Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:04 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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

Package 1782/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 2.24.0  (landing page)
Fabian Mueller
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/RnBeads
git_branch: RELEASE_3_20
git_last_commit: a6b1698
git_last_commit_date: 2024-10-29 10:01:01 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for RnBeads on nebbiolo2

To the developers/maintainers of the RnBeads package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: RnBeads
Version: 2.24.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RnBeads_2.24.0.tar.gz
StartedAt: 2024-12-20 04:53:52 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 05:04:42 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 649.7 seconds
RetCode: 0
Status:   OK  
CheckDir: RnBeads.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RnBeads_2.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/RnBeads.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘2.24.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     3.2Mb
    bin   1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘qvalue’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 loading without being on the library search path ... 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.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 ‘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’
computeDiffVar.bin.site: no visible binding for global variable
  ‘p.vals.t.na.adj’
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.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.genesymbol.of.coordinate: no visible global function definition for
  ‘getBM’
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.add.nv.heatmap: no visible binding for global variable ‘dataset’
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.biseq.coverage.hist: no visible binding for global variable
  ‘count’
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.nv.heatmap: no visible global function definition for
  ‘useMart’
rnb.plot.region.profile.density: no visible binding for global variable
  ‘relative.coord’
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.exploratory: no visible global function definition for
  ‘useMart’
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.beta.value.density.plot: no visible global function
  definition for ‘%dopar%’
rnb.section.beta.value.density.plot: no visible global function
  definition for ‘foreach’
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.diffMeth.site: no visible global function definition for
  ‘useMart’
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.na.removal.internal : <anonymous>: no visible binding for
  global variable ‘count’
rnb.section.normalization: no visible global function definition for
  ‘samples’
rnb.section.nv.probes.heatmap: 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% 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 count
  covgMedian covgPercLow covgPercUp cv.glmnet daglad dataset diffmeth
  diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency
  expectedCounts featureData featureData<- featureNames featureNames<-
  foreach geneCounts genome<- getBM 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 ... NOTE
checkRd: (-1) as.RnBeadRawSet.Rd:9: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.RnBeadRawSet.Rd:10: Lost braces in \itemize; meant \describe ?
checkRd: (-1) as.RnBeadRawSet.Rd:11: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReport.Rd:50-51: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReport.Rd:52-54: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReport.Rd:55-57: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReport.Rd:58-59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReport.Rd:60-61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReportPlot.Rd:48: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReportPlot.Rd:49: Lost braces in \itemize; meant \describe ?
checkRd: (-1) createReportPlot.Rd:50: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.combine.seq.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.combine.seq.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.combine.seq.Rd:29: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.combine.seq.Rd:30: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.execute.export.csv.Rd:40: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.execute.export.csv.Rd:41-43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.execute.export.csv.Rd:44: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.execute.export.csv.Rd:45: Lost braces in \itemize; meant \describe ?
checkRd: (-1) rnb.execute.export.csv.Rd:46: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 8 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/RnBeads.Rcheck/00check.log’
for details.

Installation output

RnBeads.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RnBeads
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘RnBeads’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RnBeads)

Tests output

RnBeads.Rcheck/tests/runTests.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname


Attaching package: 'bit'

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

    xor

Attaching package ff
- getOption("fftempdir")=="/home/biocbuild/bbs-3.20-bioc/tmpdir/RtmpbHHhtj/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 2.11-0 (2024-10-03) 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: '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 1.5-9.10 	 2024-06-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

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

    compact

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

    count

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

    desc

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

    rename

2024-12-20 05:00:30     1.2  STATUS STARTED Unit testing: differential
2024-12-20 05:00:30     1.2  STATUS     STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2024-12-20 05:00:30     1.2  STATUS     COMPLETED Testing function: rowWelchP
2024-12-20 05:00:30     1.2  STATUS     STARTED Testing function: limmaP
2024-12-20 05:00:30     1.2  STATUS     COMPLETED Testing function: limmaP
2024-12-20 05:00:30     1.2  STATUS     STARTED Testing function: computeDiffTab.extended.site
2024-12-20 05:00:30     1.2    INFO         Conducting differential analysis using limma
2024-12-20 05:00:30     1.2  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2024-12-20 05:00:30     1.2  STATUS     STARTED Testing function: computeDiffTab.default.region
2024-12-20 05:00:30     1.2    INFO         Conducting differential analysis using limma
2024-12-20 05:00:34     1.3  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2024-12-20 05:00:34     1.3  STATUS     STARTED Testing function: combineTestPvalsMeth
2024-12-20 05:00:34     1.3  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2024-12-20 05:00:34     1.3  STATUS     STARTED Testing function: get.adjustment.variables
2024-12-20 05:00:34     1.3  STATUS     COMPLETED Testing function: get.adjustment.variables
2024-12-20 05:00:34     1.3  STATUS     STARTED Testing function: get.comparison.info
2024-12-20 05:00:34     1.3  STATUS     COMPLETED Testing function: get.comparison.info
2024-12-20 05:00:34     1.3  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2024-12-20 05:00:34     1.3  STATUS         STARTED Retrieving comparison info
2024-12-20 05:00:34     1.3  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:00:34     1.3  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:00:34     1.3  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:00:34     1.3  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:00:34     1.3    INFO                     Conducting differential analysis using limma
2024-12-20 05:00:34     1.3  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:00:34     1.3  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:00:35     1.3  STATUS                     Computed table for tiling
2024-12-20 05:00:36     1.3  STATUS                     Computed table for genes
2024-12-20 05:00:37     1.3  STATUS                     Computed table for promoters
2024-12-20 05:00:37     1.3  STATUS                     Computed table for cpgislands
2024-12-20 05:00:37     1.3  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:00:37     1.4  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:00:37     1.4  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:00:37     1.4  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:00:37     1.4    INFO                     Conducting differential analysis using limma
2024-12-20 05:00:37     1.4  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:00:37     1.4  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:00:37     1.5  STATUS                     Computed table for tiling
2024-12-20 05:00:37     1.6  STATUS                     Computed table for genes
2024-12-20 05:00:38     1.7  STATUS                     Computed table for promoters
2024-12-20 05:00:38     1.7  STATUS                     Computed table for cpgislands
2024-12-20 05:00:38     1.7  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:00:38     1.7  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:00:38     1.7  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:00:38     1.7  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2024-12-20 05:00:38     1.7  STATUS     STARTED Testing function: diffVar
2024-12-20 05:00:38     1.7  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:17     4.5  STATUS         COMPLETED diffVar method
2024-12-20 05:02:17     4.5  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:18     4.5 WARNING             Could not compute p-values with diffVar, returning NA
2024-12-20 05:02:18     4.5    INFO             diffVar from missMethyl package not properly running
2024-12-20 05:02:18     4.5  STATUS         COMPLETED diffVar method
2024-12-20 05:02:18     4.5  STATUS         STARTED Testing function: apply.iEVORA
2024-12-20 05:02:18     4.5  STATUS             STARTED iEVORA method
2024-12-20 05:02:18     4.5    INFO                 No DVCs detected. All p-values set to 1.
2024-12-20 05:02:18     4.5  STATUS             COMPLETED iEVORA method
2024-12-20 05:02:18     4.5  STATUS             STARTED Testing function: rnb.execute.diffVar
2024-12-20 05:02:18     4.5  STATUS                 STARTED Differential Variability
2024-12-20 05:02:18     4.5  STATUS                     STARTED Retrieving comparison info
2024-12-20 05:02:18     4.5  STATUS                     COMPLETED Retrieving comparison info
2024-12-20 05:02:18     4.5    INFO                     No imputation method selected, 'knn' method used.
2024-12-20 05:02:18     4.5  STATUS                     STARTED Imputation procedure knn 
2024-12-20 05:02:18     4.5  STATUS                     COMPLETED Imputation procedure knn 
2024-12-20 05:02:18     4.5  STATUS                     STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:18     4.5    INFO                         Conducting differential variability using diffVar
2024-12-20 05:02:18     4.5  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:18     4.5  STATUS                         COMPLETED diffVar method
2024-12-20 05:02:18     4.6  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:19     4.6  STATUS                             Computed table for tiling
2024-12-20 05:02:19     4.7  STATUS                             Computed table for genes
2024-12-20 05:02:19     4.7  STATUS                             Computed table for promoters
2024-12-20 05:02:19     4.8  STATUS                             Computed table for cpgislands
2024-12-20 05:02:19     4.8  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:19     4.8  STATUS                     COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:19     4.8  STATUS                     STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:19     4.8    INFO                         Conducting differential variability using diffVar
2024-12-20 05:02:19     4.8  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:19     4.8  STATUS                         COMPLETED diffVar method
2024-12-20 05:02:19     4.8  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:20     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:20     5.0  STATUS                             Computed table for genes
2024-12-20 05:02:20     5.0  STATUS                             Computed table for promoters
2024-12-20 05:02:22     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:22     4.9  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:22     4.9  STATUS                     COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:22     4.9  STATUS                 COMPLETED Differential Variability
2024-12-20 05:02:22     4.9  STATUS             COMPLETED Testing function: rnb.execute.diffVar
2024-12-20 05:02:22     4.9  STATUS             STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2024-12-20 05:02:22     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:22     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:22     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:22     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:22     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:22     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:22     4.9  STATUS                             STARTED Imputation procedure knn 
2024-12-20 05:02:22     4.9  STATUS                             COMPLETED Imputation procedure knn 
2024-12-20 05:02:22     4.9    INFO                             Conducting differential variability using diffVar
2024-12-20 05:02:22     4.9  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:22     4.9  STATUS                             COMPLETED diffVar method
2024-12-20 05:02:22     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:22     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:23     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:23     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:23     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:24     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:24     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:24     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:24     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:24     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:24     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:24     4.9  STATUS                             STARTED Imputation procedure knn 
2024-12-20 05:02:24     4.9  STATUS                             COMPLETED Imputation procedure knn 
2024-12-20 05:02:24     4.9    INFO                             Conducting differential variability using diffVar
2024-12-20 05:02:24     4.9  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:24     4.9  STATUS                             COMPLETED diffVar method
2024-12-20 05:02:24     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:24     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:25     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:25     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:26     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:26     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:26     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:26     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:26     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:26     4.9  STATUS             COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2024-12-20 05:02:26     4.9  STATUS             STARTED Testing class: RnBDiffMeth
2024-12-20 05:02:26     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:26     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:26     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:26     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:26     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:26     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:26     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:26     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:26     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:26     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:27     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:27     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:27     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:27     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:27     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:27     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:27     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:27     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:27     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:28     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:28     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:28     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:28     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:28     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:28     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:28     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:28     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:28     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:28     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:28     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:28     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:28     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:28     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:28     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:29     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:29     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:29     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:29     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:29     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:29     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:29     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:29     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:29     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:29     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:29     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:29     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:29     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:29     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:30     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:30     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:30     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:30     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:30     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:30     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:30     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:30     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:30     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:30     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:30     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:30     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:30     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:30     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:30     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:30     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:30     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:30     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:30     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:30     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:31     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:31     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:31     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:31     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:31     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:31     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:31     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:31     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:31     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:31     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:31     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:31     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:31     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:31     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:31     4.9  STATUS                 STARTED Testing function: get.region.types
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Testing function: get.region.types
2024-12-20 05:02:31     4.9  STATUS                 STARTED Testing function: get.comparisons
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Testing function: get.comparisons
2024-12-20 05:02:31     4.9  STATUS                 STARTED Testing function: get.comparison.grouplabels
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Testing function: get.comparison.grouplabels
2024-12-20 05:02:31     4.9  STATUS                 STARTED Testing function: get.site.test.method
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Testing function: get.site.test.method
2024-12-20 05:02:31     4.9  STATUS                 STARTED Testing function: get.table
2024-12-20 05:02:31     4.9  STATUS                 COMPLETED Testing function: get.table
2024-12-20 05:02:31     4.9  STATUS                 STARTED Testing function: addDiffMethTable
2024-12-20 05:02:31     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:32     4.9  STATUS                 COMPLETED Testing function: addDiffMethTable
2024-12-20 05:02:32     4.9  STATUS                 STARTED Testing functions: join.diffMeth, is.valid
2024-12-20 05:02:32     4.9  STATUS                 COMPLETED Testing functions: join.diffMeth, is.valid
2024-12-20 05:02:32     4.9  STATUS                 STARTED Destructor
2024-12-20 05:02:32     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:32     4.9  STATUS                 COMPLETED Destructor
2024-12-20 05:02:32     4.9  STATUS             COMPLETED Testing class: RnBDiffMeth
2024-12-20 05:02:32     4.9  STATUS         COMPLETED Testing function: apply.iEVORA
2024-12-20 05:02:32     4.9  STATUS         STARTED Retrieving comparison info
2024-12-20 05:02:32     4.9  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:02:32     4.9  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:02:32     4.9  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:32     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:32     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:32     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:32     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:32     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:32     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:33     4.9  STATUS                     Computed table for promoters
2024-12-20 05:02:33     4.9  STATUS                     Computed table for cpgislands
2024-12-20 05:02:33     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:33     4.9  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:33     4.9  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:33     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:33     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:33     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:33     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:34     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:34     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:34     4.9  STATUS                     Computed table for promoters
2024-12-20 05:02:34     4.9  STATUS                     Computed table for cpgislands
2024-12-20 05:02:34     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:34     4.9  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:34     4.9  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:02:34     4.9  STATUS         STARTED Retrieving comparison info
2024-12-20 05:02:34     4.9  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:02:34     4.9  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:02:34     4.9  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:34     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:34     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:34     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:34     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:35     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:35     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:35     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:35     4.9  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:35     4.9  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:02:35     4.9  STATUS         STARTED Retrieving comparison info
2024-12-20 05:02:35     4.9  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:02:35     4.9  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:02:35     4.9  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:35     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:35     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:35     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:35     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:35     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:36     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:36     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:36     4.9  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:36     4.9  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:02:36     4.9  STATUS         STARTED Retrieving comparison info
2024-12-20 05:02:36     4.9  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:02:36     4.9  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:02:36     4.9  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:36     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:36     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:36     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:36     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:37     4.9  STATUS                     Computed table for promoters
2024-12-20 05:02:37     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:37     4.9  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:37     4.9  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:37     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:37     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:37     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:37     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:37     4.9  STATUS                     Computed table for promoters
2024-12-20 05:02:37     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:37     4.9  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:02:37     4.9  STATUS         STARTED Retrieving comparison info
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:02:37     4.9  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:02:37     4.9  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:37     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:37     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:37     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:37     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:37     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:37     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:37     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:37     4.9  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:02:37     4.9  STATUS         STARTED Testing function: get.region.types
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Testing function: get.region.types
2024-12-20 05:02:37     4.9  STATUS         STARTED Testing function: get.comparisons
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Testing function: get.comparisons
2024-12-20 05:02:37     4.9  STATUS         STARTED Testing function: get.comparison.grouplabels
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Testing function: get.comparison.grouplabels
2024-12-20 05:02:37     4.9  STATUS         STARTED Testing function: get.site.test.method
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Testing function: get.site.test.method
2024-12-20 05:02:37     4.9  STATUS         STARTED Testing function: get.table
2024-12-20 05:02:37     4.9  STATUS         COMPLETED Testing function: get.table
2024-12-20 05:02:37     4.9  STATUS         STARTED Testing function: addDiffMethTable
2024-12-20 05:02:37     4.9    INFO             Conducting differential analysis using limma
2024-12-20 05:02:38     4.9  STATUS         COMPLETED Testing function: addDiffMethTable
2024-12-20 05:02:38     4.9  STATUS         STARTED Testing functions: join.diffMeth, is.valid
2024-12-20 05:02:38     4.9  STATUS         COMPLETED Testing functions: join.diffMeth, is.valid
2024-12-20 05:02:38     4.9  STATUS         STARTED Destructor
2024-12-20 05:02:38     4.9  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS             COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:38     4.9  STATUS         COMPLETED Destructor
2024-12-20 05:02:38     4.9    INFO         Conducting differential analysis using limma
2024-12-20 05:02:38     4.9    INFO         Conducting differential analysis using limma
2024-12-20 05:02:38     4.9  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:38     4.9  STATUS         COMPLETED diffVar method
2024-12-20 05:02:38     4.9  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:38     4.9 WARNING             Could not compute p-values with diffVar, returning NA
2024-12-20 05:02:38     4.9    INFO             diffVar from missMethyl package not properly running
2024-12-20 05:02:38     4.9  STATUS             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:38     4.9  STATUS             COMPLETED diffVar method
2024-12-20 05:02:38     4.9  STATUS STARTED Unit testing: differential
2024-12-20 05:02:38     4.9  STATUS     STARTED Testing function: rowWelchP
2024-12-20 05:02:38     4.9  STATUS     COMPLETED Testing function: rowWelchP
2024-12-20 05:02:38     4.9  STATUS     STARTED Testing function: limmaP
2024-12-20 05:02:38     4.9  STATUS     COMPLETED Testing function: limmaP
2024-12-20 05:02:38     4.9  STATUS     STARTED Testing function: computeDiffTab.extended.site
2024-12-20 05:02:38     4.9    INFO         Conducting differential analysis using limma
2024-12-20 05:02:38     4.9  STATUS     COMPLETED Testing function: computeDiffTab.extended.site
2024-12-20 05:02:38     4.9  STATUS     STARTED Testing function: computeDiffTab.default.region
2024-12-20 05:02:38     4.9    INFO         Conducting differential analysis using limma
2024-12-20 05:02:39     4.9  STATUS     COMPLETED Testing function: computeDiffTab.default.region
2024-12-20 05:02:39     4.9  STATUS     STARTED Testing function: combineTestPvalsMeth
2024-12-20 05:02:39     4.9  STATUS     COMPLETED Testing function: combineTestPvalsMeth
2024-12-20 05:02:39     4.9  STATUS     STARTED Testing function: get.adjustment.variables
2024-12-20 05:02:39     4.9  STATUS     COMPLETED Testing function: get.adjustment.variables
2024-12-20 05:02:39     4.9  STATUS     STARTED Testing function: get.comparison.info
2024-12-20 05:02:39     4.9  STATUS     COMPLETED Testing function: get.comparison.info
2024-12-20 05:02:39     4.9  STATUS     STARTED Testing function: rnb.execute.computeDiffMeth
2024-12-20 05:02:39     4.9  STATUS         STARTED Retrieving comparison info
2024-12-20 05:02:39     4.9  STATUS         COMPLETED Retrieving comparison info
2024-12-20 05:02:39     4.9  STATUS         STARTED Computing differential methylation tables
2024-12-20 05:02:39     4.9  STATUS             STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:39     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:39     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:39     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:39     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:39     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:39     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:40     4.9  STATUS                     Computed table for promoters
2024-12-20 05:02:40     4.9  STATUS                     Computed table for cpgislands
2024-12-20 05:02:40     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:40     4.9  STATUS             COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:40     4.9  STATUS             STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:40     4.9  STATUS                 STARTED Computing Differential Methylation Table
2024-12-20 05:02:40     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:40     4.9  STATUS                 COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:40     4.9  STATUS                 STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:41     4.9  STATUS                     Computed table for tiling
2024-12-20 05:02:41     4.9  STATUS                     Computed table for genes
2024-12-20 05:02:41     4.9  STATUS                     Computed table for promoters
2024-12-20 05:02:41     4.9  STATUS                     Computed table for cpgislands
2024-12-20 05:02:41     4.9  STATUS                 COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:41     4.9  STATUS             COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:41     4.9  STATUS         COMPLETED Computing differential methylation tables
2024-12-20 05:02:41     4.9  STATUS     COMPLETED Testing function: rnb.execute.computeDiffMeth
2024-12-20 05:02:41     4.9  STATUS     STARTED Testing function: diffVar
2024-12-20 05:02:41     4.9  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:41     4.9  STATUS         COMPLETED diffVar method
2024-12-20 05:02:42     4.9  STATUS         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:42     4.9 WARNING             Could not compute p-values with diffVar, returning NA
2024-12-20 05:02:42     4.9    INFO             diffVar from missMethyl package not properly running
2024-12-20 05:02:42     4.9  STATUS         COMPLETED diffVar method
2024-12-20 05:02:42     4.9  STATUS         STARTED Testing function: apply.iEVORA
2024-12-20 05:02:42     4.9  STATUS             STARTED iEVORA method
2024-12-20 05:02:42     4.9    INFO                 No DVCs detected. All p-values set to 1.
2024-12-20 05:02:42     4.9  STATUS             COMPLETED iEVORA method
2024-12-20 05:02:42     4.9  STATUS             STARTED Testing function: rnb.execute.diffVar
2024-12-20 05:02:42     4.9  STATUS                 STARTED Differential Variability
2024-12-20 05:02:42     4.9  STATUS                     STARTED Retrieving comparison info
2024-12-20 05:02:42     4.9  STATUS                     COMPLETED Retrieving comparison info
2024-12-20 05:02:42     4.9  STATUS                     STARTED Imputation procedure knn 
2024-12-20 05:02:42     4.9  STATUS                     COMPLETED Imputation procedure knn 
2024-12-20 05:02:42     4.9  STATUS                     STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:42     4.9    INFO                         Conducting differential variability using diffVar
2024-12-20 05:02:42     4.9  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:42     4.9  STATUS                         COMPLETED diffVar method
2024-12-20 05:02:42     4.9  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:43     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:43     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:44     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:44     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:44     4.9  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:44     4.9  STATUS                     COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:44     4.9  STATUS                     STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:44     4.9    INFO                         Conducting differential variability using diffVar
2024-12-20 05:02:44     4.9  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:44     4.9  STATUS                         COMPLETED diffVar method
2024-12-20 05:02:44     4.9  STATUS                         STARTED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:44     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:44     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:44     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:45     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:45     4.9  STATUS                         COMPLETED Computing Differential Variability Tables (Region Level)
2024-12-20 05:02:45     4.9  STATUS                     COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:45     4.9  STATUS                 COMPLETED Differential Variability
2024-12-20 05:02:45     4.9  STATUS             COMPLETED Testing function: rnb.execute.diffVar
2024-12-20 05:02:45     4.9  STATUS             STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2024-12-20 05:02:45     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:45     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:45     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:45     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:45     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:45     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:45     4.9  STATUS                             STARTED Imputation procedure knn 
2024-12-20 05:02:45     4.9  STATUS                             COMPLETED Imputation procedure knn 
2024-12-20 05:02:45     4.9    INFO                             Conducting differential variability using diffVar
2024-12-20 05:02:45     4.9  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:45     4.9  STATUS                             COMPLETED diffVar method
2024-12-20 05:02:45     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:45     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:45     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:46     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:47     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:47     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:47     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:47     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:47     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:47     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:47     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:47     4.9  STATUS                             STARTED Imputation procedure knn 
2024-12-20 05:02:47     4.9  STATUS                             COMPLETED Imputation procedure knn 
2024-12-20 05:02:47     4.9    INFO                             Conducting differential variability using diffVar
2024-12-20 05:02:47     4.9  STATUS                             STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:47     4.9  STATUS                             COMPLETED diffVar method
2024-12-20 05:02:47     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:47     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:47     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:48     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:48     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:48     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:48     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:48     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:48     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:48     4.9  STATUS             COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2024-12-20 05:02:48     4.9  STATUS             STARTED Testing class: RnBDiffMeth
2024-12-20 05:02:48     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:48     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:48     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:48     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:48     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:48     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:48     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:48     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:49     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:50     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:50     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:50     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:50     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:50     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:50     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:50     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:50     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:50     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:50     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:50     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:50     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:51     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:51     4.9  STATUS                             Computed table for cpgislands
2024-12-20 05:02:51     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:51     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:51     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:51     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:51     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:51     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:51     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:51     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:51     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:51     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:51     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:51     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:52     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:52     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:52     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:52     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:52     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:52     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:52     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:52     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:52     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:52     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:52     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:52     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:52     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:53     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:53     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:53     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:53     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:53     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:53     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:53     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:53     4.9  STATUS                     STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:53     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:53     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:53     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:53     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:53     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:53     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:53     4.9  STATUS                     COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:53     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:53     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:53     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:53     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:53     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:53     4.9  STATUS                             Computed table for promoters
2024-12-20 05:02:53     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:53     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:53     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:53     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:02:53     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:02:53     4.9  STATUS                 STARTED Computing differential methylation tables
2024-12-20 05:02:53     4.9  STATUS                     STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:53     4.9  STATUS                         STARTED Computing Differential Methylation Table
2024-12-20 05:02:53     4.9    INFO                             Conducting differential analysis using limma
2024-12-20 05:02:53     4.9  STATUS                         COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:53     4.9  STATUS                         STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:53     4.9  STATUS                             Computed table for genes
2024-12-20 05:02:54     4.9  STATUS                             Computed table for tiling
2024-12-20 05:02:54     4.9  STATUS                         COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:54     4.9  STATUS                     COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Computing differential methylation tables
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing function: get.region.types
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing function: get.region.types
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing function: get.comparisons
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing function: get.comparisons
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing function: get.comparison.grouplabels
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing function: get.comparison.grouplabels
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing function: get.site.test.method
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing function: get.site.test.method
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing function: get.table
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing function: get.table
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing function: addDiffMethTable
2024-12-20 05:02:54     4.9    INFO                     Conducting differential analysis using limma
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing function: addDiffMethTable
2024-12-20 05:02:54     4.9  STATUS                 STARTED Testing functions: join.diffMeth, is.valid
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Testing functions: join.diffMeth, is.valid
2024-12-20 05:02:54     4.9  STATUS                 STARTED Destructor
2024-12-20 05:02:54     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     STARTED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                     COMPLETED Deleting RnBDiffMeth disk dump files from disk
2024-12-20 05:02:54     4.9  STATUS                 COMPLETED Destructor
2024-12-20 05:02:54     4.9  STATUS             COMPLETED Testing class: RnBDiffMeth
2024-12-20 05:02:54     4.9  STATUS         COMPLETED Testing function: apply.iEVORA
2024-12-20 05:02:54     4.9  STATUS         STARTED iEVORA method
2024-12-20 05:02:55     4.9    INFO             No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2 
2024-12-20 05:02:56     4.9  STATUS             STARTED Retrieving comparison info
2024-12-20 05:02:56     4.9  STATUS             COMPLETED Retrieving comparison info
2024-12-20 05:02:56     4.9  STATUS             STARTED Computing differential methylation tables
2024-12-20 05:02:56     4.9  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:56     4.9  STATUS                     STARTED Computing Differential Methylation Table
2024-12-20 05:02:56     4.9    INFO                         Conducting differential analysis using limma
2024-12-20 05:02:56     4.9  STATUS                     COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:56     4.9  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:56     4.9  STATUS                         Computed table for tiling
2024-12-20 05:02:56     4.9  STATUS                         Computed table for genes
2024-12-20 05:02:56     4.9  STATUS                         Computed table for promoters
2024-12-20 05:02:56     4.9  STATUS                         Computed table for cpgislands
2024-12-20 05:02:56     4.9  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:56     4.9  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:56     4.9  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:56     4.9  STATUS                     STARTED Computing Differential Methylation Table
2024-12-20 05:02:56     4.9    INFO                         Conducting differential analysis using limma
2024-12-20 05:02:56     4.9  STATUS                     COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:56     4.9  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:57     4.9  STATUS                         Computed table for tiling
2024-12-20 05:02:57     4.9  STATUS                         Computed table for genes
2024-12-20 05:02:58     4.9  STATUS                         Computed table for promoters
2024-12-20 05:02:58     4.9  STATUS                         Computed table for cpgislands
2024-12-20 05:02:58     4.9  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:58     4.9  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:02:58     4.9  STATUS             COMPLETED Computing differential methylation tables
2024-12-20 05:02:58     4.9  STATUS             STARTED Retrieving comparison info
2024-12-20 05:02:58     4.9  STATUS             COMPLETED Retrieving comparison info
2024-12-20 05:02:58     4.9  STATUS             STARTED Computing differential methylation tables
2024-12-20 05:02:58     4.9  STATUS                 STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:02:58     4.9  STATUS                     STARTED Computing Differential Methylation Table
2024-12-20 05:02:58     4.9    INFO                         Conducting differential analysis using limma
2024-12-20 05:02:58     4.9  STATUS                         STARTED Imputation procedure knn 
2024-12-20 05:02:58     4.9  STATUS                         COMPLETED Imputation procedure knn 
2024-12-20 05:02:58     4.9    INFO                         Conducting differential variability using diffVar
2024-12-20 05:02:58     4.9  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:02:58     4.9  STATUS                         COMPLETED diffVar method
2024-12-20 05:02:58     4.9  STATUS                     COMPLETED Computing Differential Methylation Table
2024-12-20 05:02:58     4.9  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:02:59     4.9  STATUS                         Computed table for tiling
2024-12-20 05:02:59     4.9  STATUS                         Computed table for genes
2024-12-20 05:02:59     4.9  STATUS                         Computed table for promoters
2024-12-20 05:03:00     4.9  STATUS                         Computed table for cpgislands
2024-12-20 05:03:00     4.9  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:03:00     4.9  STATUS                 COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:03:00     4.9  STATUS                 STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:03:00     4.9  STATUS                     STARTED Computing Differential Methylation Table
2024-12-20 05:03:00     4.9    INFO                         Conducting differential analysis using limma
2024-12-20 05:03:00     4.9  STATUS                         STARTED Imputation procedure knn 
2024-12-20 05:03:00     4.9  STATUS                         COMPLETED Imputation procedure knn 
2024-12-20 05:03:00     4.9    INFO                         Conducting differential variability using diffVar
2024-12-20 05:03:00     4.9  STATUS                         STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:03:00     4.9  STATUS                         COMPLETED diffVar method
2024-12-20 05:03:00     4.9  STATUS                     COMPLETED Computing Differential Methylation Table
2024-12-20 05:03:00     4.9  STATUS                     STARTED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:03:01     4.9  STATUS                         Computed table for tiling
2024-12-20 05:03:01     4.9  STATUS                         Computed table for genes
2024-12-20 05:03:01     4.9  STATUS                         Computed table for promoters
2024-12-20 05:03:02     4.9  STATUS                         Computed table for cpgislands
2024-12-20 05:03:02     4.9  STATUS                     COMPLETED Computing Differential Methylation Tables (Region Level)
2024-12-20 05:03:02     4.9  STATUS                 COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2024-12-20 05:03:02     4.9  STATUS             COMPLETED Computing differential methylation tables
2024-12-20 05:03:02     4.9  STATUS             STARTED Differential Variability
2024-12-20 05:03:02     4.9  STATUS                 STARTED Retrieving comparison info
2024-12-20 05:03:02     4.9  STATUS                 COMPLETED Retrieving comparison info
2024-12-20 05:03:02     4.9  STATUS                 STARTED Imputation procedure knn 
2024-12-20 05:03:02     4.9  STATUS                 COMPLETED Imputation procedure knn 
2024-12-20 05:03:02     4.9  STATUS                 STARTED Comparing  hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:03:02     4.9    INFO                     Conducting differential variability using diffVar
2024-12-20 05:03:02     4.9  STATUS                     STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:03:02     4.9  STATUS                     COMPLETED diffVar method
2024-12-20 05:03:02     4.9  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2024-12-20 05:03:02     4.9  STATUS                         Computed table for tiling
2024-12-20 05:03:02     4.9  STATUS                         Computed table for genes
2024-12-20 05:03:02     4.9  STATUS                         Computed table for promoters
2024-12-20 05:03:03     4.9  STATUS                         Computed table for cpgislands
2024-12-20 05:03:03     4.9  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2024-12-20 05:03:03     4.9  STATUS                 COMPLETED Comparing  hESC vs. hiPSC (based on Sample_Group)
2024-12-20 05:03:03     4.9  STATUS                 STARTED Comparing  KOSR vs. TeSR (based on Treatment)
2024-12-20 05:03:03     4.9    INFO                     Conducting differential variability using diffVar
2024-12-20 05:03:03     4.9  STATUS                     STARTED diffVar method
coef not specified. Using all columns of design matrix.
2024-12-20 05:03:03     4.9  STATUS                     COMPLETED diffVar method
2024-12-20 05:03:03     4.9  STATUS                     STARTED Computing Differential Variability Tables (Region Level)
2024-12-20 05:03:04     4.9  STATUS                         Computed table for tiling
2024-12-20 05:03:04     4.9  STATUS                         Computed table for genes
2024-12-20 05:03:04     4.9  STATUS                         Computed table for promoters
2024-12-20 05:03:04     4.9  STATUS                         Computed table for cpgislands
2024-12-20 05:03:04     4.9  STATUS                     COMPLETED Computing Differential Variability Tables (Region Level)
2024-12-20 05:03:04     4.9  STATUS                 COMPLETED Comparing  KOSR vs. TeSR (based on Treatment)
2024-12-20 05:03:04     4.9  STATUS             COMPLETED Differential Variability
2024-12-20 05:03:04     4.9  STATUS STARTED Analysis
2024-12-20 05:03:04     4.9    INFO     Loaded information from data.RData
2024-12-20 05:03:04     4.9  STATUS     STARTED Processing Detection P-values
2024-12-20 05:03:04     4.9    INFO         Removed 3979 probes that overlap with SNPs
2024-12-20 05:03:04     4.9    INFO         Completed Greedycut on 510 samples
2024-12-20 05:03:04     4.9  STATUS     COMPLETED Processing Detection P-values
2024-12-20 05:03:04     4.9 WARNING     File not found: data2.RData
2024-12-20 05:03:04     4.9  STATUS COMPLETED Analysis

2024-12-20 05:03:04     4.9  STATUS STARTED Testing imputation
2024-12-20 05:03:04     4.9  STATUS     STARTED Imputation procedure knn 
2024-12-20 05:03:05     4.9  STATUS     COMPLETED Imputation procedure knn 
2024-12-20 05:03:05     4.9  STATUS     STARTED Imputation procedure mean.samples 
2024-12-20 05:03:05     4.9  STATUS     COMPLETED Imputation procedure mean.samples 
2024-12-20 05:03:05     4.9  STATUS     STARTED Imputation procedure mean.cpgs 
2024-12-20 05:03:06     4.9  STATUS     COMPLETED Imputation procedure mean.cpgs 
2024-12-20 05:03:06     4.9  STATUS     STARTED Imputation procedure random 
2024-12-20 05:03:07     4.9  STATUS     COMPLETED Imputation procedure random 
2024-12-20 05:03:07     4.9  STATUS COMPLETED Testing imputation

2024-12-20 05:03:07     4.9  STATUS STARTED Testing age prediction
2024-12-20 05:03:07     4.9  STATUS     STARTED Performing Age Prediction
2024-12-20 05:03:08     5.0  STATUS     COMPLETED Performing Age Prediction
2024-12-20 05:03:08     5.0  STATUS COMPLETED Testing age prediction

2024-12-20 05:03:08     5.0  STATUS STARTED Performing Age Prediction
2024-12-20 05:03:09     5.2  STATUS COMPLETED Performing Age Prediction

2024-12-20 05:03:09     5.2  STATUS STARTED Imputation procedure knn 
2024-12-20 05:03:09     5.2  STATUS COMPLETED Imputation procedure knn 

2024-12-20 05:03:09     5.2  STATUS STARTED Imputation procedure mean.samples 
2024-12-20 05:03:09     5.2  STATUS COMPLETED Imputation procedure mean.samples 

2024-12-20 05:03:09     5.2  STATUS STARTED Imputation procedure mean.cpgs 
2024-12-20 05:03:11     5.2  STATUS COMPLETED Imputation procedure mean.cpgs 

2024-12-20 05:03:11     5.2  STATUS STARTED Imputation procedure random 
2024-12-20 05:03:11     5.2  STATUS COMPLETED Imputation procedure random 

2024-12-20 05:03:11     5.2  STATUS STARTED Testing imputation
2024-12-20 05:03:11     5.2  STATUS     STARTED Imputation procedure knn 
2024-12-20 05:03:11     5.2  STATUS     COMPLETED Imputation procedure knn 
2024-12-20 05:03:11     5.2  STATUS     STARTED Imputation procedure mean.samples 
2024-12-20 05:03:12     5.2  STATUS     COMPLETED Imputation procedure mean.samples 
2024-12-20 05:03:12     5.2  STATUS     STARTED Imputation procedure mean.cpgs 
2024-12-20 05:03:12     5.2  STATUS     COMPLETED Imputation procedure mean.cpgs 
2024-12-20 05:03:12     5.2  STATUS     STARTED Imputation procedure random 
2024-12-20 05:03:13     5.2  STATUS     COMPLETED Imputation procedure random 
2024-12-20 05:03:13     5.2  STATUS COMPLETED Testing imputation

2024-12-20 05:03:13     5.2  STATUS STARTED Testing age prediction
2024-12-20 05:03:13     5.2  STATUS     STARTED Performing Age Prediction
2024-12-20 05:03:14     5.2  STATUS     COMPLETED Performing Age Prediction
2024-12-20 05:03:14     5.2  STATUS COMPLETED Testing age prediction



RUNIT TEST PROTOCOL -- Fri Dec 20 05:03:19 2024 
*********************************************** 
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 19 warnings (use warnings() to see them)
> 
> proc.time()
   user  system elapsed 
176.141   9.399 186.249

Example timings

RnBeads.Rcheck/RnBeads-Ex.timings

nameusersystemelapsed
M-methods000
U-methods000
addDiffMethTable-RnBDiffMeth-methods000
addPheno-RnBSet-methods0.0000.0000.001
addRegionSubsegments000
annotation-methods000
assembly-methods000
combine.rnb.sets-methods000
combineTestPvalsMeth0.0000.0000.001
computeDiffTab.region000
computeDiffTab.site000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport000
createReportPlot0.0000.0010.000
downloadLolaDbs000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods000
get.comparison.info000
get.comparisons-RnBDiffMeth-methods0.0010.0000.000
get.covariates.sva000
get.covg.thres-RnBDiffMeth-methods000
get.files0.0000.0000.001
get.region.types-RnBDiffMeth-methods000
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods000
getCellTypesFromLolaDb000
getNamesFromLolaDb000
getSubCmdTokens-ClusterArchitectureLSF-methods000
getSubCmdTokens-ClusterArchitectureSGE-methods000
getSubCmdTokens-ClusterArchitectureSLURM-methods000
getTargetFromLolaDb000
has.covariates.sva0.0010.0000.000
hasCovg-methods000
includes.sites-RnBDiffMeth-methods000
is.valid-RnBDiffMeth-methods0.0000.0000.001
join.diffMeth-methods000
limmaP000
loadLolaDbs000
logger.argument000
logger.getfiles0.0010.0000.000
logger.isinitialized000
logger.validate.file000
loggerManagement0.0000.0000.001
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-methods000
qc-methods000
read.sample.annotation000
regionMapping-methods000
regions-methods000
reload-RnBDiffMeth-methods000
remove.regions-methods000
remove.samples-methods000
remove.sites-methods0.0010.0000.000
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.pOOBAH0.0610.0030.064
rnb.execute.sex.prediction000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva000
rnb.execute.tnt000
rnb.execute.variability.removal0.0010.0000.000
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.reports0.0000.0000.001
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.boxplot0.0010.0000.000
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.annotation0.0010.0000.000
rnb.run.example000
rnb.runs000
rnb.sample.groups000
rnb.sample.summary.table000
rnb.set.annotation000
rnb.write.table000
rnb.xml2options000
rowOneSampleTP000
rowWelchP000
run-RnBClusterRun-methods000
samples-methods000
save.tables-RnBDiffMeth-methods000
set.covariates.sva0.0010.0000.000
sites-methods000
summarize.regions-methods000
summarized.regions-methods000