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CHECK report for RnBeads on merida1

This page was generated on 2019-04-16 11:58:38 -0400 (Tue, 16 Apr 2019).

Package 1334/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 2.0.1
Fabian Mueller
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/RnBeads
Branch: RELEASE_3_8
Last Commit: 1e73169
Last Changed Date: 2019-01-04 13:17:35 -0400 (Fri, 04 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RnBeads
Version: 2.0.1
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_2.0.1.tar.gz
StartedAt: 2019-04-16 02:27:31 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:45:28 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 1077.4 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_2.0.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/RnBeads.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.0.1’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qvalue’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’

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

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
  'grDevices:::.smoothScatterCalcDensity'
  'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
  'minfi:::.normalizeFunnorm450k'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
  ‘stopCluster’
MethyLumiSet2RnBeadSet: no visible global function definition for
  ‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
  ‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
  ‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
  ‘varLabels’
MethyLumiSet2RnBeadSet: no visible global function definition for
  ‘featureData’
add.age.histogram: no visible binding for global variable ‘Age’
add.age.histogram: no visible binding for global variable ‘..count..’
add.age.histogram: no visible binding for global variable ‘..density..’
add.agecomparison.plot: no visible global function definition for
  ‘samples’
add.agecomparison.plot: no visible binding for global variable ‘Sample’
add.combination.plot: no visible global function definition for
  ‘samples’
add.combination.plot: no visible binding for global variable
  ‘Difference’
add.combination.plot: no visible binding for global variable ‘Density’
add.combination.plot: no visible binding for global variable ‘yint’
add.combination.plot: no visible binding for global variable ‘Measure’
add.error.plot: no visible binding for global variable ‘Value’
add.error.plot: no visible binding for global variable ‘Sample’
add.error.plot: no visible binding for global variable ‘Deviance’
add.error.plot: no visible binding for global variable ‘yint’
add.error.plot: no visible binding for global variable ‘Measure’
add.negative.control.boxplot: no visible global function definition for
  ‘samples’
add.profile.plots: no visible global function definition for ‘mclapply’
add.qc.barplots: no visible global function definition for ‘samples’
add.quantile.plot: no visible binding for global variable ‘Difference’
add.quantile.plot: no visible binding for global variable ‘..density..’
add.quantile.plot: no visible binding for global variable ‘Sample’
add.quantile.plot: no visible binding for global variable ‘Density’
add.seq.coverage.histograms: no visible global function definition for
  ‘samples’
add.seq.coverage.plot: no visible global function definition for
  ‘samples’
add.seq.coverage.violins: no visible global function definition for
  ‘samples’
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: no visible global function definition for ‘seqlengths’
getCGCounts : <anonymous>: no visible global function definition for
  ‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles: no visible global function definition for ‘mclapply’
getGLADProfiles : <anonymous>: no visible global function definition
  for ‘as.profileCGH’
getGLADProfiles : <anonymous>: no visible global function definition
  for ‘daglad’
getMergeList: no visible global function definition for ‘samples’
groupPermutationP.site.parallel: no visible global function definition
  for ‘%dopar%’
groupPermutationP.site.parallel: no visible global function definition
  for ‘foreach’
iEVORA: no visible global function definition for ‘qvalue’
imputation.low.memory.cpgs: no visible global function definition for
  ‘samples’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylationEPICmanifest’
intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
intensities.by.color: no visible global function definition for
  ‘samples’
knn.imputation: no visible global function definition for ‘impute.knn’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
loadLolaDbs: no visible global function definition for ‘loadRegionDB’
loadLolaDbs: no visible global function definition for ‘mergeRegionDBs’
locus.profile.get.base.tracks: no visible global function definition
  for ‘useMart’
locus.profile.get.base.tracks: no visible global function definition
  for ‘IdeogramTrack’
locus.profile.get.base.tracks: no visible global function definition
  for ‘GenomeAxisTrack’
locus.profile.get.base.tracks: no visible global function definition
  for ‘BiomartGeneRegionTrack’
locus.profile.get.base.tracks: no visible global function definition
  for ‘UcscTrack’
locus.profile.get.methylation.track.heatmap: no visible global function
  definition for ‘DataTrack’
locus.profile.get.methylation.track.smooth: no visible global function
  definition for ‘DataTrack’
methylumi.intensities.by.color: no visible global function definition
  for ‘featureNames’
methylumi.intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
methylumi.intensities.by.color: no visible global function definition
  for ‘assayDataElement’
parallel.setup: no visible global function definition for
  ‘registerDoParallel’
parallel.setup: no visible global function definition for
  ‘getDoParWorkers’
performLolaEnrichment.diffMeth: no visible global function definition
  for ‘runLOLA’
performLolaEnrichment.diffVar: no visible global function definition
  for ‘runLOLA’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘grid.newpage’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘grid.draw’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘melt’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘grid.newpage’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘grid.draw’
plot.heatmap.rand: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for
  ‘grid.newpage’
plot.heatmap.symm: no visible global function definition for
  ‘grid.draw’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
prepareGEOSampleInfoTemplate: no visible global function definition for
  ‘samples’
projectWBC: no visible global function definition for ‘solve.QP’
read.GS.report: no visible global function definition for
  ‘featureNames’
read.idat.files: no visible binding for global variable ‘barcode’
refFreeEWASP: no visible global function definition for ‘EstDimRMT’
refFreeEWASP: no visible global function definition for
  ‘RefFreeEwasModel’
refFreeEWASP: no visible global function definition for
  ‘PairsBootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for
  ‘BootRefFreeEwasModel’
rnb.RnBSet.to.GRangesList: no visible global function definition for
  ‘samples’
rnb.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
  ‘samples’
rnb.chromosome.lengths: no visible global function definition for
  ‘seqlengths’
rnb.combine.seq: no visible global function definition for ‘samples’
rnb.enmix.oob: no visible global function definition for ‘%dopar%’
rnb.enmix.oob: no visible global function definition for ‘foreach’
rnb.execute.dreduction: no visible global function definition for
  ‘samples’
rnb.execute.filter.summary.internal: no visible global function
  definition for ‘samples’
rnb.execute.high.coverage.removal.internal: no visible global function
  definition for ‘samples’
rnb.execute.imputation: no visible global function definition for
  ‘samples’
rnb.execute.low.coverage.masking.internal: no visible global function
  definition for ‘samples’
rnb.execute.na.removal.internal: no visible global function definition
  for ‘samples’
rnb.execute.normalization: no visible global function definition for
  ‘phenoData’
rnb.execute.normalization: no visible global function definition for
  ‘phenoData<-’
rnb.execute.normalization: no visible global function definition for
  ‘RGChannelSet’
rnb.execute.normalization: no visible global function definition for
  ‘preprocessSWAN’
rnb.execute.normalization: no visible global function definition for
  ‘getMeth’
rnb.execute.normalization: no visible global function definition for
  ‘getUnmeth’
rnb.execute.normalization: no visible global function definition for
  ‘featureNames’
rnb.execute.normalization: no visible global function definition for
  ‘samples’
rnb.execute.normalization: no visible global function definition for
  ‘mapToGenome’
rnb.execute.normalization: no visible global function definition for
  ‘addSex’
rnb.execute.normalization: no visible global function definition for
  ‘getSex’
rnb.execute.normalization: no visible global function definition for
  ‘getCN’
rnb.execute.normalization.bmiq: no visible global function definition
  for ‘%dopar%’
rnb.execute.normalization.bmiq: no visible global function definition
  for ‘foreach’
rnb.execute.quality: no visible global function definition for
  ‘samples’
rnb.execute.quality : <anonymous>: no visible global function
  definition for ‘samples’
rnb.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.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
  ‘phenoData’
rnb.section.imputation: no visible global function definition for
  ‘melt’
rnb.section.locus.profiles: no visible global function definition for
  ‘samples’
rnb.section.locus.profiles : do.plots: no visible global function
  definition for ‘plotTracks’
rnb.section.locus.profiles: no visible global function definition for
  ‘%dopar%’
rnb.section.locus.profiles: no visible global function definition for
  ‘foreach’
rnb.section.na.removal: no visible global function definition for
  ‘samples’
rnb.section.normalization: no visible global function definition for
  ‘samples’
rnb.section.region.description: no visible binding for global variable
  ‘size’
rnb.section.region.description: no visible binding for global variable
  ‘n.sites’
rnb.section.region.profiles: no visible global function definition for
  ‘samples’
rnb.section.region.subsegmentation : get.summary.df.from.list: no
  visible global function definition for ‘melt’
rnb.section.region.subsegmentation: no visible binding for global
  variable ‘region.size’
rnb.section.region.subsegmentation: no visible binding for global
  variable ‘is.subsegmentation’
rnb.section.region.subsegmentation: no visible binding for global
  variable ‘num.sites’
rnb.section.sex.prediction: no visible global function definition for
  ‘muted’
rnb.step.betadistribution.internal: no visible global function
  definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
  definition for ‘foreach’
rnb.step.cell.types: no visible global function definition for
  ‘samples’
rnb.step.clustering.internal: no visible global function definition for
  ‘samples’
rnb.step.dreduction: no visible global function definition for
  ‘%dopar%’
rnb.step.dreduction: no visible global function definition for
  ‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
  for ‘percent_format’
rnb.step.filter.summary.internal: no visible global function definition
  for ‘samples’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.na.removal: no visible binding for global variable
  ‘sites2ignore’
rnb.step.na.removal.internal: no visible global function definition for
  ‘samples’
rnb.step.normalization: no visible global function definition for
  ‘phenoData’
robustHyperGResultSummary: no visible global function definition for
  ‘sigCategories’
robustHyperGResultSummary: no visible global function definition for
  ‘pvalues’
robustHyperGResultSummary: no visible global function definition for
  ‘oddsRatios’
robustHyperGResultSummary: no visible global function definition for
  ‘expectedCounts’
robustHyperGResultSummary: no visible global function definition for
  ‘geneCounts’
robustHyperGResultSummary: no visible global function definition for
  ‘universeCounts’
robustHyperGResultSummary: no visible binding for global variable
  ‘Term’
run.cross.validation: no visible global function definition for
  ‘samples’
run.cross.validation: no visible global function definition for ‘melt’
run.cross.validation: no visible binding for global variable ‘Measure’
run.cross.validation: no visible binding for global variable ‘Error’
sampleCovgApply: no visible global function definition for ‘samples’
set.covariates.ct: no visible global function definition for ‘samples’
simpleGlmnet: no visible global function definition for ‘impute.knn’
simpleGlmnet: no visible global function definition for ‘cv.glmnet’
simpleGlmnet: no visible global function definition for ‘glmnet’
simpleGlmnetBiseq: no visible global function definition for
  ‘cv.glmnet’
simpleGlmnetBiseq: no visible global function definition for ‘glmnet’
simpleGlmnetEvaluate: no visible global function definition for
  ‘cv.glmnet’
simpleGlmnetEvaluate: no visible global function definition for
  ‘glmnet’
symmetric.melt: no visible global function definition for ‘melt’
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
  ‘reg.type’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘getManifest’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘getGreen’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘getRed’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for ‘pData’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for ‘featureData<-’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for ‘featureNames<-’
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 is.subsegmentation k letterFrequency lme loadRegionDB
  log10FDR log10P mapToGenome mclapply 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: 7 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 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/Rtmp3mVEBt"

- 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 2.2-2 (2019-03-07) 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 object is masked from 'package:ff':

    maxlength

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

2019-04-16 02:34:22     0.7  STATUS STARTED Unit testing: differential
2019-04-16 02:34:22     0.7  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2019-04-16 02:34:23     0.7  STATUS     COMPLETED Testing function: rowWelchP
2019-04-16 02:34:23     0.7  STATUS     STARTED Testing function: limmaP
2019-04-16 02:34:23     0.7  STATUS     COMPLETED Testing function: limmaP
2019-04-16 02:34:23     0.7  STATUS     STARTED Testing function: computeDiffTab.extended.site
2019-04-16 02:34:24     0.7    INFO         Conducting differential analysis using limma
2019-04-16 02:34:24     0.7  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2019-04-16 02:34:24     0.7  STATUS     STARTED Testing function: computeDiffTab.default.region
2019-04-16 02:34:25     0.7    INFO         Conducting differential analysis using limma
2019-04-16 02:34:30     0.8  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2019-04-16 02:34:31     0.8  STATUS     STARTED Testing function: combineTestPvalsMeth
2019-04-16 02:34:31     0.8  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2019-04-16 02:34:31     0.8  STATUS     STARTED Testing function: get.adjustment.variables
2019-04-16 02:34:32     0.8  STATUS     COMPLETED Testing function: get.adjustment.variables
2019-04-16 02:34:32     0.8  STATUS     STARTED Testing function: get.comparison.info
2019-04-16 02:34:32     0.8  STATUS     COMPLETED Testing function: get.comparison.info
2019-04-16 02:34:33     0.8  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2019-04-16 02:34:33     0.8  STATUS         STARTED Retrieving comparison info
2019-04-16 02:34:33     0.8  STATUS         COMPLETED Retrieving comparison info
2019-04-16 02:34:34     0.8  STATUS         STARTED Computing differential methylation tables
2019-04-16 02:34:34     0.8  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:34:34     0.8  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:34:34     0.8    INFO                     Conducting differential analysis using limma
2019-04-16 02:34:35     0.8  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:34:35     0.8  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:34:36     1.0  STATUS                     Computed table for tiling
2019-04-16 02:34:37     1.0  STATUS                     Computed table for genes
2019-04-16 02:34:38     1.0  STATUS                     Computed table for promoters
2019-04-16 02:34:38     1.0  STATUS                     Computed table for cpgislands
2019-04-16 02:34:39     1.0  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:34:39     1.0  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:34:40     1.0  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:34:40     1.0  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:34:40     1.0    INFO                     Conducting differential analysis using limma
2019-04-16 02:34:40     1.0  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:34:41     1.0  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:34:42     1.1  STATUS                     Computed table for tiling
2019-04-16 02:34:43     1.1  STATUS                     Computed table for genes
2019-04-16 02:34:43     1.1  STATUS                     Computed table for promoters
2019-04-16 02:34:44     1.1  STATUS                     Computed table for cpgislands
2019-04-16 02:34:44     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:34:44     1.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:34:45     1.1  STATUS         COMPLETED Computing differential methylation tables
2019-04-16 02:34:45     1.1  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2019-04-16 02:34:45     1.1  STATUS     STARTED Testing function: diffVar
2019-04-16 02:34:46     1.1  STATUS         STARTED diffVar method
2019-04-16 02:34:46     1.1  STATUS         COMPLETED diffVar method
2019-04-16 02:34:46     1.1  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2019-04-16 02:34:48     1.1  STATUS         COMPLETED diffVar method
2019-04-16 02:34:48     1.1  STATUS     COMPLETED Testing function: diffVar
2019-04-16 02:34:48     1.1  STATUS     STARTED Testing function: apply.iEVORA
2019-04-16 02:34:49     1.1  STATUS         STARTED iEVORA method
2019-04-16 02:34:51     1.2    INFO             No DVCs detected. All p-values set to 1.
2019-04-16 02:34:51     1.2  STATUS         COMPLETED iEVORA method
2019-04-16 02:34:51     1.2  STATUS         STARTED Testing function: rnb.execute.diffVar
2019-04-16 02:34:52     1.2  STATUS             STARTED Differential Variability
2019-04-16 02:34:52     1.2  STATUS                 STARTED Retrieving comparison info
2019-04-16 02:34:52     1.2  STATUS                 COMPLETED Retrieving comparison info
2019-04-16 02:34:53     1.2    INFO                 No imputation method selected, 'knn' method used.
2019-04-16 02:34:53     1.2  STATUS                 STARTED Imputation procedure knn 
2019-04-16 02:34:53     1.2  STATUS                 COMPLETED Imputation procedure knn 
2019-04-16 02:34:54     1.2  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:34:54     1.2    INFO                     Conducting differential variability using diffVar
2019-04-16 02:34:54     1.2  STATUS                     STARTED diffVar method
2019-04-16 02:34:55     1.2  STATUS                     COMPLETED diffVar method
2019-04-16 02:34:55     1.2  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2019-04-16 02:34:56     1.2  STATUS                         Computed table for tiling
2019-04-16 02:34:57     1.2  STATUS                         Computed table for genes
2019-04-16 02:34:57     1.2  STATUS                         Computed table for promoters
2019-04-16 02:34:58     1.2  STATUS                         Computed table for cpgislands
2019-04-16 02:34:58     1.2  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2019-04-16 02:34:58     1.2  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:34:59     1.2  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2019-04-16 02:34:59     1.2    INFO                     Conducting differential variability using diffVar
2019-04-16 02:34:59     1.2  STATUS                     STARTED diffVar method
2019-04-16 02:34:59     1.2  STATUS                     COMPLETED diffVar method
2019-04-16 02:35:00     1.2  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2019-04-16 02:35:01     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:01     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:02     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:02     1.2  STATUS                         Computed table for cpgislands
2019-04-16 02:35:03     1.2  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2019-04-16 02:35:03     1.2  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:03     1.2  STATUS             COMPLETED Differential Variability
2019-04-16 02:35:04     1.2  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2019-04-16 02:35:04     1.2  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2019-04-16 02:35:04     1.2  STATUS             STARTED Retrieving comparison info
2019-04-16 02:35:04     1.2  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:35:05     1.2  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:35:05     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:05     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:06     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:06     1.2  STATUS                         STARTED Imputation procedure knn 
2019-04-16 02:35:06     1.2  STATUS                         COMPLETED Imputation procedure knn 
2019-04-16 02:35:07     1.2    INFO                         Conducting differential variability using diffVar
2019-04-16 02:35:07     1.2  STATUS                         STARTED diffVar method
2019-04-16 02:35:07     1.2  STATUS                         COMPLETED diffVar method
2019-04-16 02:35:08     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:08     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:10     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:11     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:12     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:12     1.2  STATUS                         Computed table for cpgislands
2019-04-16 02:35:13     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:13     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:13     1.2  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:14     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:14     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:14     1.2  STATUS                         STARTED Imputation procedure knn 
2019-04-16 02:35:14     1.2  STATUS                         COMPLETED Imputation procedure knn 
2019-04-16 02:35:15     1.2    INFO                         Conducting differential variability using diffVar
2019-04-16 02:35:15     1.2  STATUS                         STARTED diffVar method
2019-04-16 02:35:15     1.2  STATUS                         COMPLETED diffVar method
2019-04-16 02:35:16     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:16     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:18     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:19     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:20     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:21     1.2  STATUS                         Computed table for cpgislands
2019-04-16 02:35:21     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:21     1.2  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:22     1.2  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:35:22     1.2  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2019-04-16 02:35:22     1.2  STATUS         STARTED Testing class: RnBDiffMeth
2019-04-16 02:35:22     1.2  STATUS             STARTED Retrieving comparison info
2019-04-16 02:35:23     1.2  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:35:23     1.2  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:35:23     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:24     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:24     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:24     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:24     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:25     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:26     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:27     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:27     1.2  STATUS                         Computed table for cpgislands
2019-04-16 02:35:27     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:28     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:28     1.2  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:28     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:29     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:29     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:29     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:30     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:31     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:31     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:32     1.2  STATUS                         Computed table for cpgislands
2019-04-16 02:35:32     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:33     1.2  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:33     1.2  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:35:33     1.2  STATUS             STARTED Retrieving comparison info
2019-04-16 02:35:34     1.2  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:35:34     1.2  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:35:34     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:34     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:35     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:35     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:35     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:36     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:37     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:37     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:38     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:38     1.2  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:35:38     1.2  STATUS             STARTED Retrieving comparison info
2019-04-16 02:35:38     1.2  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:35:39     1.2  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:35:39     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:39     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:40     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:40     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:40     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:41     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:42     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:42     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:42     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:43     1.2  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:35:43     1.2  STATUS             STARTED Retrieving comparison info
2019-04-16 02:35:43     1.2  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:35:44     1.2  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:35:44     1.2  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:44     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:44     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:45     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:45     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:46     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:46     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:46     1.2  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:35:47     1.2  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:47     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:47     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:47     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:48     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:48     1.2  STATUS                         Computed table for promoters
2019-04-16 02:35:49     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:49     1.2  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:49     1.2  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:35:50     1.2  STATUS             STARTED Retrieving comparison info
2019-04-16 02:35:50     1.2  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:35:50     1.2  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:35:50     1.2  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:51     1.2  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:35:51     1.2    INFO                         Conducting differential analysis using limma
2019-04-16 02:35:51     1.2  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:35:52     1.2  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:52     1.2  STATUS                         Computed table for genes
2019-04-16 02:35:53     1.2  STATUS                         Computed table for tiling
2019-04-16 02:35:54     1.2  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:35:54     1.2  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:35:54     1.2  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:35:54     1.2  STATUS             STARTED Testing function: get.region.types
2019-04-16 02:35:55     1.2  STATUS             COMPLETED Testing function: get.region.types
2019-04-16 02:35:55     1.2  STATUS             STARTED Testing function: get.comparisons
2019-04-16 02:35:55     1.2  STATUS             COMPLETED Testing function: get.comparisons
2019-04-16 02:35:56     1.2  STATUS             STARTED Testing function: get.comparison.grouplabels
2019-04-16 02:35:56     1.2  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2019-04-16 02:35:56     1.2  STATUS             STARTED Testing function: get.site.test.method
2019-04-16 02:35:56     1.2  STATUS             COMPLETED Testing function: get.site.test.method
2019-04-16 02:35:57     1.2  STATUS             STARTED Testing function: get.table
2019-04-16 02:35:57     1.2  STATUS             COMPLETED Testing function: get.table
2019-04-16 02:35:57     1.2  STATUS             STARTED Testing function: addDiffMethTable
2019-04-16 02:35:58     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:35:58     1.2  STATUS             COMPLETED Testing function: addDiffMethTable
2019-04-16 02:35:58     1.2  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2019-04-16 02:35:59     1.2  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2019-04-16 02:35:59     1.2  STATUS             STARTED Destructor
2019-04-16 02:35:59     1.2  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:00     1.2  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:00     1.2  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:00     1.2  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:01     1.2  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:01     1.2  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:01     1.2  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:01     1.2  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:02     1.2  STATUS             COMPLETED Destructor
2019-04-16 02:36:02     1.2  STATUS         COMPLETED Testing class: RnBDiffMeth
2019-04-16 02:36:02     1.2  STATUS     COMPLETED Testing function: apply.iEVORA
2019-04-16 02:36:03     1.2  STATUS     STARTED Retrieving comparison info
2019-04-16 02:36:03     1.2  STATUS     COMPLETED Retrieving comparison info
2019-04-16 02:36:03     1.2  STATUS     STARTED Computing differential methylation tables
2019-04-16 02:36:04     1.2  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:04     1.2  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:04     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:04     1.2  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:05     1.2  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:06     1.2  STATUS                 Computed table for tiling
2019-04-16 02:36:06     1.2  STATUS                 Computed table for genes
2019-04-16 02:36:07     1.2  STATUS                 Computed table for promoters
2019-04-16 02:36:08     1.2  STATUS                 Computed table for cpgislands
2019-04-16 02:36:08     1.2  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:08     1.2  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:09     1.2  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:09     1.2  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:09     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:10     1.2  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:10     1.2  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:11     1.2  STATUS                 Computed table for tiling
2019-04-16 02:36:12     1.2  STATUS                 Computed table for genes
2019-04-16 02:36:13     1.2  STATUS                 Computed table for promoters
2019-04-16 02:36:13     1.2  STATUS                 Computed table for cpgislands
2019-04-16 02:36:13     1.2  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:14     1.2  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:14     1.2  STATUS     COMPLETED Computing differential methylation tables
2019-04-16 02:36:14     1.2  STATUS     STARTED Retrieving comparison info
2019-04-16 02:36:15     1.2  STATUS     COMPLETED Retrieving comparison info
2019-04-16 02:36:15     1.2  STATUS     STARTED Computing differential methylation tables
2019-04-16 02:36:15     1.2  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:15     1.2  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:16     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:16     1.2  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:16     1.2  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:17     1.2  STATUS                 Computed table for genes
2019-04-16 02:36:18     1.2  STATUS                 Computed table for tiling
2019-04-16 02:36:18     1.2  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:19     1.2  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:19     1.2  STATUS     COMPLETED Computing differential methylation tables
2019-04-16 02:36:19     1.2  STATUS     STARTED Retrieving comparison info
2019-04-16 02:36:20     1.2  STATUS     COMPLETED Retrieving comparison info
2019-04-16 02:36:20     1.2  STATUS     STARTED Computing differential methylation tables
2019-04-16 02:36:20     1.2  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:20     1.2  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:21     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:21     1.2  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:21     1.2  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:22     1.2  STATUS                 Computed table for genes
2019-04-16 02:36:23     1.2  STATUS                 Computed table for tiling
2019-04-16 02:36:23     1.2  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:24     1.2  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:24     1.2  STATUS     COMPLETED Computing differential methylation tables
2019-04-16 02:36:24     1.2  STATUS     STARTED Retrieving comparison info
2019-04-16 02:36:24     1.2  STATUS     COMPLETED Retrieving comparison info
2019-04-16 02:36:25     1.2  STATUS     STARTED Computing differential methylation tables
2019-04-16 02:36:25     1.2  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:25     1.2  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:25     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:26     1.2  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:26     1.2  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:26     1.2  STATUS                 Computed table for promoters
2019-04-16 02:36:27     1.2  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:27     1.2  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:27     1.2  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:27     1.2  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:28     1.2    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:28     1.2  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:28     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:29     1.3  STATUS                 Computed table for promoters
2019-04-16 02:36:29     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:29     1.3  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:29     1.3  STATUS     COMPLETED Computing differential methylation tables
2019-04-16 02:36:30     1.3  STATUS     STARTED Retrieving comparison info
2019-04-16 02:36:30     1.3  STATUS     COMPLETED Retrieving comparison info
2019-04-16 02:36:30     1.3  STATUS     STARTED Computing differential methylation tables
2019-04-16 02:36:30     1.3  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:31     1.3  STATUS             STARTED Computing Differential Methylation Table
2019-04-16 02:36:31     1.3    INFO                 Conducting differential analysis using limma
2019-04-16 02:36:31     1.3  STATUS             COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:31     1.3  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:32     1.3  STATUS                 Computed table for genes
2019-04-16 02:36:33     1.3  STATUS                 Computed table for tiling
2019-04-16 02:36:33     1.3  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:33     1.3  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:34     1.3  STATUS     COMPLETED Computing differential methylation tables
2019-04-16 02:36:34     1.3  STATUS     STARTED Testing function: get.region.types
2019-04-16 02:36:34     1.3  STATUS     COMPLETED Testing function: get.region.types
2019-04-16 02:36:34     1.3  STATUS     STARTED Testing function: get.comparisons
2019-04-16 02:36:35     1.3  STATUS     COMPLETED Testing function: get.comparisons
2019-04-16 02:36:35     1.3  STATUS     STARTED Testing function: get.comparison.grouplabels
2019-04-16 02:36:35     1.3  STATUS     COMPLETED Testing function: get.comparison.grouplabels
2019-04-16 02:36:35     1.3  STATUS     STARTED Testing function: get.site.test.method
2019-04-16 02:36:35     1.3  STATUS     COMPLETED Testing function: get.site.test.method
2019-04-16 02:36:36     1.3  STATUS     STARTED Testing function: get.table
2019-04-16 02:36:36     1.3  STATUS     COMPLETED Testing function: get.table
2019-04-16 02:36:36     1.3  STATUS     STARTED Testing function: addDiffMethTable
2019-04-16 02:36:37     1.3    INFO         Conducting differential analysis using limma
2019-04-16 02:36:37     1.3  STATUS     COMPLETED Testing function: addDiffMethTable
2019-04-16 02:36:37     1.3  STATUS     STARTED Testing functions: join.diffMeth, is.valid
2019-04-16 02:36:38     1.3  STATUS     COMPLETED Testing functions: join.diffMeth, is.valid
2019-04-16 02:36:38     1.3  STATUS     STARTED Destructor
2019-04-16 02:36:38     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:39     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:39     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:39     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:39     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:40     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:40     1.3  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:40     1.3  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:36:41     1.3  STATUS     COMPLETED Destructor
2019-04-16 02:36:41     1.3    INFO     Conducting differential analysis using limma
2019-04-16 02:36:41     1.3    INFO     Conducting differential analysis using limma
2019-04-16 02:36:42     1.3  STATUS     STARTED diffVar method
2019-04-16 02:36:42     1.3  STATUS     COMPLETED diffVar method
2019-04-16 02:36:43     1.3  STATUS     STARTED diffVar method
Coefficients not estimable: x2x2 
2019-04-16 02:36:43     1.3  STATUS     COMPLETED diffVar method
2019-04-16 02:36:43     1.3  STATUS STARTED Unit testing: differential
2019-04-16 02:36:44     1.3  STATUS     STARTED Testing function: rowWelchP
2019-04-16 02:36:44     1.3  STATUS     COMPLETED Testing function: rowWelchP
2019-04-16 02:36:44     1.3  STATUS     STARTED Testing function: limmaP
2019-04-16 02:36:45     1.3  STATUS     COMPLETED Testing function: limmaP
2019-04-16 02:36:45     1.3  STATUS     STARTED Testing function: computeDiffTab.extended.site
2019-04-16 02:36:45     1.3    INFO         Conducting differential analysis using limma
2019-04-16 02:36:46     1.3  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2019-04-16 02:36:46     1.3  STATUS     STARTED Testing function: computeDiffTab.default.region
2019-04-16 02:36:46     1.3    INFO         Conducting differential analysis using limma
2019-04-16 02:36:47     1.3  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2019-04-16 02:36:47     1.3  STATUS     STARTED Testing function: combineTestPvalsMeth
2019-04-16 02:36:48     1.3  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2019-04-16 02:36:48     1.3  STATUS     STARTED Testing function: get.adjustment.variables
2019-04-16 02:36:48     1.3  STATUS     COMPLETED Testing function: get.adjustment.variables
2019-04-16 02:36:49     1.3  STATUS     STARTED Testing function: get.comparison.info
2019-04-16 02:36:49     1.3  STATUS     COMPLETED Testing function: get.comparison.info
2019-04-16 02:36:49     1.3  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2019-04-16 02:36:50     1.3  STATUS         STARTED Retrieving comparison info
2019-04-16 02:36:50     1.3  STATUS         COMPLETED Retrieving comparison info
2019-04-16 02:36:50     1.3  STATUS         STARTED Computing differential methylation tables
2019-04-16 02:36:50     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:51     1.3  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:36:51     1.3    INFO                     Conducting differential analysis using limma
2019-04-16 02:36:51     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:51     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:52     1.3  STATUS                     Computed table for tiling
2019-04-16 02:36:53     1.3  STATUS                     Computed table for genes
2019-04-16 02:36:54     1.3  STATUS                     Computed table for promoters
2019-04-16 02:36:54     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:36:55     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:55     1.3  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:36:55     1.3  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:36:55     1.3  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:36:56     1.3    INFO                     Conducting differential analysis using limma
2019-04-16 02:36:56     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:36:56     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:36:57     1.3  STATUS                     Computed table for tiling
2019-04-16 02:36:58     1.3  STATUS                     Computed table for genes
2019-04-16 02:36:59     1.3  STATUS                     Computed table for promoters
2019-04-16 02:36:59     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:36:59     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:00     1.3  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:00     1.3  STATUS         COMPLETED Computing differential methylation tables
2019-04-16 02:37:00     1.3  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2019-04-16 02:37:00     1.3  STATUS     STARTED Testing function: diffVar
2019-04-16 02:37:01     1.3  STATUS         STARTED diffVar method
2019-04-16 02:37:01     1.3  STATUS         COMPLETED diffVar method
2019-04-16 02:37:01     1.3  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2019-04-16 02:37:02     1.3  STATUS         COMPLETED diffVar method
2019-04-16 02:37:02     1.3  STATUS     COMPLETED Testing function: diffVar
2019-04-16 02:37:03     1.3  STATUS     STARTED Testing function: apply.iEVORA
2019-04-16 02:37:03     1.3  STATUS         STARTED iEVORA method
2019-04-16 02:37:05     1.3    INFO             No DVCs detected. All p-values set to 1.
2019-04-16 02:37:05     1.3  STATUS         COMPLETED iEVORA method
2019-04-16 02:37:06     1.3  STATUS         STARTED Testing function: rnb.execute.diffVar
2019-04-16 02:37:06     1.3  STATUS             STARTED Differential Variability
2019-04-16 02:37:06     1.3  STATUS                 STARTED Retrieving comparison info
2019-04-16 02:37:07     1.3  STATUS                 COMPLETED Retrieving comparison info
2019-04-16 02:37:07     1.3  STATUS                 STARTED Imputation procedure knn 
2019-04-16 02:37:07     1.3  STATUS                 COMPLETED Imputation procedure knn 
2019-04-16 02:37:08     1.3  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:08     1.3    INFO                     Conducting differential variability using diffVar
2019-04-16 02:37:08     1.3  STATUS                     STARTED diffVar method
2019-04-16 02:37:09     1.3  STATUS                     COMPLETED diffVar method
2019-04-16 02:37:09     1.3  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2019-04-16 02:37:10     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:11     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:12     1.3  STATUS                         Computed table for promoters
2019-04-16 02:37:12     1.3  STATUS                         Computed table for cpgislands
2019-04-16 02:37:12     1.3  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2019-04-16 02:37:13     1.3  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:13     1.3  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:13     1.3    INFO                     Conducting differential variability using diffVar
2019-04-16 02:37:14     1.3  STATUS                     STARTED diffVar method
2019-04-16 02:37:14     1.3  STATUS                     COMPLETED diffVar method
2019-04-16 02:37:15     1.3  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2019-04-16 02:37:16     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:16     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:17     1.3  STATUS                         Computed table for promoters
2019-04-16 02:37:17     1.3  STATUS                         Computed table for cpgislands
2019-04-16 02:37:18     1.3  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2019-04-16 02:37:18     1.3  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:18     1.3  STATUS             COMPLETED Differential Variability
2019-04-16 02:37:19     1.3  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2019-04-16 02:37:19     1.3  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2019-04-16 02:37:19     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:37:20     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:37:20     1.3  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:37:20     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:20     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:37:21     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:37:21     1.3  STATUS                         STARTED Imputation procedure knn 
2019-04-16 02:37:21     1.3  STATUS                         COMPLETED Imputation procedure knn 
2019-04-16 02:37:22     1.3    INFO                         Conducting differential variability using diffVar
2019-04-16 02:37:22     1.3  STATUS                         STARTED diffVar method
2019-04-16 02:37:22     1.3  STATUS                         COMPLETED diffVar method
2019-04-16 02:37:23     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:37:23     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:25     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:26     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:26     1.3  STATUS                         Computed table for promoters
2019-04-16 02:37:27     1.3  STATUS                         Computed table for cpgislands
2019-04-16 02:37:27     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:28     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:28     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:28     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:37:29     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:37:29     1.3  STATUS                         STARTED Imputation procedure knn 
2019-04-16 02:37:29     1.3  STATUS                         COMPLETED Imputation procedure knn 
2019-04-16 02:37:30     1.3    INFO                         Conducting differential variability using diffVar
2019-04-16 02:37:30     1.3  STATUS                         STARTED diffVar method
2019-04-16 02:37:30     1.3  STATUS                         COMPLETED diffVar method
2019-04-16 02:37:31     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:37:31     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:33     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:34     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:35     1.3  STATUS                         Computed table for promoters
2019-04-16 02:37:35     1.3  STATUS                         Computed table for cpgislands
2019-04-16 02:37:36     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:36     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:36     1.3  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:37:37     1.3  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2019-04-16 02:37:37     1.3  STATUS         STARTED Testing class: RnBDiffMeth
2019-04-16 02:37:37     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:37:38     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:37:38     1.3  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:37:38     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:39     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:37:39     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:37:39     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:37:40     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:41     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:42     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:42     1.3  STATUS                         Computed table for promoters
2019-04-16 02:37:43     1.3  STATUS                         Computed table for cpgislands
2019-04-16 02:37:43     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:44     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:44     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:44     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:37:45     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:37:45     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:37:45     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:47     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:47     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:48     1.3  STATUS                         Computed table for promoters
2019-04-16 02:37:49     1.3  STATUS                         Computed table for cpgislands
2019-04-16 02:37:49     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:49     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:37:50     1.3  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:37:50     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:37:50     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:37:51     1.3  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:37:51     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:51     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:37:52     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:37:52     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:37:52     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:53     1.3  STATUS                         Computed table for genes
2019-04-16 02:37:54     1.3  STATUS                         Computed table for tiling
2019-04-16 02:37:55     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:55     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:55     1.3  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:37:56     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:37:56     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:37:56     1.3  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:37:56     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:37:57     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:37:57     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:37:57     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:37:58     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:37:58     1.3  STATUS                         Computed table for genes
2019-04-16 02:38:00     1.3  STATUS                         Computed table for tiling
2019-04-16 02:38:00     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:00     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:00     1.3  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:38:01     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:38:01     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:38:01     1.3  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:38:02     1.3  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:02     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:38:02     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:38:03     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:03     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:04     1.3  STATUS                         Computed table for promoters
2019-04-16 02:38:04     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:04     1.3  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:05     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:05     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:38:05     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:38:06     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:06     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:06     1.3  STATUS                         Computed table for promoters
2019-04-16 02:38:07     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:07     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:07     1.3  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:38:08     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:38:08     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:38:08     1.3  STATUS             STARTED Computing differential methylation tables
2019-04-16 02:38:09     1.3  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:09     1.3  STATUS                     STARTED Computing Differential Methylation Table
2019-04-16 02:38:09     1.3    INFO                         Conducting differential analysis using limma
2019-04-16 02:38:10     1.3  STATUS                     COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:10     1.3  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:11     1.3  STATUS                         Computed table for genes
2019-04-16 02:38:12     1.3  STATUS                         Computed table for tiling
2019-04-16 02:38:12     1.3  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:12     1.3  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:13     1.3  STATUS             COMPLETED Computing differential methylation tables
2019-04-16 02:38:13     1.3  STATUS             STARTED Testing function: get.region.types
2019-04-16 02:38:13     1.3  STATUS             COMPLETED Testing function: get.region.types
2019-04-16 02:38:14     1.3  STATUS             STARTED Testing function: get.comparisons
2019-04-16 02:38:14     1.3  STATUS             COMPLETED Testing function: get.comparisons
2019-04-16 02:38:14     1.3  STATUS             STARTED Testing function: get.comparison.grouplabels
2019-04-16 02:38:15     1.3  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2019-04-16 02:38:15     1.3  STATUS             STARTED Testing function: get.site.test.method
2019-04-16 02:38:15     1.3  STATUS             COMPLETED Testing function: get.site.test.method
2019-04-16 02:38:15     1.3  STATUS             STARTED Testing function: get.table
2019-04-16 02:38:16     1.3  STATUS             COMPLETED Testing function: get.table
2019-04-16 02:38:16     1.3  STATUS             STARTED Testing function: addDiffMethTable
2019-04-16 02:38:16     1.3    INFO                 Conducting differential analysis using limma
2019-04-16 02:38:17     1.3  STATUS             COMPLETED Testing function: addDiffMethTable
2019-04-16 02:38:17     1.3  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2019-04-16 02:38:18     1.3  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2019-04-16 02:38:18     1.3  STATUS             STARTED Destructor
2019-04-16 02:38:18     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:19     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:19     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:19     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:19     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:20     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:20     1.3  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:20     1.3  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2019-04-16 02:38:21     1.3  STATUS             COMPLETED Destructor
2019-04-16 02:38:21     1.3  STATUS         COMPLETED Testing class: RnBDiffMeth
2019-04-16 02:38:21     1.3  STATUS     COMPLETED Testing function: apply.iEVORA
2019-04-16 02:38:22     1.3  STATUS     STARTED iEVORA method
2019-04-16 02:38:24     1.3    INFO         No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2019-04-16 02:38:24     1.3  STATUS         STARTED Retrieving comparison info
2019-04-16 02:38:25     1.3  STATUS         COMPLETED Retrieving comparison info
2019-04-16 02:38:25     1.3  STATUS         STARTED Computing differential methylation tables
2019-04-16 02:38:25     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:26     1.3  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:38:26     1.3    INFO                     Conducting differential analysis using limma
2019-04-16 02:38:26     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:27     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:28     1.3  STATUS                     Computed table for tiling
2019-04-16 02:38:29     1.3  STATUS                     Computed table for genes
2019-04-16 02:38:29     1.3  STATUS                     Computed table for promoters
2019-04-16 02:38:30     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:38:30     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:31     1.3  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:31     1.3  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:31     1.3  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:38:31     1.3    INFO                     Conducting differential analysis using limma
2019-04-16 02:38:32     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:32     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:33     1.3  STATUS                     Computed table for tiling
2019-04-16 02:38:34     1.3  STATUS                     Computed table for genes
2019-04-16 02:38:34     1.3  STATUS                     Computed table for promoters
2019-04-16 02:38:35     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:38:35     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:36     1.3  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:36     1.3  STATUS         COMPLETED Computing differential methylation tables
2019-04-16 02:38:36     1.3  STATUS         STARTED Retrieving comparison info
2019-04-16 02:38:37     1.3  STATUS         COMPLETED Retrieving comparison info
2019-04-16 02:38:37     1.3  STATUS         STARTED Computing differential methylation tables
2019-04-16 02:38:37     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:37     1.3  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:38:38     1.3    INFO                     Conducting differential analysis using limma
2019-04-16 02:38:38     1.3  STATUS                     STARTED Imputation procedure knn 
2019-04-16 02:38:38     1.3  STATUS                     COMPLETED Imputation procedure knn 
2019-04-16 02:38:39     1.3    INFO                     Conducting differential variability using diffVar
2019-04-16 02:38:39     1.3  STATUS                     STARTED diffVar method
2019-04-16 02:38:39     1.3  STATUS                     COMPLETED diffVar method
2019-04-16 02:38:40     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:40     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:42     1.3  STATUS                     Computed table for tiling
2019-04-16 02:38:42     1.3  STATUS                     Computed table for genes
2019-04-16 02:38:43     1.3  STATUS                     Computed table for promoters
2019-04-16 02:38:44     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:38:44     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:45     1.3  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:45     1.3  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:45     1.3  STATUS                 STARTED Computing Differential Methylation Table
2019-04-16 02:38:45     1.3    INFO                     Conducting differential analysis using limma
2019-04-16 02:38:46     1.3  STATUS                     STARTED Imputation procedure knn 
2019-04-16 02:38:46     1.3  STATUS                     COMPLETED Imputation procedure knn 
2019-04-16 02:38:46     1.3    INFO                     Conducting differential variability using diffVar
2019-04-16 02:38:47     1.3  STATUS                     STARTED diffVar method
2019-04-16 02:38:47     1.3  STATUS                     COMPLETED diffVar method
2019-04-16 02:38:48     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2019-04-16 02:38:48     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:49     1.3  STATUS                     Computed table for tiling
2019-04-16 02:38:50     1.3  STATUS                     Computed table for genes
2019-04-16 02:38:51     1.3  STATUS                     Computed table for promoters
2019-04-16 02:38:52     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:38:52     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2019-04-16 02:38:53     1.3  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2019-04-16 02:38:53     1.3  STATUS         COMPLETED Computing differential methylation tables
2019-04-16 02:38:53     1.3  STATUS         STARTED Differential Variability
2019-04-16 02:38:53     1.3  STATUS             STARTED Retrieving comparison info
2019-04-16 02:38:54     1.3  STATUS             COMPLETED Retrieving comparison info
2019-04-16 02:38:54     1.3  STATUS             STARTED Imputation procedure knn 
2019-04-16 02:38:54     1.3  STATUS             COMPLETED Imputation procedure knn 
2019-04-16 02:38:55     1.3  STATUS             STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:38:55     1.3    INFO                 Conducting differential variability using diffVar
2019-04-16 02:38:55     1.3  STATUS                 STARTED diffVar method
2019-04-16 02:38:56     1.3  STATUS                 COMPLETED diffVar method
2019-04-16 02:38:56     1.3  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2019-04-16 02:38:57     1.3  STATUS                     Computed table for tiling
2019-04-16 02:38:58     1.3  STATUS                     Computed table for genes
2019-04-16 02:38:58     1.3  STATUS                     Computed table for promoters
2019-04-16 02:38:59     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:38:59     1.3  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2019-04-16 02:39:00     1.3  STATUS             COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2019-04-16 02:39:00     1.3  STATUS             STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2019-04-16 02:39:00     1.3    INFO                 Conducting differential variability using diffVar
2019-04-16 02:39:00     1.3  STATUS                 STARTED diffVar method
2019-04-16 02:39:01     1.3  STATUS                 COMPLETED diffVar method
2019-04-16 02:39:01     1.3  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2019-04-16 02:39:02     1.3  STATUS                     Computed table for tiling
2019-04-16 02:39:03     1.3  STATUS                     Computed table for genes
2019-04-16 02:39:03     1.3  STATUS                     Computed table for promoters
2019-04-16 02:39:04     1.3  STATUS                     Computed table for cpgislands
2019-04-16 02:39:04     1.3  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2019-04-16 02:39:05     1.3  STATUS             COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2019-04-16 02:39:05     1.3  STATUS         COMPLETED Differential Variability
2019-04-16 02:39:05     1.3  STATUS STARTED Analysis
2019-04-16 02:39:06     1.3    INFO     Loaded information from data.RData
2019-04-16 02:39:06     1.3  STATUS     STARTED Processing Detection P-values
2019-04-16 02:39:06     1.3    INFO         Removed 3979 probes that overlap with SNPs
2019-04-16 02:39:06     1.3    INFO         Completed Greedycut on 510 samples
2019-04-16 02:39:07     1.3  STATUS     COMPLETED Processing Detection P-values
2019-04-16 02:39:07     1.3 WARNING     File not found: data2.RData
2019-04-16 02:39:07     1.3  STATUS COMPLETED Analysis

2019-04-16 02:39:08     1.3  STATUS STARTED Testing imputation
2019-04-16 02:39:08     1.3  STATUS     STARTED Imputation procedure knn 
2019-04-16 02:39:09     1.3  STATUS     COMPLETED Imputation procedure knn 
2019-04-16 02:39:10     1.3  STATUS     STARTED Imputation procedure mean.samples 
2019-04-16 02:39:11     1.3  STATUS     COMPLETED Imputation procedure mean.samples 
2019-04-16 02:39:11     1.3  STATUS     STARTED Imputation procedure mean.cpgs 
2019-04-16 02:39:12     1.3  STATUS     COMPLETED Imputation procedure mean.cpgs 
2019-04-16 02:39:13     1.3  STATUS     STARTED Imputation procedure random 
2019-04-16 02:39:14     1.3  STATUS     COMPLETED Imputation procedure random 
2019-04-16 02:39:14     1.3  STATUS COMPLETED Testing imputation

2019-04-16 02:39:14     1.3  STATUS STARTED Testing age prediction
2019-04-16 02:39:15     1.3  STATUS     STARTED Performing Age Prediction
2019-04-16 02:39:17     1.4  STATUS     COMPLETED Performing Age Prediction
2019-04-16 02:39:17     1.4  STATUS COMPLETED Testing age prediction

2019-04-16 02:39:18     1.4  STATUS STARTED Testing CNV computation
2019-04-16 02:39:18     1.4  STATUS     STARTED Copy Number Variation
2019-04-16 02:40:46     1.3  STATUS         STARTED Copy Number Variation Section
2019-04-16 02:41:07     1.3  STATUS             Added CNV profile plots
2019-04-16 02:41:07     1.3  STATUS             Added CpG counts
2019-04-16 02:41:07     1.3  STATUS         COMPLETED Copy Number Variation Section
2019-04-16 02:41:08     1.3  STATUS     COMPLETED Copy Number Variation
2019-04-16 02:41:08     1.3  STATUS COMPLETED Testing CNV computation

2019-04-16 02:41:09     1.3  STATUS STARTED Performing Age Prediction
2019-04-16 02:41:11     1.4  STATUS COMPLETED Performing Age Prediction

2019-04-16 02:41:11     1.4  STATUS STARTED Copy Number Variation
2019-04-16 02:42:40     1.4  STATUS     STARTED Copy Number Variation Section
2019-04-16 02:43:00     1.4  STATUS         Added CNV profile plots
2019-04-16 02:43:00     1.4  STATUS         Added CpG counts
2019-04-16 02:43:01     1.4  STATUS     COMPLETED Copy Number Variation Section
2019-04-16 02:43:01     1.4  STATUS COMPLETED Copy Number Variation

2019-04-16 02:43:01     1.4  STATUS STARTED Imputation procedure knn 
2019-04-16 02:43:02     1.4  STATUS COMPLETED Imputation procedure knn 

2019-04-16 02:43:03     1.4  STATUS STARTED Imputation procedure mean.samples 
2019-04-16 02:43:04     1.4  STATUS COMPLETED Imputation procedure mean.samples 

2019-04-16 02:43:04     1.4  STATUS STARTED Imputation procedure mean.cpgs 
2019-04-16 02:43:05     1.4  STATUS COMPLETED Imputation procedure mean.cpgs 

2019-04-16 02:43:05     1.4  STATUS STARTED Imputation procedure random 
2019-04-16 02:43:06     1.4  STATUS COMPLETED Imputation procedure random 

2019-04-16 02:43:07     1.4  STATUS STARTED Testing imputation
2019-04-16 02:43:07     1.4  STATUS     STARTED Imputation procedure knn 
2019-04-16 02:43:08     1.4  STATUS     COMPLETED Imputation procedure knn 
2019-04-16 02:43:08     1.4  STATUS     STARTED Imputation procedure mean.samples 
2019-04-16 02:43:09     1.4  STATUS     COMPLETED Imputation procedure mean.samples 
2019-04-16 02:43:09     1.4  STATUS     STARTED Imputation procedure mean.cpgs 
2019-04-16 02:43:10     1.4  STATUS     COMPLETED Imputation procedure mean.cpgs 
2019-04-16 02:43:10     1.4  STATUS     STARTED Imputation procedure random 
2019-04-16 02:43:11     1.4  STATUS     COMPLETED Imputation procedure random 
2019-04-16 02:43:11     1.4  STATUS COMPLETED Testing imputation

2019-04-16 02:43:12     1.4  STATUS STARTED Testing age prediction
2019-04-16 02:43:12     1.4  STATUS     STARTED Performing Age Prediction
2019-04-16 02:43:14     1.4  STATUS     COMPLETED Performing Age Prediction
2019-04-16 02:43:14     1.4  STATUS COMPLETED Testing age prediction

2019-04-16 02:43:14     1.4  STATUS STARTED Testing CNV computation
2019-04-16 02:43:15     1.4  STATUS     STARTED Copy Number Variation
2019-04-16 02:44:38     1.4  STATUS         STARTED Copy Number Variation Section
2019-04-16 02:44:59     1.4  STATUS             Added CNV profile plots
2019-04-16 02:44:59     1.4  STATUS             Added CpG counts
2019-04-16 02:44:59     1.4  STATUS         COMPLETED Copy Number Variation Section
2019-04-16 02:45:00     1.4  STATUS     COMPLETED Copy Number Variation
2019-04-16 02:45:00     1.4  STATUS COMPLETED Testing CNV computation



RUNIT TEST PROTOCOL -- Tue Apr 16 02:45:12 2019 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RnBeads RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
There were 37 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
481.304 180.790 667.286

Example timings

RnBeads.Rcheck/RnBeads-Ex.timings

nameusersystemelapsed
M-methods0.0000.0000.001
U-methods0.0010.0000.000
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods000
addRegionSubsegments000
annotation-methods0.0010.0000.000
assembly-methods000
combine-methods0.0000.0000.001
combineTestPvalsMeth000
computeDiffTab.region000
computeDiffTab.site000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport000
createReportPlot000
downloadLolaDbs000
dpval-methods0.0000.0000.001
exportDMRs2regionFile0.0000.0000.001
get.adjustment.variables0.0000.0000.001
get.comparison.grouplabels-RnBDiffMeth-methods0.0000.0000.001
get.comparison.groupsizes-RnBDiffMeth-methods0.0000.0010.001
get.comparison.info000
get.comparisons-RnBDiffMeth-methods0.0010.0000.000
get.covariates.sva0.0000.0000.001
get.covg.thres-RnBDiffMeth-methods000
get.files0.0010.0000.000
get.region.types-RnBDiffMeth-methods0.0000.0000.001
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods0.0010.0010.000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods0.0010.0000.000
getTargetFromLolaDb000
has.covariates.sva000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods000
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods0.0010.0000.000
limmaP000
loadLolaDbs0.0000.0000.001
logger.argument0.0000.0000.001
logger.getfiles0.0000.0000.001
logger.isinitialized0.0000.0000.001
logger.validate.file0.0010.0000.001
loggerManagement0.0000.0000.001
loggerMessages0.0000.0010.000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot000
mergeSamples-methods0.0010.0010.000
meth-methods000
mval-methods000
nsites-methods000
parallel.getNumWorkers000
parallel.isEnabled000
parallel.setup0.0010.0000.000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth0.0010.0000.001
performLolaEnrichment.diffMeth0.0010.0000.000
performLolaEnrichment.diffVar000
pheno-methods0.0000.0010.000
qc-methods0.0010.0000.001
read.sample.annotation0.0000.0000.001
regionMapping-methods0.0010.0000.000
regions-methods000
reload-RnBDiffMeth-methods000
remove.regions-methods000
remove.samples-methods000
remove.sites-methods0.0000.0000.001
rnb.RnBSet.to.GRangesList000
rnb.RnBSet.to.bed0.0010.0000.000
rnb.RnBSet.to.bedGraph0.0000.0000.001
rnb.add.list0.0000.0010.000
rnb.add.paragraph000
rnb.add.reference0.0000.0000.001
rnb.add.section000
rnb.annotation.size000
rnb.annotation2data.frame0.0000.0000.001
rnb.beta2mval000
rnb.execute.batcheffects0.0000.0010.000
rnb.execute.clustering000
rnb.execute.computeDiffMeth000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal000
rnb.execute.dreduction000
rnb.execute.export.csv000
rnb.execute.greedycut0.0010.0000.001
rnb.execute.import000
rnb.execute.na.removal0.0000.0000.001
rnb.execute.normalization000
rnb.execute.sex.prediction000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva000
rnb.execute.tnt0.0000.0000.001
rnb.execute.variability.removal000
rnb.export.all.annotation000
rnb.export.annotation0.0010.0000.000
rnb.export.to.ewasher000
rnb.export.to.trackhub0.0000.0000.001
rnb.get.annotation000
rnb.get.assemblies000
rnb.get.chromosomes000
rnb.get.directory000
rnb.get.mapping000
rnb.get.reference000
rnb.get.reliability.matrix0.0000.0000.001
rnb.infinium.control.targets0.0000.0000.001
rnb.initialize.reports0.0000.0000.001
rnb.is.option0.0000.0000.001
rnb.load.annotation.from.db000
rnb.message.plot000
rnb.mval2beta000
rnb.options000
rnb.options2xml000
rnb.plot.betadistribution.probeCategories000
rnb.plot.betadistribution.sampleGroups000
rnb.plot.control.barplot000
rnb.plot.control.boxplot000
rnb.plot.dreduction0.0000.0000.001
rnb.plot.locus.profile0.0000.0010.000
rnb.plot.negative.boxplot0.0000.0000.001
rnb.plot.region.profile.density000
rnb.plot.region.profiles000
rnb.plot.region.site.density000
rnb.plot.sentrix.distribution000
rnb.plot.snp.barplot000
rnb.plot.snp.boxplot0.0000.0000.001
rnb.plot.snp.heatmap000
rnb.region.types0.0000.0000.001
rnb.region.types.for.analysis0.0010.0000.000
rnb.remove.annotation0.0010.0000.000
rnb.run.example000
rnb.runs000
rnb.sample.groups000
rnb.sample.summary.table0.0000.0000.001
rnb.set.annotation000
rnb.write.table000
rnb.xml2options0.0010.0000.000
rowOneSampleTP000
rowWelchP000
run-RnBClusterRun-methods000
samples-methods000
save.tables-RnBDiffMeth-methods000
set.covariates.sva0.0010.0000.001
sites-methods0.0000.0000.001
summarize.regions-methods0.0000.0000.001
summarized.regions-methods0.0000.0000.001