.3  STATUS                         Computed table for cpgislands
2018-10-16 23:55:45     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:45     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:46     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:46     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:55:46     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:55:46     1.3  STATUS                         STARTED Imputation procedure knn 
2018-10-16 23:55:46     1.3  STATUS                         COMPLETED Imputation procedure knn 
2018-10-16 23:55:47     1.3    INFO                         Conducting differential variability using diffVar
2018-10-16 23:55:47     1.3  STATUS                         STARTED diffVar method
2018-10-16 23:55:47     1.3  STATUS                         COMPLETED diffVar method
2018-10-16 23:55:48     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:48     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:49     1.3  STATUS                         Computed table for tiling
2018-10-16 23:55:50     1.3  STATUS                         Computed table for genes
2018-10-16 23:55:51     1.3  STATUS                         Computed table for promoters
2018-10-16 23:55:51     1.3  STATUS                         Computed table for cpgislands
2018-10-16 23:55:52     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:52     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:52     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:55:52     1.3  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-16 23:55:52     1.3  STATUS         STARTED Testing class: RnBDiffMeth
2018-10-16 23:55:53     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:55:53     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:55:53     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:55:53     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:53     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:55:54     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:55:54     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:54     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:55     1.3  STATUS                         Computed table for tiling
2018-10-16 23:55:55     1.3  STATUS                         Computed table for genes
2018-10-16 23:55:56     1.3  STATUS                         Computed table for promoters
2018-10-16 23:55:56     1.3  STATUS                         Computed table for cpgislands
2018-10-16 23:55:57     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:57     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:55:57     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:55:57     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:55:58     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:55:58     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:55:58     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:55:59     1.1  STATUS                         Computed table for tiling
2018-10-16 23:56:00     1.1  STATUS                         Computed table for genes
2018-10-16 23:56:00     1.1  STATUS                         Computed table for promoters
2018-10-16 23:56:01     1.1  STATUS                         Computed table for cpgislands
2018-10-16 23:56:01     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:01     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:02     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:56:02     1.1  STATUS             STARTED Retrieving comparison info
2018-10-16 23:56:02     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:56:02     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:56:02     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:03     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:56:03     1.1    INFO                         Conducting differential analysis using limma
2018-10-16 23:56:03     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:03     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:04     1.2  STATUS                         Computed table for genes
2018-10-16 23:56:05     1.2  STATUS                         Computed table for tiling
2018-10-16 23:56:05     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:06     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:06     1.2  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:56:06     1.2  STATUS             STARTED Retrieving comparison info
2018-10-16 23:56:06     1.2  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:56:06     1.2  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:56:07     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:07     1.2  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:56:07     1.2    INFO                         Conducting differential analysis using limma
2018-10-16 23:56:07     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:08     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:08     1.3  STATUS                         Computed table for genes
2018-10-16 23:56:09     1.3  STATUS                         Computed table for tiling
2018-10-16 23:56:09     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:10     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:10     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:56:10     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:56:10     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:56:11     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:56:11     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:11     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:56:11     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:56:11     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:12     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:12     1.3  STATUS                         Computed table for promoters
2018-10-16 23:56:12     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:13     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:13     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:13     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:56:13     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:56:13     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:14     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:14     1.3  STATUS                         Computed table for promoters
2018-10-16 23:56:14     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:15     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:15     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:56:15     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:56:15     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:56:15     1.3  STATUS             STARTED Computing differential methylation tables
2018-10-16 23:56:16     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:16     1.3  STATUS                     STARTED Computing Differential Methylation Table
2018-10-16 23:56:16     1.3    INFO                         Conducting differential analysis using limma
2018-10-16 23:56:16     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:17     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:17     1.3  STATUS                         Computed table for genes
2018-10-16 23:56:18     1.3  STATUS                         Computed table for tiling
2018-10-16 23:56:18     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:19     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:19     1.3  STATUS             COMPLETED Computing differential methylation tables
2018-10-16 23:56:19     1.3  STATUS             STARTED Testing function: get.region.types
2018-10-16 23:56:19     1.3  STATUS             COMPLETED Testing function: get.region.types
2018-10-16 23:56:19     1.3  STATUS             STARTED Testing function: get.comparisons
2018-10-16 23:56:20     1.3  STATUS             COMPLETED Testing function: get.comparisons
2018-10-16 23:56:20     1.3  STATUS             STARTED Testing function: get.comparison.grouplabels
2018-10-16 23:56:20     1.3  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2018-10-16 23:56:20     1.3  STATUS             STARTED Testing function: get.site.test.method
2018-10-16 23:56:20     1.3  STATUS             COMPLETED Testing function: get.site.test.method
2018-10-16 23:56:21     1.3  STATUS             STARTED Testing function: get.table
2018-10-16 23:56:21     1.3  STATUS             COMPLETED Testing function: get.table
2018-10-16 23:56:21     1.3  STATUS             STARTED Testing function: addDiffMethTable
2018-10-16 23:56:21     1.3    INFO                 Conducting differential analysis using limma
2018-10-16 23:56:22     1.3  STATUS             COMPLETED Testing function: addDiffMethTable
2018-10-16 23:56:22     1.3  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2018-10-16 23:56:22     1.3  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-16 23:56:22     1.3  STATUS             STARTED Destructor
2018-10-16 23:56:23     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:23     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:23     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:23     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:23     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:24     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:24     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:24     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-16 23:56:24     1.3  STATUS             COMPLETED Destructor
2018-10-16 23:56:25     1.3  STATUS         COMPLETED Testing class: RnBDiffMeth
2018-10-16 23:56:25     1.3  STATUS     COMPLETED Testing function: apply.iEVORA
2018-10-16 23:56:25     1.3  STATUS     STARTED iEVORA method
2018-10-16 23:56:27     1.3    INFO         No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2018-10-16 23:56:27     1.3  STATUS         STARTED Retrieving comparison info
2018-10-16 23:56:28     1.3  STATUS         COMPLETED Retrieving comparison info
2018-10-16 23:56:28     1.3  STATUS         STARTED Computing differential methylation tables
2018-10-16 23:56:28     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:28     1.3  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:56:28     1.3    INFO                     Conducting differential analysis using limma
2018-10-16 23:56:29     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:29     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:30     1.3  STATUS                     Computed table for tiling
2018-10-16 23:56:30     1.3  STATUS                     Computed table for genes
2018-10-16 23:56:31     1.3  STATUS                     Computed table for promoters
2018-10-16 23:56:32     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:56:32     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:32     1.3  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:32     1.3  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:32     1.3  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:56:33     1.3    INFO                     Conducting differential analysis using limma
2018-10-16 23:56:33     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:33     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:34     1.3  STATUS                     Computed table for tiling
2018-10-16 23:56:35     1.3  STATUS                     Computed table for genes
2018-10-16 23:56:35     1.3  STATUS                     Computed table for promoters
2018-10-16 23:56:36     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:56:36     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:36     1.3  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:36     1.3  STATUS         COMPLETED Computing differential methylation tables
2018-10-16 23:56:36     1.3  STATUS         STARTED Retrieving comparison info
2018-10-16 23:56:37     1.3  STATUS         COMPLETED Retrieving comparison info
2018-10-16 23:56:37     1.3  STATUS         STARTED Computing differential methylation tables
2018-10-16 23:56:37     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:37     1.3  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:56:37     1.3    INFO                     Conducting differential analysis using limma
2018-10-16 23:56:38     1.3  STATUS                     STARTED Imputation procedure knn 
2018-10-16 23:56:38     1.3  STATUS                     COMPLETED Imputation procedure knn 
2018-10-16 23:56:38     1.3    INFO                     Conducting differential variability using diffVar
2018-10-16 23:56:38     1.3  STATUS                     STARTED diffVar method
2018-10-16 23:56:38     1.3  STATUS                     COMPLETED diffVar method
2018-10-16 23:56:39     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:39     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:41     1.3  STATUS                     Computed table for tiling
2018-10-16 23:56:41     1.3  STATUS                     Computed table for genes
2018-10-16 23:56:42     1.3  STATUS                     Computed table for promoters
2018-10-16 23:56:43     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:56:43     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:43     1.3  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:43     1.3  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:43     1.3  STATUS                 STARTED Computing Differential Methylation Table
2018-10-16 23:56:44     1.3    INFO                     Conducting differential analysis using limma
2018-10-16 23:56:44     1.3  STATUS                     STARTED Imputation procedure knn 
2018-10-16 23:56:44     1.3  STATUS                     COMPLETED Imputation procedure knn 
2018-10-16 23:56:44     1.3    INFO                     Conducting differential variability using diffVar
2018-10-16 23:56:44     1.3  STATUS                     STARTED diffVar method
2018-10-16 23:56:45     1.3  STATUS                     COMPLETED diffVar method
2018-10-16 23:56:45     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-16 23:56:45     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:47     1.3  STATUS                     Computed table for tiling
2018-10-16 23:56:48     1.3  STATUS                     Computed table for genes
2018-10-16 23:56:48     1.3  STATUS                     Computed table for promoters
2018-10-16 23:56:49     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:56:49     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-16 23:56:49     1.3  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:49     1.3  STATUS         COMPLETED Computing differential methylation tables
2018-10-16 23:56:50     1.3  STATUS         STARTED Differential Variability
2018-10-16 23:56:50     1.3  STATUS             STARTED Retrieving comparison info
2018-10-16 23:56:50     1.3  STATUS             COMPLETED Retrieving comparison info
2018-10-16 23:56:50     1.3  STATUS             STARTED Imputation procedure knn 
2018-10-16 23:56:51     1.3  STATUS             COMPLETED Imputation procedure knn 
2018-10-16 23:56:51     1.3  STATUS             STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:51     1.3    INFO                 Conducting differential variability using diffVar
2018-10-16 23:56:51     1.3  STATUS                 STARTED diffVar method
2018-10-16 23:56:51     1.3  STATUS                 COMPLETED diffVar method
2018-10-16 23:56:52     1.3  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2018-10-16 23:56:53     1.3  STATUS                     Computed table for tiling
2018-10-16 23:56:53     1.3  STATUS                     Computed table for genes
2018-10-16 23:56:54     1.3  STATUS                     Computed table for promoters
2018-10-16 23:56:54     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:56:54     1.3  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-16 23:56:55     1.3  STATUS             COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-16 23:56:55     1.3  STATUS             STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:55     1.3    INFO                 Conducting differential variability using diffVar
2018-10-16 23:56:55     1.3  STATUS                 STARTED diffVar method
2018-10-16 23:56:55     1.3  STATUS                 COMPLETED diffVar method
2018-10-16 23:56:56     1.3  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2018-10-16 23:56:57     1.3  STATUS                     Computed table for tiling
2018-10-16 23:56:57     1.3  STATUS                     Computed table for genes
2018-10-16 23:56:58     1.3  STATUS                     Computed table for promoters
2018-10-16 23:56:58     1.3  STATUS                     Computed table for cpgislands
2018-10-16 23:56:58     1.3  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-16 23:56:59     1.3  STATUS             COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-16 23:56:59     1.3  STATUS         COMPLETED Differential Variability
2018-10-16 23:56:59     1.3  STATUS STARTED Analysis
2018-10-16 23:56:59     1.3    INFO     Loaded information from data.RData
2018-10-16 23:56:59     1.3  STATUS     STARTED Processing Detection P-values
2018-10-16 23:57:00     1.3    INFO         Removed 3979 probes that overlap with SNPs
2018-10-16 23:57:00     1.3    INFO         Completed Greedycut on 510 samples
2018-10-16 23:57:00     1.3  STATUS     COMPLETED Processing Detection P-values
2018-10-16 23:57:00     1.3 WARNING     File not found: data2.RData
2018-10-16 23:57:00     1.3  STATUS COMPLETED Analysis

2018-10-16 23:57:01     1.3  STATUS STARTED Testing imputation
2018-10-16 23:57:01     1.3  STATUS     STARTED Imputation procedure knn 
2018-10-16 23:57:02     1.3  STATUS     COMPLETED Imputation procedure knn 
2018-10-16 23:57:02     1.3  STATUS     STARTED Imputation procedure mean.samples 
2018-10-16 23:57:03     1.3  STATUS     COMPLETED Imputation procedure mean.samples 
2018-10-16 23:57:04     1.3  STATUS     STARTED Imputation procedure mean.cpgs 
2018-10-16 23:57:04     1.3  STATUS     COMPLETED Imputation procedure mean.cpgs 
2018-10-16 23:57:05     1.3  STATUS     STARTED Imputation procedure random 
2018-10-16 23:57:05     1.3  STATUS     COMPLETED Imputation procedure random 
2018-10-16 23:57:06     1.3  STATUS COMPLETED Testing imputation

2018-10-16 23:57:06     1.3  STATUS STARTED Testing age prediction
2018-10-16 23:57:06     1.3  STATUS     STARTED Performing Age Prediction
2018-10-16 23:57:08     1.5  STATUS     COMPLETED Performing Age Prediction
2018-10-16 23:57:09     1.5  STATUS COMPLETED Testing age prediction

2018-10-16 23:57:09     1.5  STATUS STARTED Performing Age Prediction
2018-10-16 23:57:11     1.5  STATUS COMPLETED Performing Age Prediction

2018-10-16 23:57:11     1.5  STATUS STARTED Imputation procedure knn 
2018-10-16 23:57:12     1.4  STATUS COMPLETED Imputation procedure knn 

2018-10-16 23:57:12     1.4  STATUS STARTED Imputation procedure mean.samples 
2018-10-16 23:57:13     1.4  STATUS COMPLETED Imputation procedure mean.samples 

2018-10-16 23:57:13     1.4  STATUS STARTED Imputation procedure mean.cpgs 
2018-10-16 23:57:14     1.4  STATUS COMPLETED Imputation procedure mean.cpgs 

2018-10-16 23:57:15     1.4  STATUS STARTED Imputation procedure random 
2018-10-16 23:57:16     1.4  STATUS COMPLETED Imputation procedure random 

2018-10-16 23:57:16     1.4  STATUS STARTED Testing imputation
2018-10-16 23:57:16     1.4  STATUS     STARTED Imputation procedure knn 
2018-10-16 23:57:17     1.4  STATUS     COMPLETED Imputation procedure knn 
2018-10-16 23:57:17     1.4  STATUS     STARTED Imputation procedure mean.samples 
2018-10-16 23:57:18     1.4  STATUS     COMPLETED Imputation procedure mean.samples 
2018-10-16 23:57:18     1.4  STATUS     STARTED Imputation procedure mean.cpgs 
2018-10-16 23:57:20     1.2  STATUS     COMPLETED Imputation procedure mean.cpgs 
2018-10-16 23:57:20     1.2  STATUS     STARTED Imputation procedure random 
2018-10-16 23:57:21     1.3  STATUS     COMPLETED Imputation procedure random 
2018-10-16 23:57:21     1.3  STATUS COMPLETED Testing imputation

2018-10-16 23:57:21     1.3  STATUS STARTED Testing age prediction
2018-10-16 23:57:21     1.3  STATUS     STARTED Performing Age Prediction
2018-10-16 23:57:23     1.5  STATUS     COMPLETED Performing Age Prediction
2018-10-16 23:57:24     1.5  STATUS COMPLETED Testing age prediction



RUNIT TEST PROTOCOL -- Tue Oct 16 23:57:36 2018 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RnBeads RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
There were 37 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
149.182 112.869 265.486

Example timings

RnBeads.Rcheck/RnBeads-Ex.timings

nameusersystemelapsed
M-methods0.0010.0000.001
U-methods0.0010.0000.001
addDiffMethTable-RnBDiffMeth-methods0.0000.0000.001
addPheno-RnBSet-methods0.0010.0010.001
addRegionSubsegments0.0010.0000.001
annotation-methods0.0000.0000.002
assembly-methods0.0010.0000.001
combine-methods0.0010.0000.001
combineTestPvalsMeth0.0010.0000.001
computeDiffTab.region0.0010.0000.001
computeDiffTab.site0.0010.0000.001
covg-methods0.0010.0000.000
create.densityScatter0.0010.0000.001
create.scatter.dens.points0.0010.0000.001
createReport0.0010.0000.001
createReportPlot0.0020.0000.001
downloadLolaDbs0.0010.0000.001
dpval-methods0.0010.0000.001
exportDMRs2regionFile0.0010.0000.001
get.adjustment.variables0.0010.0000.001
get.comparison.grouplabels-RnBDiffMeth-methods0.0010.0010.001
get.comparison.groupsizes-RnBDiffMeth-methods0.0010.0000.002
get.comparison.info0.0010.0000.001
get.comparisons-RnBDiffMeth-methods0.0010.0010.003
get.covariates.sva0.0010.0000.001
get.covg.thres-RnBDiffMeth-methods0.0000.0000.001
get.files0.0010.0010.001
get.region.types-RnBDiffMeth-methods0.0020.0000.002
get.site.test.method-RnBDiffMeth-methods0.0010.0000.001
get.table-RnBDiffMeth-methods0.0010.0010.001
getCellTypesFromLolaDb000
getNamesFromLolaDb0.0010.0000.001
getSubCmdTokens-ClusterArchitectureSGE-methods0.0010.0000.000
getTargetFromLolaDb0.0010.0000.001
has.covariates.sva0.0000.0000.001
hasCovg-methods000
includes.sites-RnBDiffMeth-methods0.0000.0000.001
is.valid-RnBDiffMeth-methods0.0010.0010.001
join.diffMeth-methods0.0010.0000.001
limmaP0.0000.0000.001
loadLolaDbs0.0000.0010.001
logger.argument0.0010.0000.001
logger.getfiles0.0000.0000.001
logger.isinitialized0.0010.0010.001
logger.validate.file0.0010.0000.001
loggerManagement0.0010.0000.001
loggerMessages0.0000.0000.001
lolaBarPlot0.0010.0000.001
lolaBoxPlotPerTarget0.0010.0000.001
lolaVolcanoPlot0.0010.0000.001
mergeSamples-methods000
meth-methods0.0000.0000.001
mval-methods0.0010.0000.001
nsites-methods0.0020.0000.002
parallel.getNumWorkers0.0000.0000.001
parallel.isEnabled0.0020.0000.001
parallel.setup0.0010.0000.001
parallel.teardown0.0010.0000.001
performGOEnrichment.diffVar0.0010.0000.001
performGOenrichment.diffMeth.entrez0.0010.0000.001
performGoEnrichment.diffMeth0.0020.0000.001
performLolaEnrichment.diffMeth0.0000.0000.001
performLolaEnrichment.diffVar0.0020.0000.002
pheno-methods0.0010.0000.002
qc-methods0.0010.0010.001
read.sample.annotation0.0010.0000.001
regionMapping-methods0.0020.0000.001
regions-methods0.0010.0000.001
reload-RnBDiffMeth-methods0.0010.0000.001
remove.regions-methods0.0010.0000.001
remove.samples-methods0.0010.0010.001
remove.sites-methods0.0010.0000.001
rnb.RnBSet.to.GRangesList0.0010.0000.001
rnb.RnBSet.to.bed0.0010.0000.001
rnb.RnBSet.to.bedGraph000
rnb.add.list0.0000.0000.001
rnb.add.paragraph0.0010.0000.001
rnb.add.reference0.0010.0000.000
rnb.add.section0.0010.0000.001
rnb.annotation.size0.0020.0000.001
rnb.annotation2data.frame0.0010.0000.001
rnb.beta2mval0.0010.0000.002
rnb.execute.batcheffects0.0020.0000.001
rnb.execute.clustering0.0010.0000.001
rnb.execute.computeDiffMeth0.0010.0000.000
rnb.execute.context.removal0.0010.0000.001
rnb.execute.cross.reactive.removal0.0000.0000.001
rnb.execute.dreduction0.0010.0000.001
rnb.execute.export.csv0.0010.0000.000
rnb.execute.gender.prediction0.0010.0000.001
rnb.execute.greedycut000
rnb.execute.import0.0000.0000.001
rnb.execute.na.removal0.0010.0000.001
rnb.execute.normalization0.0010.0000.000
rnb.execute.sex.removal0.0010.0000.001
rnb.execute.snp.removal0.0010.0000.001
rnb.execute.sva0.0010.0000.001
rnb.execute.tnt0.0000.0000.001
rnb.execute.variability.removal000
rnb.export.all.annotation0.0010.0000.001
rnb.export.annotation0.0010.0000.000
rnb.export.to.ewasher0.0010.0000.001
rnb.export.to.trackhub0.0010.0000.001
rnb.get.annotation0.0000.0010.001
rnb.get.assemblies0.0000.0000.001
rnb.get.chromosomes0.0010.0000.001
rnb.get.directory0.0010.0000.001
rnb.get.mapping0.0010.0010.000
rnb.get.reference0.0000.0000.001
rnb.get.reliability.matrix000
rnb.infinium.control.targets0.0010.0000.001
rnb.initialize.reports0.0010.0000.001
rnb.is.option0.0010.0000.001
rnb.load.annotation.from.db0.0000.0000.001
rnb.message.plot000
rnb.mval2beta0.0010.0000.001
rnb.options0.0010.0000.000
rnb.options2xml0.0010.0000.001
rnb.plot.betadistribution.probeCategories000
rnb.plot.betadistribution.sampleGroups0.0000.0000.001
rnb.plot.control.barplot0.0010.0000.001
rnb.plot.control.boxplot0.0010.0000.001
rnb.plot.dreduction0.0010.0000.001
rnb.plot.locus.profile0.0000.0000.001
rnb.plot.negative.boxplot0.0010.0000.001
rnb.plot.region.profile.density0.0010.0000.001
rnb.plot.region.profiles0.0010.0000.001
rnb.plot.region.site.density0.0000.0000.001
rnb.plot.sentrix.distribution0.0010.0000.000
rnb.plot.snp.barplot0.0010.0000.001
rnb.plot.snp.boxplot0.0000.0000.001
rnb.plot.snp.heatmap0.0010.0000.001
rnb.region.types0.0010.0000.001
rnb.region.types.for.analysis0.0010.0000.001
rnb.remove.annotation0.0010.0000.000
rnb.run.example0.0000.0010.001
rnb.runs0.0010.0000.000
rnb.sample.groups0.0010.0000.001
rnb.sample.summary.table0.0020.0010.001
rnb.set.annotation0.0010.0000.001
rnb.write.table0.0010.0000.001
rnb.xml2options0.0010.0000.001
rowOneSampleTP0.0010.0000.001
rowWelchP0.0000.0000.001
run-RnBClusterRun-methods0.0010.0000.002
samples-methods0.0010.0000.002
save.tables-RnBDiffMeth-methods0.0010.0000.001
set.covariates.sva0.0010.0000.001
sites-methods0.0000.0010.001
summarize.regions-methods0.0010.0000.000
summarized.regions-methods0.0010.0000.001