Back to Build/check report for BioC 3.17
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This page was generated on 2023-01-02 09:00:48 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RnBeads on palomino5


To the developers/maintainers of the RnBeads package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1693/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 2.17.0  (landing page)
Fabian Mueller
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/RnBeads
git_branch: master
git_last_commit: 31d842d
git_last_commit_date: 2022-11-01 11:11:37 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  

Summary

Package: RnBeads
Version: 2.17.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RnBeads.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings RnBeads_2.17.0.tar.gz
StartedAt: 2022-12-29 03:00:02 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 03:07:58 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 476.4 seconds
RetCode: 0
Status:   OK  
CheckDir: RnBeads.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RnBeads.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings RnBeads_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/RnBeads.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'RnBeads/DESCRIPTION' ... OK
* this is package 'RnBeads' version '2.17.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
  'ff', 'fields', 'ggplot2', 'gplots', 'grid', '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  5.4Mb
  sub-directories of 1Mb or more:
    R   3.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'qvalue'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from 'RnBeads' for: 'samples'

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

Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'grid'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
  'grDevices:::.smoothScatterCalcDensity'
  'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
  'minfi:::.normalizeFunnorm450k'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
  'stopCluster'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'phenoData'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'assayDataElementNames'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'featureNames'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'varLabels'
MethyLumiSet2RnBeadSet: no visible global function definition for
  'featureData'
add.age.histogram: no visible binding for global variable 'Age'
add.age.histogram: no visible binding for global variable '..count..'
add.age.histogram: no visible binding for global variable '..density..'
add.agecomparison.plot: no visible global function definition for
  'samples'
add.agecomparison.plot: no visible binding for global variable 'Sample'
add.agecomparison.plot: no visible global function definition for
  '%dopar%'
add.agecomparison.plot: no visible global function definition for
  'foreach'
add.agecomparison.plot: no visible binding for global variable 'i'
add.combination.plot: no visible global function definition for
  'samples'
add.combination.plot: no visible binding for global variable
  'Difference'
add.combination.plot: no visible binding for global variable 'Density'
add.combination.plot: no visible binding for global variable 'yint'
add.combination.plot: no visible binding for global variable 'Measure'
add.error.plot: no visible binding for global variable 'Value'
add.error.plot: no visible binding for global variable 'Sample'
add.error.plot: no visible binding for global variable 'Deviance'
add.error.plot: no visible binding for global variable 'yint'
add.error.plot: no visible binding for global variable 'Measure'
add.negative.control.boxplot: no visible global function definition for
  'samples'
add.profile.plots: no visible global function definition for 'mclapply'
add.qc.barplots: no visible global function definition for 'samples'
add.quantile.plot: no visible binding for global variable 'Difference'
add.quantile.plot: no visible binding for global variable '..density..'
add.quantile.plot: no visible binding for global variable 'Sample'
add.quantile.plot: no visible binding for global variable 'Density'
add.seq.coverage.histograms: no visible global function definition for
  'samples'
add.seq.coverage.plot: no visible global function definition for
  'samples'
add.seq.coverage.violins: no visible global function definition for
  'samples'
add.stratification.plot: no visible global function definition for
  '%dopar%'
add.stratification.plot: no visible global function definition for
  'foreach'
add.stratification.plot: no visible binding for global variable 'Group'
add.stratification.plot: no visible binding for global variable
  'Increase'
add.stratification.plot: no visible binding for global variable
  'Predicted'
add.stratification.plot: no visible binding for global variable
  'Annotated'
add.stratification.plot.immune: no visible global function definition
  for '%dopar%'
add.stratification.plot.immune: no visible global function definition
  for 'foreach'
add.stratification.plot.immune: no visible binding for global variable
  'Group'
add.stratification.plot.immune: no visible binding for global variable
  'Immune'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'var.diff'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'log10P'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'combinedRank.var'
addReportPlot.diffVar.volcano: no visible binding for global variable
  'log10FDR'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'mean.diff'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'diffmeth.p.val'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'combinedRank'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'mean.quot.log2'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
  variable 'diffmeth.p.adj.fdr'
agePredictorBiseq: no visible global function definition for
  'impute.knn'
agePredictorBiseq: no visible global function definition for 'samples'
agePredictorChip: no visible global function definition for
  'impute.knn'
append.cpg.stats: no visible global function definition for '%dopar%'
append.cpg.stats: no visible global function definition for 'foreach'
append.cpg.stats: no visible binding for global variable 'chrom'
basic_combine: no visible global function definition for 'samples'
computeDiffTab.default.region: no visible global function definition
  for '%dopar%'
computeDiffTab.default.region: no visible global function definition
  for 'foreach'
computeDiffTab.default.region: no visible binding for global variable
  'i'
computeDiffTab.default.site: no visible binding for global variable
  'p.vals.t.na.adj'
computeDiffTab.default.site : <anonymous>: no visible binding for
  global variable '.inds.g2'
computeDiffVar.bin.site: no visible binding for global variable
  'p.vals.t.na.adj'
computeDiffVar.bin.site : <anonymous>: no visible binding for global
  variable 'eps'
computeDiffVar.bin.site : <anonymous>: no visible binding for global
  variable '.inds.g2'
computeDiffVar.default.region: no visible global function definition
  for '%dopar%'
computeDiffVar.default.region: no visible global function definition
  for 'foreach'
computeDiffVar.default.region: no visible binding for global variable
  'i'
create.densityScatter: no visible binding for global variable
  '..density..'
create.diffMeth.diffVar.subsample: no visible binding for global
  variable '..density..'
create.ucsc.track.hub: no visible global function definition for
  'samples'
createPredictor : ret: no visible global function definition for
  'impute.knn'
cv.array: no visible global function definition for 'impute.knn'
data.frame2GRanges: no visible global function definition for
  'seqlevels<-'
data.frame2GRanges: no visible global function definition for
  'genome<-'
diffVar: no visible global function definition for 'varFit'
diffVar: no visible binding for global variable 'group1'
diffVar: no visible binding for global variable 'group2'
estimateProportionsCP: no visible global function definition for 'lme'
estimateProportionsCP: no visible global function definition for
  'getVarCov'
general.cv: no visible global function definition for '%dopar%'
general.cv: no visible global function definition for 'foreach'
general.cv: no visible binding for global variable 'i'
get.adjustment.variables: no visible global function definition for
  'samples'
get.comparison.info : rm.na.from.adj.tab: no visible global function
  definition for 'samples'
get.components.isva: no visible global function definition for 'DoISVA'
get.components.sva: no visible global function definition for 'sva'
get.cpg.stats: no visible global function definition for
  'dinucleotideFrequency'
get.cpg.stats: no visible global function definition for
  'letterFrequency'
get.dataset.matrix: no visible global function definition for 'samples'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
  variable 'report'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
  variable 'refText'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
  variable 'diffmeth'
get.platform.tokens: no visible global function definition for
  'setNames'
getCGCounts: no visible global function definition for 'seqlengths'
getCGCounts : <anonymous>: no visible global function definition for
  'ChrNumeric'
getGLADProfiles: no visible global function definition for 'samples'
getGLADProfiles: no visible global function definition for 'mclapply'
getGLADProfiles : <anonymous>: no visible global function definition
  for 'as.profileCGH'
getGLADProfiles : <anonymous>: no visible global function definition
  for 'daglad'
getMergeList: no visible global function definition for 'samples'
groupPermutationP.site.parallel: no visible global function definition
  for '%dopar%'
groupPermutationP.site.parallel: no visible global function definition
  for 'foreach'
iEVORA: no visible global function definition for 'qvalue'
imputation.low.memory.cpgs: no visible global function definition for
  'samples'
inferWBCbyLme: no visible global function definition for 'lme'
inferWBCbyLme: no visible global function definition for 'getVarCov'
intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylationEPICmanifest'
intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylation450kmanifest'
intensities.by.color: no visible global function definition for
  'samples'
knn.imputation: no visible global function definition for 'impute.knn'
limmaP: no visible binding for global variable 'group1'
limmaP: no visible binding for global variable 'group2'
loadLolaDbs: no visible global function definition for 'loadRegionDB'
loadLolaDbs: no visible global function definition for 'mergeRegionDBs'
locus.profile.get.base.tracks: no visible global function definition
  for 'useMart'
locus.profile.get.base.tracks: no visible global function definition
  for 'IdeogramTrack'
locus.profile.get.base.tracks: no visible global function definition
  for 'GenomeAxisTrack'
locus.profile.get.base.tracks: no visible global function definition
  for 'BiomartGeneRegionTrack'
locus.profile.get.base.tracks: no visible global function definition
  for 'UcscTrack'
locus.profile.get.methylation.track.heatmap: no visible global function
  definition for 'DataTrack'
locus.profile.get.methylation.track.smooth: no visible global function
  definition for 'DataTrack'
methylumi.intensities.by.color: no visible global function definition
  for 'featureNames'
methylumi.intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylation450kmanifest'
methylumi.intensities.by.color: no visible global function definition
  for 'assayDataElement'
parallel.setup: no visible global function definition for
  'registerDoParallel'
parallel.setup: no visible global function definition for
  'getDoParWorkers'
performLolaEnrichment.diffMeth: no visible global function definition
  for 'runLOLA'
performLolaEnrichment.diffVar: no visible global function definition
  for 'runLOLA'
plot.heatmap.pc.correlations: no visible global function definition for
  'melt'
plot.heatmap.pc.correlations: no visible global function definition for
  'grid.newpage'
plot.heatmap.pc.correlations: no visible global function definition for
  'grid.draw'
plot.heatmap.pc.pvalues: no visible global function definition for
  'melt'
plot.heatmap.pc.pvalues: no visible global function definition for
  'grid.newpage'
plot.heatmap.pc.pvalues: no visible global function definition for
  'grid.draw'
plot.heatmap.rand: no visible global function definition for 'melt'
plot.heatmap.symm: no visible global function definition for 'melt'
plot.heatmap.symm: no visible global function definition for
  'grid.newpage'
plot.heatmap.symm: no visible global function definition for
  'grid.draw'
plotCGHProfile: no visible global function definition for 'ChrNumeric'
prepareGEOSampleInfoTemplate: no visible global function definition for
  'samples'
projectWBC: no visible global function definition for 'solve.QP'
read.GS.report: no visible global function definition for
  'featureNames'
read.idat.files: no visible binding for global variable 'barcode'
rnb.RnBSet.to.GRangesList: no visible global function definition for
  'samples'
rnb.RnBSet.to.bed: no visible global function definition for 'samples'
rnb.RnBSet.to.bedGraph: no visible global function definition for
  'samples'
rnb.bed.from.segmentation: no visible global function definition for
  'samples'
rnb.boxplot.from.segmentation: no visible global function definition
  for 'samples'
rnb.boxplot.from.segmentation: no visible binding for global variable
  'Segment'
rnb.boxplot.from.segmentation: no visible binding for global variable
  'AvgMeth'
rnb.chromosome.lengths: no visible global function definition for
  'seqlengths'
rnb.combine.seq: no visible global function definition for 'samples'
rnb.enmix.oob: no visible global function definition for '%dopar%'
rnb.enmix.oob: no visible global function definition for 'foreach'
rnb.execute.dreduction: no visible global function definition for
  'samples'
rnb.execute.filter.summary.internal: no visible global function
  definition for 'samples'
rnb.execute.high.coverage.removal.internal: no visible global function
  definition for 'samples'
rnb.execute.high.dpval.masking.internal: no visible global function
  definition for 'samples'
rnb.execute.imputation: no visible global function definition for
  'samples'
rnb.execute.low.coverage.masking.internal: no visible global function
  definition for 'samples'
rnb.execute.na.removal.internal: no visible global function definition
  for 'samples'
rnb.execute.normalization: no visible global function definition for
  'phenoData'
rnb.execute.normalization: no visible global function definition for
  'phenoData<-'
rnb.execute.normalization: no visible global function definition for
  'RGChannelSet'
rnb.execute.normalization: no visible global function definition for
  'preprocessSWAN'
rnb.execute.normalization: no visible global function definition for
  'getMeth'
rnb.execute.normalization: no visible global function definition for
  'getUnmeth'
rnb.execute.normalization: no visible global function definition for
  'featureNames'
rnb.execute.normalization: no visible global function definition for
  'samples'
rnb.execute.normalization: no visible global function definition for
  'mapToGenome'
rnb.execute.normalization: no visible global function definition for
  'addSex'
rnb.execute.normalization: no visible global function definition for
  'getSex'
rnb.execute.normalization: no visible global function definition for
  'getCN'
rnb.execute.normalization.bmiq: no visible global function definition
  for '%dopar%'
rnb.execute.normalization.bmiq: no visible global function definition
  for 'foreach'
rnb.execute.pOOBAH: no visible global function definition for 'samples'
rnb.execute.pOOBAH: no visible global function definition for 'SigDF'
rnb.execute.pOOBAH: no visible global function definition for 'pOOBAH'
rnb.execute.pOOBAH: no visible binding for global variable 'sigset.l'
rnb.execute.pOOBAH: no visible binding for global variable 'pIG'
rnb.execute.pOOBAH: no visible binding for global variable 'pII'
rnb.execute.pOOBAH: no visible binding for global variable 'pIR'
rnb.execute.quality: no visible global function definition for
  'samples'
rnb.execute.quality : <anonymous>: no visible global function
  definition for 'samples'
rnb.execute.segmentation: no visible binding for global variable
  'Hsapiens'
rnb.execute.segmentation: no visible binding for global variable
  'Mmusculus'
rnb.execute.segmentation: no visible global function definition for
  'seqlengths'
rnb.execute.segmentation: no visible global function definition for
  'browserSession'
rnb.execute.segmentation: no visible global function definition for
  'genome<-'
rnb.execute.segmentation: no visible global function definition for
  'ucscTableQuery'
rnb.execute.segmentation: no visible global function definition for
  'getTable'
rnb.execute.segmentation: no visible global function definition for
  'samples'
rnb.execute.segmentation: no visible global function definition for
  'readMethylome'
rnb.execute.segmentation: no visible global function definition for
  'readSNPTable'
rnb.execute.segmentation: no visible global function definition for
  'removeSNPs'
rnb.execute.segmentation: no visible global function definition for
  'segmentPMDs'
rnb.execute.segmentation: no visible global function definition for
  'plotAlphaDistributionOneChr'
rnb.execute.segmentation: no visible global function definition for
  'calculateFDRs'
rnb.execute.segmentation: no visible global function definition for
  'segmentUMRsLMRs'
rnb.export.to.ewasher: no visible global function definition for
  'samples'
rnb.filter.dataset: no visible global function definition for 'samples'
rnb.final.segmentation: no visible global function definition for
  'samples'
rnb.get.reliability.counts.per.sample: no visible global function
  definition for 'samples'
rnb.options.description.table.fromRd: no visible global function
  definition for 'Rd2HTML'
rnb.options.description.table.fromRd: no visible binding for global
  variable 'xmlValue'
rnb.plot.beta.density.group: no visible binding for global variable
  'group'
rnb.plot.biseq.coverage: no visible global function definition for
  'samples'
rnb.plot.biseq.coverage.hist: no visible global function definition for
  'samples'
rnb.plot.control.barplot: no visible global function definition for
  'samples'
rnb.plot.control.barplot: no visible binding for global variable
  'Target'
rnb.plot.control.barplot: no visible binding for global variable
  'Index'
rnb.plot.control.barplot: no visible binding for global variable 'ID'
rnb.plot.control.barplot: no visible binding for global variable
  'Address'
rnb.plot.control.barplot: no visible global function definition for
  'grid.newpage'
rnb.plot.control.barplot: no visible binding for global variable
  'Intensity'
rnb.plot.control.barplot: no visible global function definition for
  'grid.draw'
rnb.plot.control.boxplot: no visible global function definition for
  'grid.newpage'
rnb.plot.control.boxplot: no visible binding for global variable
  'Probe'
rnb.plot.control.boxplot: no visible binding for global variable
  'Intensity'
rnb.plot.control.boxplot: no visible global function definition for
  'grid.draw'
rnb.plot.ct.heatmap: no visible binding for global variable 'x'
rnb.plot.ct.heatmap: no visible binding for global variable 'y'
rnb.plot.ct.heatmap: no visible binding for global variable 'v'
rnb.plot.ct.heatmap: no visible global function definition for
  'grid.newpage'
rnb.plot.ct.heatmap: no visible global function definition for
  'grid.draw'
rnb.plot.dreduction: no visible global function definition for 'tsne'
rnb.plot.locus.profile: no visible global function definition for
  'plotTracks'
rnb.plot.marker.fstat: no visible binding for global variable 'x'
rnb.plot.marker.fstat: no visible binding for global variable 'y'
rnb.plot.marker.fstat: no visible global function definition for
  'muted'
rnb.plot.negative.boxplot: no visible global function definition for
  'samples'
rnb.plot.negative.boxplot: no visible binding for global variable
  'numeric.names'
rnb.plot.negative.boxplot: no visible binding for global variable
  'type'
rnb.plot.negative.boxplot: no visible binding for global variable
  'types'
rnb.plot.negative.boxplot: no visible global function definition for
  'grid.newpage'
rnb.plot.negative.boxplot: no visible binding for global variable
  'Sample'
rnb.plot.negative.boxplot: no visible binding for global variable
  'Intensity'
rnb.plot.negative.boxplot: no visible global function definition for
  'grid.draw'
rnb.plot.num.sites.covg: no visible global function definition for
  'samples'
rnb.plot.num.sites.covg : <anonymous>: no visible global function
  definition for 'samples'
rnb.plot.num.sites.covg: no visible binding for global variable
  'numSites'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgMedian'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgPercLow'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgPercUp'
rnb.plot.num.sites.covg: no visible binding for global variable 'comma'
rnb.plot.region.profile.density: no visible binding for global variable
  'relative.coord'
rnb.plot.region.profile.density: no visible binding for global variable
  '..density..'
rnb.plot.region.profiles : <anonymous>: no visible global function
  definition for 'samples'
rnb.plot.region.profiles: no visible binding for global variable
  'relative.coord'
rnb.plot.region.profiles: no visible binding for global variable
  'group'
rnb.plot.region.site.density: no visible binding for global variable
  'relative.coord'
rnb.plot.segmentation.distributions: no visible binding for global
  variable 'x2'
rnb.plot.segmentation.distributions: no visible binding for global
  variable 'y2'
rnb.plot.segmentation.distributions: no visible binding for global
  variable 'texthere'
rnb.plot.segmentation.final: no visible global function definition for
  'plotFinalSegmentation'
rnb.plot.sentrix.distributions: no visible global function definition
  for 'samples'
rnb.plot.sentrix.distributions: no visible binding for global variable
  'Slide'
rnb.plot.snp.boxplot: no visible binding for global variable 'SNP'
rnb.plot.snp.boxplot: no visible binding for global variable 'bv'
rnb.run.example: no visible global function definition for 'install'
rnb.run.preprocessing : logger.completed.filtering: no visible global
  function definition for 'samples'
rnb.sample.summary.table: no visible global function definition for
  'samples'
rnb.section.ageprediction: no visible global function definition for
  'samples'
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
  function definition for 'samples'
rnb.section.clustering: no visible global function definition for
  'samples'
rnb.section.diffMeth.region: no visible global function definition for
  '%dopar%'
rnb.section.diffMeth.region: no visible global function definition for
  'foreach'
rnb.section.diffMeth.region: no visible binding for global variable 'k'
rnb.section.diffMeth.region : do.enrichment.table: no visible global
  function definition for 'sigCategories'
rnb.section.diffMeth.region : do.enrichment.table.var: no visible
  global function definition for 'sigCategories'
rnb.section.diffMeth.site: no visible global function definition for
  '%dopar%'
rnb.section.diffMeth.site: no visible global function definition for
  'foreach'
rnb.section.diffVar: no visible global function definition for
  '%dopar%'
rnb.section.diffVar: no visible global function definition for
  'foreach'
rnb.section.diffVar.region: no visible global function definition for
  '%dopar%'
rnb.section.diffVar.region: no visible global function definition for
  'foreach'
rnb.section.diffVar.region: no visible binding for global variable 'k'
rnb.section.import: no visible global function definition for 'samples'
rnb.section.import: no visible global function definition for
  'phenoData'
rnb.section.imputation: no visible global function definition for
  'melt'
rnb.section.locus.profiles: no visible global function definition for
  'samples'
rnb.section.locus.profiles : do.plots: no visible global function
  definition for 'plotTracks'
rnb.section.locus.profiles: no visible global function definition for
  '%dopar%'
rnb.section.locus.profiles: no visible global function definition for
  'foreach'
rnb.section.na.removal: no visible global function definition for
  'samples'
rnb.section.normalization: no visible global function definition for
  'samples'
rnb.section.region.description: no visible binding for global variable
  'size'
rnb.section.region.description: no visible binding for global variable
  'n.sites'
rnb.section.region.profiles: no visible global function definition for
  'samples'
rnb.section.region.subsegmentation : get.summary.df.from.list: no
  visible global function definition for 'melt'
rnb.section.region.subsegmentation: no visible binding for global
  variable 'region.size'
rnb.section.region.subsegmentation: no visible binding for global
  variable 'is.subsegmentation'
rnb.section.region.subsegmentation: no visible binding for global
  variable 'num.sites'
rnb.section.sex.prediction: no visible global function definition for
  'muted'
rnb.step.betadistribution.internal: no visible global function
  definition for '%dopar%'
rnb.step.betadistribution.internal: no visible global function
  definition for 'foreach'
rnb.step.cell.types: no visible global function definition for
  'samples'
rnb.step.clustering.internal: no visible global function definition for
  'samples'
rnb.step.dreduction: no visible global function definition for
  '%dopar%'
rnb.step.dreduction: no visible global function definition for
  'foreach'
rnb.step.dreduction: no visible binding for global variable 'target'
rnb.step.filter.summary.internal: no visible global function definition
  for 'percent_format'
rnb.step.filter.summary.internal: no visible global function definition
  for 'samples'
rnb.step.import: no visible global function definition for 'samples'
rnb.step.import: no visible global function definition for 'phenoData'
rnb.step.na.removal: no visible binding for global variable
  'sites2ignore'
rnb.step.na.removal.internal: no visible global function definition for
  'samples'
rnb.step.normalization: no visible global function definition for
  'phenoData'
robustHyperGResultSummary: no visible global function definition for
  'sigCategories'
robustHyperGResultSummary: no visible global function definition for
  'pvalues'
robustHyperGResultSummary: no visible global function definition for
  'oddsRatios'
robustHyperGResultSummary: no visible global function definition for
  'expectedCounts'
robustHyperGResultSummary: no visible global function definition for
  'geneCounts'
robustHyperGResultSummary: no visible global function definition for
  'universeCounts'
robustHyperGResultSummary: no visible binding for global variable
  'Term'
run.cross.validation: no visible global function definition for
  'samples'
run.cross.validation: no visible global function definition for 'melt'
run.cross.validation: no visible binding for global variable 'Measure'
run.cross.validation: no visible binding for global variable 'Error'
sampleCovgApply: no visible global function definition for 'samples'
set.covariates.ct: no visible global function definition for 'samples'
simpleGlmnet: no visible global function definition for 'impute.knn'
simpleGlmnet: no visible global function definition for 'cv.glmnet'
simpleGlmnet: no visible global function definition for 'glmnet'
simpleGlmnetBiseq: no visible global function definition for
  'cv.glmnet'
simpleGlmnetBiseq: no visible global function definition for 'glmnet'
simpleGlmnetEvaluate: no visible global function definition for
  'cv.glmnet'
simpleGlmnetEvaluate: no visible global function definition for
  'glmnet'
symmetric.melt: no visible global function definition for 'melt'
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
  'reg.type'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'getManifest'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'getGreen'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'getRed'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
  for 'pData'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for 'featureData<-'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for 'featureNames<-'
coerce,RnBeadRawSet-RGChannelSet: no visible global function definition
  for 'RGChannelSet'
join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function
  definition for 'clone'
mask.sites.meth,RnBSet: no visible global function definition for
  'samples'
remove.samples,RnBSet: no visible global function definition for
  'samples'
remove.samples,RnBeadRawSet: no visible global function definition for
  'samples'
remove.samples,RnBeadSet: no visible global function definition for
  'samples'
remove.sites,RnBSet: no visible global function definition for
  'samples'
sampleCovgApply,RnBSet: no visible global function definition for
  'samples'
sampleMethApply,RnBSet: no visible global function definition for
  'samples'
summarize.regions,RnBSet: no visible global function definition for
  'samples'
summarize.regions,RnBSet: multiple local function definitions for
  'aggr.f' with different formal arguments
updateMethylationSites,RnBSet: no visible global function definition
  for 'samples'
Undefined global functions or variables:
  %dopar% ..count.. ..density.. .inds.g2 Address Age Annotated AvgMeth
  BiomartGeneRegionTrack ChrNumeric DataTrack Density Deviance
  Difference DoISVA Error GenomeAxisTrack Group Hsapiens ID
  IdeogramTrack IlluminaHumanMethylation450kmanifest
  IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity
  Measure Mmusculus Predicted Probe RGChannelSet Rd2HTML SNP Sample
  Segment SigDF Slide Target Term UcscTrack Value addSex as.profileCGH
  assayDataElement assayDataElementNames barcode browserSession bv
  calculateFDRs chrom clone combinedRank combinedRank.var comma
  covgMedian covgPercLow covgPercUp cv.glmnet daglad diffmeth
  diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency eps
  expectedCounts featureData featureData<- featureNames featureNames<-
  foreach geneCounts genome<- getCN getDoParWorkers getGreen
  getManifest getMeth getRed getSex getTable getUnmeth getVarCov glmnet
  grid.draw grid.newpage group group1 group2 i impute.knn install
  is.subsegmentation k letterFrequency lme loadRegionDB log10FDR log10P
  mapToGenome mclapply mean.diff mean.quot.log2 melt mergeRegionDBs
  muted n.sites num.sites numSites numeric.names oddsRatios
  p.vals.t.na.adj pData pIG pII pIR pOOBAH percent_format phenoData
  phenoData<- plotAlphaDistributionOneChr plotFinalSegmentation
  plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable
  refText reg.type region.size registerDoParallel relative.coord
  removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs
  seqlengths seqlevels<- setNames sigCategories sigset.l sites2ignore
  size solve.QP stopCluster sva target texthere tsne type types
  ucscTableQuery universeCounts useMart v var.diff varFit varLabels x
  x2 xmlValue y y2 yint
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
rnb.execute.pOOBAH 13.98   1.51   15.88
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 7 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/RnBeads.Rcheck/00check.log'
for details.

Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL RnBeads
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'RnBeads' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RnBeads)

Tests output

RnBeads.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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:stats':

    IQR, mad, sd, var, xtabs

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

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


Attaching package: 'S4Vectors'

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

    I, expand.grid, unname


Attaching package: 'IRanges'

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

    windows


Attaching package: 'bit'

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

    xor

Attaching package ff
- getOption("fftempdir")=="F:/biocbuild/bbs-3.17-bioc-rtools43/tmpdir/Rtmp6nflt0/ff"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    mle

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

    backsolve, forwardsolve


Try help(fields) to get started.

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: 'grid'

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

    pattern


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: 'scales'

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

    viridis_pal


Attaching package: 'AnnotationDbi'

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

    select



Attaching package: 'MatrixGenerics'

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

    rowMedians

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

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


Attaching package: 'Biostrings'

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

    pattern

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

    mismatch, pattern

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

    strsplit

locfit 1.5-9.6 	 2022-07-11
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

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

    compact

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

    count

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

    desc

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

    rename

2022-12-29 03:05:40     Inf  STATUS STARTED Unit testing: differential
2022-12-29 03:05:40     Inf  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2022-12-29 03:05:40     Inf  STATUS     COMPLETED Testing function: rowWelchP
2022-12-29 03:05:40     Inf  STATUS     STARTED Testing function: limmaP
2022-12-29 03:05:40     Inf  STATUS     COMPLETED Testing function: limmaP
2022-12-29 03:05:40     Inf  STATUS     STARTED Testing function: computeDiffTab.extended.site
2022-12-29 03:05:40     Inf    INFO         Conducting differential analysis using limma
2022-12-29 03:05:40     Inf  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2022-12-29 03:05:40     Inf  STATUS     STARTED Testing function: computeDiffTab.default.region
2022-12-29 03:05:40     Inf    INFO         Conducting differential analysis using limma
2022-12-29 03:05:43     Inf  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2022-12-29 03:05:43     Inf  STATUS     STARTED Testing function: combineTestPvalsMeth
2022-12-29 03:05:43     Inf  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2022-12-29 03:05:43     Inf  STATUS     STARTED Testing function: get.adjustment.variables
2022-12-29 03:05:43     Inf  STATUS     COMPLETED Testing function: get.adjustment.variables
2022-12-29 03:05:43     Inf  STATUS     STARTED Testing function: get.comparison.info
2022-12-29 03:05:44     Inf  STATUS     COMPLETED Testing function: get.comparison.info
2022-12-29 03:05:44     Inf  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2022-12-29 03:05:44     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:05:44     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:05:44     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:05:44     Inf  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:05:44     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:05:44     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:05:44     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:05:44     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:05:45     Inf  STATUS                     Computed table for tiling
2022-12-29 03:05:45     Inf  STATUS                     Computed table for genes
2022-12-29 03:05:45     Inf  STATUS                     Computed table for promoters
2022-12-29 03:05:45     Inf  STATUS                     Computed table for cpgislands
2022-12-29 03:05:45     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:05:46     Inf  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:05:46     Inf  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:05:46     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:05:46     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:05:46     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:05:46     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:05:46     Inf  STATUS                     Computed table for tiling
2022-12-29 03:05:46     Inf  STATUS                     Computed table for genes
2022-12-29 03:05:46     Inf  STATUS                     Computed table for promoters
2022-12-29 03:05:46     Inf  STATUS                     Computed table for cpgislands
2022-12-29 03:05:46     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:05:47     Inf  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:05:47     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:05:47     Inf  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2022-12-29 03:05:47     Inf  STATUS     STARTED Testing function: diffVar
2022-12-29 03:05:47     Inf  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:35     Inf  STATUS         COMPLETED diffVar method
2022-12-29 03:06:35     Inf  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:35     Inf WARNING             Could not compute p-values with diffVar, returning NA
2022-12-29 03:06:35     Inf    INFO             diffVar from missMethyl package not properly running
2022-12-29 03:06:35     Inf  STATUS         COMPLETED diffVar method
2022-12-29 03:06:35     Inf  STATUS         STARTED Testing function: apply.iEVORA
2022-12-29 03:06:35     Inf  STATUS             STARTED iEVORA method
2022-12-29 03:06:35     Inf    INFO                 No DVCs detected. All p-values set to 1.
2022-12-29 03:06:35     Inf  STATUS             COMPLETED iEVORA method
2022-12-29 03:06:35     Inf  STATUS             STARTED Testing function: rnb.execute.diffVar
2022-12-29 03:06:35     Inf  STATUS                 STARTED Differential Variability
2022-12-29 03:06:35     Inf  STATUS                     STARTED Retrieving comparison info
2022-12-29 03:06:35     Inf  STATUS                     COMPLETED Retrieving comparison info
2022-12-29 03:06:35     Inf    INFO                     No imputation method selected, 'knn' method used.
2022-12-29 03:06:35     Inf  STATUS                     STARTED Imputation procedure knn 
2022-12-29 03:06:35     Inf  STATUS                     COMPLETED Imputation procedure knn 
2022-12-29 03:06:35     Inf  STATUS                     STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:35     Inf    INFO                         Conducting differential variability using diffVar
2022-12-29 03:06:35     Inf  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:35     Inf  STATUS                         COMPLETED diffVar method
2022-12-29 03:06:35     Inf  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:36     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:36     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:36     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:36     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:36     Inf  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:36     Inf  STATUS                     COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:36     Inf  STATUS                     STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:36     Inf    INFO                         Conducting differential variability using diffVar
2022-12-29 03:06:36     Inf  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:36     Inf  STATUS                         COMPLETED diffVar method
2022-12-29 03:06:36     Inf  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:37     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:37     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:37     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:37     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:37     Inf  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:38     Inf  STATUS                     COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:38     Inf  STATUS                 COMPLETED Differential Variability
2022-12-29 03:06:38     Inf  STATUS             COMPLETED Testing function: rnb.execute.diffVar
2022-12-29 03:06:38     Inf  STATUS             STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2022-12-29 03:06:38     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:06:38     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:06:38     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:06:38     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:38     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:38     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:38     Inf  STATUS                             STARTED Imputation procedure knn 
2022-12-29 03:06:38     Inf  STATUS                             COMPLETED Imputation procedure knn 
2022-12-29 03:06:38     Inf    INFO                             Conducting differential variability using diffVar
2022-12-29 03:06:38     Inf  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:38     Inf  STATUS                             COMPLETED diffVar method
2022-12-29 03:06:38     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:38     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:38     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:38     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:40     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:40     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:40     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:40     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:40     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:40     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:40     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:40     Inf  STATUS                             STARTED Imputation procedure knn 
2022-12-29 03:06:40     Inf  STATUS                             COMPLETED Imputation procedure knn 
2022-12-29 03:06:40     Inf    INFO                             Conducting differential variability using diffVar
2022-12-29 03:06:40     Inf  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:40     Inf  STATUS                             COMPLETED diffVar method
2022-12-29 03:06:40     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:40     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:41     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:41     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:41     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:44     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:44     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:44     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:44     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:06:44     Inf  STATUS             COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2022-12-29 03:06:44     Inf  STATUS             STARTED Testing class: RnBDiffMeth
2022-12-29 03:06:44     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:06:44     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:06:44     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:06:44     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:44     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:44     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:44     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:44     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:44     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:45     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:45     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:45     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:45     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:45     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:45     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:45     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:45     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:45     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:45     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:45     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:45     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:46     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:46     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:46     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:46     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:46     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:06:46     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:06:46     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:06:46     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:06:46     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:46     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:46     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:46     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:46     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:46     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:47     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:47     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:47     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:47     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:06:47     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:06:47     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:06:47     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:06:47     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:47     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:47     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:47     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:47     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:47     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:47     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:47     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:47     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:47     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:06:47     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:06:47     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:06:47     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:06:47     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:47     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:47     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:47     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:47     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:47     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:47     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:47     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:47     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:47     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:47     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:47     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:47     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:48     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:48     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:48     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:06:48     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:06:48     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:06:48     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:48     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:06:48     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:06:48     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:48     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:48     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:48     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:48     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:48     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:06:48     Inf  STATUS                 STARTED Testing function: get.region.types
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Testing function: get.region.types
2022-12-29 03:06:48     Inf  STATUS                 STARTED Testing function: get.comparisons
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Testing function: get.comparisons
2022-12-29 03:06:48     Inf  STATUS                 STARTED Testing function: get.comparison.grouplabels
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Testing function: get.comparison.grouplabels
2022-12-29 03:06:48     Inf  STATUS                 STARTED Testing function: get.site.test.method
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Testing function: get.site.test.method
2022-12-29 03:06:48     Inf  STATUS                 STARTED Testing function: get.table
2022-12-29 03:06:48     Inf  STATUS                 COMPLETED Testing function: get.table
2022-12-29 03:06:48     Inf  STATUS                 STARTED Testing function: addDiffMethTable
2022-12-29 03:06:48     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:49     Inf  STATUS                 COMPLETED Testing function: addDiffMethTable
2022-12-29 03:06:49     Inf  STATUS                 STARTED Testing functions: join.diffMeth, is.valid
2022-12-29 03:06:49     Inf  STATUS                 COMPLETED Testing functions: join.diffMeth, is.valid
2022-12-29 03:06:49     Inf  STATUS                 STARTED Destructor
2022-12-29 03:06:49     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:49     Inf  STATUS                 COMPLETED Destructor
2022-12-29 03:06:49     Inf  STATUS             COMPLETED Testing class: RnBDiffMeth
2022-12-29 03:06:49     Inf  STATUS         COMPLETED Testing function: apply.iEVORA
2022-12-29 03:06:49     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:06:49     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:06:49     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:06:49     Inf  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:49     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:49     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:49     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:49     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:49     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:50     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:50     Inf  STATUS                     Computed table for promoters
2022-12-29 03:06:50     Inf  STATUS                     Computed table for cpgislands
2022-12-29 03:06:50     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:50     Inf  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:50     Inf  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:50     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:50     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:50     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:50     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:50     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:50     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:51     Inf  STATUS                     Computed table for promoters
2022-12-29 03:06:51     Inf  STATUS                     Computed table for cpgislands
2022-12-29 03:06:51     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:51     Inf  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:51     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:06:51     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:06:51     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:06:51     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:06:51     Inf  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:51     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:51     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:51     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:51     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:51     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:52     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:52     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:52     Inf  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:52     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:06:52     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:06:52     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:06:52     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:06:52     Inf  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:52     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:52     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:52     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:52     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:52     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:52     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:52     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:52     Inf  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:52     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:06:52     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:06:52     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:06:52     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:06:52     Inf  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:52     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:52     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:52     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:52     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:52     Inf  STATUS                     Computed table for promoters
2022-12-29 03:06:52     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:52     Inf  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:52     Inf  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:52     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:52     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:52     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:52     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:53     Inf  STATUS                     Computed table for promoters
2022-12-29 03:06:53     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:53     Inf  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:53     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:06:53     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:06:53     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:06:53     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:06:53     Inf  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:53     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:53     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:53     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:53     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:53     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:54     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:54     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:54     Inf  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing function: get.region.types
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing function: get.region.types
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing function: get.comparisons
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing function: get.comparisons
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing function: get.comparison.grouplabels
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing function: get.comparison.grouplabels
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing function: get.site.test.method
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing function: get.site.test.method
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing function: get.table
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing function: get.table
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing function: addDiffMethTable
2022-12-29 03:06:54     Inf    INFO             Conducting differential analysis using limma
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing function: addDiffMethTable
2022-12-29 03:06:54     Inf  STATUS         STARTED Testing functions: join.diffMeth, is.valid
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Testing functions: join.diffMeth, is.valid
2022-12-29 03:06:54     Inf  STATUS         STARTED Destructor
2022-12-29 03:06:54     Inf  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:06:54     Inf  STATUS         COMPLETED Destructor
2022-12-29 03:06:54     Inf    INFO         Conducting differential analysis using limma
2022-12-29 03:06:54     Inf    INFO         Conducting differential analysis using limma
2022-12-29 03:06:54     Inf  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:54     Inf  STATUS         COMPLETED diffVar method
2022-12-29 03:06:54     Inf  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:54     Inf WARNING             Could not compute p-values with diffVar, returning NA
2022-12-29 03:06:54     Inf    INFO             diffVar from missMethyl package not properly running
2022-12-29 03:06:54     Inf  STATUS             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:54     Inf  STATUS             COMPLETED diffVar method
2022-12-29 03:06:54     Inf  STATUS STARTED Unit testing: differential
2022-12-29 03:06:54     Inf  STATUS     STARTED Testing function: rowWelchP
2022-12-29 03:06:54     Inf  STATUS     COMPLETED Testing function: rowWelchP
2022-12-29 03:06:54     Inf  STATUS     STARTED Testing function: limmaP
2022-12-29 03:06:54     Inf  STATUS     COMPLETED Testing function: limmaP
2022-12-29 03:06:54     Inf  STATUS     STARTED Testing function: computeDiffTab.extended.site
2022-12-29 03:06:55     Inf    INFO         Conducting differential analysis using limma
2022-12-29 03:06:55     Inf  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2022-12-29 03:06:55     Inf  STATUS     STARTED Testing function: computeDiffTab.default.region
2022-12-29 03:06:55     Inf    INFO         Conducting differential analysis using limma
2022-12-29 03:06:55     Inf  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2022-12-29 03:06:55     Inf  STATUS     STARTED Testing function: combineTestPvalsMeth
2022-12-29 03:06:55     Inf  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2022-12-29 03:06:55     Inf  STATUS     STARTED Testing function: get.adjustment.variables
2022-12-29 03:06:55     Inf  STATUS     COMPLETED Testing function: get.adjustment.variables
2022-12-29 03:06:55     Inf  STATUS     STARTED Testing function: get.comparison.info
2022-12-29 03:06:55     Inf  STATUS     COMPLETED Testing function: get.comparison.info
2022-12-29 03:06:55     Inf  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2022-12-29 03:06:55     Inf  STATUS         STARTED Retrieving comparison info
2022-12-29 03:06:55     Inf  STATUS         COMPLETED Retrieving comparison info
2022-12-29 03:06:55     Inf  STATUS         STARTED Computing differential methylation tables
2022-12-29 03:06:55     Inf  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:55     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:55     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:55     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:55     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:55     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:55     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:55     Inf  STATUS                     Computed table for promoters
2022-12-29 03:06:56     Inf  STATUS                     Computed table for cpgislands
2022-12-29 03:06:56     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:56     Inf  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:56     Inf  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:56     Inf  STATUS                 STARTED Computing Differential Methylation Table
2022-12-29 03:06:56     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:06:56     Inf  STATUS                 COMPLETED Computing Differential Methylation Table
2022-12-29 03:06:56     Inf  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:57     Inf  STATUS                     Computed table for tiling
2022-12-29 03:06:57     Inf  STATUS                     Computed table for genes
2022-12-29 03:06:57     Inf  STATUS                     Computed table for promoters
2022-12-29 03:06:57     Inf  STATUS                     Computed table for cpgislands
2022-12-29 03:06:57     Inf  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:06:57     Inf  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:57     Inf  STATUS         COMPLETED Computing differential methylation tables
2022-12-29 03:06:57     Inf  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2022-12-29 03:06:57     Inf  STATUS     STARTED Testing function: diffVar
2022-12-29 03:06:57     Inf  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:57     Inf  STATUS         COMPLETED diffVar method
2022-12-29 03:06:57     Inf  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:57     Inf WARNING             Could not compute p-values with diffVar, returning NA
2022-12-29 03:06:57     Inf    INFO             diffVar from missMethyl package not properly running
2022-12-29 03:06:57     Inf  STATUS         COMPLETED diffVar method
2022-12-29 03:06:57     Inf  STATUS         STARTED Testing function: apply.iEVORA
2022-12-29 03:06:57     Inf  STATUS             STARTED iEVORA method
2022-12-29 03:06:58     Inf    INFO                 No DVCs detected. All p-values set to 1.
2022-12-29 03:06:58     Inf  STATUS             COMPLETED iEVORA method
2022-12-29 03:06:58     Inf  STATUS             STARTED Testing function: rnb.execute.diffVar
2022-12-29 03:06:58     Inf  STATUS                 STARTED Differential Variability
2022-12-29 03:06:58     Inf  STATUS                     STARTED Retrieving comparison info
2022-12-29 03:06:58     Inf  STATUS                     COMPLETED Retrieving comparison info
2022-12-29 03:06:58     Inf  STATUS                     STARTED Imputation procedure knn 
2022-12-29 03:06:58     Inf  STATUS                     COMPLETED Imputation procedure knn 
2022-12-29 03:06:58     Inf  STATUS                     STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:58     Inf    INFO                         Conducting differential variability using diffVar
2022-12-29 03:06:58     Inf  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:58     Inf  STATUS                         COMPLETED diffVar method
2022-12-29 03:06:58     Inf  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:59     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:59     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:59     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:59     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:59     Inf  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:59     Inf  STATUS                     COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:06:59     Inf  STATUS                     STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2022-12-29 03:06:59     Inf    INFO                         Conducting differential variability using diffVar
2022-12-29 03:06:59     Inf  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:06:59     Inf  STATUS                         COMPLETED diffVar method
2022-12-29 03:06:59     Inf  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2022-12-29 03:06:59     Inf  STATUS                             Computed table for tiling
2022-12-29 03:06:59     Inf  STATUS                             Computed table for genes
2022-12-29 03:06:59     Inf  STATUS                             Computed table for promoters
2022-12-29 03:06:59     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:06:59     Inf  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2022-12-29 03:07:00     Inf  STATUS                     COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:00     Inf  STATUS                 COMPLETED Differential Variability
2022-12-29 03:07:00     Inf  STATUS             COMPLETED Testing function: rnb.execute.diffVar
2022-12-29 03:07:00     Inf  STATUS             STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2022-12-29 03:07:00     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:00     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:00     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:07:00     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:00     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:00     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:00     Inf  STATUS                             STARTED Imputation procedure knn 
2022-12-29 03:07:00     Inf  STATUS                             COMPLETED Imputation procedure knn 
2022-12-29 03:07:00     Inf    INFO                             Conducting differential variability using diffVar
2022-12-29 03:07:00     Inf  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:07:00     Inf  STATUS                             COMPLETED diffVar method
2022-12-29 03:07:00     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:00     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:01     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:01     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:01     Inf  STATUS                             Computed table for promoters
2022-12-29 03:07:01     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:07:01     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:01     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:01     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:01     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:01     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:01     Inf  STATUS                             STARTED Imputation procedure knn 
2022-12-29 03:07:01     Inf  STATUS                             COMPLETED Imputation procedure knn 
2022-12-29 03:07:01     Inf    INFO                             Conducting differential variability using diffVar
2022-12-29 03:07:01     Inf  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:07:01     Inf  STATUS                             COMPLETED diffVar method
2022-12-29 03:07:01     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:02     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:02     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:03     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:03     Inf  STATUS                             Computed table for promoters
2022-12-29 03:07:03     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:07:03     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:03     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:03     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:07:03     Inf  STATUS             COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2022-12-29 03:07:03     Inf  STATUS             STARTED Testing class: RnBDiffMeth
2022-12-29 03:07:03     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:03     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:03     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:07:03     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:03     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:03     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:03     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:03     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:03     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:04     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:04     Inf  STATUS                             Computed table for promoters
2022-12-29 03:07:04     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:07:04     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:04     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:04     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:04     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:04     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:04     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:04     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:05     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:05     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:05     Inf  STATUS                             Computed table for promoters
2022-12-29 03:07:05     Inf  STATUS                             Computed table for cpgislands
2022-12-29 03:07:05     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:05     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:05     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:07:05     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:05     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:05     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:07:05     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:05     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:05     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:05     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:05     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:05     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:06     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:06     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:06     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:06     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:07:06     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:06     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:06     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:07:06     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:06     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:06     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:06     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:06     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:06     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:06     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:06     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:07:07     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:07     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:07:07     Inf  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:07     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:07     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:07     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:07     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                             Computed table for promoters
2022-12-29 03:07:07     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:07     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:07     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:07     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:07     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:07     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                             Computed table for promoters
2022-12-29 03:07:07     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:07:07     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:07     Inf  STATUS                 STARTED Computing differential methylation tables
2022-12-29 03:07:07     Inf  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:07     Inf  STATUS                         STARTED Computing Differential Methylation Table
2022-12-29 03:07:07     Inf    INFO                             Conducting differential analysis using limma
2022-12-29 03:07:07     Inf  STATUS                         COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:07     Inf  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                             Computed table for genes
2022-12-29 03:07:07     Inf  STATUS                             Computed table for tiling
2022-12-29 03:07:07     Inf  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:07     Inf  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Computing differential methylation tables
2022-12-29 03:07:07     Inf  STATUS                 STARTED Testing function: get.region.types
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Testing function: get.region.types
2022-12-29 03:07:07     Inf  STATUS                 STARTED Testing function: get.comparisons
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Testing function: get.comparisons
2022-12-29 03:07:07     Inf  STATUS                 STARTED Testing function: get.comparison.grouplabels
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Testing function: get.comparison.grouplabels
2022-12-29 03:07:07     Inf  STATUS                 STARTED Testing function: get.site.test.method
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Testing function: get.site.test.method
2022-12-29 03:07:07     Inf  STATUS                 STARTED Testing function: get.table
2022-12-29 03:07:07     Inf  STATUS                 COMPLETED Testing function: get.table
2022-12-29 03:07:08     Inf  STATUS                 STARTED Testing function: addDiffMethTable
2022-12-29 03:07:08     Inf    INFO                     Conducting differential analysis using limma
2022-12-29 03:07:08     Inf  STATUS                 COMPLETED Testing function: addDiffMethTable
2022-12-29 03:07:08     Inf  STATUS                 STARTED Testing functions: join.diffMeth, is.valid
2022-12-29 03:07:08     Inf  STATUS                 COMPLETED Testing functions: join.diffMeth, is.valid
2022-12-29 03:07:08     Inf  STATUS                 STARTED Destructor
2022-12-29 03:07:08     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2022-12-29 03:07:08     Inf  STATUS                 COMPLETED Destructor
2022-12-29 03:07:08     Inf  STATUS             COMPLETED Testing class: RnBDiffMeth
2022-12-29 03:07:08     Inf  STATUS         COMPLETED Testing function: apply.iEVORA
2022-12-29 03:07:08     Inf  STATUS         STARTED iEVORA method
2022-12-29 03:07:09     Inf    INFO             No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2022-12-29 03:07:09     Inf  STATUS             STARTED Retrieving comparison info
2022-12-29 03:07:09     Inf  STATUS             COMPLETED Retrieving comparison info
2022-12-29 03:07:09     Inf  STATUS             STARTED Computing differential methylation tables
2022-12-29 03:07:09     Inf  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:09     Inf  STATUS                     STARTED Computing Differential Methylation Table
2022-12-29 03:07:09     Inf    INFO                         Conducting differential analysis using limma
2022-12-29 03:07:09     Inf  STATUS                     COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:09     Inf  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:09     Inf  STATUS                         Computed table for tiling
2022-12-29 03:07:09     Inf  STATUS                         Computed table for genes
2022-12-29 03:07:10     Inf  STATUS                         Computed table for promoters
2022-12-29 03:07:10     Inf  STATUS                         Computed table for cpgislands
2022-12-29 03:07:10     Inf  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:10     Inf  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:10     Inf  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:10     Inf  STATUS                     STARTED Computing Differential Methylation Table
2022-12-29 03:07:10     Inf    INFO                         Conducting differential analysis using limma
2022-12-29 03:07:10     Inf  STATUS                     COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:10     Inf  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:11     Inf  STATUS                         Computed table for tiling
2022-12-29 03:07:11     Inf  STATUS                         Computed table for genes
2022-12-29 03:07:11     Inf  STATUS                         Computed table for promoters
2022-12-29 03:07:11     Inf  STATUS                         Computed table for cpgislands
2022-12-29 03:07:11     Inf  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:11     Inf  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:11     Inf  STATUS             COMPLETED Computing differential methylation tables
2022-12-29 03:07:11     Inf  STATUS             STARTED Retrieving comparison info
2022-12-29 03:07:11     Inf  STATUS             COMPLETED Retrieving comparison info
2022-12-29 03:07:11     Inf  STATUS             STARTED Computing differential methylation tables
2022-12-29 03:07:11     Inf  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:11     Inf  STATUS                     STARTED Computing Differential Methylation Table
2022-12-29 03:07:11     Inf    INFO                         Conducting differential analysis using limma
2022-12-29 03:07:11     Inf  STATUS                         STARTED Imputation procedure knn 
2022-12-29 03:07:11     Inf  STATUS                         COMPLETED Imputation procedure knn 
2022-12-29 03:07:11     Inf    INFO                         Conducting differential variability using diffVar
2022-12-29 03:07:11     Inf  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:07:11     Inf  STATUS                         COMPLETED diffVar method
2022-12-29 03:07:11     Inf  STATUS                     COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:11     Inf  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:12     Inf  STATUS                         Computed table for tiling
2022-12-29 03:07:12     Inf  STATUS                         Computed table for genes
2022-12-29 03:07:12     Inf  STATUS                         Computed table for promoters
2022-12-29 03:07:13     Inf  STATUS                         Computed table for cpgislands
2022-12-29 03:07:13     Inf  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:13     Inf  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:13     Inf  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:13     Inf  STATUS                     STARTED Computing Differential Methylation Table
2022-12-29 03:07:13     Inf    INFO                         Conducting differential analysis using limma
2022-12-29 03:07:13     Inf  STATUS                         STARTED Imputation procedure knn 
2022-12-29 03:07:13     Inf  STATUS                         COMPLETED Imputation procedure knn 
2022-12-29 03:07:13     Inf    INFO                         Conducting differential variability using diffVar
2022-12-29 03:07:13     Inf  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:07:13     Inf  STATUS                         COMPLETED diffVar method
2022-12-29 03:07:13     Inf  STATUS                     COMPLETED Computing Differential Methylation Table
2022-12-29 03:07:13     Inf  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:13     Inf  STATUS                         Computed table for tiling
2022-12-29 03:07:14     Inf  STATUS                         Computed table for genes
2022-12-29 03:07:14     Inf  STATUS                         Computed table for promoters
2022-12-29 03:07:14     Inf  STATUS                         Computed table for cpgislands
2022-12-29 03:07:14     Inf  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2022-12-29 03:07:14     Inf  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:14     Inf  STATUS             COMPLETED Computing differential methylation tables
2022-12-29 03:07:14     Inf  STATUS             STARTED Differential Variability
2022-12-29 03:07:14     Inf  STATUS                 STARTED Retrieving comparison info
2022-12-29 03:07:14     Inf  STATUS                 COMPLETED Retrieving comparison info
2022-12-29 03:07:14     Inf  STATUS                 STARTED Imputation procedure knn 
2022-12-29 03:07:14     Inf  STATUS                 COMPLETED Imputation procedure knn 
2022-12-29 03:07:14     Inf  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:14     Inf    INFO                     Conducting differential variability using diffVar
2022-12-29 03:07:14     Inf  STATUS                     STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:07:14     Inf  STATUS                     COMPLETED diffVar method
2022-12-29 03:07:15     Inf  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2022-12-29 03:07:15     Inf  STATUS                         Computed table for tiling
2022-12-29 03:07:15     Inf  STATUS                         Computed table for genes
2022-12-29 03:07:15     Inf  STATUS                         Computed table for promoters
2022-12-29 03:07:15     Inf  STATUS                         Computed table for cpgislands
2022-12-29 03:07:15     Inf  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2022-12-29 03:07:15     Inf  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2022-12-29 03:07:15     Inf  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:15     Inf    INFO                     Conducting differential variability using diffVar
2022-12-29 03:07:15     Inf  STATUS                     STARTED diffVar method
coef not specified. Using all columns of design matrix.
2022-12-29 03:07:15     Inf  STATUS                     COMPLETED diffVar method
2022-12-29 03:07:15     Inf  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2022-12-29 03:07:15     Inf  STATUS                         Computed table for tiling
2022-12-29 03:07:16     Inf  STATUS                         Computed table for genes
2022-12-29 03:07:16     Inf  STATUS                         Computed table for promoters
2022-12-29 03:07:16     Inf  STATUS                         Computed table for cpgislands
2022-12-29 03:07:16     Inf  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2022-12-29 03:07:16     Inf  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2022-12-29 03:07:16     Inf  STATUS             COMPLETED Differential Variability
2022-12-29 03:07:16     Inf  STATUS STARTED Analysis
2022-12-29 03:07:16     Inf    INFO     Loaded information from data.RData
2022-12-29 03:07:16     Inf  STATUS     STARTED Processing Detection P-values
2022-12-29 03:07:16     Inf    INFO         Removed 3979 probes that overlap with SNPs
2022-12-29 03:07:16     Inf    INFO         Completed Greedycut on 510 samples
2022-12-29 03:07:16     Inf  STATUS     COMPLETED Processing Detection P-values
2022-12-29 03:07:16     Inf WARNING     File not found: data2.RData
2022-12-29 03:07:16     Inf  STATUS COMPLETED Analysis

2022-12-29 03:07:16     Inf  STATUS STARTED Testing imputation
2022-12-29 03:07:16     Inf  STATUS     STARTED Imputation procedure knn 
2022-12-29 03:07:17     Inf  STATUS     COMPLETED Imputation procedure knn 
2022-12-29 03:07:17     Inf  STATUS     STARTED Imputation procedure mean.samples 
2022-12-29 03:07:17     Inf  STATUS     COMPLETED Imputation procedure mean.samples 
2022-12-29 03:07:17     Inf  STATUS     STARTED Imputation procedure mean.cpgs 
2022-12-29 03:07:18     Inf  STATUS     COMPLETED Imputation procedure mean.cpgs 
2022-12-29 03:07:18     Inf  STATUS     STARTED Imputation procedure random 
2022-12-29 03:07:18     Inf  STATUS     COMPLETED Imputation procedure random 
2022-12-29 03:07:18     Inf  STATUS COMPLETED Testing imputation

2022-12-29 03:07:18     Inf  STATUS STARTED Testing age prediction
2022-12-29 03:07:18     Inf  STATUS     STARTED Performing Age Prediction
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:19     Inf  STATUS     COMPLETED Performing Age Prediction
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:19     Inf  STATUS COMPLETED Testing age prediction

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:19     Inf  STATUS STARTED Performing Age Prediction
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:20     Inf  STATUS COMPLETED Performing Age Prediction

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:20     Inf  STATUS STARTED Imputation procedure knn 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:20     Inf  STATUS COMPLETED Imputation procedure knn 

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:20     Inf  STATUS STARTED Imputation procedure mean.samples 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:21     Inf  STATUS COMPLETED Imputation procedure mean.samples 

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:21     Inf  STATUS STARTED Imputation procedure mean.cpgs 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:21     Inf  STATUS COMPLETED Imputation procedure mean.cpgs 

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:21     Inf  STATUS STARTED Imputation procedure random 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:21     Inf  STATUS COMPLETED Imputation procedure random 

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:21     Inf  STATUS STARTED Testing imputation
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:22     Inf  STATUS     STARTED Imputation procedure knn 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:22     Inf  STATUS     COMPLETED Imputation procedure knn 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:22     Inf  STATUS     STARTED Imputation procedure mean.samples 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS     COMPLETED Imputation procedure mean.samples 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS     STARTED Imputation procedure mean.cpgs 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS     COMPLETED Imputation procedure mean.cpgs 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS     STARTED Imputation procedure random 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS     COMPLETED Imputation procedure random 
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS COMPLETED Testing imputation

Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS STARTED Testing age prediction
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:23     Inf  STATUS     STARTED Performing Age Prediction
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:24     Inf  STATUS     COMPLETED Performing Age Prediction
Warning: 'memory.size()' is no longer supported
2022-12-29 03:07:24     Inf  STATUS COMPLETED Testing age prediction

Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported
Warning: 'memory.size()' is no longer supported


RUNIT TEST PROTOCOL -- Thu Dec 29 03:07:40 2022 
*********************************************** 
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RnBeads RUnit Tests - 24 test functions, 0 errors, 0 failures
Number of test functions: 24 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
 113.37    4.65  134.29

Example timings

RnBeads.Rcheck/RnBeads-Ex.timings

nameusersystemelapsed
M-methods000
U-methods000
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods000
addRegionSubsegments000
annotation-methods000
assembly-methods000
combine.rnb.sets-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-methods0.010.000.02
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getSubCmdTokens-ClusterArchitectureSLURM-methods000
getTargetFromLolaDb000
has.covariates.sva000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods000
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods000
limmaP000
loadLolaDbs000
logger.argument000
logger.getfiles000
logger.isinitialized000
logger.validate.file000
loggerManagement000
loggerMessages000
lolaBarPlot000
lolaBoxPlotPerTarget000
lolaVolcanoPlot000
mergeSamples-methods000
meth-methods000
mval-methods000
nsites-methods000
parallel.getNumWorkers000
parallel.isEnabled000
parallel.setup000
parallel.teardown000
performGOEnrichment.diffVar000
performGOenrichment.diffMeth.entrez000
performGoEnrichment.diffMeth000
performLolaEnrichment.diffMeth000
performLolaEnrichment.diffVar000
pheno-methods0.000.010.02
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.greedycut000
rnb.execute.import000
rnb.execute.na.removal000
rnb.execute.normalization000
rnb.execute.pOOBAH13.98 1.5115.88
rnb.execute.sex.prediction000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva000
rnb.execute.tnt000
rnb.execute.variability.removal000
rnb.export.all.annotation000
rnb.export.annotation000
rnb.export.to.ewasher000
rnb.export.to.trackhub000
rnb.get.annotation000
rnb.get.assemblies000
rnb.get.chromosomes000
rnb.get.directory000
rnb.get.mapping000
rnb.get.reference000
rnb.get.reliability.matrix000
rnb.infinium.control.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.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.runs0.000.010.01
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