Fabian Mueller
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/RnBeads |
| git_branch: RELEASE_3_17 |
| git_last_commit: d20e31c |
| git_last_commit_date: 2023-08-01 03:45:58 -0400 (Tue, 01 Aug 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:10 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1749/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RnBeads 2.18.1 (landing page) Fabian Mueller
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the RnBeads package: - 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. |
| Package: RnBeads |
| Version: 2.18.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RnBeads_2.18.1.tar.gz |
| StartedAt: 2023-10-18 20:04:12 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 20:23:31 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 1158.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RnBeads.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RnBeads_2.18.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RnBeads.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘2.18.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
'ff', 'fields', 'ggplot2', 'gplots', '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 5.4Mb
sub-directories of 1Mb or more:
R 3.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘qvalue’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'grid'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
‘stopCluster’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘varLabels’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureData’
add.age.histogram: no visible binding for global variable ‘Age’
add.age.histogram: no visible binding for global variable ‘..count..’
add.age.histogram: no visible binding for global variable ‘..density..’
add.agecomparison.plot: no visible global function definition for
‘samples’
add.agecomparison.plot: no visible binding for global variable ‘Sample’
add.agecomparison.plot: no visible global function definition for
‘%dopar%’
add.agecomparison.plot: no visible global function definition for
‘foreach’
add.agecomparison.plot: no visible binding for global variable ‘i’
add.combination.plot: no visible global function definition for
‘samples’
add.combination.plot: no visible binding for global variable
‘Difference’
add.combination.plot: no visible binding for global variable ‘Density’
add.combination.plot: no visible binding for global variable ‘yint’
add.combination.plot: no visible binding for global variable ‘Measure’
add.error.plot: no visible binding for global variable ‘Value’
add.error.plot: no visible binding for global variable ‘Sample’
add.error.plot: no visible binding for global variable ‘Deviance’
add.error.plot: no visible binding for global variable ‘yint’
add.error.plot: no visible binding for global variable ‘Measure’
add.negative.control.boxplot: no visible global function definition for
‘samples’
add.profile.plots: no visible global function definition for ‘mclapply’
add.qc.barplots: no visible global function definition for ‘samples’
add.quantile.plot: no visible binding for global variable ‘Difference’
add.quantile.plot: no visible binding for global variable ‘..density..’
add.quantile.plot: no visible binding for global variable ‘Sample’
add.quantile.plot: no visible binding for global variable ‘Density’
add.seq.coverage.histograms: no visible global function definition for
‘samples’
add.seq.coverage.plot: no visible global function definition for
‘samples’
add.seq.coverage.violins: no visible global function definition for
‘samples’
add.stratification.plot: no visible global function definition for
‘%dopar%’
add.stratification.plot: no visible global function definition for
‘foreach’
add.stratification.plot: no visible binding for global variable ‘Group’
add.stratification.plot: no visible binding for global variable
‘Increase’
add.stratification.plot: no visible binding for global variable
‘Predicted’
add.stratification.plot: no visible binding for global variable
‘Annotated’
add.stratification.plot.immune: no visible global function definition
for ‘%dopar%’
add.stratification.plot.immune: no visible global function definition
for ‘foreach’
add.stratification.plot.immune: no visible binding for global variable
‘Group’
add.stratification.plot.immune: no visible binding for global variable
‘Immune’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘var.diff’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘log10P’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘combinedRank.var’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘log10FDR’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.diff’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.val’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.quot.log2’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.adj.fdr’
agePredictorBiseq: no visible global function definition for
‘impute.knn’
agePredictorBiseq: no visible global function definition for ‘samples’
agePredictorChip: no visible global function definition for
‘impute.knn’
append.cpg.stats: no visible global function definition for ‘%dopar%’
append.cpg.stats: no visible global function definition for ‘foreach’
append.cpg.stats: no visible binding for global variable ‘chrom’
basic_combine: no visible global function definition for ‘samples’
computeDiffTab.default.region: no visible global function definition
for ‘%dopar%’
computeDiffTab.default.region: no visible global function definition
for ‘foreach’
computeDiffTab.default.region: no visible binding for global variable
‘i’
computeDiffTab.default.site: no visible binding for global variable
‘p.vals.t.na.adj’
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.densityScatter: no visible binding for global variable
‘..density..’
create.diffMeth.diffVar.subsample: no visible binding for global
variable ‘..density..’
create.ucsc.track.hub: no visible global function definition for
‘samples’
createPredictor : ret: no visible global function definition for
‘impute.knn’
cv.array: no visible global function definition for ‘impute.knn’
data.frame2GRanges: no visible global function definition for
‘seqlevels<-’
data.frame2GRanges: no visible global function definition for
‘genome<-’
diffVar: no visible global function definition for ‘varFit’
diffVar: no visible binding for global variable ‘group1’
diffVar: no visible binding for global variable ‘group2’
estimateProportionsCP: no visible global function definition for ‘lme’
estimateProportionsCP: no visible global function definition for
‘getVarCov’
general.cv: no visible global function definition for ‘%dopar%’
general.cv: no visible global function definition for ‘foreach’
general.cv: no visible binding for global variable ‘i’
get.adjustment.variables: no visible global function definition for
‘samples’
get.comparison.info : rm.na.from.adj.tab: no visible global function
definition for ‘samples’
get.components.isva: no visible global function definition for ‘DoISVA’
get.components.sva: no visible global function definition for ‘sva’
get.cpg.stats: no visible global function definition for
‘dinucleotideFrequency’
get.cpg.stats: no visible global function definition for
‘letterFrequency’
get.dataset.matrix: no visible global function definition for ‘samples’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘report’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘refText’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘diffmeth’
get.platform.tokens: no visible global function definition for
‘setNames’
getCGCounts: no visible global function definition for ‘seqlengths’
getCGCounts : <anonymous>: no visible global function definition for
‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles: no visible global function definition for ‘mclapply’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘as.profileCGH’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘daglad’
getMergeList: no visible global function definition for ‘samples’
groupPermutationP.site.parallel: no visible global function definition
for ‘%dopar%’
groupPermutationP.site.parallel: no visible global function definition
for ‘foreach’
iEVORA: no visible global function definition for ‘qvalue’
imputation.low.memory.cpgs: no visible global function definition for
‘samples’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylationEPICmanifest’
intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
intensities.by.color: no visible global function definition for
‘samples’
knn.imputation: no visible global function definition for ‘impute.knn’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
loadLolaDbs: no visible global function definition for ‘loadRegionDB’
loadLolaDbs: no visible global function definition for ‘mergeRegionDBs’
locus.profile.get.base.tracks: no visible global function definition
for ‘useMart’
locus.profile.get.base.tracks: no visible global function definition
for ‘IdeogramTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘GenomeAxisTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘BiomartGeneRegionTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘UcscTrack’
locus.profile.get.methylation.track.heatmap: no visible global function
definition for ‘DataTrack’
locus.profile.get.methylation.track.smooth: no visible global function
definition for ‘DataTrack’
methylumi.intensities.by.color: no visible global function definition
for ‘featureNames’
methylumi.intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
methylumi.intensities.by.color: no visible global function definition
for ‘assayDataElement’
parallel.setup: no visible global function definition for
‘registerDoParallel’
parallel.setup: no visible global function definition for
‘getDoParWorkers’
performLolaEnrichment.diffMeth: no visible global function definition
for ‘runLOLA’
performLolaEnrichment.diffVar: no visible global function definition
for ‘runLOLA’
plot.heatmap.pc.correlations: no visible global function definition for
‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
‘grid.newpage’
plot.heatmap.pc.correlations: no visible global function definition for
‘grid.draw’
plot.heatmap.pc.pvalues: no visible global function definition for
‘melt’
plot.heatmap.pc.pvalues: no visible global function definition for
‘grid.newpage’
plot.heatmap.pc.pvalues: no visible global function definition for
‘grid.draw’
plot.heatmap.rand: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for
‘grid.newpage’
plot.heatmap.symm: no visible global function definition for
‘grid.draw’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
prepareGEOSampleInfoTemplate: no visible global function definition for
‘samples’
projectWBC: no visible global function definition for ‘solve.QP’
read.GS.report: no visible global function definition for
‘featureNames’
read.idat.files: no visible binding for global variable ‘barcode’
rnb.RnBSet.to.GRangesList: no visible global function definition for
‘samples’
rnb.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
‘samples’
rnb.bed.from.segmentation: no visible global function definition for
‘samples’
rnb.boxplot.from.segmentation: no visible global function definition
for ‘samples’
rnb.boxplot.from.segmentation: no visible binding for global variable
‘Segment’
rnb.boxplot.from.segmentation: no visible binding for global variable
‘AvgMeth’
rnb.chromosome.lengths: no visible global function definition for
‘seqlengths’
rnb.combine.seq: no visible global function definition for ‘samples’
rnb.enmix.oob: no visible global function definition for ‘%dopar%’
rnb.enmix.oob: no visible global function definition for ‘foreach’
rnb.execute.dreduction: no visible global function definition for
‘samples’
rnb.execute.filter.summary.internal: no visible global function
definition for ‘samples’
rnb.execute.high.coverage.removal.internal: no visible global function
definition for ‘samples’
rnb.execute.high.dpval.masking.internal: no visible global function
definition for ‘samples’
rnb.execute.imputation: no visible global function definition for
‘samples’
rnb.execute.low.coverage.masking.internal: no visible global function
definition for ‘samples’
rnb.execute.na.removal.internal: no visible global function definition
for ‘samples’
rnb.execute.normalization: no visible global function definition for
‘phenoData’
rnb.execute.normalization: no visible global function definition for
‘phenoData<-’
rnb.execute.normalization: no visible global function definition for
‘RGChannelSet’
rnb.execute.normalization: no visible global function definition for
‘preprocessSWAN’
rnb.execute.normalization: no visible global function definition for
‘getMeth’
rnb.execute.normalization: no visible global function definition for
‘getUnmeth’
rnb.execute.normalization: no visible global function definition for
‘featureNames’
rnb.execute.normalization: no visible global function definition for
‘samples’
rnb.execute.normalization: no visible global function definition for
‘mapToGenome’
rnb.execute.normalization: no visible global function definition for
‘addSex’
rnb.execute.normalization: no visible global function definition for
‘getSex’
rnb.execute.normalization: no visible global function definition for
‘getCN’
rnb.execute.normalization.bmiq: no visible global function definition
for ‘%dopar%’
rnb.execute.normalization.bmiq: no visible global function definition
for ‘foreach’
rnb.execute.pOOBAH: no visible global function definition for ‘samples’
rnb.execute.pOOBAH: no visible global function definition for ‘SigDF’
rnb.execute.pOOBAH: no visible global function definition for ‘pOOBAH’
rnb.execute.pOOBAH: no visible binding for global variable ‘sigset.l’
rnb.execute.pOOBAH: no visible binding for global variable ‘pIG’
rnb.execute.pOOBAH: no visible binding for global variable ‘pII’
rnb.execute.pOOBAH: no visible binding for global variable ‘pIR’
rnb.execute.quality: no visible global function definition for
‘samples’
rnb.execute.quality : <anonymous>: no visible global function
definition for ‘samples’
rnb.execute.segmentation: no visible binding for global variable
‘Hsapiens’
rnb.execute.segmentation: no visible binding for global variable
‘Mmusculus’
rnb.execute.segmentation: no visible global function definition for
‘seqlengths’
rnb.execute.segmentation: no visible global function definition for
‘browserSession’
rnb.execute.segmentation: no visible global function definition for
‘genome<-’
rnb.execute.segmentation: no visible global function definition for
‘ucscTableQuery’
rnb.execute.segmentation: no visible global function definition for
‘getTable’
rnb.execute.segmentation: no visible global function definition for
‘samples’
rnb.execute.segmentation: no visible global function definition for
‘readMethylome’
rnb.execute.segmentation: no visible global function definition for
‘readSNPTable’
rnb.execute.segmentation: no visible global function definition for
‘removeSNPs’
rnb.execute.segmentation: no visible global function definition for
‘segmentPMDs’
rnb.execute.segmentation: no visible global function definition for
‘plotAlphaDistributionOneChr’
rnb.execute.segmentation: no visible global function definition for
‘calculateFDRs’
rnb.execute.segmentation: no visible global function definition for
‘segmentUMRsLMRs’
rnb.export.to.ewasher: no visible global function definition for
‘samples’
rnb.filter.dataset: no visible global function definition for ‘samples’
rnb.final.segmentation: no visible global function definition for
‘samples’
rnb.get.reliability.counts.per.sample: no visible global function
definition for ‘samples’
rnb.options.description.table.fromRd: no visible global function
definition for ‘Rd2HTML’
rnb.options.description.table.fromRd: no visible binding for global
variable ‘xmlValue’
rnb.plot.beta.density.group: no visible binding for global variable
‘group’
rnb.plot.biseq.coverage: no visible global function definition for
‘samples’
rnb.plot.biseq.coverage.hist: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible binding for global variable
‘Target’
rnb.plot.control.barplot: no visible binding for global variable
‘Index’
rnb.plot.control.barplot: no visible binding for global variable ‘ID’
rnb.plot.control.barplot: no visible binding for global variable
‘Address’
rnb.plot.control.barplot: no visible global function definition for
‘grid.newpage’
rnb.plot.control.barplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.barplot: no visible global function definition for
‘grid.draw’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.newpage’
rnb.plot.control.boxplot: no visible binding for global variable
‘Probe’
rnb.plot.control.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.ct.heatmap: no visible binding for global variable ‘x’
rnb.plot.ct.heatmap: no visible binding for global variable ‘y’
rnb.plot.ct.heatmap: no visible binding for global variable ‘v’
rnb.plot.ct.heatmap: no visible global function definition for
‘grid.newpage’
rnb.plot.ct.heatmap: no visible global function definition for
‘grid.draw’
rnb.plot.dreduction: no visible global function definition for ‘tsne’
rnb.plot.locus.profile: no visible global function definition for
‘plotTracks’
rnb.plot.marker.fstat: no visible binding for global variable ‘x’
rnb.plot.marker.fstat: no visible binding for global variable ‘y’
rnb.plot.marker.fstat: no visible global function definition for
‘muted’
rnb.plot.negative.boxplot: no visible global function definition for
‘samples’
rnb.plot.negative.boxplot: no visible binding for global variable
‘numeric.names’
rnb.plot.negative.boxplot: no visible binding for global variable
‘type’
rnb.plot.negative.boxplot: no visible binding for global variable
‘types’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.newpage’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Sample’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.num.sites.covg: no visible global function definition for
‘samples’
rnb.plot.num.sites.covg : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.num.sites.covg: no visible binding for global variable
‘numSites’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgMedian’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercLow’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercUp’
rnb.plot.num.sites.covg: no visible binding for global variable ‘comma’
rnb.plot.region.profile.density: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profile.density: no visible binding for global variable
‘..density..’
rnb.plot.region.profiles : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.region.profiles: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profiles: no visible binding for global variable
‘group’
rnb.plot.region.site.density: no visible binding for global variable
‘relative.coord’
rnb.plot.segmentation.distributions: no visible binding for global
variable ‘x2’
rnb.plot.segmentation.distributions: no visible binding for global
variable ‘y2’
rnb.plot.segmentation.distributions: no visible binding for global
variable ‘texthere’
rnb.plot.segmentation.final: no visible global function definition for
‘plotFinalSegmentation’
rnb.plot.sentrix.distributions: no visible global function definition
for ‘samples’
rnb.plot.sentrix.distributions: no visible binding for global variable
‘Slide’
rnb.plot.snp.boxplot: no visible binding for global variable ‘SNP’
rnb.plot.snp.boxplot: no visible binding for global variable ‘bv’
rnb.run.example: no visible global function definition for ‘install’
rnb.run.preprocessing : logger.completed.filtering: no visible global
function definition for ‘samples’
rnb.sample.summary.table: no visible global function definition for
‘samples’
rnb.section.ageprediction: no visible global function definition for
‘samples’
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
function definition for ‘samples’
rnb.section.clustering: no visible global function definition for
‘samples’
rnb.section.diffMeth.region: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.region: no visible global function definition for
‘foreach’
rnb.section.diffMeth.region: no visible binding for global variable ‘k’
rnb.section.diffMeth.region : do.enrichment.table: no visible global
function definition for ‘sigCategories’
rnb.section.diffMeth.region : do.enrichment.table.var: no visible
global function definition for ‘sigCategories’
rnb.section.diffMeth.site: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
‘foreach’
rnb.section.diffVar: no visible global function definition for
‘%dopar%’
rnb.section.diffVar: no visible global function definition for
‘foreach’
rnb.section.diffVar.region: no visible global function definition for
‘%dopar%’
rnb.section.diffVar.region: no visible global function definition for
‘foreach’
rnb.section.diffVar.region: no visible binding for global variable ‘k’
rnb.section.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
‘phenoData’
rnb.section.imputation: no visible global function definition for
‘melt’
rnb.section.locus.profiles: no visible global function definition for
‘samples’
rnb.section.locus.profiles : do.plots: no visible global function
definition for ‘plotTracks’
rnb.section.locus.profiles: no visible global function definition for
‘%dopar%’
rnb.section.locus.profiles: no visible global function definition for
‘foreach’
rnb.section.na.removal: no visible global function definition for
‘samples’
rnb.section.normalization: no visible global function definition for
‘samples’
rnb.section.region.description: no visible binding for global variable
‘size’
rnb.section.region.description: no visible binding for global variable
‘n.sites’
rnb.section.region.profiles: no visible global function definition for
‘samples’
rnb.section.region.subsegmentation : get.summary.df.from.list: no
visible global function definition for ‘melt’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘region.size’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘is.subsegmentation’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘num.sites’
rnb.section.sex.prediction: no visible global function definition for
‘muted’
rnb.step.betadistribution.internal: no visible global function
definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
definition for ‘foreach’
rnb.step.cell.types: no visible global function definition for
‘samples’
rnb.step.clustering.internal: no visible global function definition for
‘samples’
rnb.step.dreduction: no visible global function definition for
‘%dopar%’
rnb.step.dreduction: no visible global function definition for
‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
for ‘percent_format’
rnb.step.filter.summary.internal: no visible global function definition
for ‘samples’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.na.removal: no visible binding for global variable
‘sites2ignore’
rnb.step.na.removal.internal: no visible global function definition for
‘samples’
rnb.step.normalization: no visible global function definition for
‘phenoData’
robustHyperGResultSummary: no visible global function definition for
‘sigCategories’
robustHyperGResultSummary: no visible global function definition for
‘pvalues’
robustHyperGResultSummary: no visible global function definition for
‘oddsRatios’
robustHyperGResultSummary: no visible global function definition for
‘expectedCounts’
robustHyperGResultSummary: no visible global function definition for
‘geneCounts’
robustHyperGResultSummary: no visible global function definition for
‘universeCounts’
robustHyperGResultSummary: no visible binding for global variable
‘Term’
run.cross.validation: no visible global function definition for
‘samples’
run.cross.validation: no visible global function definition for ‘melt’
run.cross.validation: no visible binding for global variable ‘Measure’
run.cross.validation: no visible binding for global variable ‘Error’
sampleCovgApply: no visible global function definition for ‘samples’
set.covariates.ct: no visible global function definition for ‘samples’
simpleGlmnet: no visible global function definition for ‘impute.knn’
simpleGlmnet: no visible global function definition for ‘cv.glmnet’
simpleGlmnet: no visible global function definition for ‘glmnet’
simpleGlmnetBiseq: no visible global function definition for
‘cv.glmnet’
simpleGlmnetBiseq: no visible global function definition for ‘glmnet’
simpleGlmnetEvaluate: no visible global function definition for
‘cv.glmnet’
simpleGlmnetEvaluate: no visible global function definition for
‘glmnet’
symmetric.melt: no visible global function definition for ‘melt’
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
‘reg.type’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘getManifest’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘getGreen’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘getRed’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘pData’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureData<-’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureNames<-’
coerce,RnBeadRawSet-RGChannelSet: no visible global function definition
for ‘RGChannelSet’
join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function
definition for ‘clone’
mask.sites.meth,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
‘samples’
remove.samples,RnBeadSet: no visible global function definition for
‘samples’
remove.sites,RnBSet: no visible global function definition for
‘samples’
sampleCovgApply,RnBSet: no visible global function definition for
‘samples’
sampleMethApply,RnBSet: no visible global function definition for
‘samples’
summarize.regions,RnBSet: no visible global function definition for
‘samples’
summarize.regions,RnBSet: multiple local function definitions for
‘aggr.f’ with different formal arguments
updateMethylationSites,RnBSet: no visible global function definition
for ‘samples’
Undefined global functions or variables:
%dopar% ..count.. ..density.. Address Age Annotated AvgMeth
BiomartGeneRegionTrack ChrNumeric DataTrack Density Deviance
Difference DoISVA Error GenomeAxisTrack Group Hsapiens ID
IdeogramTrack IlluminaHumanMethylation450kmanifest
IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity
Measure Mmusculus Predicted Probe RGChannelSet Rd2HTML SNP Sample
Segment SigDF Slide Target Term UcscTrack Value addSex as.profileCGH
assayDataElement assayDataElementNames barcode browserSession bv
calculateFDRs chrom clone combinedRank combinedRank.var comma
covgMedian covgPercLow covgPercUp cv.glmnet daglad diffmeth
diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency
expectedCounts featureData featureData<- featureNames featureNames<-
foreach geneCounts genome<- getCN getDoParWorkers getGreen
getManifest getMeth getRed getSex getTable getUnmeth getVarCov glmnet
grid.draw grid.newpage group group1 group2 i impute.knn install
is.subsegmentation k letterFrequency lme loadRegionDB log10FDR log10P
mapToGenome mclapply mean.diff mean.quot.log2 melt mergeRegionDBs
muted n.sites num.sites numSites numeric.names oddsRatios
p.vals.t.na.adj pData pIG pII pIR pOOBAH percent_format phenoData
phenoData<- plotAlphaDistributionOneChr plotFinalSegmentation
plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable
refText reg.type region.size registerDoParallel relative.coord
removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs
seqlengths seqlevels<- setNames sigCategories sigset.l sites2ignore
size solve.QP stopCluster sva target texthere tsne type types
ucscTableQuery universeCounts useMart v var.diff varFit varLabels x
x2 xmlValue y y2 yint
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
rnb.execute.pOOBAH 21.396 2.474 37.165
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 7 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/RnBeads.Rcheck/00check.log’
for details.
RnBeads.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RnBeads ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)
RnBeads.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("RnBeads")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following 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")=="/tmp/RtmpY7SIoJ/ff"
- getOption("ffextension")=="ff"
- getOption("ffdrop")==TRUE
- getOption("fffinonexit")==TRUE
- getOption("ffpagesize")==65536
- getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes
- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Spam version 2.9-1 (2022-08-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.
Attaching package: 'spam'
The following object is masked from 'package:stats4':
mle
The following objects are masked from 'package:base':
backsolve, forwardsolve
Try help(fields) to get started.
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'grid'
The following object is masked from 'package:ff':
pattern
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'scales'
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viridis_pal
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
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Attaching package: 'MatrixGenerics'
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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 1.5-9.8 2023-06-11
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
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count
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The following object is masked from 'package:S4Vectors':
rename
2023-10-18 20:16:30 0.9 STATUS STARTED Unit testing: differential
2023-10-18 20:16:30 0.9 STATUS STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2023-10-18 20:16:31 0.9 STATUS COMPLETED Testing function: rowWelchP
2023-10-18 20:16:31 0.9 STATUS STARTED Testing function: limmaP
2023-10-18 20:16:31 0.9 STATUS COMPLETED Testing function: limmaP
2023-10-18 20:16:31 0.9 STATUS STARTED Testing function: computeDiffTab.extended.site
2023-10-18 20:16:32 0.9 INFO Conducting differential analysis using limma
2023-10-18 20:16:32 0.9 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2023-10-18 20:16:32 0.9 STATUS STARTED Testing function: computeDiffTab.default.region
2023-10-18 20:16:33 0.9 INFO Conducting differential analysis using limma
2023-10-18 20:16:39 1.0 STATUS COMPLETED Testing function: computeDiffTab.default.region
2023-10-18 20:16:39 1.0 STATUS STARTED Testing function: combineTestPvalsMeth
2023-10-18 20:16:40 1.0 STATUS COMPLETED Testing function: combineTestPvalsMeth
2023-10-18 20:16:40 1.0 STATUS STARTED Testing function: get.adjustment.variables
2023-10-18 20:16:40 1.0 STATUS COMPLETED Testing function: get.adjustment.variables
2023-10-18 20:16:40 1.0 STATUS STARTED Testing function: get.comparison.info
2023-10-18 20:16:41 1.0 STATUS COMPLETED Testing function: get.comparison.info
2023-10-18 20:16:41 1.0 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2023-10-18 20:16:41 1.0 STATUS STARTED Retrieving comparison info
2023-10-18 20:16:41 1.0 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:16:42 1.0 STATUS STARTED Computing differential methylation tables
2023-10-18 20:16:42 1.0 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:16:42 1.0 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:16:42 1.0 INFO Conducting differential analysis using limma
2023-10-18 20:16:43 1.0 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:16:43 1.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:16:46 1.0 STATUS Computed table for tiling
2023-10-18 20:16:46 1.0 STATUS Computed table for genes
2023-10-18 20:16:47 1.1 STATUS Computed table for promoters
2023-10-18 20:16:48 1.2 STATUS Computed table for cpgislands
2023-10-18 20:16:48 1.2 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:16:48 1.2 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:16:49 1.2 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:16:49 1.2 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:16:49 1.2 INFO Conducting differential analysis using limma
2023-10-18 20:16:49 1.2 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:16:50 1.2 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:16:51 1.3 STATUS Computed table for tiling
2023-10-18 20:16:51 1.4 STATUS Computed table for genes
2023-10-18 20:16:52 1.4 STATUS Computed table for promoters
2023-10-18 20:16:53 1.4 STATUS Computed table for cpgislands
2023-10-18 20:16:53 1.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:16:53 1.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:16:53 1.4 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:16:54 1.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2023-10-18 20:16:54 1.4 STATUS STARTED Testing function: diffVar
2023-10-18 20:16:54 1.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:18:40 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:18:40 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:18:41 3.8 WARNING Could not compute p-values with diffVar, returning NA
2023-10-18 20:18:41 3.8 INFO diffVar from missMethyl package not properly running
2023-10-18 20:18:41 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:18:41 3.8 STATUS STARTED Testing function: apply.iEVORA
2023-10-18 20:18:42 3.8 STATUS STARTED iEVORA method
2023-10-18 20:18:43 3.9 INFO No DVCs detected. All p-values set to 1.
2023-10-18 20:18:43 3.9 STATUS COMPLETED iEVORA method
2023-10-18 20:18:43 3.9 STATUS STARTED Testing function: rnb.execute.diffVar
2023-10-18 20:18:44 3.9 STATUS STARTED Differential Variability
2023-10-18 20:18:44 3.9 STATUS STARTED Retrieving comparison info
2023-10-18 20:18:44 3.9 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:18:44 3.9 INFO No imputation method selected, 'knn' method used.
2023-10-18 20:18:44 3.9 STATUS STARTED Imputation procedure knn
2023-10-18 20:18:45 3.9 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:18:45 3.9 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:18:45 3.9 INFO Conducting differential variability using diffVar
2023-10-18 20:18:45 3.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:18:46 3.9 STATUS COMPLETED diffVar method
2023-10-18 20:18:46 3.9 STATUS STARTED Computing Differential Variability Tables (Region Level)
2023-10-18 20:18:48 3.8 STATUS Computed table for tiling
2023-10-18 20:18:49 3.8 STATUS Computed table for genes
2023-10-18 20:18:49 3.8 STATUS Computed table for promoters
2023-10-18 20:18:50 3.8 STATUS Computed table for cpgislands
2023-10-18 20:18:50 3.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2023-10-18 20:18:50 3.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:18:50 3.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2023-10-18 20:18:51 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:18:51 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:18:51 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:18:51 3.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2023-10-18 20:18:55 3.9 STATUS Computed table for tiling
2023-10-18 20:18:56 3.9 STATUS Computed table for genes
2023-10-18 20:18:56 3.9 STATUS Computed table for promoters
2023-10-18 20:18:57 3.9 STATUS Computed table for cpgislands
2023-10-18 20:18:57 3.9 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2023-10-18 20:18:57 3.9 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2023-10-18 20:18:58 3.9 STATUS COMPLETED Differential Variability
2023-10-18 20:18:58 3.9 STATUS COMPLETED Testing function: rnb.execute.diffVar
2023-10-18 20:18:58 3.9 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2023-10-18 20:18:58 3.9 STATUS STARTED Retrieving comparison info
2023-10-18 20:18:58 3.9 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:18:59 3.9 STATUS STARTED Computing differential methylation tables
2023-10-18 20:18:59 3.9 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:18:59 3.9 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:18:59 3.9 INFO Conducting differential analysis using limma
2023-10-18 20:19:00 3.9 STATUS STARTED Imputation procedure knn
2023-10-18 20:19:00 3.9 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:19:00 3.9 INFO Conducting differential variability using diffVar
2023-10-18 20:19:00 3.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:19:00 3.9 STATUS COMPLETED diffVar method
2023-10-18 20:19:01 3.9 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:01 3.9 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:09 3.2 STATUS Computed table for tiling
2023-10-18 20:19:09 3.2 STATUS Computed table for genes
2023-10-18 20:19:10 3.2 STATUS Computed table for promoters
2023-10-18 20:19:11 3.3 STATUS Computed table for cpgislands
2023-10-18 20:19:11 3.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:11 3.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:11 3.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:12 3.3 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:12 3.3 INFO Conducting differential analysis using limma
2023-10-18 20:19:12 3.3 STATUS STARTED Imputation procedure knn
2023-10-18 20:19:12 3.3 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:19:13 3.3 INFO Conducting differential variability using diffVar
2023-10-18 20:19:13 3.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:19:13 3.3 STATUS COMPLETED diffVar method
2023-10-18 20:19:14 3.3 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:14 3.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:15 3.5 STATUS Computed table for tiling
2023-10-18 20:19:16 3.6 STATUS Computed table for genes
2023-10-18 20:19:17 3.7 STATUS Computed table for promoters
2023-10-18 20:19:19 3.7 STATUS Computed table for cpgislands
2023-10-18 20:19:19 3.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:20 3.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:20 3.7 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:19:20 3.7 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2023-10-18 20:19:20 3.7 STATUS STARTED Testing class: RnBDiffMeth
2023-10-18 20:19:21 3.7 STATUS STARTED Retrieving comparison info
2023-10-18 20:19:21 3.7 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:19:21 3.7 STATUS STARTED Computing differential methylation tables
2023-10-18 20:19:21 3.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:22 3.7 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:22 3.7 INFO Conducting differential analysis using limma
2023-10-18 20:19:22 3.7 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:22 3.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:23 3.7 STATUS Computed table for tiling
2023-10-18 20:19:24 3.7 STATUS Computed table for genes
2023-10-18 20:19:24 3.7 STATUS Computed table for promoters
2023-10-18 20:19:25 3.7 STATUS Computed table for cpgislands
2023-10-18 20:19:25 3.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:25 3.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:25 3.7 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:26 3.7 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:26 3.7 INFO Conducting differential analysis using limma
2023-10-18 20:19:26 3.7 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:26 3.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:27 3.7 STATUS Computed table for tiling
2023-10-18 20:19:28 3.7 STATUS Computed table for genes
2023-10-18 20:19:29 3.7 STATUS Computed table for promoters
2023-10-18 20:19:29 3.7 STATUS Computed table for cpgislands
2023-10-18 20:19:29 3.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:29 3.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:30 3.7 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:19:30 3.7 STATUS STARTED Retrieving comparison info
2023-10-18 20:19:30 3.7 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:19:30 3.7 STATUS STARTED Computing differential methylation tables
2023-10-18 20:19:31 3.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:31 3.7 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:31 3.7 INFO Conducting differential analysis using limma
2023-10-18 20:19:31 3.7 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:32 3.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:32 3.7 STATUS Computed table for genes
2023-10-18 20:19:34 3.8 STATUS Computed table for tiling
2023-10-18 20:19:35 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:35 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:35 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:19:35 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:19:36 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:19:36 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:19:36 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:36 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:37 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:19:37 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:37 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:38 3.8 STATUS Computed table for genes
2023-10-18 20:19:39 3.8 STATUS Computed table for tiling
2023-10-18 20:19:39 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:39 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:39 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:19:39 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:19:40 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:19:40 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:19:40 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:40 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:41 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:19:41 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:41 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:41 3.8 STATUS Computed table for promoters
2023-10-18 20:19:42 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:42 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:42 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:42 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:43 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:19:43 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:43 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:44 3.8 STATUS Computed table for promoters
2023-10-18 20:19:44 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:44 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:44 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:19:45 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:19:45 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:19:45 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:19:45 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:46 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:46 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:19:46 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:46 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:47 3.8 STATUS Computed table for genes
2023-10-18 20:19:48 3.8 STATUS Computed table for tiling
2023-10-18 20:19:48 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:48 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:19:48 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:19:49 3.8 STATUS STARTED Testing function: get.region.types
2023-10-18 20:19:49 3.8 STATUS COMPLETED Testing function: get.region.types
2023-10-18 20:19:49 3.8 STATUS STARTED Testing function: get.comparisons
2023-10-18 20:19:49 3.8 STATUS COMPLETED Testing function: get.comparisons
2023-10-18 20:19:49 3.8 STATUS STARTED Testing function: get.comparison.grouplabels
2023-10-18 20:19:50 3.8 STATUS COMPLETED Testing function: get.comparison.grouplabels
2023-10-18 20:19:50 3.8 STATUS STARTED Testing function: get.site.test.method
2023-10-18 20:19:50 3.8 STATUS COMPLETED Testing function: get.site.test.method
2023-10-18 20:19:50 3.8 STATUS STARTED Testing function: get.table
2023-10-18 20:19:51 3.8 STATUS COMPLETED Testing function: get.table
2023-10-18 20:19:51 3.8 STATUS STARTED Testing function: addDiffMethTable
2023-10-18 20:19:51 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:19:52 3.8 STATUS COMPLETED Testing function: addDiffMethTable
2023-10-18 20:19:52 3.8 STATUS STARTED Testing functions: join.diffMeth, is.valid
2023-10-18 20:19:52 3.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2023-10-18 20:19:53 3.8 STATUS STARTED Destructor
2023-10-18 20:19:53 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:53 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:53 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:53 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:54 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:54 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:54 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:54 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:19:55 3.8 STATUS COMPLETED Destructor
2023-10-18 20:19:55 3.8 STATUS COMPLETED Testing class: RnBDiffMeth
2023-10-18 20:19:55 3.8 STATUS COMPLETED Testing function: apply.iEVORA
2023-10-18 20:19:55 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:19:56 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:19:56 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:19:56 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:19:56 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:19:56 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:19:57 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:19:57 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:19:59 3.8 STATUS Computed table for tiling
2023-10-18 20:20:00 3.8 STATUS Computed table for genes
2023-10-18 20:20:00 3.8 STATUS Computed table for promoters
2023-10-18 20:20:01 3.8 STATUS Computed table for cpgislands
2023-10-18 20:20:01 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:01 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:01 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:02 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:02 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:02 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:02 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:03 3.8 STATUS Computed table for tiling
2023-10-18 20:20:04 3.8 STATUS Computed table for genes
2023-10-18 20:20:04 3.8 STATUS Computed table for promoters
2023-10-18 20:20:05 3.8 STATUS Computed table for cpgislands
2023-10-18 20:20:05 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:05 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:05 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:20:06 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:06 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:06 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:20:06 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:06 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:07 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:07 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:07 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:08 3.8 STATUS Computed table for genes
2023-10-18 20:20:10 3.8 STATUS Computed table for tiling
2023-10-18 20:20:10 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:10 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:10 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:20:11 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:11 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:11 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:20:11 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:11 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:12 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:12 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:12 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:13 3.8 STATUS Computed table for genes
2023-10-18 20:20:13 3.8 STATUS Computed table for tiling
2023-10-18 20:20:14 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:14 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:14 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:20:14 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:14 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:15 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:20:15 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:15 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:15 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:15 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:16 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:16 3.8 STATUS Computed table for promoters
2023-10-18 20:20:16 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:17 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:17 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:17 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:17 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:17 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:18 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:18 3.8 STATUS Computed table for promoters
2023-10-18 20:20:18 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:18 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:19 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:20:19 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:19 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:19 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:20:19 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:20 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:20 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:20 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:20 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:21 3.8 STATUS Computed table for genes
2023-10-18 20:20:21 3.8 STATUS Computed table for tiling
2023-10-18 20:20:22 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:22 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:22 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:20:22 3.8 STATUS STARTED Testing function: get.region.types
2023-10-18 20:20:22 3.8 STATUS COMPLETED Testing function: get.region.types
2023-10-18 20:20:22 3.8 STATUS STARTED Testing function: get.comparisons
2023-10-18 20:20:23 3.8 STATUS COMPLETED Testing function: get.comparisons
2023-10-18 20:20:23 3.8 STATUS STARTED Testing function: get.comparison.grouplabels
2023-10-18 20:20:23 3.8 STATUS COMPLETED Testing function: get.comparison.grouplabels
2023-10-18 20:20:23 3.8 STATUS STARTED Testing function: get.site.test.method
2023-10-18 20:20:23 3.8 STATUS COMPLETED Testing function: get.site.test.method
2023-10-18 20:20:23 3.8 STATUS STARTED Testing function: get.table
2023-10-18 20:20:24 3.8 STATUS COMPLETED Testing function: get.table
2023-10-18 20:20:24 3.8 STATUS STARTED Testing function: addDiffMethTable
2023-10-18 20:20:24 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:25 3.8 STATUS COMPLETED Testing function: addDiffMethTable
2023-10-18 20:20:25 3.8 STATUS STARTED Testing functions: join.diffMeth, is.valid
2023-10-18 20:20:25 3.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2023-10-18 20:20:25 3.8 STATUS STARTED Destructor
2023-10-18 20:20:25 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:25 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:20:26 3.8 STATUS COMPLETED Destructor
2023-10-18 20:20:27 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:27 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:27 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:28 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:20:28 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:28 3.8 WARNING Could not compute p-values with diffVar, returning NA
2023-10-18 20:20:28 3.8 INFO diffVar from missMethyl package not properly running
2023-10-18 20:20:28 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:29 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:20:29 3.8 STATUS STARTED Unit testing: differential
2023-10-18 20:20:29 3.8 STATUS STARTED Testing function: rowWelchP
2023-10-18 20:20:29 3.8 STATUS COMPLETED Testing function: rowWelchP
2023-10-18 20:20:29 3.8 STATUS STARTED Testing function: limmaP
2023-10-18 20:20:30 3.8 STATUS COMPLETED Testing function: limmaP
2023-10-18 20:20:30 3.8 STATUS STARTED Testing function: computeDiffTab.extended.site
2023-10-18 20:20:30 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:30 3.8 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2023-10-18 20:20:30 3.8 STATUS STARTED Testing function: computeDiffTab.default.region
2023-10-18 20:20:31 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:31 3.8 STATUS COMPLETED Testing function: computeDiffTab.default.region
2023-10-18 20:20:31 3.8 STATUS STARTED Testing function: combineTestPvalsMeth
2023-10-18 20:20:32 3.8 STATUS COMPLETED Testing function: combineTestPvalsMeth
2023-10-18 20:20:32 3.8 STATUS STARTED Testing function: get.adjustment.variables
2023-10-18 20:20:32 3.8 STATUS COMPLETED Testing function: get.adjustment.variables
2023-10-18 20:20:32 3.8 STATUS STARTED Testing function: get.comparison.info
2023-10-18 20:20:32 3.8 STATUS COMPLETED Testing function: get.comparison.info
2023-10-18 20:20:33 3.8 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2023-10-18 20:20:33 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:33 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:33 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:20:33 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:34 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:34 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:34 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:34 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:36 3.8 STATUS Computed table for tiling
2023-10-18 20:20:37 3.8 STATUS Computed table for genes
2023-10-18 20:20:37 3.8 STATUS Computed table for promoters
2023-10-18 20:20:38 3.8 STATUS Computed table for cpgislands
2023-10-18 20:20:38 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:38 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:39 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:39 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:39 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:39 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:20:40 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:41 3.8 STATUS Computed table for tiling
2023-10-18 20:20:41 3.8 STATUS Computed table for genes
2023-10-18 20:20:42 3.8 STATUS Computed table for promoters
2023-10-18 20:20:42 3.8 STATUS Computed table for cpgislands
2023-10-18 20:20:42 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:20:42 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:43 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:20:43 3.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2023-10-18 20:20:43 3.8 STATUS STARTED Testing function: diffVar
2023-10-18 20:20:43 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:44 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:20:44 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:44 3.8 WARNING Could not compute p-values with diffVar, returning NA
2023-10-18 20:20:44 3.8 INFO diffVar from missMethyl package not properly running
2023-10-18 20:20:45 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:20:45 3.8 STATUS STARTED Testing function: apply.iEVORA
2023-10-18 20:20:45 3.8 STATUS STARTED iEVORA method
2023-10-18 20:20:48 3.8 INFO No DVCs detected. All p-values set to 1.
2023-10-18 20:20:48 3.8 STATUS COMPLETED iEVORA method
2023-10-18 20:20:48 3.8 STATUS STARTED Testing function: rnb.execute.diffVar
2023-10-18 20:20:48 3.8 STATUS STARTED Differential Variability
2023-10-18 20:20:49 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:49 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:49 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:20:49 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:20:50 3.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:50 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:20:50 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:50 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:20:50 3.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2023-10-18 20:20:51 3.8 STATUS Computed table for tiling
2023-10-18 20:20:52 3.8 STATUS Computed table for genes
2023-10-18 20:20:52 3.8 STATUS Computed table for promoters
2023-10-18 20:20:52 3.8 STATUS Computed table for cpgislands
2023-10-18 20:20:53 3.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2023-10-18 20:20:53 3.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:53 3.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:53 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:20:54 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:20:54 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:20:54 3.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2023-10-18 20:20:55 3.8 STATUS Computed table for tiling
2023-10-18 20:20:55 3.8 STATUS Computed table for genes
2023-10-18 20:20:56 3.8 STATUS Computed table for promoters
2023-10-18 20:20:56 3.8 STATUS Computed table for cpgislands
2023-10-18 20:20:57 3.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2023-10-18 20:20:57 3.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2023-10-18 20:20:57 3.8 STATUS COMPLETED Differential Variability
2023-10-18 20:20:57 3.8 STATUS COMPLETED Testing function: rnb.execute.diffVar
2023-10-18 20:20:57 3.8 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2023-10-18 20:20:58 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:20:58 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:20:58 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:20:58 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:20:58 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:20:59 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:20:59 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:20:59 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:20:59 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:21:00 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:21:00 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:21:00 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:00 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:03 3.8 STATUS Computed table for tiling
2023-10-18 20:21:03 3.8 STATUS Computed table for genes
2023-10-18 20:21:04 3.8 STATUS Computed table for promoters
2023-10-18 20:21:05 3.8 STATUS Computed table for cpgislands
2023-10-18 20:21:05 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:05 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:06 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:06 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:06 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:06 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:21:06 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:21:07 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:21:07 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:21:07 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:21:07 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:08 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:09 3.8 STATUS Computed table for tiling
2023-10-18 20:21:09 3.8 STATUS Computed table for genes
2023-10-18 20:21:10 3.8 STATUS Computed table for promoters
2023-10-18 20:21:11 3.8 STATUS Computed table for cpgislands
2023-10-18 20:21:11 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:11 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:11 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:12 3.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2023-10-18 20:21:12 3.8 STATUS STARTED Testing class: RnBDiffMeth
2023-10-18 20:21:12 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:12 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:13 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:13 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:13 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:13 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:15 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:15 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:16 3.8 STATUS Computed table for tiling
2023-10-18 20:21:16 3.8 STATUS Computed table for genes
2023-10-18 20:21:17 3.8 STATUS Computed table for promoters
2023-10-18 20:21:17 3.8 STATUS Computed table for cpgislands
2023-10-18 20:21:18 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:18 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:18 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:18 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:19 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:19 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:19 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:20 3.8 STATUS Computed table for tiling
2023-10-18 20:21:20 3.8 STATUS Computed table for genes
2023-10-18 20:21:21 3.8 STATUS Computed table for promoters
2023-10-18 20:21:22 3.8 STATUS Computed table for cpgislands
2023-10-18 20:21:22 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:22 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:22 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:22 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:23 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:23 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:23 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:23 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:23 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:24 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:24 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:24 3.8 STATUS Computed table for genes
2023-10-18 20:21:26 3.8 STATUS Computed table for tiling
2023-10-18 20:21:27 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:27 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:27 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:27 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:28 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:28 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:28 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:28 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:28 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:29 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:29 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:29 3.8 STATUS Computed table for genes
2023-10-18 20:21:30 3.8 STATUS Computed table for tiling
2023-10-18 20:21:30 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:30 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:31 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:31 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:31 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:31 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:31 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:32 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:32 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:32 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:32 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:33 3.8 STATUS Computed table for promoters
2023-10-18 20:21:33 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:33 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:34 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:34 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:34 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:34 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:35 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:35 3.8 STATUS Computed table for promoters
2023-10-18 20:21:35 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:35 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:36 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:36 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:36 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:36 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:37 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:37 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:37 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:37 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:37 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:38 3.8 STATUS Computed table for genes
2023-10-18 20:21:39 3.8 STATUS Computed table for tiling
2023-10-18 20:21:39 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:39 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:39 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:39 3.8 STATUS STARTED Testing function: get.region.types
2023-10-18 20:21:40 3.8 STATUS COMPLETED Testing function: get.region.types
2023-10-18 20:21:40 3.8 STATUS STARTED Testing function: get.comparisons
2023-10-18 20:21:40 3.8 STATUS COMPLETED Testing function: get.comparisons
2023-10-18 20:21:40 3.8 STATUS STARTED Testing function: get.comparison.grouplabels
2023-10-18 20:21:41 3.8 STATUS COMPLETED Testing function: get.comparison.grouplabels
2023-10-18 20:21:41 3.8 STATUS STARTED Testing function: get.site.test.method
2023-10-18 20:21:41 3.8 STATUS COMPLETED Testing function: get.site.test.method
2023-10-18 20:21:41 3.8 STATUS STARTED Testing function: get.table
2023-10-18 20:21:42 3.8 STATUS COMPLETED Testing function: get.table
2023-10-18 20:21:42 3.8 STATUS STARTED Testing function: addDiffMethTable
2023-10-18 20:21:42 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:43 3.8 STATUS COMPLETED Testing function: addDiffMethTable
2023-10-18 20:21:43 3.8 STATUS STARTED Testing functions: join.diffMeth, is.valid
2023-10-18 20:21:43 3.8 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2023-10-18 20:21:43 3.8 STATUS STARTED Destructor
2023-10-18 20:21:43 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:44 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:44 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:44 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:44 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:44 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:45 3.8 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:45 3.8 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2023-10-18 20:21:45 3.8 STATUS COMPLETED Destructor
2023-10-18 20:21:45 3.8 STATUS COMPLETED Testing class: RnBDiffMeth
2023-10-18 20:21:46 3.8 STATUS COMPLETED Testing function: apply.iEVORA
2023-10-18 20:21:46 3.8 STATUS STARTED iEVORA method
2023-10-18 20:21:48 3.8 INFO No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2
2023-10-18 20:21:49 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:49 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:49 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:50 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:50 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:50 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:50 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:51 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:51 3.8 STATUS Computed table for tiling
2023-10-18 20:21:52 3.8 STATUS Computed table for genes
2023-10-18 20:21:52 3.8 STATUS Computed table for promoters
2023-10-18 20:21:53 3.8 STATUS Computed table for cpgislands
2023-10-18 20:21:53 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:53 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:54 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:54 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:54 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:54 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:21:54 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:55 3.8 STATUS Computed table for tiling
2023-10-18 20:21:56 3.8 STATUS Computed table for genes
2023-10-18 20:21:56 3.8 STATUS Computed table for promoters
2023-10-18 20:21:57 3.8 STATUS Computed table for cpgislands
2023-10-18 20:21:57 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:21:57 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:21:57 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:21:58 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:21:58 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:21:58 3.8 STATUS STARTED Computing differential methylation tables
2023-10-18 20:21:58 3.8 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:21:59 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:21:59 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:21:59 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:21:59 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:22:00 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:22:00 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:22:00 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:22:00 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:22:01 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:22:03 3.8 STATUS Computed table for tiling
2023-10-18 20:22:04 3.8 STATUS Computed table for genes
2023-10-18 20:22:05 3.8 STATUS Computed table for promoters
2023-10-18 20:22:05 3.8 STATUS Computed table for cpgislands
2023-10-18 20:22:05 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:22:06 3.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:22:06 3.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:22:06 3.8 STATUS STARTED Computing Differential Methylation Table
2023-10-18 20:22:06 3.8 INFO Conducting differential analysis using limma
2023-10-18 20:22:06 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:22:07 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:22:07 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:22:07 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:22:07 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:22:08 3.8 STATUS COMPLETED Computing Differential Methylation Table
2023-10-18 20:22:08 3.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:22:09 3.8 STATUS Computed table for tiling
2023-10-18 20:22:10 3.8 STATUS Computed table for genes
2023-10-18 20:22:12 3.8 STATUS Computed table for promoters
2023-10-18 20:22:12 3.8 STATUS Computed table for cpgislands
2023-10-18 20:22:13 3.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2023-10-18 20:22:13 3.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2023-10-18 20:22:13 3.8 STATUS COMPLETED Computing differential methylation tables
2023-10-18 20:22:13 3.8 STATUS STARTED Differential Variability
2023-10-18 20:22:13 3.8 STATUS STARTED Retrieving comparison info
2023-10-18 20:22:14 3.8 STATUS COMPLETED Retrieving comparison info
2023-10-18 20:22:14 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:22:14 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:22:14 3.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:22:15 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:22:15 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:22:15 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:22:15 3.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2023-10-18 20:22:16 3.8 STATUS Computed table for tiling
2023-10-18 20:22:16 3.8 STATUS Computed table for genes
2023-10-18 20:22:17 3.8 STATUS Computed table for promoters
2023-10-18 20:22:17 3.8 STATUS Computed table for cpgislands
2023-10-18 20:22:18 3.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2023-10-18 20:22:18 3.8 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2023-10-18 20:22:18 3.8 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2023-10-18 20:22:18 3.8 INFO Conducting differential variability using diffVar
2023-10-18 20:22:18 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2023-10-18 20:22:19 3.8 STATUS COMPLETED diffVar method
2023-10-18 20:22:19 3.8 STATUS STARTED Computing Differential Variability Tables (Region Level)
2023-10-18 20:22:20 3.8 STATUS Computed table for tiling
2023-10-18 20:22:20 3.8 STATUS Computed table for genes
2023-10-18 20:22:20 3.8 STATUS Computed table for promoters
2023-10-18 20:22:21 3.8 STATUS Computed table for cpgislands
2023-10-18 20:22:21 3.8 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2023-10-18 20:22:21 3.8 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2023-10-18 20:22:22 3.8 STATUS COMPLETED Differential Variability
2023-10-18 20:22:22 3.8 STATUS STARTED Analysis
2023-10-18 20:22:22 3.8 INFO Loaded information from data.RData
2023-10-18 20:22:22 3.8 STATUS STARTED Processing Detection P-values
2023-10-18 20:22:22 3.8 INFO Removed 3979 probes that overlap with SNPs
2023-10-18 20:22:23 3.8 INFO Completed Greedycut on 510 samples
2023-10-18 20:22:23 3.8 STATUS COMPLETED Processing Detection P-values
2023-10-18 20:22:23 3.8 WARNING File not found: data2.RData
2023-10-18 20:22:23 3.8 STATUS COMPLETED Analysis
2023-10-18 20:22:23 3.8 STATUS STARTED Testing imputation
2023-10-18 20:22:24 3.8 STATUS STARTED Imputation procedure knn
2023-10-18 20:22:27 3.8 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:22:27 3.8 STATUS STARTED Imputation procedure mean.samples
2023-10-18 20:22:28 3.8 STATUS COMPLETED Imputation procedure mean.samples
2023-10-18 20:22:28 3.8 STATUS STARTED Imputation procedure mean.cpgs
2023-10-18 20:22:29 3.8 STATUS COMPLETED Imputation procedure mean.cpgs
2023-10-18 20:22:29 3.8 STATUS STARTED Imputation procedure random
2023-10-18 20:22:30 3.8 STATUS COMPLETED Imputation procedure random
2023-10-18 20:22:30 3.8 STATUS COMPLETED Testing imputation
2023-10-18 20:22:30 3.8 STATUS STARTED Testing age prediction
2023-10-18 20:22:30 3.8 STATUS STARTED Performing Age Prediction
2023-10-18 20:22:32 3.9 STATUS COMPLETED Performing Age Prediction
2023-10-18 20:22:32 3.9 STATUS COMPLETED Testing age prediction
2023-10-18 20:22:33 3.9 STATUS STARTED Performing Age Prediction
2023-10-18 20:22:34 4.1 STATUS COMPLETED Performing Age Prediction
2023-10-18 20:22:35 4.1 STATUS STARTED Imputation procedure knn
2023-10-18 20:22:37 3.9 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:22:37 3.9 STATUS STARTED Imputation procedure mean.samples
2023-10-18 20:22:38 3.9 STATUS COMPLETED Imputation procedure mean.samples
2023-10-18 20:22:38 3.9 STATUS STARTED Imputation procedure mean.cpgs
2023-10-18 20:22:39 3.9 STATUS COMPLETED Imputation procedure mean.cpgs
2023-10-18 20:22:39 3.9 STATUS STARTED Imputation procedure random
2023-10-18 20:22:40 3.9 STATUS COMPLETED Imputation procedure random
2023-10-18 20:22:41 3.9 STATUS STARTED Testing imputation
2023-10-18 20:22:41 3.9 STATUS STARTED Imputation procedure knn
2023-10-18 20:22:42 3.9 STATUS COMPLETED Imputation procedure knn
2023-10-18 20:22:42 3.9 STATUS STARTED Imputation procedure mean.samples
2023-10-18 20:22:44 3.9 STATUS COMPLETED Imputation procedure mean.samples
2023-10-18 20:22:45 3.9 STATUS STARTED Imputation procedure mean.cpgs
2023-10-18 20:22:45 3.9 STATUS COMPLETED Imputation procedure mean.cpgs
2023-10-18 20:22:46 3.9 STATUS STARTED Imputation procedure random
2023-10-18 20:22:47 3.9 STATUS COMPLETED Imputation procedure random
2023-10-18 20:22:47 3.9 STATUS COMPLETED Testing imputation
2023-10-18 20:22:47 3.9 STATUS STARTED Testing age prediction
2023-10-18 20:22:47 3.9 STATUS STARTED Performing Age Prediction
2023-10-18 20:22:49 3.9 STATUS COMPLETED Performing Age Prediction
2023-10-18 20:22:49 3.9 STATUS COMPLETED Testing age prediction
RUNIT TEST PROTOCOL -- Wed Oct 18 20:23:02 2023
***********************************************
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 13 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
194.599 113.996 423.371
RnBeads.Rcheck/RnBeads-Ex.timings
| name | user | system | elapsed | |
| M-methods | 0 | 0 | 0 | |
| U-methods | 0 | 0 | 0 | |
| addDiffMethTable-RnBDiffMeth-methods | 0 | 0 | 0 | |
| addPheno-RnBSet-methods | 0 | 0 | 0 | |
| addRegionSubsegments | 0 | 0 | 0 | |
| annotation-methods | 0 | 0 | 0 | |
| assembly-methods | 0 | 0 | 0 | |
| combine.rnb.sets-methods | 0 | 0 | 0 | |
| combineTestPvalsMeth | 0 | 0 | 0 | |
| computeDiffTab.region | 0.000 | 0.001 | 0.001 | |
| computeDiffTab.site | 0 | 0 | 0 | |
| covg-methods | 0 | 0 | 0 | |
| create.densityScatter | 0 | 0 | 0 | |
| create.scatter.dens.points | 0 | 0 | 0 | |
| createReport | 0 | 0 | 0 | |
| createReportPlot | 0 | 0 | 0 | |
| downloadLolaDbs | 0.000 | 0.000 | 0.001 | |
| dpval-methods | 0 | 0 | 0 | |
| exportDMRs2regionFile | 0 | 0 | 0 | |
| get.adjustment.variables | 0 | 0 | 0 | |
| get.comparison.grouplabels-RnBDiffMeth-methods | 0.000 | 0.001 | 0.001 | |
| get.comparison.groupsizes-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.comparison.info | 0 | 0 | 0 | |
| get.comparisons-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.covariates.sva | 0 | 0 | 0 | |
| get.covg.thres-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| get.files | 0.001 | 0.000 | 0.002 | |
| get.region.types-RnBDiffMeth-methods | 0.001 | 0.000 | 0.000 | |
| get.site.test.method-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.table-RnBDiffMeth-methods | 0.000 | 0.001 | 0.000 | |
| getCellTypesFromLolaDb | 0 | 0 | 0 | |
| getNamesFromLolaDb | 0 | 0 | 0 | |
| getSubCmdTokens-ClusterArchitectureSGE-methods | 0 | 0 | 0 | |
| getSubCmdTokens-ClusterArchitectureSLURM-methods | 0 | 0 | 0 | |
| getTargetFromLolaDb | 0 | 0 | 0 | |
| has.covariates.sva | 0 | 0 | 0 | |
| hasCovg-methods | 0 | 0 | 0 | |
| includes.sites-RnBDiffMeth-methods | 0 | 0 | 0 | |
| is.valid-RnBDiffMeth-methods | 0 | 0 | 0 | |
| join.diffMeth-methods | 0.000 | 0.001 | 0.001 | |
| limmaP | 0 | 0 | 0 | |
| loadLolaDbs | 0.000 | 0.000 | 0.001 | |
| logger.argument | 0 | 0 | 0 | |
| logger.getfiles | 0.000 | 0.001 | 0.000 | |
| logger.isinitialized | 0 | 0 | 0 | |
| logger.validate.file | 0 | 0 | 0 | |
| loggerManagement | 0.001 | 0.000 | 0.000 | |
| loggerMessages | 0 | 0 | 0 | |
| lolaBarPlot | 0 | 0 | 0 | |
| lolaBoxPlotPerTarget | 0 | 0 | 0 | |
| lolaVolcanoPlot | 0 | 0 | 0 | |
| mergeSamples-methods | 0 | 0 | 0 | |
| meth-methods | 0 | 0 | 0 | |
| mval-methods | 0 | 0 | 0 | |
| nsites-methods | 0 | 0 | 0 | |
| parallel.getNumWorkers | 0.000 | 0.000 | 0.001 | |
| parallel.isEnabled | 0.001 | 0.000 | 0.000 | |
| parallel.setup | 0 | 0 | 0 | |
| parallel.teardown | 0 | 0 | 0 | |
| performGOEnrichment.diffVar | 0 | 0 | 0 | |
| performGOenrichment.diffMeth.entrez | 0 | 0 | 0 | |
| performGoEnrichment.diffMeth | 0 | 0 | 0 | |
| performLolaEnrichment.diffMeth | 0 | 0 | 0 | |
| performLolaEnrichment.diffVar | 0.000 | 0.001 | 0.000 | |
| pheno-methods | 0 | 0 | 0 | |
| qc-methods | 0 | 0 | 0 | |
| read.sample.annotation | 0 | 0 | 0 | |
| regionMapping-methods | 0.000 | 0.000 | 0.001 | |
| regions-methods | 0 | 0 | 0 | |
| reload-RnBDiffMeth-methods | 0 | 0 | 0 | |
| remove.regions-methods | 0 | 0 | 0 | |
| remove.samples-methods | 0 | 0 | 0 | |
| remove.sites-methods | 0 | 0 | 0 | |
| rnb.RnBSet.to.GRangesList | 0 | 0 | 0 | |
| rnb.RnBSet.to.bed | 0.000 | 0.000 | 0.001 | |
| rnb.RnBSet.to.bedGraph | 0 | 0 | 0 | |
| rnb.add.list | 0 | 0 | 0 | |
| rnb.add.paragraph | 0.001 | 0.000 | 0.000 | |
| rnb.add.reference | 0 | 0 | 0 | |
| rnb.add.section | 0 | 0 | 0 | |
| rnb.annotation.size | 0 | 0 | 0 | |
| rnb.annotation2data.frame | 0 | 0 | 0 | |
| rnb.beta2mval | 0.000 | 0.000 | 0.002 | |
| rnb.execute.batcheffects | 0 | 0 | 0 | |
| rnb.execute.clustering | 0.000 | 0.001 | 0.000 | |
| rnb.execute.computeDiffMeth | 0 | 0 | 0 | |
| rnb.execute.context.removal | 0.000 | 0.001 | 0.000 | |
| rnb.execute.cross.reactive.removal | 0 | 0 | 0 | |
| rnb.execute.dreduction | 0 | 0 | 0 | |
| rnb.execute.export.csv | 0 | 0 | 0 | |
| rnb.execute.greedycut | 0.000 | 0.000 | 0.001 | |
| rnb.execute.import | 0.000 | 0.000 | 0.001 | |
| rnb.execute.na.removal | 0.000 | 0.000 | 0.001 | |
| rnb.execute.normalization | 0.001 | 0.000 | 0.000 | |
| rnb.execute.pOOBAH | 21.396 | 2.474 | 37.165 | |
| rnb.execute.sex.prediction | 0 | 0 | 0 | |
| rnb.execute.sex.removal | 0 | 0 | 0 | |
| rnb.execute.snp.removal | 0 | 0 | 0 | |
| rnb.execute.sva | 0.001 | 0.000 | 0.000 | |
| rnb.execute.tnt | 0.000 | 0.000 | 0.001 | |
| rnb.execute.variability.removal | 0 | 0 | 0 | |
| rnb.export.all.annotation | 0 | 0 | 0 | |
| rnb.export.annotation | 0 | 0 | 0 | |
| rnb.export.to.ewasher | 0.000 | 0.000 | 0.001 | |
| rnb.export.to.trackhub | 0 | 0 | 0 | |
| rnb.get.annotation | 0.001 | 0.000 | 0.000 | |
| rnb.get.assemblies | 0 | 0 | 0 | |
| rnb.get.chromosomes | 0 | 0 | 0 | |
| rnb.get.directory | 0 | 0 | 0 | |
| rnb.get.mapping | 0.000 | 0.001 | 0.000 | |
| rnb.get.reference | 0 | 0 | 0 | |
| rnb.get.reliability.matrix | 0 | 0 | 0 | |
| rnb.infinium.control.targets | 0 | 0 | 0 | |
| rnb.initialize.reports | 0 | 0 | 0 | |
| rnb.is.option | 0.000 | 0.000 | 0.001 | |
| rnb.load.annotation.from.db | 0.000 | 0.000 | 0.002 | |
| rnb.message.plot | 0 | 0 | 0 | |
| rnb.mval2beta | 0 | 0 | 0 | |
| rnb.options | 0 | 0 | 0 | |
| rnb.options2xml | 0 | 0 | 0 | |
| rnb.plot.betadistribution.probeCategories | 0.000 | 0.000 | 0.001 | |
| rnb.plot.betadistribution.sampleGroups | 0 | 0 | 0 | |
| rnb.plot.control.barplot | 0 | 0 | 0 | |
| rnb.plot.control.boxplot | 0 | 0 | 0 | |
| rnb.plot.dreduction | 0.000 | 0.000 | 0.001 | |
| rnb.plot.locus.profile | 0.000 | 0.000 | 0.001 | |
| rnb.plot.negative.boxplot | 0 | 0 | 0 | |
| rnb.plot.region.profile.density | 0 | 0 | 0 | |
| rnb.plot.region.profiles | 0 | 0 | 0 | |
| rnb.plot.region.site.density | 0 | 0 | 0 | |
| rnb.plot.sentrix.distribution | 0.000 | 0.000 | 0.002 | |
| rnb.plot.snp.barplot | 0.000 | 0.001 | 0.000 | |
| rnb.plot.snp.boxplot | 0 | 0 | 0 | |
| rnb.plot.snp.heatmap | 0 | 0 | 0 | |
| rnb.region.types | 0 | 0 | 0 | |
| rnb.region.types.for.analysis | 0 | 0 | 0 | |
| rnb.remove.annotation | 0 | 0 | 0 | |
| rnb.run.example | 0.001 | 0.000 | 0.001 | |
| rnb.runs | 0 | 0 | 0 | |
| rnb.sample.groups | 0.000 | 0.000 | 0.004 | |
| rnb.sample.summary.table | 0 | 0 | 0 | |
| rnb.set.annotation | 0 | 0 | 0 | |
| rnb.write.table | 0 | 0 | 0 | |
| rnb.xml2options | 0 | 0 | 0 | |
| rowOneSampleTP | 0 | 0 | 0 | |
| rowWelchP | 0 | 0 | 0 | |
| run-RnBClusterRun-methods | 0 | 0 | 0 | |
| samples-methods | 0.000 | 0.000 | 0.001 | |
| save.tables-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| set.covariates.sva | 0.000 | 0.000 | 0.001 | |
| sites-methods | 0.000 | 0.000 | 0.001 | |
| summarize.regions-methods | 0 | 0 | 0 | |
| summarized.regions-methods | 0 | 0 | 0 | |