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CHECK report for RnBeads on tokay2

This page was generated on 2018-10-17 08:40:30 -0400 (Wed, 17 Oct 2018).

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

Summary

Package: RnBeads
Version: 1.12.1
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RnBeads_1.12.1.tar.gz
StartedAt: 2018-10-17 04:30:07 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:42:58 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 771.4 seconds
RetCode: 0
Status:  OK  
CheckDir: RnBeads.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings RnBeads_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/RnBeads.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RnBeads/DESCRIPTION' ... OK
* this is package 'RnBeads' version '1.12.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'GenomicRanges' 'MASS' 'cluster' 'ff'
  'fields' 'ggplot2' 'gplots' 'gridExtra' 'limma' 'matrixStats'
  'illuminaio' 'methylumi' 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RnBeads' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R      3.0Mb
    html   1.4Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from 'RnBeads' for: 'samples'

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

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from 'RnBeads' for: 'samples'

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

Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
  'grDevices:::.smoothScatterCalcDensity'
  'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
  'minfi:::.normalizeFunnorm450k'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
  'stopCluster'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'phenoData'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'assayDataElementNames'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'featureNames'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'varLabels'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'featureData'
add.age.histogram: no visible binding for global variable 'Age'
add.age.histogram: no visible binding for global variable '..count..'
add.age.histogram: no visible binding for global variable '..density..'
add.agecomparison.plot: no visible global function definition for
  'samples'
add.agecomparison.plot: no visible binding for global variable 'Sample'
add.combination.plot: no visible global function definition for
  'samples'
add.combination.plot: no visible binding for global variable
  'Difference'
add.combination.plot: no visible binding for global variable 'Density'
add.combination.plot: no visible binding for global variable 'yint'
add.combination.plot: no visible binding for global variable 'Measure'
add.error.plot: no visible binding for global variable 'Value'
add.error.plot: no visible binding for global variable 'Sample'
add.error.plot: no visible binding for global variable 'Deviance'
add.error.plot: no visible binding for global variable 'yint'
add.error.plot: no visible binding for global variable 'Measure'
add.negative.control.boxplot: no visible global function definition for
  'samples'
add.qc.barplots: no visible global function definition for 'samples'
add.quantile.plot: no visible binding for global variable 'Difference'
add.quantile.plot: no visible binding for global variable '..density..'
add.quantile.plot: no visible binding for global variable 'Sample'
add.quantile.plot: no visible binding for global variable 'Density'
add.seq.coverage.histograms: no visible global function definition for
  'samples'
add.seq.coverage.plot: no visible global function definition for
  'samples'
add.seq.coverage.violins: no visible global function definition for
  'samples'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'var.diff'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'log10P'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'combinedRank.var'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'log10FDR'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'mean.diff'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'diffmeth.p.val'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'combinedRank'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'mean.quot.log2'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'diffmeth.p.adj.fdr'
agePredictorBiseq: no visible global function definition for
  'impute.knn'
agePredictorBiseq: no visible global function definition for 'samples'
agePredictorChip: no visible global function definition for
  'impute.knn'
append.cpg.stats: no visible global function definition for '%dopar%'
append.cpg.stats: no visible global function definition for 'foreach'
append.cpg.stats: no visible binding for global variable 'chrom'
basic_combine: no visible global function definition for 'samples'
computeDiffTab.default.region: no visible global function definition
  for '%dopar%'
computeDiffTab.default.region: no visible global function definition
  for 'foreach'
computeDiffTab.default.region: no visible binding for global variable
  'i'
computeDiffTab.default.site: no visible binding for global variable
  'p.vals.t.na.adj'
computeDiffTab.default.site : <anonymous>: no visible binding for
  global variable '.inds.g2'
computeDiffVar.bin.site: no visible binding for global variable
  'p.vals.t.na.adj'
computeDiffVar.bin.site : <anonymous>: no visible binding for global
  variable 'eps'
computeDiffVar.bin.site : <anonymous>: no visible binding for global
  variable '.inds.g2'
computeDiffVar.default.region: no visible global function definition
  for '%dopar%'
computeDiffVar.default.region: no visible global function definition
  for 'foreach'
computeDiffVar.default.region: no visible binding for global variable
  'i'
create.densityScatter: no visible binding for global variable
  '..density..'
create.diffMeth.diffVar.subsample: no visible binding for global
  variable '..density..'
create.ucsc.track.hub: no visible global function definition for
  'samples'
createPredictor : ret: no visible global function definition for
  'impute.knn'
cv.array: no visible global function definition for 'impute.knn'
data.frame2GRanges: no visible global function definition for
  'seqlevels<-'
data.frame2GRanges: no visible global function definition for
  'genome<-'
diffVar: no visible binding for global variable 'ng.2'
diffVar: no visible global function definition for 'varFit'
diffVar: no visible binding for global variable 'group1'
diffVar: no visible binding for global variable 'group2'
estimateProportionsCP: no visible global function definition for 'lme'
estimateProportionsCP: no visible global function definition for
  'getVarCov'
general.cv: no visible global function definition for '%dopar%'
general.cv: no visible global function definition for 'foreach'
general.cv: no visible binding for global variable 'i'
get.adjustment.variables: no visible global function definition for
  'samples'
get.comparison.info : rm.na.from.adj.tab: no visible global function
  definition for 'samples'
get.components.isva: no visible global function definition for 'DoISVA'
get.components.sva: no visible global function definition for 'sva'
get.cpg.stats: no visible global function definition for
  'dinucleotideFrequency'
get.cpg.stats: no visible global function definition for
  'letterFrequency'
get.dataset.matrix: no visible global function definition for 'samples'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
  variable 'report'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
  variable 'refText'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
  variable 'diffmeth'
getCGCounts : <anonymous>: no visible global function definition for
  'ChrNumeric'
getGLADProfiles: no visible global function definition for 'samples'
getGLADProfiles : <anonymous>: no visible global function definition
  for 'as.profileCGH'
getGLADProfiles : <anonymous>: no visible global function definition
  for 'daglad'
getMergeList: no visible global function definition for 'samples'
groupPermutationP.site.parallel: no visible global function definition
  for '%dopar%'
groupPermutationP.site.parallel: no visible global function definition
  for 'foreach'
iEVORA: no visible global function definition for 'qvalue'
imputation.low.memory.cpgs: no visible global function definition for
  'samples'
inferWBCbyLme: no visible global function definition for 'lme'
inferWBCbyLme: no visible global function definition for 'getVarCov'
intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylationEPICmanifest'
intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylation450kmanifest'
intensities.by.color: no visible global function definition for
  'samples'
knn.imputation: no visible global function definition for 'impute.knn'
limmaP: no visible binding for global variable 'group1'
limmaP: no visible binding for global variable 'group2'
loadLolaDbs: no visible global function definition for 'loadRegionDB'
loadLolaDbs: no visible global function definition for 'mergeRegionDBs'
locus.profile.get.base.tracks: no visible global function definition
  for 'useMart'
locus.profile.get.base.tracks: no visible global function definition
  for 'IdeogramTrack'
locus.profile.get.base.tracks: no visible global function definition
  for 'GenomeAxisTrack'
locus.profile.get.base.tracks: no visible global function definition
  for 'BiomartGeneRegionTrack'
locus.profile.get.base.tracks: no visible global function definition
  for 'UcscTrack'
locus.profile.get.methylation.track.heatmap: no visible global function
  definition for 'DataTrack'
locus.profile.get.methylation.track.smooth: no visible global function
  definition for 'DataTrack'
methylumi.intensities.by.color: no visible global function definition
  for 'featureNames'
methylumi.intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylation450kmanifest'
methylumi.intensities.by.color: no visible global function definition
  for 'assayDataElement'
parallel.setup: no visible global function definition for
  'registerDoParallel'
parallel.setup: no visible global function definition for
  'getDoParWorkers'
performLolaEnrichment.diffMeth: no visible global function definition
  for 'runLOLA'
performLolaEnrichment.diffVar: no visible global function definition
  for 'runLOLA'
plot.heatmap.pc.correlations: no visible global function definition for
  'melt'
plot.heatmap.pc.correlations: no visible global function definition for
  'grid.newpage'
plot.heatmap.pc.correlations: no visible global function definition for
  'grid.draw'
plot.heatmap.pc.pvalues: no visible global function definition for
  'melt'
plot.heatmap.pc.pvalues: no visible global function definition for
  'grid.newpage'
plot.heatmap.pc.pvalues: no visible global function definition for
  'grid.draw'
plot.heatmap.rand: no visible global function definition for 'melt'
plot.heatmap.symm: no visible global function definition for 'melt'
plot.heatmap.symm: no visible global function definition for
  'grid.newpage'
plot.heatmap.symm: no visible global function definition for
  'grid.draw'
plotCGHProfile: no visible global function definition for 'ChrNumeric'
prepareGEOSampleInfoTemplate: no visible global function definition for
  'samples'
projectWBC: no visible global function definition for 'solve.QP'
read.GS.report: no visible global function definition for
  'featureNames'
read.idat.files: no visible binding for global variable 'barcode'
refFreeEWASP: no visible global function definition for 'EstDimRMT'
refFreeEWASP: no visible global function definition for
  'RefFreeEwasModel'
refFreeEWASP: no visible global function definition for
  'PairsBootRefFreeEwasModel'
refFreeEWASP: no visible global function definition for
  'BootRefFreeEwasModel'
rnb.RnBSet.to.GRangesList: no visible global function definition for
  'samples'
rnb.RnBSet.to.bed: no visible global function definition for 'samples'
rnb.RnBSet.to.bedGraph: no visible global function definition for
  'samples'
rnb.add.snp.distances: no visible global function definition for
  'grid.newpage'
rnb.add.snp.distances: no visible global function definition for
  'grid.draw'
rnb.chromosome.lengths: no visible global function definition for
  'seqlengths'
rnb.combine.seq: no visible global function definition for 'samples'
rnb.enmix.oob: no visible global function definition for '%dopar%'
rnb.enmix.oob: no visible global function definition for 'foreach'
rnb.execute.dreduction: no visible global function definition for
  'samples'
rnb.execute.filter.summary.internal: no visible global function
  definition for 'samples'
rnb.execute.high.coverage.removal.internal: no visible global function
  definition for 'samples'
rnb.execute.low.coverage.masking.internal: no visible global function
  definition for 'samples'
rnb.execute.na.removal.internal: no visible global function definition
  for 'samples'
rnb.execute.normalization: no visible global function definition for
  'phenoData'
rnb.execute.normalization: no visible global function definition for
  'phenoData<-'
rnb.execute.normalization: no visible global function definition for
  'RGChannelSet'
rnb.execute.normalization: no visible global function definition for
  'preprocessSWAN'
rnb.execute.normalization: no visible global function definition for
  'getMeth'
rnb.execute.normalization: no visible global function definition for
  'getUnmeth'
rnb.execute.normalization: no visible global function definition for
  'featureNames'
rnb.execute.normalization: no visible global function definition for
  'samples'
rnb.execute.normalization: no visible global function definition for
  'mapToGenome'
rnb.execute.normalization: no visible global function definition for
  'addSex'
rnb.execute.normalization: no visible global function definition for
  'getSex'
rnb.execute.normalization: no visible global function definition for
  'getCN'
rnb.execute.normalization.bmiq: no visible global function definition
  for '%dopar%'
rnb.execute.normalization.bmiq: no visible global function definition
  for 'foreach'
rnb.execute.quality: no visible global function definition for
  'samples'
rnb.execute.quality : <anonymous>: no visible global function
  definition for 'samples'
rnb.export.to.ewasher: no visible global function definition for
  'samples'
rnb.filter.dataset: no visible global function definition for 'samples'
rnb.get.reliability.counts.per.sample: no visible global function
  definition for 'samples'
rnb.options.description.table.fromRd: no visible global function
  definition for 'Rd2HTML'
rnb.options.description.table.fromRd: no visible binding for global
  variable 'xmlValue'
rnb.plot.beta.density.group: no visible binding for global variable
  'group'
rnb.plot.biseq.coverage: no visible global function definition for
  'samples'
rnb.plot.biseq.coverage.hist: no visible global function definition for
  'samples'
rnb.plot.control.barplot: no visible global function definition for
  'samples'
rnb.plot.control.barplot: no visible binding for global variable
  'Target'
rnb.plot.control.barplot: no visible binding for global variable
  'Index'
rnb.plot.control.barplot: no visible binding for global variable 'ID'
rnb.plot.control.barplot: no visible binding for global variable
  'Address'
rnb.plot.control.barplot: no visible global function definition for
  'grid.newpage'
rnb.plot.control.barplot: no visible binding for global variable
  'Intensity'
rnb.plot.control.barplot: no visible global function definition for
  'grid.draw'
rnb.plot.control.boxplot: no visible global function definition for
  'grid.newpage'
rnb.plot.control.boxplot: no visible binding for global variable
  'Probe'
rnb.plot.control.boxplot: no visible binding for global variable
  'Intensity'
rnb.plot.control.boxplot: no visible global function definition for
  'grid.draw'
rnb.plot.ct.heatmap: no visible binding for global variable 'x'
rnb.plot.ct.heatmap: no visible binding for global variable 'y'
rnb.plot.ct.heatmap: no visible binding for global variable 'v'
rnb.plot.ct.heatmap: no visible global function definition for
  'grid.newpage'
rnb.plot.ct.heatmap: no visible global function definition for
  'grid.draw'
rnb.plot.dreduction: no visible global function definition for 'tsne'
rnb.plot.locus.profile: no visible global function definition for
  'plotTracks'
rnb.plot.marker.fstat: no visible binding for global variable 'x'
rnb.plot.marker.fstat: no visible binding for global variable 'y'
rnb.plot.marker.fstat: no visible global function definition for
  'muted'
rnb.plot.negative.boxplot: no visible global function definition for
  'samples'
rnb.plot.negative.boxplot: no visible binding for global variable
  'numeric.names'
rnb.plot.negative.boxplot: no visible binding for global variable
  'type'
rnb.plot.negative.boxplot: no visible binding for global variable
  'types'
rnb.plot.negative.boxplot: no visible global function definition for
  'grid.newpage'
rnb.plot.negative.boxplot: no visible binding for global variable
  'Sample'
rnb.plot.negative.boxplot: no visible binding for global variable
  'Intensity'
rnb.plot.negative.boxplot: no visible global function definition for
  'grid.draw'
rnb.plot.num.sites.covg: no visible global function definition for
  'samples'
rnb.plot.num.sites.covg : <anonymous>: no visible global function
  definition for 'samples'
rnb.plot.num.sites.covg: no visible binding for global variable
  'numSites'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgMedian'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgPercLow'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgPercUp'
rnb.plot.num.sites.covg: no visible binding for global variable 'comma'
rnb.plot.region.profile.density: no visible binding for global variable
  'relative.coord'
rnb.plot.region.profile.density: no visible binding for global variable
  '..density..'
rnb.plot.region.profiles : <anonymous>: no visible global function
  definition for 'samples'
rnb.plot.region.profiles: no visible binding for global variable
  'relative.coord'
rnb.plot.region.profiles: no visible binding for global variable
  'group'
rnb.plot.region.site.density: no visible binding for global variable
  'relative.coord'
rnb.plot.sentrix.distributions: no visible global function definition
  for 'samples'
rnb.plot.sentrix.distributions: no visible binding for global variable
  'Slide'
rnb.plot.snp.boxplot: no visible binding for global variable 'SNP'
rnb.plot.snp.boxplot: no visible binding for global variable 'bv'
rnb.run.preprocessing : logger.completed.filtering: no visible global
  function definition for 'samples'
rnb.sample.summary.table: no visible global function definition for
  'samples'
rnb.section.ageprediction: no visible global function definition for
  'samples'
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
  function definition for 'samples'
rnb.section.clustering: no visible global function definition for
  'samples'
rnb.section.diffMeth.region: no visible global function definition for
  '%dopar%'
rnb.section.diffMeth.region: no visible global function definition for
  'foreach'
rnb.section.diffMeth.region: no visible binding for global variable 'k'
rnb.section.diffMeth.region : do.enrichment.table: no visible global
  function definition for 'sigCategories'
rnb.section.diffMeth.region : do.enrichment.table.var: no visible
  global function definition for 'sigCategories'
rnb.section.diffMeth.site: no visible global function definition for
  '%dopar%'
rnb.section.diffMeth.site: no visible global function definition for
  'foreach'
rnb.section.diffVar: no visible global function definition for
  '%dopar%'
rnb.section.diffVar: no visible global function definition for
  'foreach'
rnb.section.diffVar.region: no visible global function definition for
  '%dopar%'
rnb.section.diffVar.region: no visible global function definition for
  'foreach'
rnb.section.diffVar.region: no visible binding for global variable 'k'
rnb.section.gender.prediction: no visible global function definition
  for 'muted'
rnb.section.import: no visible global function definition for 'samples'
rnb.section.import: no visible global function definition for
  'phenoData'
rnb.section.imputation: no visible global function definition for
  'melt'
rnb.section.locus.profiles: no visible global function definition for
  'samples'
rnb.section.locus.profiles : do.plots: no visible global function
  definition for 'plotTracks'
rnb.section.locus.profiles: no visible global function definition for
  '%dopar%'
rnb.section.locus.profiles: no visible global function definition for
  'foreach'
rnb.section.na.removal: no visible global function definition for
  'samples'
rnb.section.normalization: no visible global function definition for
  'samples'
rnb.section.region.description: no visible binding for global variable
  'size'
rnb.section.region.description: no visible binding for global variable
  'n.sites'
rnb.section.region.profiles: no visible global function definition for
  'samples'
rnb.section.region.subsegmentation : get.summary.df.from.list: no
  visible global function definition for 'melt'
rnb.section.region.subsegmentation: no visible binding for global
  variable 'region.size'
rnb.section.region.subsegmentation: no visible binding for global
  variable 'is.subsegmentation'
rnb.section.region.subsegmentation: no visible binding for global
  variable 'num.sites'
rnb.step.betadistribution.internal: no visible global function
  definition for '%dopar%'
rnb.step.betadistribution.internal: no visible global function
  definition for 'foreach'
rnb.step.cell.types: no visible global function definition for
  'samples'
rnb.step.clustering.internal: no visible global function definition for
  'samples'
rnb.step.cnv: no visible binding for global variable 'intensities'
rnb.step.dreduction: no visible global function definition for
  '%dopar%'
rnb.step.dreduction: no visible global function definition for
  'foreach'
rnb.step.dreduction: no visible binding for global variable 'target'
rnb.step.filter.summary.internal: no visible global function definition
  for 'percent_format'
rnb.step.filter.summary.internal: no visible global function definition
  for 'samples'
rnb.step.import: no visible global function definition for 'samples'
rnb.step.import: no visible global function definition for 'phenoData'
rnb.step.na.removal: no visible binding for global variable
  'sites2ignore'
rnb.step.na.removal.internal: no visible global function definition for
  'samples'
rnb.step.normalization: no visible global function definition for
  'phenoData'
robustHyperGResultSummary: no visible global function definition for
  'sigCategories'
robustHyperGResultSummary: no visible global function definition for
  'pvalues'
robustHyperGResultSummary: no visible global function definition for
  'oddsRatios'
robustHyperGResultSummary: no visible global function definition for
  'expectedCounts'
robustHyperGResultSummary: no visible global function definition for
  'geneCounts'
robustHyperGResultSummary: no visible global function definition for
  'universeCounts'
robustHyperGResultSummary: no visible binding for global variable
  'Term'
run.cross.validation: no visible global function definition for
  'samples'
run.cross.validation: no visible global function definition for 'melt'
run.cross.validation: no visible binding for global variable 'Measure'
run.cross.validation: no visible binding for global variable 'Error'
sampleCovgApply: no visible global function definition for 'samples'
set.covariates.ct: no visible global function definition for 'samples'
simpleGlmnet: no visible global function definition for 'impute.knn'
simpleGlmnet: no visible global function definition for 'cv.glmnet'
simpleGlmnet: no visible global function definition for 'glmnet'
simpleGlmnetBiseq: no visible global function definition for
  'cv.glmnet'
simpleGlmnetBiseq: no visible global function definition for 'glmnet'
simpleGlmnetEvaluate: no visible global function definition for
  'cv.glmnet'
simpleGlmnetEvaluate: no visible global function definition for
  'glmnet'
symmetric.melt: no visible global function definition for 'melt'
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
  'reg.type'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'getManifest'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'getGreen'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'getRed'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'pData'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for 'featureData<-'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for 'featureNames<-'
mask.sites.meth,RnBSet: no visible global function definition for
  'samples'
remove.samples,RnBSet: no visible global function definition for
  'samples'
remove.samples,RnBeadRawSet: no visible global function definition for
  'samples'
remove.samples,RnBeadSet: no visible global function definition for
  'samples'
remove.sites,RnBSet: no visible global function definition for
  'samples'
sampleCovgApply,RnBSet: no visible global function definition for
  'samples'
sampleMethApply,RnBSet: no visible global function definition for
  'samples'
summarize.regions,RnBSet: no visible global function definition for
  'samples'
summarize.regions,RnBSet: multiple local function definitions for
  'aggr.f' with different formal arguments
updateMethylationSites,RnBSet: no visible global function definition
  for 'samples'
Undefined global functions or variables:
  %dopar% ..count.. ..density.. .inds.g2 Address Age
  BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
  Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack ID
  IdeogramTrack IlluminaHumanMethylation450kmanifest
  IlluminaHumanMethylationEPICmanifest Index Intensity Measure
  PairsBootRefFreeEwasModel Probe RGChannelSet Rd2HTML RefFreeEwasModel
  SNP Sample Slide Target Term UcscTrack Value addSex as.profileCGH
  assayDataElement assayDataElementNames barcode bv chrom combinedRank
  combinedRank.var comma covgMedian covgPercLow covgPercUp cv.glmnet
  daglad diffmeth diffmeth.p.adj.fdr diffmeth.p.val
  dinucleotideFrequency eps expectedCounts featureData featureData<-
  featureNames featureNames<- foreach geneCounts genome<- getCN
  getDoParWorkers getGreen getManifest getMeth getRed getSex getUnmeth
  getVarCov glmnet grid.draw grid.newpage group group1 group2 i
  impute.knn intensities is.subsegmentation k letterFrequency lme
  loadRegionDB log10FDR log10P mapToGenome mean.diff mean.quot.log2
  melt mergeRegionDBs muted n.sites ng.2 num.sites numSites
  numeric.names oddsRatios p.vals.t.na.adj pData percent_format
  phenoData phenoData<- plotTracks preprocessSWAN pvalues qvalue
  refText reg.type region.size registerDoParallel relative.coord report
  runLOLA samples seqlengths seqlevels<- sigCategories sites2ignore
  size solve.QP stopCluster sva target tsne type types universeCounts
  useMart v var.diff varFit varLabels x xmlValue y yint
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/RnBeads.Rcheck/00check.log'
for details.

Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/RnBeads_1.12.1.tar.gz && rm -rf RnBeads.buildbin-libdir && mkdir RnBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.buildbin-libdir RnBeads_1.12.1.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL RnBeads_1.12.1.zip && rm RnBeads_1.12.1.tar.gz RnBeads_1.12.1.zip
###
##############################################################################
##############################################################################


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install for i386

* installing *source* package 'RnBeads' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RnBeads'
    finding HTML links ... done
    BMIQ                                    html  
    ClusterArchitecture-class               html  
    ClusterArchitectureSGE-class            html  
    M-methods                               html  
    Report-class                            html  
    ReportGgPlot-class                      html  
    ReportPlot-class                        html  
    RnBClusterRun-class                     html  
    RnBDiffMeth-class                       html  
    RnBSet-class                            html  
    RnBeadClustering-class                  html  
    RnBeadRawSet-class                      html  
    RnBeadSet-class                         html  
    RnBeads                                 html  
    RnBeads.data                            html  
    RnBiseqSet-class                        html  
    U-methods                               html  
    accepted                                html  
    addDiffMethTable-RnBDiffMeth-methods    html  
    addPheno-RnBSet-methods                 html  
    addRegionSubsegments                    html  
    annotation-methods                      html  
    apply.iEVORA                            html  
    as.RnBeadRawSet                         html  
    assembly-methods                        html  
    auto.select.rank.cut                    html  
    coercion-methods                        html  
    finding level-2 HTML links ... done

    cols.to.rank                            html  
    combine-methods                         html  
    combine.diffMeth.objs                   html  
    combineTestPvalsMeth                    html  
    computeDiffTab.region                   html  
    computeDiffTab.site                     html  
    covg-methods                            html  
    create.densityScatter                   html  
    create.hex.summary.plot                 html  
    create.scatter.dens.points              html  
    createReport                            html  
    createReportGgPlot                      html  
    createReportPlot                        html  
    data.frame2GRanges                      html  
    densRanks                               html  
    destroy-RnBDiffMeth-methods             html  
    destroy-methods                         html  
    deviation.plot.beta                     html  
    diffVar                                 html  
    dim-BigFfMat-method                     html  
    downloadLolaDbs                         html  
    dpval-methods                           html  
    estimateProportionsCP                   html  
    exportDMRs2regionFile                   html  
    get.adjustment.variables                html  
    get.comparison.grouplabels-RnBDiffMeth-methods
                                            html  
    get.comparison.groupsizes-RnBDiffMeth-methods
                                            html  
    get.comparison.info                     html  
    get.comparisons-RnBDiffMeth-methods     html  
    get.covariates.ct                       html  
    get.covariates.sva                      html  
    get.covg.thres-RnBDiffMeth-methods      html  
    get.cpg.stats                           html  
    get.files                               html  
    get.region.types-RnBDiffMeth-methods    html  
    get.site.test.method-RnBDiffMeth-methods
                                            html  
    get.table-RnBDiffMeth-methods           html  
    get.table.ids                           html  
    get.variability.method-RnBDiffMeth-methods
                                            html  
    getCellTypesFromLolaDb                  html  
    getExecutable-ClusterArchitecture-methods
                                            html  
    getModuleNumCores-RnBClusterRun-methods
                                            html  
    getNamesFromLolaDb                      html  
    getNumNaMeth-methods                    html  
    getSubCmdStr-ClusterArchitecture-methods
                                            html  
    getSubCmdTokens-ClusterArchitecture-methods
                                            html  
    getSubCmdTokens-ClusterArchitectureSGE-methods
                                            html  
    getTargetFromLolaDb                     html  
    greedycut.filter.matrix                 html  
    greedycut.get.statistics                html  
    greedycut.get.submatrix                 html  
    has.covariates.ct                       html  
    has.covariates.sva                      html  
    hasCovg-methods                         html  
    includes.sites-RnBDiffMeth-methods      html  
    initialize-ClusterArchitecture-method   html  
    initialize-ClusterArchitectureSGE-method
                                            html  
    initialize-RnBClusterRun-method         html  
    initialize-RnBDiffMeth-method           html  
    intensities.by.color                    html  
    is.valid-RnBDiffMeth-methods            html  
    isImputed-RnBSet-method                 html  
    join.diffMeth-methods                   html  
    limmaP                                  html  
    load.region.subsegment.annotation       html  
    load.rnb.diffmeth                       html  
    load.rnb.set                            html  
    loadLolaDbs                             html  
    logger.argument                         html  
    logger.getfiles                         html  
    logger.isinitialized                    html  
    logger.machine.name                     html  
    logger.validate.file                    html  
    loggerManagement                        html  
    loggerMessages                          html  
    lolaBarPlot                             html  
    lolaBoxPlotPerTarget                    html  
    lolaVolcanoPlot                         html  
    lump.hg19                               html  
    mask.sites.meth-methods                 html  
    mergeSamples-methods                    html  
    meth-methods                            html  
    mval-methods                            html  
    nsites-methods                          html  
    off-methods                             html  
    parallel.getNumWorkers                  html  
    parallel.isEnabled                      html  
    parallel.setup                          html  
    parallel.teardown                       html  
    performGOEnrichment.diffVar             html  
    performGOenrichment.diffMeth.entrez     html  
    performGoEnrichment.diffMeth            html  
    performLolaEnrichment.diffMeth          html  
    performLolaEnrichment.diffVar           html  
    pheno-methods                           html  
    prepareSOFTfileForGEO                   html  
    qc-methods                              html  
    read.GS.report                          html  
    read.bed.files                          html  
    read.data.dir                           html  
    read.idat.files                         html  
    read.idat.files2                        html  
    read.sample.annotation                  html  
    read.single.bed                         html  
    refFreeEWASP                            html  
    regionMapping-methods                   html  
    regions-methods                         html  
    reload-RnBDiffMeth-methods              html  
    remove.regions-methods                  html  
    remove.samples-methods                  html  
    remove.sites-methods                    html  
    rnb.RnBSet.to.GRangesList               html  
    rnb.RnBSet.to.bed                       html  
    rnb.RnBSet.to.bedGraph                  html  
    rnb.add.figure                          html  
    rnb.add.list                            html  
    rnb.add.paragraph                       html  
    rnb.add.reference                       html  
    rnb.add.section                         html  
    rnb.add.table                           html  
    rnb.add.tables                          html  
    rnb.annotation.size                     html  
    rnb.annotation2data.frame               html  
    rnb.beta2mval                           html  
    rnb.build.index                         html  
    rnb.call.destructor                     html  
    rnb.color.legends                       html  
    rnb.combine.arrays                      html  
    rnb.execute.age.prediction              html  
    rnb.execute.batch.qc                    html  
    rnb.execute.batcheffects                html  
    rnb.execute.clustering                  html  
    rnb.execute.clustering.all              html  
    rnb.execute.computeDiffMeth             html  
    rnb.execute.context.removal             html  
    rnb.execute.cross.reactive.removal      html  
    rnb.execute.ct.estimation               html  
    rnb.execute.diffVar                     html  
    rnb.execute.dreduction                  html  
    rnb.execute.export.csv                  html  
    rnb.execute.filter.summary              html  
    rnb.execute.gender.prediction           html  
    rnb.execute.genomewide                  html  
    rnb.execute.greedycut                   html  
    rnb.execute.high.coverage.removal       html  
    rnb.execute.import                      html  
    rnb.execute.imputation                  html  
    rnb.execute.low.coverage.masking        html  
    rnb.execute.lump                        html  
    rnb.execute.na.removal                  html  
    rnb.execute.normalization               html  
    rnb.execute.quality                     html  
    rnb.execute.sex.removal                 html  
    rnb.execute.snp.removal                 html  
    rnb.execute.sva                         html  
    rnb.execute.tnt                         html  
    rnb.execute.training                    html  
    rnb.execute.variability.removal         html  
    rnb.export.all.annotation               html  
    rnb.export.annotation                   html  
    rnb.export.to.ewasher                   html  
    rnb.export.to.trackhub                  html  
    rnb.find.relative.site.coord            html  
    rnb.get.annotation                      html  
    rnb.get.assemblies                      html  
    rnb.get.chromosomes                     html  
    rnb.get.directory                       html  
    rnb.get.mapping                         html  
    rnb.get.reference                       html  
    rnb.get.reliability.matrix              html  
    rnb.infinium.control.targets            html  
    rnb.initialize.reports                  html  
    rnb.is.option                           html  
    rnb.load.annotation                     html  
    rnb.load.annotation.from.db             html  
    rnb.load.sitelist                       html  
    rnb.message.plot                        html  
    rnb.mval2beta                           html  
    rnb.options                             html  
    rnb.options2xml                         html  
    rnb.performance.profile                 html  
    rnb.plot.beta.comparison                html  
    rnb.plot.betadistribution.probeCategories
                                            html  
    rnb.plot.betadistribution.sampleGroups
                                            html  
    rnb.plot.biseq.coverage                 html  
    rnb.plot.biseq.coverage.hist            html  
    rnb.plot.biseq.coverage.violin          html  
    rnb.plot.control.barplot                html  
    rnb.plot.control.boxplot                html  
    rnb.plot.coverage.thresholds            html  
    rnb.plot.ct.heatmap                     html  
    rnb.plot.dreduction                     html  
    rnb.plot.locus.profile                  html  
    rnb.plot.marker.fstat                   html  
    rnb.plot.negative.boxplot               html  
    rnb.plot.num.sites.covg                 html  
    rnb.plot.pheno.categories               html  
    rnb.plot.region.profile.density         html  
    rnb.plot.region.profiles                html  
    rnb.plot.region.site.density            html  
    rnb.plot.sentrix.distribution           html  
    rnb.plot.sentrix.distributions          html  
    rnb.plot.snp.barplot                    html  
    rnb.plot.snp.boxplot                    html  
    rnb.plot.snp.heatmap                    html  
    rnb.read.geo                            html  
    rnb.region.types                        html  
    rnb.region.types.for.analysis           html  
    rnb.remove.annotation                   html  
    rnb.run.analysis                        html  
    rnb.run.dj                              html  
    rnb.run.example                         html  
    rnb.run.xml                             html  
    rnb.runs                                html  
    rnb.sample.groups                       html  
    rnb.sample.replicates                   html  
    rnb.sample.summary.table                html  
    rnb.save.annotation                     html  
    rnb.section.diffVar.region              html  
    rnb.set.annotation                      html  
    rnb.set.annotation.and.cpg.stats        html  
    rnb.show.report                         html  
    rnb.step.betadistribution               html  
    rnb.write.table                         html  
    rnb.xml2options                         html  
    rowOneSampleTP                          html  
    rowPairedTP                             html  
    rowWelchP                               html  
    run-RnBClusterRun-methods               html  
    run.cross.validation                    html  
    sampleCovgApply-methods                 html  
    sampleMethApply-methods                 html  
    samples-methods                         html  
    save.rnb.diffmeth                       html  
    save.rnb.set                            html  
    save.tables-RnBDiffMeth-methods         html  
    set.covariates.ct                       html  
    set.covariates.sva                      html  
    setExecutable-ClusterArchitecture-methods
                                            html  
    setModuleNumCores-RnBClusterRun-methods
                                            html  
    setModuleResourceRequirements-RnBClusterRun-methods
                                            html  
    sites-methods                           html  
    sub-BigFfMat-ANY-ANY-ANY-method         html  
    subset-BigFfMat-ANY-ANY-ANY-method      html  
    summarize.regions-methods               html  
    summarized.regions-methods              html  
    updateMethylationSites-methods          html  
    updateRegionSummaries                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'RnBeads' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RnBeads' as RnBeads_1.12.1.zip
* DONE (RnBeads)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'RnBeads' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

RnBeads.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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

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

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

> BiocGenerics:::testPackage("RnBeads")

Attaching package: 'BiocGenerics'

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

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

    windows

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")=="C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/Rtmp6DAh47"

- 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")==37570478.08 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system


Attaching package: 'ff'

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

    clone, clone.default, clone.list

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Spam version 2.2-0 (2018-06-19) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    mle

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

    backsolve, forwardsolve


Attaching package: 'maps'

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

    votes.repub

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

Attaching package: 'gplots'

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

    space

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

    space

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

    lowess


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'limma'

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

    plotMA

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    anyMissing, rowMedians


Attaching package: 'AnnotationDbi'

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

    select



Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply


Attaching package: 'Biostrings'

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

    type

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

    mismatch, pattern

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

    strsplit

locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

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

    compact

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

    count

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

    ozone

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

    desc

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

    rename

2018-10-17 04:38:11     0.4  STATUS STARTED Unit testing: differential
2018-10-17 04:38:11     0.4  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2018-10-17 04:38:11     0.4  STATUS     COMPLETED Testing function: rowWelchP
2018-10-17 04:38:11     0.4  STATUS     STARTED Testing function: limmaP
2018-10-17 04:38:12     0.4  STATUS     COMPLETED Testing function: limmaP
2018-10-17 04:38:12     0.4  STATUS     STARTED Testing function: computeDiffTab.extended.site
2018-10-17 04:38:12     0.4    INFO         Conducting differential analysis using limma
2018-10-17 04:38:12     0.4  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2018-10-17 04:38:12     0.4  STATUS     STARTED Testing function: computeDiffTab.default.region
2018-10-17 04:38:12     0.4    INFO         Conducting differential analysis using limma
2018-10-17 04:38:17     0.5  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2018-10-17 04:38:17     0.5  STATUS     STARTED Testing function: combineTestPvalsMeth
2018-10-17 04:38:17     0.5  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2018-10-17 04:38:17     0.5  STATUS     STARTED Testing function: get.adjustment.variables
2018-10-17 04:38:17     0.5  STATUS     COMPLETED Testing function: get.adjustment.variables
2018-10-17 04:38:17     0.5  STATUS     STARTED Testing function: get.comparison.info
2018-10-17 04:38:17     0.5  STATUS     COMPLETED Testing function: get.comparison.info
2018-10-17 04:38:17     0.5  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:38:17     0.5  STATUS         STARTED Retrieving comparison info
2018-10-17 04:38:17     0.5  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:38:17     0.5  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:38:17     0.5  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:17     0.5  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:38:17     0.5    INFO                     Conducting differential analysis using limma
2018-10-17 04:38:18     0.5  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:18     0.5  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:19     0.5  STATUS                     Computed table for tiling
2018-10-17 04:38:20     0.6  STATUS                     Computed table for genes
2018-10-17 04:38:20     0.6  STATUS                     Computed table for promoters
2018-10-17 04:38:20     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:38:20     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:21     0.6  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:21     0.6  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:21     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:38:21     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:38:21     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:21     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:21     0.6  STATUS                     Computed table for tiling
2018-10-17 04:38:22     0.6  STATUS                     Computed table for genes
2018-10-17 04:38:22     0.6  STATUS                     Computed table for promoters
2018-10-17 04:38:22     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:38:22     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:22     0.6  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:22     0.6  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:38:22     0.6  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:38:22     0.6  STATUS     STARTED Testing function: diffVar
2018-10-17 04:38:22     0.6  STATUS         STARTED diffVar method
2018-10-17 04:38:22     0.6  STATUS         COMPLETED diffVar method
2018-10-17 04:38:23     0.6  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-17 04:38:23     0.6  STATUS         COMPLETED diffVar method
2018-10-17 04:38:23     0.6  STATUS     COMPLETED Testing function: diffVar
2018-10-17 04:38:23     0.6  STATUS     STARTED Testing function: apply.iEVORA
2018-10-17 04:38:23     0.6  STATUS         STARTED iEVORA method
2018-10-17 04:38:24     0.6    INFO             No DVCs detected. All p-values set to 1.
2018-10-17 04:38:24     0.6  STATUS         COMPLETED iEVORA method
2018-10-17 04:38:24     0.6  STATUS         STARTED Testing function: rnb.execute.diffVar
2018-10-17 04:38:24     0.6  STATUS             STARTED Differential Variability
2018-10-17 04:38:24     0.6  STATUS                 STARTED Retrieving comparison info
2018-10-17 04:38:25     0.6  STATUS                 COMPLETED Retrieving comparison info
2018-10-17 04:38:25     0.6    INFO                 No imputation method selected, 'knn' method used.
2018-10-17 04:38:25     0.6  STATUS                 STARTED Imputation procedure knn 
2018-10-17 04:38:25     0.6  STATUS                 COMPLETED Imputation procedure knn 
2018-10-17 04:38:25     0.6  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:25     0.6    INFO                     Conducting differential variability using diffVar
2018-10-17 04:38:25     0.6  STATUS                     STARTED diffVar method
2018-10-17 04:38:25     0.6  STATUS                     COMPLETED diffVar method
2018-10-17 04:38:25     0.6  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:38:26     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:26     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:26     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:26     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:38:26     0.6  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:38:26     0.6  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:26     0.6  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:26     0.6    INFO                     Conducting differential variability using diffVar
2018-10-17 04:38:26     0.6  STATUS                     STARTED diffVar method
2018-10-17 04:38:26     0.6  STATUS                     COMPLETED diffVar method
2018-10-17 04:38:27     0.6  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:38:27     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:27     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:28     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:28     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:38:28     0.6  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:38:28     0.6  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:28     0.6  STATUS             COMPLETED Differential Variability
2018-10-17 04:38:28     0.6  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2018-10-17 04:38:28     0.6  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:38:28     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:38:28     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:38:28     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:38:28     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:28     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:28     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:28     0.6  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:38:28     0.6  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:38:28     0.6    INFO                         Conducting differential variability using diffVar
2018-10-17 04:38:29     0.6  STATUS                         STARTED diffVar method
2018-10-17 04:38:29     0.6  STATUS                         COMPLETED diffVar method
2018-10-17 04:38:29     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:29     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:30     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:31     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:31     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:32     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:38:32     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:32     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:32     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:32     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:32     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:32     0.6  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:38:32     0.6  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:38:32     0.6    INFO                         Conducting differential variability using diffVar
2018-10-17 04:38:32     0.6  STATUS                         STARTED diffVar method
2018-10-17 04:38:32     0.6  STATUS                         COMPLETED diffVar method
2018-10-17 04:38:33     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:33     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:34     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:35     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:35     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:36     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:38:36     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:36     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:36     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:38:36     0.6  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:38:36     0.6  STATUS         STARTED Testing class: RnBDiffMeth
2018-10-17 04:38:36     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:38:36     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:38:36     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:38:36     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:36     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:36     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:36     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:36     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:37     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:37     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:37     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:38     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:38:38     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:38     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:38     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:38     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:38     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:38     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:38     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:39     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:39     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:39     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:39     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:38:39     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:40     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:40     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:38:40     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:38:40     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:38:40     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:38:40     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:40     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:40     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:40     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:40     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:40     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:41     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:41     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:41     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:41     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:38:41     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:38:41     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:38:41     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:38:42     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:42     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:42     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:42     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:42     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:42     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:43     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:43     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:43     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:43     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:38:43     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:38:43     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:38:43     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:38:43     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:43     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:43     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:43     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:43     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:44     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:44     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:44     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:44     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:44     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:44     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:44     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:44     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:45     0.6  STATUS                         Computed table for promoters
2018-10-17 04:38:45     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:45     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:45     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:38:45     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:38:45     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:38:45     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:38:45     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:45     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:38:45     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:38:45     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:45     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:46     0.6  STATUS                         Computed table for genes
2018-10-17 04:38:46     0.6  STATUS                         Computed table for tiling
2018-10-17 04:38:46     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:46     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:46     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:38:46     0.6  STATUS             STARTED Testing function: get.region.types
2018-10-17 04:38:46     0.6  STATUS             COMPLETED Testing function: get.region.types
2018-10-17 04:38:46     0.6  STATUS             STARTED Testing function: get.comparisons
2018-10-17 04:38:47     0.6  STATUS             COMPLETED Testing function: get.comparisons
2018-10-17 04:38:47     0.6  STATUS             STARTED Testing function: get.comparison.grouplabels
2018-10-17 04:38:47     0.6  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2018-10-17 04:38:47     0.6  STATUS             STARTED Testing function: get.site.test.method
2018-10-17 04:38:47     0.6  STATUS             COMPLETED Testing function: get.site.test.method
2018-10-17 04:38:47     0.6  STATUS             STARTED Testing function: get.table
2018-10-17 04:38:47     0.6  STATUS             COMPLETED Testing function: get.table
2018-10-17 04:38:47     0.6  STATUS             STARTED Testing function: addDiffMethTable
2018-10-17 04:38:47     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:47     0.6  STATUS             COMPLETED Testing function: addDiffMethTable
2018-10-17 04:38:47     0.6  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2018-10-17 04:38:47     0.6  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-17 04:38:47     0.6  STATUS             STARTED Destructor
2018-10-17 04:38:48     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:48     0.6  STATUS             COMPLETED Destructor
2018-10-17 04:38:48     0.6  STATUS         COMPLETED Testing class: RnBDiffMeth
2018-10-17 04:38:48     0.6  STATUS     COMPLETED Testing function: apply.iEVORA
2018-10-17 04:38:48     0.6  STATUS     STARTED Retrieving comparison info
2018-10-17 04:38:48     0.6  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:38:48     0.6  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:38:48     0.6  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:48     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:48     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:48     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:48     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:49     0.6  STATUS                 Computed table for tiling
2018-10-17 04:38:49     0.6  STATUS                 Computed table for genes
2018-10-17 04:38:50     0.6  STATUS                 Computed table for promoters
2018-10-17 04:38:50     0.6  STATUS                 Computed table for cpgislands
2018-10-17 04:38:50     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:50     0.6  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:51     0.6  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:51     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:51     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:51     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:51     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:51     0.6  STATUS                 Computed table for tiling
2018-10-17 04:38:52     0.6  STATUS                 Computed table for genes
2018-10-17 04:38:52     0.6  STATUS                 Computed table for promoters
2018-10-17 04:38:52     0.6  STATUS                 Computed table for cpgislands
2018-10-17 04:38:52     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:52     0.6  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:52     0.6  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:38:52     0.6  STATUS     STARTED Retrieving comparison info
2018-10-17 04:38:52     0.6  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:38:52     0.6  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:38:52     0.6  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:52     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:52     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:53     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:53     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:53     0.6  STATUS                 Computed table for genes
2018-10-17 04:38:53     0.6  STATUS                 Computed table for tiling
2018-10-17 04:38:53     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:53     0.6  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:53     0.6  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:38:53     0.6  STATUS     STARTED Retrieving comparison info
2018-10-17 04:38:53     0.6  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:38:54     0.6  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:38:54     0.6  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:54     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:54     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:54     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:54     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:54     0.6  STATUS                 Computed table for genes
2018-10-17 04:38:54     0.6  STATUS                 Computed table for tiling
2018-10-17 04:38:55     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:55     0.6  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:55     0.6  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:38:55     0.6  STATUS     STARTED Retrieving comparison info
2018-10-17 04:38:55     0.6  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:38:55     0.6  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:38:55     0.6  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:55     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:55     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:55     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:55     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:55     0.6  STATUS                 Computed table for promoters
2018-10-17 04:38:55     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:55     0.6  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:38:55     0.6  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:55     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:55     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:55     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:56     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:56     0.6  STATUS                 Computed table for promoters
2018-10-17 04:38:56     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:56     0.6  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:56     0.6  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:38:56     0.6  STATUS     STARTED Retrieving comparison info
2018-10-17 04:38:56     0.6  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:38:56     0.6  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:38:56     0.6  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:56     0.6  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:38:56     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:38:56     0.6  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:38:57     0.6  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:57     0.6  STATUS                 Computed table for genes
2018-10-17 04:38:57     0.6  STATUS                 Computed table for tiling
2018-10-17 04:38:58     0.6  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:38:58     0.6  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing function: get.region.types
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing function: get.region.types
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing function: get.comparisons
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing function: get.comparisons
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing function: get.comparison.grouplabels
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing function: get.comparison.grouplabels
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing function: get.site.test.method
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing function: get.site.test.method
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing function: get.table
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing function: get.table
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing function: addDiffMethTable
2018-10-17 04:38:58     0.6    INFO         Conducting differential analysis using limma
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing function: addDiffMethTable
2018-10-17 04:38:58     0.6  STATUS     STARTED Testing functions: join.diffMeth, is.valid
2018-10-17 04:38:58     0.6  STATUS     COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-17 04:38:58     0.6  STATUS     STARTED Destructor
2018-10-17 04:38:59     0.6  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:38:59     0.6  STATUS     COMPLETED Destructor
2018-10-17 04:38:59     0.6    INFO     Conducting differential analysis using limma
2018-10-17 04:38:59     0.6    INFO     Conducting differential analysis using limma
2018-10-17 04:38:59     0.6  STATUS     STARTED diffVar method
2018-10-17 04:38:59     0.6  STATUS     COMPLETED diffVar method
2018-10-17 04:38:59     0.6  STATUS     STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-17 04:39:00     0.6  STATUS     COMPLETED diffVar method
2018-10-17 04:39:00     0.6  STATUS STARTED Unit testing: differential
2018-10-17 04:39:00     0.6  STATUS     STARTED Testing function: rowWelchP
2018-10-17 04:39:00     0.6  STATUS     COMPLETED Testing function: rowWelchP
2018-10-17 04:39:00     0.6  STATUS     STARTED Testing function: limmaP
2018-10-17 04:39:00     0.6  STATUS     COMPLETED Testing function: limmaP
2018-10-17 04:39:00     0.6  STATUS     STARTED Testing function: computeDiffTab.extended.site
2018-10-17 04:39:00     0.6    INFO         Conducting differential analysis using limma
2018-10-17 04:39:00     0.6  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2018-10-17 04:39:00     0.6  STATUS     STARTED Testing function: computeDiffTab.default.region
2018-10-17 04:39:00     0.6    INFO         Conducting differential analysis using limma
2018-10-17 04:39:01     0.6  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2018-10-17 04:39:01     0.6  STATUS     STARTED Testing function: combineTestPvalsMeth
2018-10-17 04:39:01     0.6  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2018-10-17 04:39:01     0.6  STATUS     STARTED Testing function: get.adjustment.variables
2018-10-17 04:39:01     0.6  STATUS     COMPLETED Testing function: get.adjustment.variables
2018-10-17 04:39:01     0.6  STATUS     STARTED Testing function: get.comparison.info
2018-10-17 04:39:01     0.6  STATUS     COMPLETED Testing function: get.comparison.info
2018-10-17 04:39:01     0.6  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:39:01     0.6  STATUS         STARTED Retrieving comparison info
2018-10-17 04:39:01     0.6  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:39:01     0.6  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:39:01     0.6  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:01     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:39:01     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:39:01     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:01     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:02     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:02     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:02     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:03     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:03     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:03     0.6  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:03     0.6  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:03     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:39:03     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:39:03     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:03     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:03     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:04     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:04     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:04     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:04     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:04     0.6  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:04     0.6  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:39:04     0.6  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:39:04     0.6  STATUS     STARTED Testing function: diffVar
2018-10-17 04:39:04     0.6  STATUS         STARTED diffVar method
2018-10-17 04:39:04     0.6  STATUS         COMPLETED diffVar method
2018-10-17 04:39:05     0.6  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-17 04:39:05     0.6  STATUS         COMPLETED diffVar method
2018-10-17 04:39:05     0.6  STATUS     COMPLETED Testing function: diffVar
2018-10-17 04:39:05     0.6  STATUS     STARTED Testing function: apply.iEVORA
2018-10-17 04:39:05     0.6  STATUS         STARTED iEVORA method
2018-10-17 04:39:06     0.6    INFO             No DVCs detected. All p-values set to 1.
2018-10-17 04:39:06     0.6  STATUS         COMPLETED iEVORA method
2018-10-17 04:39:06     0.6  STATUS         STARTED Testing function: rnb.execute.diffVar
2018-10-17 04:39:07     0.6  STATUS             STARTED Differential Variability
2018-10-17 04:39:07     0.6  STATUS                 STARTED Retrieving comparison info
2018-10-17 04:39:07     0.6  STATUS                 COMPLETED Retrieving comparison info
2018-10-17 04:39:07     0.6  STATUS                 STARTED Imputation procedure knn 
2018-10-17 04:39:07     0.6  STATUS                 COMPLETED Imputation procedure knn 
2018-10-17 04:39:07     0.6  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:07     0.6    INFO                     Conducting differential variability using diffVar
2018-10-17 04:39:07     0.6  STATUS                     STARTED diffVar method
2018-10-17 04:39:07     0.6  STATUS                     COMPLETED diffVar method
2018-10-17 04:39:07     0.6  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:08     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:08     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:08     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:08     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:39:08     0.6  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:08     0.6  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:08     0.6  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:08     0.6    INFO                     Conducting differential variability using diffVar
2018-10-17 04:39:09     0.6  STATUS                     STARTED diffVar method
2018-10-17 04:39:09     0.6  STATUS                     COMPLETED diffVar method
2018-10-17 04:39:09     0.6  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:09     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:09     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:10     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:10     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:39:10     0.6  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:10     0.6  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:10     0.6  STATUS             COMPLETED Differential Variability
2018-10-17 04:39:10     0.6  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2018-10-17 04:39:10     0.6  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:39:10     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:10     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:10     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:39:10     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:10     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:10     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:10     0.6  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:39:10     0.6  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:39:10     0.6    INFO                         Conducting differential variability using diffVar
2018-10-17 04:39:10     0.6  STATUS                         STARTED diffVar method
2018-10-17 04:39:11     0.6  STATUS                         COMPLETED diffVar method
2018-10-17 04:39:11     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:11     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:12     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:13     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:13     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:14     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:39:14     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:14     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:14     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:14     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:14     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:14     0.6  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:39:14     0.6  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:39:14     0.6    INFO                         Conducting differential variability using diffVar
2018-10-17 04:39:14     0.6  STATUS                         STARTED diffVar method
2018-10-17 04:39:14     0.6  STATUS                         COMPLETED diffVar method
2018-10-17 04:39:15     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:15     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:15     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:16     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:16     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:16     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:39:16     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:17     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:17     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:39:17     0.6  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:39:17     0.6  STATUS         STARTED Testing class: RnBDiffMeth
2018-10-17 04:39:17     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:17     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:17     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:39:17     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:17     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:17     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:17     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:17     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:18     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:18     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:18     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:18     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:39:18     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:18     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:19     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:19     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:19     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:19     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:19     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:19     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:19     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:20     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:20     0.6  STATUS                         Computed table for cpgislands
2018-10-17 04:39:20     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:20     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:20     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:39:20     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:20     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:20     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:39:20     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:20     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:20     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:20     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:20     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:21     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:21     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:21     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:21     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:21     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:39:21     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:21     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:21     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:39:22     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:22     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:22     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:22     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:22     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:22     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:23     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:23     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:23     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:23     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:39:23     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:23     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:23     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:39:23     0.6  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:23     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:23     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:23     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:23     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:23     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:23     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:23     0.6  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:23     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:23     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:24     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:24     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:24     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:24     0.6  STATUS                         Computed table for promoters
2018-10-17 04:39:24     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:24     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:24     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:39:24     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:24     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:24     0.6  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:39:24     0.6  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:24     0.6  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:39:24     0.6    INFO                         Conducting differential analysis using limma
2018-10-17 04:39:24     0.6  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:24     0.6  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:25     0.6  STATUS                         Computed table for genes
2018-10-17 04:39:25     0.6  STATUS                         Computed table for tiling
2018-10-17 04:39:25     0.6  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:25     0.6  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:25     0.6  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:39:25     0.6  STATUS             STARTED Testing function: get.region.types
2018-10-17 04:39:25     0.6  STATUS             COMPLETED Testing function: get.region.types
2018-10-17 04:39:25     0.6  STATUS             STARTED Testing function: get.comparisons
2018-10-17 04:39:25     0.6  STATUS             COMPLETED Testing function: get.comparisons
2018-10-17 04:39:25     0.6  STATUS             STARTED Testing function: get.comparison.grouplabels
2018-10-17 04:39:26     0.6  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2018-10-17 04:39:26     0.6  STATUS             STARTED Testing function: get.site.test.method
2018-10-17 04:39:26     0.6  STATUS             COMPLETED Testing function: get.site.test.method
2018-10-17 04:39:26     0.6  STATUS             STARTED Testing function: get.table
2018-10-17 04:39:26     0.6  STATUS             COMPLETED Testing function: get.table
2018-10-17 04:39:26     0.6  STATUS             STARTED Testing function: addDiffMethTable
2018-10-17 04:39:26     0.6    INFO                 Conducting differential analysis using limma
2018-10-17 04:39:26     0.6  STATUS             COMPLETED Testing function: addDiffMethTable
2018-10-17 04:39:26     0.6  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2018-10-17 04:39:26     0.6  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-17 04:39:26     0.6  STATUS             STARTED Destructor
2018-10-17 04:39:26     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:26     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:26     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:27     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:27     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:27     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:27     0.6  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:27     0.6  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:39:27     0.6  STATUS             COMPLETED Destructor
2018-10-17 04:39:27     0.6  STATUS         COMPLETED Testing class: RnBDiffMeth
2018-10-17 04:39:27     0.6  STATUS     COMPLETED Testing function: apply.iEVORA
2018-10-17 04:39:27     0.6  STATUS     STARTED iEVORA method
2018-10-17 04:39:28     0.6    INFO         No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2018-10-17 04:39:28     0.6  STATUS         STARTED Retrieving comparison info
2018-10-17 04:39:28     0.6  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:39:28     0.6  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:39:28     0.6  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:28     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:39:29     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:39:29     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:29     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:29     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:29     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:30     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:30     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:30     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:30     0.6  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:30     0.6  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:30     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:39:30     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:39:30     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:30     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:31     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:31     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:31     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:31     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:31     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:31     0.6  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:31     0.6  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:39:31     0.6  STATUS         STARTED Retrieving comparison info
2018-10-17 04:39:32     0.6  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:39:32     0.6  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:39:32     0.6  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:32     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:39:32     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:39:32     0.6  STATUS                     STARTED Imputation procedure knn 
2018-10-17 04:39:32     0.6  STATUS                     COMPLETED Imputation procedure knn 
2018-10-17 04:39:32     0.6    INFO                     Conducting differential variability using diffVar
2018-10-17 04:39:32     0.6  STATUS                     STARTED diffVar method
2018-10-17 04:39:32     0.6  STATUS                     COMPLETED diffVar method
2018-10-17 04:39:32     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:32     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:33     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:33     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:34     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:34     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:34     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:34     0.6  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:34     0.6  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:34     0.6  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:39:34     0.6    INFO                     Conducting differential analysis using limma
2018-10-17 04:39:34     0.6  STATUS                     STARTED Imputation procedure knn 
2018-10-17 04:39:34     0.6  STATUS                     COMPLETED Imputation procedure knn 
2018-10-17 04:39:34     0.6    INFO                     Conducting differential variability using diffVar
2018-10-17 04:39:34     0.6  STATUS                     STARTED diffVar method
2018-10-17 04:39:34     0.6  STATUS                     COMPLETED diffVar method
2018-10-17 04:39:35     0.6  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:39:35     0.6  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:35     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:36     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:36     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:37     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:37     0.6  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:39:37     0.6  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:37     0.6  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:39:37     0.6  STATUS         STARTED Differential Variability
2018-10-17 04:39:37     0.6  STATUS             STARTED Retrieving comparison info
2018-10-17 04:39:37     0.6  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:39:37     0.6  STATUS             STARTED Imputation procedure knn 
2018-10-17 04:39:37     0.6  STATUS             COMPLETED Imputation procedure knn 
2018-10-17 04:39:37     0.6  STATUS             STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:37     0.6    INFO                 Conducting differential variability using diffVar
2018-10-17 04:39:37     0.6  STATUS                 STARTED diffVar method
2018-10-17 04:39:37     0.6  STATUS                 COMPLETED diffVar method
2018-10-17 04:39:37     0.6  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:38     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:38     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:38     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:38     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:38     0.6  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:38     0.6  STATUS             COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:39:39     0.6  STATUS             STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:39     0.6    INFO                 Conducting differential variability using diffVar
2018-10-17 04:39:39     0.6  STATUS                 STARTED diffVar method
2018-10-17 04:39:39     0.6  STATUS                 COMPLETED diffVar method
2018-10-17 04:39:39     0.6  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:39     0.6  STATUS                     Computed table for tiling
2018-10-17 04:39:39     0.6  STATUS                     Computed table for genes
2018-10-17 04:39:40     0.6  STATUS                     Computed table for promoters
2018-10-17 04:39:40     0.6  STATUS                     Computed table for cpgislands
2018-10-17 04:39:40     0.6  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:39:40     0.6  STATUS             COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:39:40     0.6  STATUS         COMPLETED Differential Variability
2018-10-17 04:39:40     0.6  STATUS STARTED Analysis
2018-10-17 04:39:40     0.6    INFO     Loaded information from data.RData
2018-10-17 04:39:40     0.6  STATUS     STARTED Processing Detection P-values
2018-10-17 04:39:40     0.6    INFO         Removed 3979 probes that overlap with SNPs
2018-10-17 04:39:40     0.6    INFO         Completed Greedycut on 510 samples
2018-10-17 04:39:40     0.6  STATUS     COMPLETED Processing Detection P-values
2018-10-17 04:39:40     0.6 WARNING     File not found: data2.RData
2018-10-17 04:39:40     0.6  STATUS COMPLETED Analysis

2018-10-17 04:39:40     0.6  STATUS STARTED Testing imputation
2018-10-17 04:39:40     0.6  STATUS     STARTED Imputation procedure knn 
2018-10-17 04:39:41     0.6  STATUS     COMPLETED Imputation procedure knn 
2018-10-17 04:39:41     0.6  STATUS     STARTED Imputation procedure mean.samples 
2018-10-17 04:39:42     0.6  STATUS     COMPLETED Imputation procedure mean.samples 
2018-10-17 04:39:42     0.6  STATUS     STARTED Imputation procedure mean.cpgs 
2018-10-17 04:39:42     0.6  STATUS     COMPLETED Imputation procedure mean.cpgs 
2018-10-17 04:39:42     0.6  STATUS     STARTED Imputation procedure random 
2018-10-17 04:39:43     0.6  STATUS     COMPLETED Imputation procedure random 
2018-10-17 04:39:43     0.6  STATUS COMPLETED Testing imputation

2018-10-17 04:39:43     0.6  STATUS STARTED Testing age prediction
2018-10-17 04:39:43     0.6  STATUS     STARTED Performing Age Prediction
2018-10-17 04:39:46     0.6  STATUS     COMPLETED Performing Age Prediction
2018-10-17 04:39:46     0.6  STATUS COMPLETED Testing age prediction

2018-10-17 04:39:46     0.6  STATUS STARTED Performing Age Prediction
2018-10-17 04:39:50     0.7  STATUS COMPLETED Performing Age Prediction

2018-10-17 04:39:50     0.7  STATUS STARTED Imputation procedure knn 
2018-10-17 04:39:50     0.6  STATUS COMPLETED Imputation procedure knn 

2018-10-17 04:39:50     0.6  STATUS STARTED Imputation procedure mean.samples 
2018-10-17 04:39:51     0.6  STATUS COMPLETED Imputation procedure mean.samples 

2018-10-17 04:39:51     0.6  STATUS STARTED Imputation procedure mean.cpgs 
2018-10-17 04:39:52     0.6  STATUS COMPLETED Imputation procedure mean.cpgs 

2018-10-17 04:39:52     0.6  STATUS STARTED Imputation procedure random 
2018-10-17 04:39:53     0.6  STATUS COMPLETED Imputation procedure random 

2018-10-17 04:39:53     0.6  STATUS STARTED Testing imputation
2018-10-17 04:39:53     0.6  STATUS     STARTED Imputation procedure knn 
2018-10-17 04:39:53     0.6  STATUS     COMPLETED Imputation procedure knn 
2018-10-17 04:39:53     0.6  STATUS     STARTED Imputation procedure mean.samples 
2018-10-17 04:39:54     0.6  STATUS     COMPLETED Imputation procedure mean.samples 
2018-10-17 04:39:54     0.6  STATUS     STARTED Imputation procedure mean.cpgs 
2018-10-17 04:39:54     0.6  STATUS     COMPLETED Imputation procedure mean.cpgs 
2018-10-17 04:39:54     0.6  STATUS     STARTED Imputation procedure random 
2018-10-17 04:39:55     0.6  STATUS     COMPLETED Imputation procedure random 
2018-10-17 04:39:55     0.6  STATUS COMPLETED Testing imputation

2018-10-17 04:39:55     0.6  STATUS STARTED Testing age prediction
2018-10-17 04:39:55     0.6  STATUS     STARTED Performing Age Prediction
2018-10-17 04:39:56     0.7  STATUS     COMPLETED Performing Age Prediction
2018-10-17 04:39:57     0.7  STATUS COMPLETED Testing age prediction



RUNIT TEST PROTOCOL -- Wed Oct 17 04:40:20 2018 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RnBeads RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
There were 25 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 115.93    4.03  142.98

RnBeads.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

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

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

> BiocGenerics:::testPackage("RnBeads")

Attaching package: 'BiocGenerics'

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

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

    windows

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")=="C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpMJRSvo"

- 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")==685831618.56 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system


Attaching package: 'ff'

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

    clone, clone.default, clone.list

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Spam version 2.2-0 (2018-06-19) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    mle

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

    backsolve, forwardsolve


Attaching package: 'maps'

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

    votes.repub

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

Attaching package: 'gplots'

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

    space

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

    space

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

    lowess


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'limma'

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

    plotMA

Welcome to Bioconductor

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


Attaching package: 'Biobase'

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

    anyMissing, rowMedians


Attaching package: 'AnnotationDbi'

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

    select



Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply


Attaching package: 'Biostrings'

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

    type

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

    mismatch, pattern

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

    strsplit

locfit 1.5-9.1 	 2013-03-22
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

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

    compact

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

    count

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

    ozone

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

    desc

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

    rename

2018-10-17 04:40:38     0.6  STATUS STARTED Unit testing: differential
2018-10-17 04:40:38     0.6  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2018-10-17 04:40:38     0.6  STATUS     COMPLETED Testing function: rowWelchP
2018-10-17 04:40:38     0.6  STATUS     STARTED Testing function: limmaP
2018-10-17 04:40:38     0.6  STATUS     COMPLETED Testing function: limmaP
2018-10-17 04:40:38     0.6  STATUS     STARTED Testing function: computeDiffTab.extended.site
2018-10-17 04:40:38     0.6    INFO         Conducting differential analysis using limma
2018-10-17 04:40:38     0.6  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2018-10-17 04:40:38     0.6  STATUS     STARTED Testing function: computeDiffTab.default.region
2018-10-17 04:40:38     0.6    INFO         Conducting differential analysis using limma
2018-10-17 04:40:42     0.7  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2018-10-17 04:40:42     0.7  STATUS     STARTED Testing function: combineTestPvalsMeth
2018-10-17 04:40:42     0.7  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2018-10-17 04:40:42     0.7  STATUS     STARTED Testing function: get.adjustment.variables
2018-10-17 04:40:43     0.7  STATUS     COMPLETED Testing function: get.adjustment.variables
2018-10-17 04:40:43     0.7  STATUS     STARTED Testing function: get.comparison.info
2018-10-17 04:40:43     0.7  STATUS     COMPLETED Testing function: get.comparison.info
2018-10-17 04:40:43     0.7  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:40:43     0.7  STATUS         STARTED Retrieving comparison info
2018-10-17 04:40:43     0.7  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:40:43     0.7  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:40:43     0.7  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:40:43     0.7  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:40:43     0.7    INFO                     Conducting differential analysis using limma
2018-10-17 04:40:43     0.7  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:40:43     0.7  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:40:44     0.9  STATUS                     Computed table for tiling
2018-10-17 04:40:44     0.9  STATUS                     Computed table for genes
2018-10-17 04:40:45     0.9  STATUS                     Computed table for promoters
2018-10-17 04:40:45     0.9  STATUS                     Computed table for cpgislands
2018-10-17 04:40:45     0.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:40:45     1.0  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:40:45     1.0  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:40:45     1.0  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:40:45     1.0    INFO                     Conducting differential analysis using limma
2018-10-17 04:40:45     1.0  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:40:45     1.0  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:40:46     1.0  STATUS                     Computed table for tiling
2018-10-17 04:40:46     0.8  STATUS                     Computed table for genes
2018-10-17 04:40:46     0.8  STATUS                     Computed table for promoters
2018-10-17 04:40:47     0.8  STATUS                     Computed table for cpgislands
2018-10-17 04:40:47     0.8  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:40:47     0.8  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:40:47     0.8  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:40:47     0.8  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:40:47     0.8  STATUS     STARTED Testing function: diffVar
2018-10-17 04:40:47     0.8  STATUS         STARTED diffVar method
2018-10-17 04:40:47     0.9  STATUS         COMPLETED diffVar method
2018-10-17 04:40:47     0.9  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-17 04:40:49     0.9  STATUS         COMPLETED diffVar method
2018-10-17 04:40:49     0.9  STATUS     COMPLETED Testing function: diffVar
2018-10-17 04:40:49     0.9  STATUS     STARTED Testing function: apply.iEVORA
2018-10-17 04:40:49     0.9  STATUS         STARTED iEVORA method
2018-10-17 04:40:51     1.0    INFO             No DVCs detected. All p-values set to 1.
2018-10-17 04:40:51     1.0  STATUS         COMPLETED iEVORA method
2018-10-17 04:40:51     1.0  STATUS         STARTED Testing function: rnb.execute.diffVar
2018-10-17 04:40:51     1.0  STATUS             STARTED Differential Variability
2018-10-17 04:40:51     1.0  STATUS                 STARTED Retrieving comparison info
2018-10-17 04:40:51     1.0  STATUS                 COMPLETED Retrieving comparison info
2018-10-17 04:40:51     1.0    INFO                 No imputation method selected, 'knn' method used.
2018-10-17 04:40:51     1.0  STATUS                 STARTED Imputation procedure knn 
2018-10-17 04:40:51     1.0  STATUS                 COMPLETED Imputation procedure knn 
2018-10-17 04:40:51     1.0  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:40:51     1.0    INFO                     Conducting differential variability using diffVar
2018-10-17 04:40:51     1.0  STATUS                     STARTED diffVar method
2018-10-17 04:40:51     1.1  STATUS                     COMPLETED diffVar method
2018-10-17 04:40:51     1.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:40:52     1.1  STATUS                         Computed table for tiling
2018-10-17 04:40:52     1.1  STATUS                         Computed table for genes
2018-10-17 04:40:52     1.1  STATUS                         Computed table for promoters
2018-10-17 04:40:53     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:40:53     1.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:40:53     1.1  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:40:53     1.1  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:40:53     1.1    INFO                     Conducting differential variability using diffVar
2018-10-17 04:40:53     1.1  STATUS                     STARTED diffVar method
2018-10-17 04:40:53     1.1  STATUS                     COMPLETED diffVar method
2018-10-17 04:40:53     1.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:40:54     1.1  STATUS                         Computed table for tiling
2018-10-17 04:40:54     1.1  STATUS                         Computed table for genes
2018-10-17 04:40:55     1.1  STATUS                         Computed table for promoters
2018-10-17 04:40:55     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:40:55     1.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:40:55     1.1  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:40:55     1.1  STATUS             COMPLETED Differential Variability
2018-10-17 04:40:55     1.1  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2018-10-17 04:40:55     1.1  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:40:55     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:40:55     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:40:55     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:40:55     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:40:55     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:40:55     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:40:55     1.1  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:40:56     1.1  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:40:56     1.1    INFO                         Conducting differential variability using diffVar
2018-10-17 04:40:56     1.1  STATUS                         STARTED diffVar method
2018-10-17 04:40:56     1.1  STATUS                         COMPLETED diffVar method
2018-10-17 04:40:56     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:40:56     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:40:57     1.1  STATUS                         Computed table for tiling
2018-10-17 04:40:57     0.9  STATUS                         Computed table for genes
2018-10-17 04:40:58     0.9  STATUS                         Computed table for promoters
2018-10-17 04:40:58     1.0  STATUS                         Computed table for cpgislands
2018-10-17 04:40:58     1.0  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:40:58     1.0  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:40:58     1.0  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:40:58     1.0  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:40:58     1.0    INFO                         Conducting differential analysis using limma
2018-10-17 04:40:58     1.0  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:40:58     1.0  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:40:58     1.0    INFO                         Conducting differential variability using diffVar
2018-10-17 04:40:58     1.0  STATUS                         STARTED diffVar method
2018-10-17 04:40:58     1.0  STATUS                         COMPLETED diffVar method
2018-10-17 04:40:59     1.0  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:40:59     1.0  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:00     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:00     1.0  STATUS                         Computed table for genes
2018-10-17 04:41:01     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:01     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:01     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:01     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:01     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:01     1.1  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:41:01     1.1  STATUS         STARTED Testing class: RnBDiffMeth
2018-10-17 04:41:01     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:01     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:01     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:01     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:01     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:02     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:02     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:02     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:02     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:03     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:03     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:04     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:04     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:04     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:04     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:04     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:04     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:04     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:04     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:05     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:05     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:05     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:06     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:06     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:06     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:06     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:06     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:06     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:06     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:06     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:06     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:06     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:06     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:06     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:07     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:07     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:07     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:07     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:07     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:07     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:07     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:07     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:07     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:07     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:07     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:08     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:08     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:08     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:08     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:09     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:09     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:09     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:09     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:09     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:09     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:09     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:09     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:09     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:09     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:09     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:09     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:09     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:09     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:09     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:09     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:09     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:09     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:10     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:10     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:10     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:10     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:10     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:10     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:10     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:10     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:10     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:10     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:10     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:10     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:10     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:11     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:11     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:11     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:11     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:11     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:11     1.1  STATUS             STARTED Testing function: get.region.types
2018-10-17 04:41:11     1.1  STATUS             COMPLETED Testing function: get.region.types
2018-10-17 04:41:11     1.1  STATUS             STARTED Testing function: get.comparisons
2018-10-17 04:41:11     1.1  STATUS             COMPLETED Testing function: get.comparisons
2018-10-17 04:41:11     1.1  STATUS             STARTED Testing function: get.comparison.grouplabels
2018-10-17 04:41:11     1.1  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2018-10-17 04:41:11     1.1  STATUS             STARTED Testing function: get.site.test.method
2018-10-17 04:41:11     1.1  STATUS             COMPLETED Testing function: get.site.test.method
2018-10-17 04:41:11     1.1  STATUS             STARTED Testing function: get.table
2018-10-17 04:41:11     1.1  STATUS             COMPLETED Testing function: get.table
2018-10-17 04:41:11     1.1  STATUS             STARTED Testing function: addDiffMethTable
2018-10-17 04:41:12     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:12     1.1  STATUS             COMPLETED Testing function: addDiffMethTable
2018-10-17 04:41:12     1.1  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2018-10-17 04:41:12     1.1  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-17 04:41:12     1.1  STATUS             STARTED Destructor
2018-10-17 04:41:13     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:13     1.1  STATUS             COMPLETED Destructor
2018-10-17 04:41:13     1.1  STATUS         COMPLETED Testing class: RnBDiffMeth
2018-10-17 04:41:13     1.1  STATUS     COMPLETED Testing function: apply.iEVORA
2018-10-17 04:41:13     1.1  STATUS     STARTED Retrieving comparison info
2018-10-17 04:41:13     1.1  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:41:13     1.1  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:41:13     1.1  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:13     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:13     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:13     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:13     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:14     1.1  STATUS                 Computed table for tiling
2018-10-17 04:41:14     1.1  STATUS                 Computed table for genes
2018-10-17 04:41:14     1.1  STATUS                 Computed table for promoters
2018-10-17 04:41:15     1.1  STATUS                 Computed table for cpgislands
2018-10-17 04:41:15     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:15     1.1  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:15     1.1  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:15     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:15     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:15     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:15     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:15     1.1  STATUS                 Computed table for tiling
2018-10-17 04:41:16     1.1  STATUS                 Computed table for genes
2018-10-17 04:41:16     1.1  STATUS                 Computed table for promoters
2018-10-17 04:41:16     1.1  STATUS                 Computed table for cpgislands
2018-10-17 04:41:16     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:17     1.1  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:17     1.1  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:41:17     1.1  STATUS     STARTED Retrieving comparison info
2018-10-17 04:41:17     1.1  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:41:17     1.1  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:41:17     1.1  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:17     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:17     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:17     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:17     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:17     1.1  STATUS                 Computed table for genes
2018-10-17 04:41:18     1.1  STATUS                 Computed table for tiling
2018-10-17 04:41:18     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:18     1.1  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:18     1.1  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:41:18     1.1  STATUS     STARTED Retrieving comparison info
2018-10-17 04:41:18     1.1  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:41:18     1.1  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:41:18     1.1  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:18     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:18     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:18     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:18     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:19     1.1  STATUS                 Computed table for genes
2018-10-17 04:41:19     1.1  STATUS                 Computed table for tiling
2018-10-17 04:41:19     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:19     1.1  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:19     1.1  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:41:19     1.1  STATUS     STARTED Retrieving comparison info
2018-10-17 04:41:19     1.1  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:41:19     1.1  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:41:20     1.1  STATUS         STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:20     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:20     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:20     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:20     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:20     1.1  STATUS                 Computed table for promoters
2018-10-17 04:41:20     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:20     1.1  STATUS         COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:20     1.1  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:20     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:20     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:20     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:20     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:21     1.1  STATUS                 Computed table for promoters
2018-10-17 04:41:21     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:21     1.1  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:21     1.1  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:41:21     1.1  STATUS     STARTED Retrieving comparison info
2018-10-17 04:41:21     1.1  STATUS     COMPLETED Retrieving comparison info
2018-10-17 04:41:21     1.1  STATUS     STARTED Computing differential methylation tables
2018-10-17 04:41:21     1.1  STATUS         STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:21     1.1  STATUS             STARTED Computing Differential Methylation Table
2018-10-17 04:41:21     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:21     1.1  STATUS             COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:21     1.1  STATUS             STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:21     1.1  STATUS                 Computed table for genes
2018-10-17 04:41:22     1.1  STATUS                 Computed table for tiling
2018-10-17 04:41:22     1.1  STATUS             COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:22     1.1  STATUS         COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:22     1.1  STATUS     COMPLETED Computing differential methylation tables
2018-10-17 04:41:22     1.1  STATUS     STARTED Testing function: get.region.types
2018-10-17 04:41:22     1.1  STATUS     COMPLETED Testing function: get.region.types
2018-10-17 04:41:22     1.1  STATUS     STARTED Testing function: get.comparisons
2018-10-17 04:41:22     1.1  STATUS     COMPLETED Testing function: get.comparisons
2018-10-17 04:41:22     1.1  STATUS     STARTED Testing function: get.comparison.grouplabels
2018-10-17 04:41:22     1.1  STATUS     COMPLETED Testing function: get.comparison.grouplabels
2018-10-17 04:41:22     1.1  STATUS     STARTED Testing function: get.site.test.method
2018-10-17 04:41:22     1.1  STATUS     COMPLETED Testing function: get.site.test.method
2018-10-17 04:41:22     1.1  STATUS     STARTED Testing function: get.table
2018-10-17 04:41:22     1.1  STATUS     COMPLETED Testing function: get.table
2018-10-17 04:41:22     1.1  STATUS     STARTED Testing function: addDiffMethTable
2018-10-17 04:41:22     1.1    INFO         Conducting differential analysis using limma
2018-10-17 04:41:23     1.1  STATUS     COMPLETED Testing function: addDiffMethTable
2018-10-17 04:41:23     1.1  STATUS     STARTED Testing functions: join.diffMeth, is.valid
2018-10-17 04:41:23     1.1  STATUS     COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-17 04:41:23     1.1  STATUS     STARTED Destructor
2018-10-17 04:41:23     1.1  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS         COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:23     1.1  STATUS     COMPLETED Destructor
2018-10-17 04:41:23     1.1    INFO     Conducting differential analysis using limma
2018-10-17 04:41:23     1.1    INFO     Conducting differential analysis using limma
2018-10-17 04:41:23     1.1  STATUS     STARTED diffVar method
2018-10-17 04:41:24     1.1  STATUS     COMPLETED diffVar method
2018-10-17 04:41:24     1.1  STATUS     STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-17 04:41:24     1.1  STATUS     COMPLETED diffVar method
2018-10-17 04:41:24     1.1  STATUS STARTED Unit testing: differential
2018-10-17 04:41:24     1.1  STATUS     STARTED Testing function: rowWelchP
2018-10-17 04:41:24     1.1  STATUS     COMPLETED Testing function: rowWelchP
2018-10-17 04:41:24     1.1  STATUS     STARTED Testing function: limmaP
2018-10-17 04:41:24     1.1  STATUS     COMPLETED Testing function: limmaP
2018-10-17 04:41:24     1.1  STATUS     STARTED Testing function: computeDiffTab.extended.site
2018-10-17 04:41:24     1.1    INFO         Conducting differential analysis using limma
2018-10-17 04:41:24     1.1  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2018-10-17 04:41:24     1.1  STATUS     STARTED Testing function: computeDiffTab.default.region
2018-10-17 04:41:25     1.1    INFO         Conducting differential analysis using limma
2018-10-17 04:41:25     1.1  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2018-10-17 04:41:25     1.1  STATUS     STARTED Testing function: combineTestPvalsMeth
2018-10-17 04:41:25     1.1  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2018-10-17 04:41:25     1.1  STATUS     STARTED Testing function: get.adjustment.variables
2018-10-17 04:41:25     1.1  STATUS     COMPLETED Testing function: get.adjustment.variables
2018-10-17 04:41:25     1.1  STATUS     STARTED Testing function: get.comparison.info
2018-10-17 04:41:25     1.1  STATUS     COMPLETED Testing function: get.comparison.info
2018-10-17 04:41:25     1.1  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:41:25     1.1  STATUS         STARTED Retrieving comparison info
2018-10-17 04:41:25     1.1  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:41:26     1.1  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:41:26     1.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:26     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:41:26     1.1    INFO                     Conducting differential analysis using limma
2018-10-17 04:41:26     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:26     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:26     1.1  STATUS                     Computed table for tiling
2018-10-17 04:41:26     1.1  STATUS                     Computed table for genes
2018-10-17 04:41:27     1.1  STATUS                     Computed table for promoters
2018-10-17 04:41:27     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:41:27     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:27     1.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:27     1.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:27     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:41:27     1.1    INFO                     Conducting differential analysis using limma
2018-10-17 04:41:27     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:27     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:28     1.1  STATUS                     Computed table for tiling
2018-10-17 04:41:28     1.1  STATUS                     Computed table for genes
2018-10-17 04:41:28     1.1  STATUS                     Computed table for promoters
2018-10-17 04:41:28     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:41:29     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:29     1.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:29     1.1  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:41:29     1.1  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2018-10-17 04:41:29     1.1  STATUS     STARTED Testing function: diffVar
2018-10-17 04:41:29     1.1  STATUS         STARTED diffVar method
2018-10-17 04:41:29     1.1  STATUS         COMPLETED diffVar method
2018-10-17 04:41:29     1.1  STATUS         STARTED diffVar method
Coefficients not estimable: x2x2 
2018-10-17 04:41:29     1.1  STATUS         COMPLETED diffVar method
2018-10-17 04:41:29     1.1  STATUS     COMPLETED Testing function: diffVar
2018-10-17 04:41:29     1.1  STATUS     STARTED Testing function: apply.iEVORA
2018-10-17 04:41:29     1.1  STATUS         STARTED iEVORA method
2018-10-17 04:41:31     1.1    INFO             No DVCs detected. All p-values set to 1.
2018-10-17 04:41:31     1.1  STATUS         COMPLETED iEVORA method
2018-10-17 04:41:31     1.1  STATUS         STARTED Testing function: rnb.execute.diffVar
2018-10-17 04:41:31     1.1  STATUS             STARTED Differential Variability
2018-10-17 04:41:31     1.1  STATUS                 STARTED Retrieving comparison info
2018-10-17 04:41:31     1.1  STATUS                 COMPLETED Retrieving comparison info
2018-10-17 04:41:31     1.1  STATUS                 STARTED Imputation procedure knn 
2018-10-17 04:41:31     1.1  STATUS                 COMPLETED Imputation procedure knn 
2018-10-17 04:41:31     1.1  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:31     1.1    INFO                     Conducting differential variability using diffVar
2018-10-17 04:41:31     1.1  STATUS                     STARTED diffVar method
2018-10-17 04:41:31     1.1  STATUS                     COMPLETED diffVar method
2018-10-17 04:41:31     1.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:41:32     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:32     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:32     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:32     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:32     1.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:41:32     1.1  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:32     1.1  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:32     1.1    INFO                     Conducting differential variability using diffVar
2018-10-17 04:41:33     1.1  STATUS                     STARTED diffVar method
2018-10-17 04:41:33     1.1  STATUS                     COMPLETED diffVar method
2018-10-17 04:41:33     1.1  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:41:33     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:33     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:34     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:34     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:34     1.1  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:41:34     1.1  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:34     1.1  STATUS             COMPLETED Differential Variability
2018-10-17 04:41:34     1.1  STATUS         COMPLETED Testing function: rnb.execute.diffVar
2018-10-17 04:41:34     1.1  STATUS         STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:41:34     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:34     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:34     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:34     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:34     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:34     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:34     1.1  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:41:34     1.1  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:41:34     1.1    INFO                         Conducting differential variability using diffVar
2018-10-17 04:41:34     1.1  STATUS                         STARTED diffVar method
2018-10-17 04:41:34     1.1  STATUS                         COMPLETED diffVar method
2018-10-17 04:41:35     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:35     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:36     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:36     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:37     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:37     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:37     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:37     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:37     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:37     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:37     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:38     1.1  STATUS                         STARTED Imputation procedure knn 
2018-10-17 04:41:38     1.1  STATUS                         COMPLETED Imputation procedure knn 
2018-10-17 04:41:38     1.1    INFO                         Conducting differential variability using diffVar
2018-10-17 04:41:38     1.1  STATUS                         STARTED diffVar method
2018-10-17 04:41:38     1.1  STATUS                         COMPLETED diffVar method
2018-10-17 04:41:38     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:38     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:39     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:40     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:40     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:40     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:40     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:40     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:40     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:40     1.1  STATUS         COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2018-10-17 04:41:40     1.1  STATUS         STARTED Testing class: RnBDiffMeth
2018-10-17 04:41:41     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:41     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:41     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:41     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:41     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:41     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:41     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:41     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:42     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:43     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:43     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:43     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:43     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:43     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:43     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:43     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:43     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:43     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:43     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:44     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:45     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:45     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:45     1.1  STATUS                         Computed table for cpgislands
2018-10-17 04:41:45     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:45     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:45     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:46     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:46     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:46     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:46     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:46     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:46     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:46     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:46     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:46     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:47     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:47     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:47     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:47     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:47     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:47     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:47     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:47     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:47     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:47     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:47     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:47     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:48     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:48     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:48     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:48     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:48     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:48     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:48     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:48     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:48     1.1  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:49     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:49     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:49     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:49     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:49     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:49     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:49     1.1  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:49     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:49     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:49     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:49     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:49     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:50     1.1  STATUS                         Computed table for promoters
2018-10-17 04:41:50     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:50     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:50     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:50     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:41:50     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:41:50     1.1  STATUS             STARTED Computing differential methylation tables
2018-10-17 04:41:50     1.1  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:50     1.1  STATUS                     STARTED Computing Differential Methylation Table
2018-10-17 04:41:50     1.1    INFO                         Conducting differential analysis using limma
2018-10-17 04:41:50     1.1  STATUS                     COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:50     1.1  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:50     1.1  STATUS                         Computed table for genes
2018-10-17 04:41:51     1.1  STATUS                         Computed table for tiling
2018-10-17 04:41:51     1.1  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:51     1.1  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:51     1.1  STATUS             COMPLETED Computing differential methylation tables
2018-10-17 04:41:51     1.1  STATUS             STARTED Testing function: get.region.types
2018-10-17 04:41:51     1.1  STATUS             COMPLETED Testing function: get.region.types
2018-10-17 04:41:51     1.1  STATUS             STARTED Testing function: get.comparisons
2018-10-17 04:41:51     1.1  STATUS             COMPLETED Testing function: get.comparisons
2018-10-17 04:41:51     1.1  STATUS             STARTED Testing function: get.comparison.grouplabels
2018-10-17 04:41:51     1.1  STATUS             COMPLETED Testing function: get.comparison.grouplabels
2018-10-17 04:41:51     1.1  STATUS             STARTED Testing function: get.site.test.method
2018-10-17 04:41:51     1.1  STATUS             COMPLETED Testing function: get.site.test.method
2018-10-17 04:41:51     1.1  STATUS             STARTED Testing function: get.table
2018-10-17 04:41:51     1.1  STATUS             COMPLETED Testing function: get.table
2018-10-17 04:41:51     1.1  STATUS             STARTED Testing function: addDiffMethTable
2018-10-17 04:41:51     1.1    INFO                 Conducting differential analysis using limma
2018-10-17 04:41:52     1.1  STATUS             COMPLETED Testing function: addDiffMethTable
2018-10-17 04:41:52     1.1  STATUS             STARTED Testing functions: join.diffMeth, is.valid
2018-10-17 04:41:52     1.1  STATUS             COMPLETED Testing functions: join.diffMeth, is.valid
2018-10-17 04:41:52     1.1  STATUS             STARTED Destructor
2018-10-17 04:41:52     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 STARTED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS                 COMPLETED Deleting RnBDiffMeth disk dump files from disk
2018-10-17 04:41:52     1.1  STATUS             COMPLETED Destructor
2018-10-17 04:41:52     1.1  STATUS         COMPLETED Testing class: RnBDiffMeth
2018-10-17 04:41:52     1.1  STATUS     COMPLETED Testing function: apply.iEVORA
2018-10-17 04:41:52     1.1  STATUS     STARTED iEVORA method
2018-10-17 04:41:54     1.1    INFO         No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2018-10-17 04:41:54     1.1  STATUS         STARTED Retrieving comparison info
2018-10-17 04:41:54     1.1  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:41:54     1.1  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:41:54     1.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:54     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:41:54     1.1    INFO                     Conducting differential analysis using limma
2018-10-17 04:41:54     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:54     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:55     1.1  STATUS                     Computed table for tiling
2018-10-17 04:41:55     1.1  STATUS                     Computed table for genes
2018-10-17 04:41:56     1.1  STATUS                     Computed table for promoters
2018-10-17 04:41:56     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:41:56     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:56     1.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:56     1.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:56     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:41:56     1.1    INFO                     Conducting differential analysis using limma
2018-10-17 04:41:56     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:56     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:56     1.1  STATUS                     Computed table for tiling
2018-10-17 04:41:57     1.1  STATUS                     Computed table for genes
2018-10-17 04:41:57     1.1  STATUS                     Computed table for promoters
2018-10-17 04:41:57     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:41:57     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:57     1.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:41:57     1.1  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:41:57     1.1  STATUS         STARTED Retrieving comparison info
2018-10-17 04:41:58     1.1  STATUS         COMPLETED Retrieving comparison info
2018-10-17 04:41:58     1.1  STATUS         STARTED Computing differential methylation tables
2018-10-17 04:41:58     1.1  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:41:58     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:41:58     1.1    INFO                     Conducting differential analysis using limma
2018-10-17 04:41:58     1.1  STATUS                     STARTED Imputation procedure knn 
2018-10-17 04:41:58     1.1  STATUS                     COMPLETED Imputation procedure knn 
2018-10-17 04:41:58     1.1    INFO                     Conducting differential variability using diffVar
2018-10-17 04:41:58     1.1  STATUS                     STARTED diffVar method
2018-10-17 04:41:58     1.1  STATUS                     COMPLETED diffVar method
2018-10-17 04:41:58     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:41:58     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:41:59     1.1  STATUS                     Computed table for tiling
2018-10-17 04:42:00     1.1  STATUS                     Computed table for genes
2018-10-17 04:42:00     1.1  STATUS                     Computed table for promoters
2018-10-17 04:42:00     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:42:00     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:42:00     1.1  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:42:00     1.1  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:42:00     1.1  STATUS                 STARTED Computing Differential Methylation Table
2018-10-17 04:42:00     1.1    INFO                     Conducting differential analysis using limma
2018-10-17 04:42:00     1.1  STATUS                     STARTED Imputation procedure knn 
2018-10-17 04:42:01     1.1  STATUS                     COMPLETED Imputation procedure knn 
2018-10-17 04:42:01     1.1    INFO                     Conducting differential variability using diffVar
2018-10-17 04:42:01     1.1  STATUS                     STARTED diffVar method
2018-10-17 04:42:01     1.1  STATUS                     COMPLETED diffVar method
2018-10-17 04:42:01     1.1  STATUS                 COMPLETED Computing Differential Methylation Table
2018-10-17 04:42:01     1.1  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:42:02     1.1  STATUS                     Computed table for tiling
2018-10-17 04:42:02     1.1  STATUS                     Computed table for genes
2018-10-17 04:42:02     1.1  STATUS                     Computed table for promoters
2018-10-17 04:42:03     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:42:03     1.1  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2018-10-17 04:42:03     1.1  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2018-10-17 04:42:03     1.1  STATUS         COMPLETED Computing differential methylation tables
2018-10-17 04:42:03     1.1  STATUS         STARTED Differential Variability
2018-10-17 04:42:03     1.1  STATUS             STARTED Retrieving comparison info
2018-10-17 04:42:03     1.1  STATUS             COMPLETED Retrieving comparison info
2018-10-17 04:42:03     1.1  STATUS             STARTED Imputation procedure knn 
2018-10-17 04:42:03     1.1  STATUS             COMPLETED Imputation procedure knn 
2018-10-17 04:42:03     1.1  STATUS             STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:42:03     1.1    INFO                 Conducting differential variability using diffVar
2018-10-17 04:42:03     1.1  STATUS                 STARTED diffVar method
2018-10-17 04:42:03     1.1  STATUS                 COMPLETED diffVar method
2018-10-17 04:42:04     1.1  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:42:04     1.1  STATUS                     Computed table for tiling
2018-10-17 04:42:04     1.1  STATUS                     Computed table for genes
2018-10-17 04:42:04     1.1  STATUS                     Computed table for promoters
2018-10-17 04:42:05     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:42:05     1.1  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:42:05     1.1  STATUS             COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2018-10-17 04:42:05     1.1  STATUS             STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:42:05     1.1    INFO                 Conducting differential variability using diffVar
2018-10-17 04:42:05     1.1  STATUS                 STARTED diffVar method
2018-10-17 04:42:05     1.1  STATUS                 COMPLETED diffVar method
2018-10-17 04:42:05     1.1  STATUS                 STARTED Computing Differential Variability Tables (Region Level)
2018-10-17 04:42:05     1.1  STATUS                     Computed table for tiling
2018-10-17 04:42:06     1.1  STATUS                     Computed table for genes
2018-10-17 04:42:06     1.1  STATUS                     Computed table for promoters
2018-10-17 04:42:06     1.1  STATUS                     Computed table for cpgislands
2018-10-17 04:42:06     1.1  STATUS                 COMPLETED Computing Differential Variability Tables (Region Level)
2018-10-17 04:42:06     1.1  STATUS             COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2018-10-17 04:42:06     1.1  STATUS         COMPLETED Differential Variability
2018-10-17 04:42:06     1.1  STATUS STARTED Analysis
2018-10-17 04:42:06     1.1    INFO     Loaded information from data.RData
2018-10-17 04:42:06     1.1  STATUS     STARTED Processing Detection P-values
2018-10-17 04:42:06     1.1    INFO         Removed 3979 probes that overlap with SNPs
2018-10-17 04:42:06     1.1    INFO         Completed Greedycut on 510 samples
2018-10-17 04:42:06     1.1  STATUS     COMPLETED Processing Detection P-values
2018-10-17 04:42:06     1.1 WARNING     File not found: data2.RData
2018-10-17 04:42:06     1.1  STATUS COMPLETED Analysis

2018-10-17 04:42:06     1.1  STATUS STARTED Testing imputation
2018-10-17 04:42:06     1.1  STATUS     STARTED Imputation procedure knn 
2018-10-17 04:42:07     1.1  STATUS     COMPLETED Imputation procedure knn 
2018-10-17 04:42:07     1.1  STATUS     STARTED Imputation procedure mean.samples 
2018-10-17 04:42:08     1.1  STATUS     COMPLETED Imputation procedure mean.samples 
2018-10-17 04:42:08     1.1  STATUS     STARTED Imputation procedure mean.cpgs 
2018-10-17 04:42:08     1.1  STATUS     COMPLETED Imputation procedure mean.cpgs 
2018-10-17 04:42:08     1.1  STATUS     STARTED Imputation procedure random 
2018-10-17 04:42:09     1.1  STATUS     COMPLETED Imputation procedure random 
2018-10-17 04:42:09     1.1  STATUS COMPLETED Testing imputation

2018-10-17 04:42:09     1.1  STATUS STARTED Testing age prediction
2018-10-17 04:42:09     1.1  STATUS     STARTED Performing Age Prediction
2018-10-17 04:42:11     1.2  STATUS     COMPLETED Performing Age Prediction
2018-10-17 04:42:11     1.2  STATUS COMPLETED Testing age prediction

2018-10-17 04:42:11     1.2  STATUS STARTED Performing Age Prediction
2018-10-17 04:42:13     1.0  STATUS COMPLETED Performing Age Prediction

2018-10-17 04:42:13     1.0  STATUS STARTED Imputation procedure knn 
2018-10-17 04:42:13     0.9  STATUS COMPLETED Imputation procedure knn 

2018-10-17 04:42:13     0.9  STATUS STARTED Imputation procedure mean.samples 
2018-10-17 04:42:14     1.0  STATUS COMPLETED Imputation procedure mean.samples 

2018-10-17 04:42:14     1.0  STATUS STARTED Imputation procedure mean.cpgs 
2018-10-17 04:42:14     1.1  STATUS COMPLETED Imputation procedure mean.cpgs 

2018-10-17 04:42:14     1.1  STATUS STARTED Imputation procedure random 
2018-10-17 04:42:15     1.1  STATUS COMPLETED Imputation procedure random 

2018-10-17 04:42:15     1.1  STATUS STARTED Testing imputation
2018-10-17 04:42:15     1.1  STATUS     STARTED Imputation procedure knn 
2018-10-17 04:42:15     1.1  STATUS     COMPLETED Imputation procedure knn 
2018-10-17 04:42:15     1.1  STATUS     STARTED Imputation procedure mean.samples 
2018-10-17 04:42:16     1.1  STATUS     COMPLETED Imputation procedure mean.samples 
2018-10-17 04:42:16     1.1  STATUS     STARTED Imputation procedure mean.cpgs 
2018-10-17 04:42:16     1.1  STATUS     COMPLETED Imputation procedure mean.cpgs 
2018-10-17 04:42:17     1.1  STATUS     STARTED Imputation procedure random 
2018-10-17 04:42:17     1.1  STATUS     COMPLETED Imputation procedure random 
2018-10-17 04:42:17     1.1  STATUS COMPLETED Testing imputation

2018-10-17 04:42:17     1.1  STATUS STARTED Testing age prediction
2018-10-17 04:42:17     1.1  STATUS     STARTED Performing Age Prediction
2018-10-17 04:42:19     1.2  STATUS     COMPLETED Performing Age Prediction
2018-10-17 04:42:19     1.2  STATUS COMPLETED Testing age prediction



RUNIT TEST PROTOCOL -- Wed Oct 17 04:42:41 2018 
*********************************************** 
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RnBeads RUnit Tests - 23 test functions, 0 errors, 0 failures
Number of test functions: 23 
Number of errors: 0 
Number of failures: 0 
There were 37 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
 117.65    2.45  139.46

Example timings

RnBeads.Rcheck/examples_i386/RnBeads-Ex.timings

nameusersystemelapsed
M-methods000
U-methods000
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods000
addRegionSubsegments000
annotation-methods000
assembly-methods000
combine-methods000
combineTestPvalsMeth000
computeDiffTab.region000
computeDiffTab.site000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport000
createReportPlot000
downloadLolaDbs000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods000
get.comparison.info000
get.comparisons-RnBDiffMeth-methods000
get.covariates.sva000
get.covg.thres-RnBDiffMeth-methods000
get.files000
get.region.types-RnBDiffMeth-methods000
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getTargetFromLolaDb000
has.covariates.sva000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods000
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods000
limmaP000
loadLolaDbs000
logger.argument000
logger.getfiles000
logger.isinitialized000
logger.validate.file000
loggerManagement000
loggerMessages000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot0.020.000.02
mergeSamples-methods000
meth-methods000
mval-methods000
nsites-methods000
parallel.getNumWorkers000
parallel.isEnabled000
parallel.setup000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth000
performLolaEnrichment.diffMeth000
performLolaEnrichment.diffVar000
pheno-methods000
qc-methods000
read.sample.annotation000
regionMapping-methods000
regions-methods000
reload-RnBDiffMeth-methods000
remove.regions-methods000
remove.samples-methods000
remove.sites-methods000
rnb.RnBSet.to.GRangesList000
rnb.RnBSet.to.bed000
rnb.RnBSet.to.bedGraph000
rnb.add.list000
rnb.add.paragraph000
rnb.add.reference000
rnb.add.section000
rnb.annotation.size000
rnb.annotation2data.frame000
rnb.beta2mval000
rnb.execute.batcheffects000
rnb.execute.clustering000
rnb.execute.computeDiffMeth000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal000
rnb.execute.dreduction000
rnb.execute.export.csv000
rnb.execute.gender.prediction000
rnb.execute.greedycut000
rnb.execute.import000
rnb.execute.na.removal000
rnb.execute.normalization000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva000
rnb.execute.tnt000
rnb.execute.variability.removal000
rnb.export.all.annotation000
rnb.export.annotation0.020.000.02
rnb.export.to.ewasher000
rnb.export.to.trackhub000
rnb.get.annotation000
rnb.get.assemblies000
rnb.get.chromosomes000
rnb.get.directory000
rnb.get.mapping000
rnb.get.reference000
rnb.get.reliability.matrix000
rnb.infinium.control.targets000
rnb.initialize.reports000
rnb.is.option000
rnb.load.annotation.from.db0.020.000.02
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.dreduction000
rnb.plot.locus.profile000
rnb.plot.negative.boxplot000
rnb.plot.region.profile.density000
rnb.plot.region.profiles0.020.000.02
rnb.plot.region.site.density000
rnb.plot.sentrix.distribution000
rnb.plot.snp.barplot000
rnb.plot.snp.boxplot000
rnb.plot.snp.heatmap000
rnb.region.types000
rnb.region.types.for.analysis000
rnb.remove.annotation000
rnb.run.example000
rnb.runs000
rnb.sample.groups000
rnb.sample.summary.table000
rnb.set.annotation000
rnb.write.table000
rnb.xml2options000
rowOneSampleTP000
rowWelchP000
run-RnBClusterRun-methods000
samples-methods000
save.tables-RnBDiffMeth-methods000
set.covariates.sva000
sites-methods000
summarize.regions-methods000
summarized.regions-methods000

RnBeads.Rcheck/examples_x64/RnBeads-Ex.timings

nameusersystemelapsed
M-methods0.010.000.02
U-methods000
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods000
addRegionSubsegments000
annotation-methods000
assembly-methods000
combine-methods000
combineTestPvalsMeth000
computeDiffTab.region000
computeDiffTab.site000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport000
createReportPlot000
downloadLolaDbs000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods000
get.comparison.info000
get.comparisons-RnBDiffMeth-methods000
get.covariates.sva000
get.covg.thres-RnBDiffMeth-methods000
get.files000
get.region.types-RnBDiffMeth-methods000
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getTargetFromLolaDb000
has.covariates.sva000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods000
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods000
limmaP000
loadLolaDbs000
logger.argument000
logger.getfiles000
logger.isinitialized000
logger.validate.file000
loggerManagement000
loggerMessages000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot000
mergeSamples-methods000
meth-methods000
mval-methods000
nsites-methods000
parallel.getNumWorkers000
parallel.isEnabled0.020.000.01
parallel.setup000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth000
performLolaEnrichment.diffMeth000
performLolaEnrichment.diffVar000
pheno-methods000
qc-methods000
read.sample.annotation000
regionMapping-methods000
regions-methods000
reload-RnBDiffMeth-methods000
remove.regions-methods000
remove.samples-methods000
remove.sites-methods000
rnb.RnBSet.to.GRangesList000
rnb.RnBSet.to.bed000
rnb.RnBSet.to.bedGraph000
rnb.add.list000
rnb.add.paragraph000
rnb.add.reference000
rnb.add.section0.020.000.01
rnb.annotation.size000
rnb.annotation2data.frame000
rnb.beta2mval000
rnb.execute.batcheffects000
rnb.execute.clustering000
rnb.execute.computeDiffMeth000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal000
rnb.execute.dreduction000
rnb.execute.export.csv000
rnb.execute.gender.prediction000
rnb.execute.greedycut000
rnb.execute.import000
rnb.execute.na.removal000
rnb.execute.normalization000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva000
rnb.execute.tnt000
rnb.execute.variability.removal000
rnb.export.all.annotation000
rnb.export.annotation000
rnb.export.to.ewasher000
rnb.export.to.trackhub000
rnb.get.annotation000
rnb.get.assemblies000
rnb.get.chromosomes000
rnb.get.directory000
rnb.get.mapping000
rnb.get.reference000
rnb.get.reliability.matrix0.010.000.02
rnb.infinium.control.targets000
rnb.initialize.reports000
rnb.is.option000
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.dreduction000
rnb.plot.locus.profile000
rnb.plot.negative.boxplot000
rnb.plot.region.profile.density000
rnb.plot.region.profiles000
rnb.plot.region.site.density000
rnb.plot.sentrix.distribution0.010.000.01
rnb.plot.snp.barplot000
rnb.plot.snp.boxplot000
rnb.plot.snp.heatmap000
rnb.region.types000
rnb.region.types.for.analysis000
rnb.remove.annotation0.020.000.02
rnb.run.example000
rnb.runs000
rnb.sample.groups000
rnb.sample.summary.table000
rnb.set.annotation000
rnb.write.table000
rnb.xml2options000
rowOneSampleTP000
rowWelchP000
run-RnBClusterRun-methods000
samples-methods000
save.tables-RnBDiffMeth-methods000
set.covariates.sva0.010.000.02
sites-methods000
summarize.regions-methods000
summarized.regions-methods000