Fabian Mueller
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/RnBeads |
| git_branch: RELEASE_3_13 |
| git_last_commit: 8929f8e |
| git_last_commit_date: 2021-05-21 03:15:12 -0400 (Fri, 21 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:20 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the RnBeads package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1614/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RnBeads 2.10.0 (landing page) Fabian Mueller
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RnBeads |
| Version: 2.10.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RnBeads_2.10.0.tar.gz |
| StartedAt: 2021-10-15 04:45:40 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 05:02:53 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 1033.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RnBeads.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RnBeads_2.10.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/RnBeads.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RnBeads/DESCRIPTION' ... OK
* this is package 'RnBeads' version '2.10.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
'ff', 'fields', 'ggplot2', 'gplots', 'gridExtra', 'limma',
'matrixStats', 'illuminaio', 'methylumi', 'plyr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'RnBeads' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.6Mb
sub-directories of 1Mb or more:
R 3.1Mb
help 1.4Mb
html 1.5Mb
* 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from 'RnBeads' for: 'samples'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from 'RnBeads' for: 'samples'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
'stopCluster'
MethyLumiSet2RnBeadSet: no visible global function definition for
'phenoData'
MethyLumiSet2RnBeadSet: no visible global function definition for
'assayDataElementNames'
MethyLumiSet2RnBeadSet: no visible global function definition for
'featureNames'
MethyLumiSet2RnBeadSet: no visible global function definition for
'varLabels'
MethyLumiSet2RnBeadSet: no visible global function definition for
'featureData'
add.age.histogram: no visible binding for global variable 'Age'
add.age.histogram: no visible binding for global variable '..count..'
add.age.histogram: no visible binding for global variable '..density..'
add.agecomparison.plot: no visible global function definition for
'samples'
add.agecomparison.plot: no visible binding for global variable 'Sample'
add.agecomparison.plot: no visible global function definition for
'%dopar%'
add.agecomparison.plot: no visible global function definition for
'foreach'
add.agecomparison.plot: no visible binding for global variable 'i'
add.combination.plot: no visible global function definition for
'samples'
add.combination.plot: no visible binding for global variable
'Difference'
add.combination.plot: no visible binding for global variable 'Density'
add.combination.plot: no visible binding for global variable 'yint'
add.combination.plot: no visible binding for global variable 'Measure'
add.error.plot: no visible binding for global variable 'Value'
add.error.plot: no visible binding for global variable 'Sample'
add.error.plot: no visible binding for global variable 'Deviance'
add.error.plot: no visible binding for global variable 'yint'
add.error.plot: no visible binding for global variable 'Measure'
add.negative.control.boxplot: no visible global function definition for
'samples'
add.profile.plots: no visible global function definition for 'mclapply'
add.qc.barplots: no visible global function definition for 'samples'
add.quantile.plot: no visible binding for global variable 'Difference'
add.quantile.plot: no visible binding for global variable '..density..'
add.quantile.plot: no visible binding for global variable 'Sample'
add.quantile.plot: no visible binding for global variable 'Density'
add.seq.coverage.histograms: no visible global function definition for
'samples'
add.seq.coverage.plot: no visible global function definition for
'samples'
add.seq.coverage.violins: no visible global function definition for
'samples'
add.stratification.plot: no visible global function definition for
'%dopar%'
add.stratification.plot: no visible global function definition for
'foreach'
add.stratification.plot: no visible binding for global variable 'Group'
add.stratification.plot: no visible binding for global variable
'Increase'
add.stratification.plot: no visible binding for global variable
'Predicted'
add.stratification.plot: no visible binding for global variable
'Annotated'
add.stratification.plot.immune: no visible global function definition
for '%dopar%'
add.stratification.plot.immune: no visible global function definition
for 'foreach'
add.stratification.plot.immune: no visible binding for global variable
'Group'
add.stratification.plot.immune: no visible binding for global variable
'Immune'
addReportPlot.diffVar.volcano: no visible binding for global variable
'var.diff'
addReportPlot.diffVar.volcano: no visible binding for global variable
'log10P'
addReportPlot.diffVar.volcano: no visible binding for global variable
'combinedRank.var'
addReportPlot.diffVar.volcano: no visible binding for global variable
'log10FDR'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable 'mean.diff'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable 'diffmeth.p.val'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable 'combinedRank'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable 'mean.quot.log2'
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable 'diffmeth.p.adj.fdr'
agePredictorBiseq: no visible global function definition for
'impute.knn'
agePredictorBiseq: no visible global function definition for 'samples'
agePredictorChip: no visible global function definition for
'impute.knn'
append.cpg.stats: no visible global function definition for '%dopar%'
append.cpg.stats: no visible global function definition for 'foreach'
append.cpg.stats: no visible binding for global variable 'chrom'
basic_combine: no visible global function definition for 'samples'
computeDiffTab.default.region: no visible global function definition
for '%dopar%'
computeDiffTab.default.region: no visible global function definition
for 'foreach'
computeDiffTab.default.region: no visible binding for global variable
'i'
computeDiffTab.default.site: no visible binding for global variable
'p.vals.t.na.adj'
computeDiffTab.default.site : <anonymous>: no visible binding for
global variable '.inds.g2'
computeDiffVar.bin.site: no visible binding for global variable
'p.vals.t.na.adj'
computeDiffVar.bin.site : <anonymous>: no visible binding for global
variable 'eps'
computeDiffVar.bin.site : <anonymous>: no visible binding for global
variable '.inds.g2'
computeDiffVar.default.region: no visible global function definition
for '%dopar%'
computeDiffVar.default.region: no visible global function definition
for 'foreach'
computeDiffVar.default.region: no visible binding for global variable
'i'
create.densityScatter: no visible binding for global variable
'..density..'
create.diffMeth.diffVar.subsample: no visible binding for global
variable '..density..'
create.ucsc.track.hub: no visible global function definition for
'samples'
createPredictor : ret: no visible global function definition for
'impute.knn'
cv.array: no visible global function definition for 'impute.knn'
data.frame2GRanges: no visible global function definition for
'seqlevels<-'
data.frame2GRanges: no visible global function definition for
'genome<-'
diffVar: no visible global function definition for 'varFit'
diffVar: no visible binding for global variable 'group1'
diffVar: no visible binding for global variable 'group2'
estimateProportionsCP: no visible global function definition for 'lme'
estimateProportionsCP: no visible global function definition for
'getVarCov'
general.cv: no visible global function definition for '%dopar%'
general.cv: no visible global function definition for 'foreach'
general.cv: no visible binding for global variable 'i'
get.adjustment.variables: no visible global function definition for
'samples'
get.comparison.info : rm.na.from.adj.tab: no visible global function
definition for 'samples'
get.components.isva: no visible global function definition for 'DoISVA'
get.components.sva: no visible global function definition for 'sva'
get.cpg.stats: no visible global function definition for
'dinucleotideFrequency'
get.cpg.stats: no visible global function definition for
'letterFrequency'
get.dataset.matrix: no visible global function definition for 'samples'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable 'report'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable 'refText'
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable 'diffmeth'
get.platform.tokens: no visible global function definition for
'setNames'
getCGCounts: no visible global function definition for 'seqlengths'
getCGCounts : <anonymous>: no visible global function definition for
'ChrNumeric'
getGLADProfiles: no visible global function definition for 'samples'
getGLADProfiles: no visible global function definition for 'mclapply'
getGLADProfiles : <anonymous>: no visible global function definition
for 'as.profileCGH'
getGLADProfiles : <anonymous>: no visible global function definition
for 'daglad'
getMergeList: no visible global function definition for 'samples'
groupPermutationP.site.parallel: no visible global function definition
for '%dopar%'
groupPermutationP.site.parallel: no visible global function definition
for 'foreach'
iEVORA: no visible global function definition for 'qvalue'
imputation.low.memory.cpgs: no visible global function definition for
'samples'
inferWBCbyLme: no visible global function definition for 'lme'
inferWBCbyLme: no visible global function definition for 'getVarCov'
intensities.by.color: no visible binding for global variable
'IlluminaHumanMethylationEPICmanifest'
intensities.by.color: no visible binding for global variable
'IlluminaHumanMethylation450kmanifest'
intensities.by.color: no visible global function definition for
'samples'
knn.imputation: no visible global function definition for 'impute.knn'
limmaP: no visible binding for global variable 'group1'
limmaP: no visible binding for global variable 'group2'
loadLolaDbs: no visible global function definition for 'loadRegionDB'
loadLolaDbs: no visible global function definition for 'mergeRegionDBs'
locus.profile.get.base.tracks: no visible global function definition
for 'useMart'
locus.profile.get.base.tracks: no visible global function definition
for 'IdeogramTrack'
locus.profile.get.base.tracks: no visible global function definition
for 'GenomeAxisTrack'
locus.profile.get.base.tracks: no visible global function definition
for 'BiomartGeneRegionTrack'
locus.profile.get.base.tracks: no visible global function definition
for 'UcscTrack'
locus.profile.get.methylation.track.heatmap: no visible global function
definition for 'DataTrack'
locus.profile.get.methylation.track.smooth: no visible global function
definition for 'DataTrack'
methylumi.intensities.by.color: no visible global function definition
for 'featureNames'
methylumi.intensities.by.color: no visible binding for global variable
'IlluminaHumanMethylation450kmanifest'
methylumi.intensities.by.color: no visible global function definition
for 'assayDataElement'
parallel.setup: no visible global function definition for
'registerDoParallel'
parallel.setup: no visible global function definition for
'getDoParWorkers'
performLolaEnrichment.diffMeth: no visible global function definition
for 'runLOLA'
performLolaEnrichment.diffVar: no visible global function definition
for 'runLOLA'
plot.heatmap.pc.correlations: no visible global function definition for
'melt'
plot.heatmap.pc.correlations: no visible global function definition for
'grid.newpage'
plot.heatmap.pc.correlations: no visible global function definition for
'grid.draw'
plot.heatmap.pc.pvalues: no visible global function definition for
'melt'
plot.heatmap.pc.pvalues: no visible global function definition for
'grid.newpage'
plot.heatmap.pc.pvalues: no visible global function definition for
'grid.draw'
plot.heatmap.rand: no visible global function definition for 'melt'
plot.heatmap.symm: no visible global function definition for 'melt'
plot.heatmap.symm: no visible global function definition for
'grid.newpage'
plot.heatmap.symm: no visible global function definition for
'grid.draw'
plotCGHProfile: no visible global function definition for 'ChrNumeric'
prepareGEOSampleInfoTemplate: no visible global function definition for
'samples'
projectWBC: no visible global function definition for 'solve.QP'
read.GS.report: no visible global function definition for
'featureNames'
read.idat.files: no visible binding for global variable 'barcode'
refFreeEWASP: no visible global function definition for 'EstDimRMT'
refFreeEWASP: no visible global function definition for
'RefFreeEwasModel'
refFreeEWASP: no visible global function definition for
'PairsBootRefFreeEwasModel'
refFreeEWASP: no visible global function definition for
'BootRefFreeEwasModel'
rnb.RnBSet.to.GRangesList: no visible global function definition for
'samples'
rnb.RnBSet.to.bed: no visible global function definition for 'samples'
rnb.RnBSet.to.bedGraph: no visible global function definition for
'samples'
rnb.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 'SigSet'
rnb.execute.pOOBAH: no visible global function definition for 'IG<-'
rnb.execute.pOOBAH: no visible global function definition for 'IR<-'
rnb.execute.pOOBAH: no visible global function definition for 'II<-'
rnb.execute.pOOBAH: no visible global function definition for 'oobG<-'
rnb.execute.pOOBAH: no visible global function definition for 'oobR<-'
rnb.execute.pOOBAH: no visible global function definition for 'oobG'
rnb.execute.pOOBAH: no visible global function definition for 'oobR'
rnb.execute.pOOBAH: no visible global function definition for 'IR'
rnb.execute.pOOBAH: no visible global function definition for 'IG'
rnb.execute.pOOBAH: no visible global function definition for 'II'
rnb.execute.quality: no visible global function definition for
'samples'
rnb.execute.quality : <anonymous>: no visible global function
definition for 'samples'
rnb.execute.segmentation: no visible binding for global variable
'Hsapiens'
rnb.execute.segmentation: no visible binding for global variable
'Mmusculus'
rnb.execute.segmentation: no visible global function definition for
'seqlengths'
rnb.execute.segmentation: no visible global function definition for
'browserSession'
rnb.execute.segmentation: no visible global function definition for
'genome<-'
rnb.execute.segmentation: no visible global function definition for
'ucscTableQuery'
rnb.execute.segmentation: no visible global function definition for
'getTable'
rnb.execute.segmentation: no visible global function definition for
'samples'
rnb.execute.segmentation: no visible global function definition for
'readMethylome'
rnb.execute.segmentation: no visible global function definition for
'readSNPTable'
rnb.execute.segmentation: no visible global function definition for
'removeSNPs'
rnb.execute.segmentation: no visible global function definition for
'segmentPMDs'
rnb.execute.segmentation: no visible global function definition for
'plotAlphaDistributionOneChr'
rnb.execute.segmentation: no visible global function definition for
'calculateFDRs'
rnb.execute.segmentation: no visible global function definition for
'segmentUMRsLMRs'
rnb.export.to.ewasher: no visible global function definition for
'samples'
rnb.filter.dataset: no visible global function definition for 'samples'
rnb.final.segmentation: no visible global function definition for
'samples'
rnb.get.reliability.counts.per.sample: no visible global function
definition for 'samples'
rnb.options.description.table.fromRd: no visible global function
definition for 'Rd2HTML'
rnb.options.description.table.fromRd: no visible binding for global
variable 'xmlValue'
rnb.plot.beta.density.group: no visible binding for global variable
'group'
rnb.plot.biseq.coverage: no visible global function definition for
'samples'
rnb.plot.biseq.coverage.hist: no visible global function definition for
'samples'
rnb.plot.control.barplot: no visible global function definition for
'samples'
rnb.plot.control.barplot: no visible binding for global variable
'Target'
rnb.plot.control.barplot: no visible binding for global variable
'Index'
rnb.plot.control.barplot: no visible binding for global variable 'ID'
rnb.plot.control.barplot: no visible binding for global variable
'Address'
rnb.plot.control.barplot: no visible global function definition for
'grid.newpage'
rnb.plot.control.barplot: no visible binding for global variable
'Intensity'
rnb.plot.control.barplot: no visible global function definition for
'grid.draw'
rnb.plot.control.boxplot: no visible global function definition for
'grid.newpage'
rnb.plot.control.boxplot: no visible binding for global variable
'Probe'
rnb.plot.control.boxplot: no visible binding for global variable
'Intensity'
rnb.plot.control.boxplot: no visible global function definition for
'grid.draw'
rnb.plot.ct.heatmap: no visible binding for global variable 'x'
rnb.plot.ct.heatmap: no visible binding for global variable 'y'
rnb.plot.ct.heatmap: no visible binding for global variable 'v'
rnb.plot.ct.heatmap: no visible global function definition for
'grid.newpage'
rnb.plot.ct.heatmap: no visible global function definition for
'grid.draw'
rnb.plot.dreduction: no visible global function definition for 'tsne'
rnb.plot.locus.profile: no visible global function definition for
'plotTracks'
rnb.plot.marker.fstat: no visible binding for global variable 'x'
rnb.plot.marker.fstat: no visible binding for global variable 'y'
rnb.plot.marker.fstat: no visible global function definition for
'muted'
rnb.plot.negative.boxplot: no visible global function definition for
'samples'
rnb.plot.negative.boxplot: no visible binding for global variable
'numeric.names'
rnb.plot.negative.boxplot: no visible binding for global variable
'type'
rnb.plot.negative.boxplot: no visible binding for global variable
'types'
rnb.plot.negative.boxplot: no visible global function definition for
'grid.newpage'
rnb.plot.negative.boxplot: no visible binding for global variable
'Sample'
rnb.plot.negative.boxplot: no visible binding for global variable
'Intensity'
rnb.plot.negative.boxplot: no visible global function definition for
'grid.draw'
rnb.plot.num.sites.covg: no visible global function definition for
'samples'
rnb.plot.num.sites.covg : <anonymous>: no visible global function
definition for 'samples'
rnb.plot.num.sites.covg: no visible binding for global variable
'numSites'
rnb.plot.num.sites.covg: no visible binding for global variable
'covgMedian'
rnb.plot.num.sites.covg: no visible binding for global variable
'covgPercLow'
rnb.plot.num.sites.covg: no visible binding for global variable
'covgPercUp'
rnb.plot.num.sites.covg: no visible binding for global variable 'comma'
rnb.plot.region.profile.density: no visible binding for global variable
'relative.coord'
rnb.plot.region.profile.density: no visible binding for global variable
'..density..'
rnb.plot.region.profiles : <anonymous>: no visible global function
definition for 'samples'
rnb.plot.region.profiles: no visible binding for global variable
'relative.coord'
rnb.plot.region.profiles: no visible binding for global variable
'group'
rnb.plot.region.site.density: no visible binding for global variable
'relative.coord'
rnb.plot.segmentation.distributions: no visible binding for global
variable 'x2'
rnb.plot.segmentation.distributions: no visible binding for global
variable 'y2'
rnb.plot.segmentation.distributions: no visible binding for global
variable 'texthere'
rnb.plot.segmentation.final: no visible global function definition for
'plotFinalSegmentation'
rnb.plot.sentrix.distributions: no visible global function definition
for 'samples'
rnb.plot.sentrix.distributions: no visible binding for global variable
'Slide'
rnb.plot.snp.boxplot: no visible binding for global variable 'SNP'
rnb.plot.snp.boxplot: no visible binding for global variable 'bv'
rnb.run.example: no visible global function definition for 'install'
rnb.run.preprocessing : logger.completed.filtering: no visible global
function definition for 'samples'
rnb.sample.summary.table: no visible global function definition for
'samples'
rnb.section.ageprediction: no visible global function definition for
'samples'
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
function definition for 'samples'
rnb.section.clustering: no visible global function definition for
'samples'
rnb.section.diffMeth.region: no visible global function definition for
'%dopar%'
rnb.section.diffMeth.region: no visible global function definition for
'foreach'
rnb.section.diffMeth.region: no visible binding for global variable 'k'
rnb.section.diffMeth.region : do.enrichment.table: no visible global
function definition for 'sigCategories'
rnb.section.diffMeth.region : do.enrichment.table.var: no visible
global function definition for 'sigCategories'
rnb.section.diffMeth.site: no visible global function definition for
'%dopar%'
rnb.section.diffMeth.site: no visible global function definition for
'foreach'
rnb.section.diffVar: no visible global function definition for
'%dopar%'
rnb.section.diffVar: no visible global function definition for
'foreach'
rnb.section.diffVar.region: no visible global function definition for
'%dopar%'
rnb.section.diffVar.region: no visible global function definition for
'foreach'
rnb.section.diffVar.region: no visible binding for global variable 'k'
rnb.section.import: no visible global function definition for 'samples'
rnb.section.import: no visible global function definition for
'phenoData'
rnb.section.imputation: no visible global function definition for
'melt'
rnb.section.locus.profiles: no visible global function definition for
'samples'
rnb.section.locus.profiles : do.plots: no visible global function
definition for 'plotTracks'
rnb.section.locus.profiles: no visible global function definition for
'%dopar%'
rnb.section.locus.profiles: no visible global function definition for
'foreach'
rnb.section.na.removal: no visible global function definition for
'samples'
rnb.section.normalization: no visible global function definition for
'samples'
rnb.section.region.description: no visible binding for global variable
'size'
rnb.section.region.description: no visible binding for global variable
'n.sites'
rnb.section.region.profiles: no visible global function definition for
'samples'
rnb.section.region.subsegmentation : get.summary.df.from.list: no
visible global function definition for 'melt'
rnb.section.region.subsegmentation: no visible binding for global
variable 'region.size'
rnb.section.region.subsegmentation: no visible binding for global
variable 'is.subsegmentation'
rnb.section.region.subsegmentation: no visible binding for global
variable 'num.sites'
rnb.section.sex.prediction: no visible global function definition for
'muted'
rnb.step.betadistribution.internal: no visible global function
definition for '%dopar%'
rnb.step.betadistribution.internal: no visible global function
definition for 'foreach'
rnb.step.cell.types: no visible global function definition for
'samples'
rnb.step.clustering.internal: no visible global function definition for
'samples'
rnb.step.dreduction: no visible global function definition for
'%dopar%'
rnb.step.dreduction: no visible global function definition for
'foreach'
rnb.step.dreduction: no visible binding for global variable 'target'
rnb.step.filter.summary.internal: no visible global function definition
for 'percent_format'
rnb.step.filter.summary.internal: no visible global function definition
for 'samples'
rnb.step.import: no visible global function definition for 'samples'
rnb.step.import: no visible global function definition for 'phenoData'
rnb.step.na.removal: no visible binding for global variable
'sites2ignore'
rnb.step.na.removal.internal: no visible global function definition for
'samples'
rnb.step.normalization: no visible global function definition for
'phenoData'
robustHyperGResultSummary: no visible global function definition for
'sigCategories'
robustHyperGResultSummary: no visible global function definition for
'pvalues'
robustHyperGResultSummary: no visible global function definition for
'oddsRatios'
robustHyperGResultSummary: no visible global function definition for
'expectedCounts'
robustHyperGResultSummary: no visible global function definition for
'geneCounts'
robustHyperGResultSummary: no visible global function definition for
'universeCounts'
robustHyperGResultSummary: no visible binding for global variable
'Term'
run.cross.validation: no visible global function definition for
'samples'
run.cross.validation: no visible global function definition for 'melt'
run.cross.validation: no visible binding for global variable 'Measure'
run.cross.validation: no visible binding for global variable 'Error'
sampleCovgApply: no visible global function definition for 'samples'
set.covariates.ct: no visible global function definition for 'samples'
simpleGlmnet: no visible global function definition for 'impute.knn'
simpleGlmnet: no visible global function definition for 'cv.glmnet'
simpleGlmnet: no visible global function definition for 'glmnet'
simpleGlmnetBiseq: no visible global function definition for
'cv.glmnet'
simpleGlmnetBiseq: no visible global function definition for 'glmnet'
simpleGlmnetEvaluate: no visible global function definition for
'cv.glmnet'
simpleGlmnetEvaluate: no visible global function definition for
'glmnet'
symmetric.melt: no visible global function definition for 'melt'
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
'reg.type'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for 'getManifest'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for 'getGreen'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for 'getRed'
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for 'pData'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for 'featureData<-'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for 'featureNames<-'
coerce,RnBeadRawSet-RGChannelSet: no visible global function definition
for 'RGChannelSet'
join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function
definition for 'clone'
mask.sites.meth,RnBSet: no visible global function definition for
'samples'
remove.samples,RnBSet: no visible global function definition for
'samples'
remove.samples,RnBeadRawSet: no visible global function definition for
'samples'
remove.samples,RnBeadSet: no visible global function definition for
'samples'
remove.sites,RnBSet: no visible global function definition for
'samples'
sampleCovgApply,RnBSet: no visible global function definition for
'samples'
sampleMethApply,RnBSet: no visible global function definition for
'samples'
summarize.regions,RnBSet: no visible global function definition for
'samples'
summarize.regions,RnBSet: multiple local function definitions for
'aggr.f' with different formal arguments
updateMethylationSites,RnBSet: no visible global function definition
for 'samples'
Undefined global functions or variables:
%dopar% ..count.. ..density.. .inds.g2 Address Age Annotated AvgMeth
BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack
Group Hsapiens ID IG IG<- II II<- IR IR<- IdeogramTrack
IlluminaHumanMethylation450kmanifest
IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity
Measure Mmusculus PairsBootRefFreeEwasModel Predicted Probe
RGChannelSet Rd2HTML RefFreeEwasModel SNP Sample Segment SigSet Slide
Target Term UcscTrack Value addSex as.profileCGH assayDataElement
assayDataElementNames barcode browserSession bv calculateFDRs chrom
clone combinedRank combinedRank.var comma covgMedian covgPercLow
covgPercUp cv.glmnet daglad diffmeth diffmeth.p.adj.fdr
diffmeth.p.val dinucleotideFrequency eps expectedCounts featureData
featureData<- featureNames featureNames<- foreach geneCounts genome<-
getCN getDoParWorkers getGreen getManifest getMeth getRed getSex
getTable getUnmeth getVarCov glmnet grid.draw grid.newpage group
group1 group2 i impute.knn install is.subsegmentation k
letterFrequency lme loadRegionDB log10FDR log10P mapToGenome mclapply
mean.diff mean.quot.log2 melt mergeRegionDBs muted n.sites num.sites
numSites numeric.names oddsRatios oobG oobG<- oobR oobR<-
p.vals.t.na.adj pData 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 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
rnb.execute.pOOBAH 21.29 1.64 23.37
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
rnb.execute.pOOBAH 20.23 0.6 20.83
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 8 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/RnBeads.Rcheck/00check.log'
for details.
RnBeads.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/RnBeads_2.10.0.tar.gz && rm -rf RnBeads.buildbin-libdir && mkdir RnBeads.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.buildbin-libdir RnBeads_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RnBeads_2.10.0.zip && rm RnBeads_2.10.0.tar.gz RnBeads_2.10.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
18 3931k 18 735k 0 0 773k 0 0:00:05 --:--:-- 0:00:05 773k
52 3931k 52 2052k 0 0 1057k 0 0:00:03 0:00:01 0:00:02 1057k
100 3931k 100 3931k 0 0 1405k 0 0:00:02 0:00:02 --:--:-- 1405k
install for i386
* installing *source* package 'RnBeads' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RnBeads'
finding HTML links ... done
BMIQ html
ClusterArchitecture-class html
ClusterArchitectureSGE-class html
ClusterArchitectureSLURM-class html
M-methods html
Report-class html
ReportGgPlot-class html
ReportPlot-class html
RnBClusterRun-class html
RnBDiffMeth-class html
RnBSet-class html
RnBeadClustering-class html
RnBeadRawSet-class html
RnBeadSet-class html
RnBeads html
RnBeads.data html
RnBiseqSet-class html
U-methods html
accepted html
addDiffMethTable-RnBDiffMeth-methods html
addPheno-RnBSet-methods html
addRegionSubsegments html
annotation-methods html
apply.iEVORA html
as.RnBeadRawSet html
assembly-methods html
auto.select.rank.cut html
coercion-methods html
finding level-2 HTML links ... done
cols.to.rank html
combine.diffMeth.objs html
combine.rnb.sets-methods html
combineTestPvalsMeth html
computeDiffTab.region html
computeDiffTab.site html
covg-methods html
create.densityScatter html
create.hex.summary.plot html
create.scatter.dens.points html
createReport html
createReportGgPlot html
createReportPlot html
data.frame2GRanges html
densRanks html
destroy-RnBDiffMeth-methods html
destroy-methods html
deviation.plot.beta html
diffVar html
dim-BigFfMat-method html
downloadLolaDbs html
dpval-methods html
estimateProportionsCP html
exportDMRs2regionFile html
get.adjustment.variables html
get.comparison.grouplabels-RnBDiffMeth-methods
html
get.comparison.groupsizes-RnBDiffMeth-methods
html
get.comparison.info html
get.comparisons-RnBDiffMeth-methods html
get.covariates.ct html
get.covariates.sva html
get.covg.thres-RnBDiffMeth-methods html
get.cpg.stats html
get.files html
get.region.types-RnBDiffMeth-methods html
get.site.test.method-RnBDiffMeth-methods
html
get.table-RnBDiffMeth-methods html
get.table.ids html
get.variability.method-RnBDiffMeth-methods
html
getCellTypesFromLolaDb html
getExecutable-ClusterArchitecture-methods
html
getModuleNumCores-RnBClusterRun-methods
html
getNamesFromLolaDb html
getNumNaMeth-methods html
getSubCmdStr-ClusterArchitecture-methods
html
getSubCmdTokens-ClusterArchitecture-methods
html
getSubCmdTokens-ClusterArchitectureSGE-methods
html
getSubCmdTokens-ClusterArchitectureSLURM-methods
html
getTargetFromLolaDb html
greedycut.filter.matrix html
greedycut.get.statistics html
greedycut.get.submatrix html
has.covariates.ct html
has.covariates.sva html
hasCovg-methods html
includes.sites-RnBDiffMeth-methods html
initialize-ClusterArchitecture-method html
initialize-ClusterArchitectureSGE-method
html
initialize-ClusterArchitectureSLURM-method
html
initialize-RnBClusterRun-method html
initialize-RnBDiffMeth-method html
intensities.by.color html
is.valid-RnBDiffMeth-methods html
isImputed-RnBSet-method html
join.diffMeth-methods html
limmaP html
load.region.subsegment.annotation html
load.rnb.diffmeth html
load.rnb.set html
loadLolaDbs html
logger.argument html
logger.getfiles html
logger.isinitialized html
logger.machine.name html
logger.validate.file html
loggerManagement html
loggerMessages html
lolaBarPlot html
lolaBoxPlotPerTarget html
lolaVolcanoPlot html
lump.hg19 html
lump.hg38 html
mask.sites.meth-methods html
mergeSamples-methods html
meth-methods html
mval-methods html
nsites-methods html
off-methods html
parallel.getNumWorkers html
parallel.isEnabled html
parallel.setup html
parallel.teardown html
performGOEnrichment.diffVar html
performGOenrichment.diffMeth.entrez html
performGoEnrichment.diffMeth html
performLolaEnrichment.diffMeth html
performLolaEnrichment.diffVar html
pheno-methods html
prepareSOFTfileForGEO html
qc-methods html
read.GS.report html
read.bed.files html
read.data.dir html
read.idat.files html
read.idat.files2 html
read.sample.annotation html
read.single.bed html
refFreeEWASP html
regionMapping-methods html
regions-methods html
reload-RnBDiffMeth-methods html
remove.regions-methods html
remove.samples-methods html
remove.sites-methods html
rnb.RnBSet.to.GRangesList html
rnb.RnBSet.to.bed html
rnb.RnBSet.to.bedGraph html
rnb.add.figure html
rnb.add.list html
rnb.add.paragraph html
rnb.add.reference html
rnb.add.section html
rnb.add.table html
rnb.add.tables html
rnb.annotation.size html
rnb.annotation2data.frame html
rnb.bed.from.segmentation html
rnb.beta2mval html
rnb.boxplot.from.segmentation html
rnb.build.index html
rnb.call.destructor html
rnb.color.legends html
rnb.combine.arrays html
rnb.combine.seq html
rnb.execute.age.prediction html
rnb.execute.batch.qc html
rnb.execute.batcheffects html
rnb.execute.clustering html
rnb.execute.clustering.all html
rnb.execute.computeDiffMeth html
rnb.execute.context.removal html
rnb.execute.cross.reactive.removal html
rnb.execute.ct.estimation html
rnb.execute.diffVar html
rnb.execute.dreduction html
rnb.execute.export.csv html
rnb.execute.filter.summary html
rnb.execute.gender.prediction html
rnb.execute.genomewide html
rnb.execute.greedycut html
rnb.execute.high.coverage.removal html
rnb.execute.high.dpval.masking html
rnb.execute.import html
rnb.execute.imputation html
rnb.execute.low.coverage.masking html
rnb.execute.lump html
rnb.execute.na.removal html
rnb.execute.normalization html
rnb.execute.pOOBAH html
rnb.execute.quality html
rnb.execute.segmentation html
rnb.execute.sex.prediction html
rnb.execute.sex.removal html
rnb.execute.snp.removal html
rnb.execute.sva html
rnb.execute.tnt html
rnb.execute.training html
rnb.execute.variability.removal html
rnb.export.all.annotation html
rnb.export.annotation html
rnb.export.to.ewasher html
rnb.export.to.trackhub html
rnb.find.relative.site.coord html
rnb.get.annotation html
rnb.get.assemblies html
rnb.get.chromosomes html
rnb.get.directory html
rnb.get.mapping html
rnb.get.reference html
rnb.get.reliability.matrix html
rnb.infinium.control.targets html
rnb.initialize.reports html
rnb.is.option html
rnb.load.annotation html
rnb.load.annotation.from.db html
rnb.load.sitelist html
rnb.message.plot html
rnb.mval2beta html
rnb.options html
rnb.options2xml html
rnb.performance.profile html
rnb.plot.beta.comparison html
rnb.plot.betadistribution.probeCategories
html
rnb.plot.betadistribution.sampleGroups
html
rnb.plot.biseq.coverage html
rnb.plot.biseq.coverage.hist html
rnb.plot.biseq.coverage.violin html
rnb.plot.control.barplot html
rnb.plot.control.boxplot html
rnb.plot.coverage.thresholds html
rnb.plot.ct.heatmap html
rnb.plot.dreduction html
rnb.plot.locus.profile html
rnb.plot.marker.fstat html
rnb.plot.negative.boxplot html
rnb.plot.num.sites.covg html
rnb.plot.pheno.categories html
rnb.plot.region.profile.density html
rnb.plot.region.profiles html
rnb.plot.region.site.density html
rnb.plot.sentrix.distribution html
rnb.plot.sentrix.distributions html
rnb.plot.snp.barplot html
rnb.plot.snp.boxplot html
rnb.plot.snp.heatmap html
rnb.read.geo html
rnb.region.types html
rnb.region.types.for.analysis html
rnb.remove.annotation html
rnb.run.analysis html
rnb.run.dj html
rnb.run.example html
rnb.run.xml html
rnb.runs html
rnb.sample.groups html
rnb.sample.replicates html
rnb.sample.summary.table html
rnb.save.annotation html
rnb.section.diffVar.region html
rnb.set.annotation html
rnb.set.annotation.and.cpg.stats html
rnb.show.report html
rnb.step.betadistribution html
rnb.step.cnv html
rnb.write.table html
rnb.xml2options html
rowOneSampleTP html
rowPairedTP html
rowWelchP html
run-RnBClusterRun-methods html
run.cross.validation html
sampleCovgApply-methods html
sampleMethApply-methods html
samples-methods html
save.rnb.diffmeth html
save.rnb.set html
save.tables-RnBDiffMeth-methods html
set.covariates.ct html
set.covariates.sva html
setExecutable-ClusterArchitecture-methods
html
setModuleNumCores-RnBClusterRun-methods
html
setModuleResourceRequirements-RnBClusterRun-methods
html
sites-methods html
sub-BigFfMat-ANY-ANY-ANY-method html
subset-BigFfMat-ANY-ANY-ANY-method html
summarize.regions-methods html
summarized.regions-methods html
updateMethylationSites-methods html
updateRegionSummaries html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'RnBeads' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RnBeads' as RnBeads_2.10.0.zip
* DONE (RnBeads)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'RnBeads' successfully unpacked and MD5 sums checked
|
RnBeads.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("RnBeads")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpO2GZFH/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")==37570478.08 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==1878523904 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Attaching package: 'grid'
The following object is masked from 'package:ff':
pattern
Spam version 2.7-0 (2021-06-25) 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
See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'scales'
The following object is masked from 'package:viridis':
viridis_pal
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Attaching package: 'MatrixGenerics'
The following object is masked from 'package:Biobase':
rowMedians
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following objects are masked from 'package:ff':
mismatch, pattern
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
2021-10-15 04:54:54 0.4 STATUS STARTED Unit testing: differential
2021-10-15 04:54:54 0.4 STATUS STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2021-10-15 04:54:54 0.5 STATUS COMPLETED Testing function: rowWelchP
2021-10-15 04:54:54 0.5 STATUS STARTED Testing function: limmaP
2021-10-15 04:54:54 0.5 STATUS COMPLETED Testing function: limmaP
2021-10-15 04:54:54 0.5 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-10-15 04:54:55 0.5 INFO Conducting differential analysis using limma
2021-10-15 04:54:55 0.4 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-10-15 04:54:55 0.4 STATUS STARTED Testing function: computeDiffTab.default.region
2021-10-15 04:54:55 0.4 INFO Conducting differential analysis using limma
2021-10-15 04:55:03 0.7 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-10-15 04:55:03 0.7 STATUS STARTED Testing function: combineTestPvalsMeth
2021-10-15 04:55:03 0.7 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-10-15 04:55:03 0.7 STATUS STARTED Testing function: get.adjustment.variables
2021-10-15 04:55:04 0.7 STATUS COMPLETED Testing function: get.adjustment.variables
2021-10-15 04:55:04 0.7 STATUS STARTED Testing function: get.comparison.info
2021-10-15 04:55:04 0.7 STATUS COMPLETED Testing function: get.comparison.info
2021-10-15 04:55:04 0.7 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-10-15 04:55:04 0.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:55:04 0.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:55:04 0.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:55:04 0.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:55:04 0.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:55:04 0.7 INFO Conducting differential analysis using limma
2021-10-15 04:55:04 0.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:55:04 0.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:55:05 0.7 STATUS Computed table for tiling
2021-10-15 04:55:05 0.8 STATUS Computed table for genes
2021-10-15 04:55:05 0.8 STATUS Computed table for promoters
2021-10-15 04:55:05 0.8 STATUS Computed table for cpgislands
2021-10-15 04:55:05 0.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:55:06 0.8 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:55:06 0.8 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:55:06 0.8 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:55:06 0.8 INFO Conducting differential analysis using limma
2021-10-15 04:55:06 0.8 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:55:06 0.8 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:55:06 0.8 STATUS Computed table for tiling
2021-10-15 04:55:06 0.8 STATUS Computed table for genes
2021-10-15 04:55:07 0.8 STATUS Computed table for promoters
2021-10-15 04:55:07 0.8 STATUS Computed table for cpgislands
2021-10-15 04:55:07 0.8 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:55:07 0.8 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:55:07 0.8 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:55:07 0.8 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-10-15 04:55:07 0.8 STATUS STARTED Testing function: diffVar
2021-10-15 04:55:08 0.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:56:06 2.8 STATUS COMPLETED diffVar method
2021-10-15 04:56:06 2.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:56:06 2.8 WARNING Could not compute p-values with diffVar, returning NA
2021-10-15 04:56:06 2.8 INFO diffVar from missMethyl package not properly running
2021-10-15 04:56:06 2.8 STATUS COMPLETED diffVar method
2021-10-15 04:56:06 2.8 STATUS STARTED Testing function: apply.iEVORA
2021-10-15 04:56:07 2.8 STATUS STARTED iEVORA method
2021-10-15 04:56:08 2.9 INFO No DVCs detected. All p-values set to 1.
2021-10-15 04:56:08 2.9 STATUS COMPLETED iEVORA method
2021-10-15 04:56:08 2.9 STATUS STARTED Testing function: rnb.execute.diffVar
2021-10-15 04:56:08 2.9 STATUS STARTED Differential Variability
2021-10-15 04:56:08 2.9 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:08 2.9 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:08 2.9 INFO No imputation method selected, 'knn' method used.
2021-10-15 04:56:08 2.9 STATUS STARTED Imputation procedure knn
2021-10-15 04:56:09 2.9 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:56:09 2.9 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:09 2.9 INFO Conducting differential variability using diffVar
2021-10-15 04:56:09 2.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:56:09 2.9 STATUS COMPLETED diffVar method
2021-10-15 04:56:09 2.9 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 04:56:11 2.6 STATUS Computed table for tiling
2021-10-15 04:56:11 2.6 STATUS Computed table for genes
2021-10-15 04:56:11 2.6 STATUS Computed table for promoters
2021-10-15 04:56:12 2.6 STATUS Computed table for cpgislands
2021-10-15 04:56:12 2.6 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 04:56:12 2.6 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:12 2.6 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:12 2.6 INFO Conducting differential variability using diffVar
2021-10-15 04:56:12 2.6 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:56:12 2.7 STATUS COMPLETED diffVar method
2021-10-15 04:56:12 2.7 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 04:56:13 2.6 STATUS Computed table for tiling
2021-10-15 04:56:14 2.6 STATUS Computed table for genes
2021-10-15 04:56:14 2.7 STATUS Computed table for promoters
2021-10-15 04:56:14 2.7 STATUS Computed table for cpgislands
2021-10-15 04:56:14 2.7 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 04:56:14 2.7 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:14 2.7 STATUS COMPLETED Differential Variability
2021-10-15 04:56:14 2.7 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-10-15 04:56:15 2.7 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 04:56:15 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:15 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:15 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:15 2.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:15 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:15 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:15 2.7 STATUS STARTED Imputation procedure knn
2021-10-15 04:56:15 2.7 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:56:15 2.7 INFO Conducting differential variability using diffVar
2021-10-15 04:56:16 2.7 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:56:16 2.7 STATUS COMPLETED diffVar method
2021-10-15 04:56:16 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:16 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:17 2.6 STATUS Computed table for tiling
2021-10-15 04:56:18 2.7 STATUS Computed table for genes
2021-10-15 04:56:18 2.7 STATUS Computed table for promoters
2021-10-15 04:56:19 2.6 STATUS Computed table for cpgislands
2021-10-15 04:56:19 2.6 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:19 2.6 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:19 2.6 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:19 2.6 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:19 2.6 INFO Conducting differential analysis using limma
2021-10-15 04:56:20 2.6 STATUS STARTED Imputation procedure knn
2021-10-15 04:56:20 2.6 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:56:20 2.6 INFO Conducting differential variability using diffVar
2021-10-15 04:56:20 2.6 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:56:20 2.7 STATUS COMPLETED diffVar method
2021-10-15 04:56:20 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:20 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:22 2.6 STATUS Computed table for tiling
2021-10-15 04:56:22 2.7 STATUS Computed table for genes
2021-10-15 04:56:22 2.7 STATUS Computed table for promoters
2021-10-15 04:56:23 2.7 STATUS Computed table for cpgislands
2021-10-15 04:56:23 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:23 2.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:23 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:23 2.7 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 04:56:23 2.7 STATUS STARTED Testing class: RnBDiffMeth
2021-10-15 04:56:23 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:23 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:24 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:24 2.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:24 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:24 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:24 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:24 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:25 2.7 STATUS Computed table for tiling
2021-10-15 04:56:25 2.7 STATUS Computed table for genes
2021-10-15 04:56:26 2.7 STATUS Computed table for promoters
2021-10-15 04:56:26 2.6 STATUS Computed table for cpgislands
2021-10-15 04:56:27 2.6 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:28 2.6 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:28 2.6 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:28 2.6 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:28 2.6 INFO Conducting differential analysis using limma
2021-10-15 04:56:28 2.6 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:29 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:29 2.7 STATUS Computed table for tiling
2021-10-15 04:56:29 2.7 STATUS Computed table for genes
2021-10-15 04:56:30 2.7 STATUS Computed table for promoters
2021-10-15 04:56:31 2.6 STATUS Computed table for cpgislands
2021-10-15 04:56:31 2.6 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:31 2.6 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:31 2.6 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:31 2.6 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:31 2.6 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:31 2.6 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:31 2.6 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:31 2.6 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:32 2.6 INFO Conducting differential analysis using limma
2021-10-15 04:56:32 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:32 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:32 2.7 STATUS Computed table for genes
2021-10-15 04:56:33 2.7 STATUS Computed table for tiling
2021-10-15 04:56:33 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:33 2.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:33 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:33 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:33 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:33 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:33 2.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:33 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:33 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:33 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:34 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:35 2.6 STATUS Computed table for genes
2021-10-15 04:56:35 2.7 STATUS Computed table for tiling
2021-10-15 04:56:35 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:35 2.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:35 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:35 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:36 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:36 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:36 2.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:36 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:36 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:36 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:36 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:36 2.7 STATUS Computed table for promoters
2021-10-15 04:56:37 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:37 2.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:37 2.7 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:37 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:37 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:37 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:37 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:37 2.7 STATUS Computed table for promoters
2021-10-15 04:56:38 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:38 2.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:38 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:38 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:38 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:38 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:38 2.7 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:38 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:38 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:38 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:38 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:39 2.7 STATUS Computed table for genes
2021-10-15 04:56:40 2.7 STATUS Computed table for tiling
2021-10-15 04:56:40 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:40 2.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:40 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:40 2.7 STATUS STARTED Testing function: get.region.types
2021-10-15 04:56:40 2.7 STATUS COMPLETED Testing function: get.region.types
2021-10-15 04:56:40 2.7 STATUS STARTED Testing function: get.comparisons
2021-10-15 04:56:40 2.7 STATUS COMPLETED Testing function: get.comparisons
2021-10-15 04:56:41 2.7 STATUS STARTED Testing function: get.comparison.grouplabels
2021-10-15 04:56:41 2.7 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-10-15 04:56:41 2.7 STATUS STARTED Testing function: get.site.test.method
2021-10-15 04:56:41 2.7 STATUS COMPLETED Testing function: get.site.test.method
2021-10-15 04:56:41 2.7 STATUS STARTED Testing function: get.table
2021-10-15 04:56:41 2.7 STATUS COMPLETED Testing function: get.table
2021-10-15 04:56:41 2.7 STATUS STARTED Testing function: addDiffMethTable
2021-10-15 04:56:41 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:41 2.7 STATUS COMPLETED Testing function: addDiffMethTable
2021-10-15 04:56:42 2.7 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-10-15 04:56:42 2.7 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-10-15 04:56:42 2.7 STATUS STARTED Destructor
2021-10-15 04:56:42 2.7 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:42 2.7 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:42 2.7 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:42 2.7 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:42 2.7 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:42 2.7 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:42 2.7 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:43 2.7 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:56:43 2.7 STATUS COMPLETED Destructor
2021-10-15 04:56:43 2.7 STATUS COMPLETED Testing class: RnBDiffMeth
2021-10-15 04:56:43 2.7 STATUS COMPLETED Testing function: apply.iEVORA
2021-10-15 04:56:44 2.6 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:44 2.6 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:44 2.6 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:44 2.6 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:44 2.6 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:44 2.6 INFO Conducting differential analysis using limma
2021-10-15 04:56:44 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:44 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:45 2.7 STATUS Computed table for tiling
2021-10-15 04:56:45 2.7 STATUS Computed table for genes
2021-10-15 04:56:45 2.7 STATUS Computed table for promoters
2021-10-15 04:56:46 2.6 STATUS Computed table for cpgislands
2021-10-15 04:56:46 2.6 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:46 2.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:46 2.7 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:46 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:46 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:47 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:47 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:47 2.7 STATUS Computed table for tiling
2021-10-15 04:56:47 2.7 STATUS Computed table for genes
2021-10-15 04:56:48 2.7 STATUS Computed table for promoters
2021-10-15 04:56:48 2.7 STATUS Computed table for cpgislands
2021-10-15 04:56:48 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:49 2.7 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:49 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:49 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:49 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:49 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:49 2.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:49 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:49 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:49 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:49 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:50 2.7 STATUS Computed table for genes
2021-10-15 04:56:50 2.7 STATUS Computed table for tiling
2021-10-15 04:56:50 2.7 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:52 2.7 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:52 2.7 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:52 2.7 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:52 2.7 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:53 2.7 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:53 2.7 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:53 2.7 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:53 2.7 INFO Conducting differential analysis using limma
2021-10-15 04:56:53 2.7 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:53 2.7 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:57 2.0 STATUS Computed table for genes
2021-10-15 04:56:57 2.0 STATUS Computed table for tiling
2021-10-15 04:56:57 2.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:57 2.0 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:57 2.0 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:56:57 2.0 STATUS STARTED Retrieving comparison info
2021-10-15 04:56:58 2.0 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:56:58 2.0 STATUS STARTED Computing differential methylation tables
2021-10-15 04:56:58 2.0 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:58 2.0 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:58 2.0 INFO Conducting differential analysis using limma
2021-10-15 04:56:58 2.0 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:58 2.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:58 2.0 STATUS Computed table for promoters
2021-10-15 04:56:58 2.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:56:58 2.0 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:56:59 2.0 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:56:59 2.0 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:56:59 2.0 INFO Conducting differential analysis using limma
2021-10-15 04:56:59 2.0 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:56:59 2.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:00 2.0 STATUS Computed table for promoters
2021-10-15 04:57:00 2.0 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:00 2.0 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:00 2.0 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:00 2.0 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:00 2.0 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:00 2.0 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:00 2.0 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:00 2.0 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:00 2.0 INFO Conducting differential analysis using limma
2021-10-15 04:57:01 2.0 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:01 2.0 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:01 2.1 STATUS Computed table for genes
2021-10-15 04:57:02 2.2 STATUS Computed table for tiling
2021-10-15 04:57:03 2.2 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:03 2.2 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:03 2.2 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:03 2.2 STATUS STARTED Testing function: get.region.types
2021-10-15 04:57:03 2.2 STATUS COMPLETED Testing function: get.region.types
2021-10-15 04:57:03 2.2 STATUS STARTED Testing function: get.comparisons
2021-10-15 04:57:03 2.2 STATUS COMPLETED Testing function: get.comparisons
2021-10-15 04:57:03 2.2 STATUS STARTED Testing function: get.comparison.grouplabels
2021-10-15 04:57:03 2.2 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-10-15 04:57:03 2.2 STATUS STARTED Testing function: get.site.test.method
2021-10-15 04:57:03 2.2 STATUS COMPLETED Testing function: get.site.test.method
2021-10-15 04:57:04 2.2 STATUS STARTED Testing function: get.table
2021-10-15 04:57:04 2.2 STATUS COMPLETED Testing function: get.table
2021-10-15 04:57:04 2.2 STATUS STARTED Testing function: addDiffMethTable
2021-10-15 04:57:04 2.2 INFO Conducting differential analysis using limma
2021-10-15 04:57:05 2.2 STATUS COMPLETED Testing function: addDiffMethTable
2021-10-15 04:57:05 2.2 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-10-15 04:57:05 2.2 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-10-15 04:57:05 2.2 STATUS STARTED Destructor
2021-10-15 04:57:05 2.2 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:05 2.2 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:05 2.2 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:05 2.2 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:05 2.2 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:06 2.2 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:06 2.2 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:06 2.2 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:06 2.2 STATUS COMPLETED Destructor
2021-10-15 04:57:06 2.2 INFO Conducting differential analysis using limma
2021-10-15 04:57:07 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:07 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:07 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:08 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:08 2.3 WARNING Could not compute p-values with diffVar, returning NA
2021-10-15 04:57:08 2.3 INFO diffVar from missMethyl package not properly running
2021-10-15 04:57:08 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:08 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:09 2.3 STATUS STARTED Unit testing: differential
2021-10-15 04:57:09 2.3 STATUS STARTED Testing function: rowWelchP
2021-10-15 04:57:09 2.3 STATUS COMPLETED Testing function: rowWelchP
2021-10-15 04:57:09 2.3 STATUS STARTED Testing function: limmaP
2021-10-15 04:57:09 2.3 STATUS COMPLETED Testing function: limmaP
2021-10-15 04:57:09 2.3 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-10-15 04:57:10 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:10 2.3 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-10-15 04:57:10 2.3 STATUS STARTED Testing function: computeDiffTab.default.region
2021-10-15 04:57:10 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:11 2.4 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-10-15 04:57:11 2.4 STATUS STARTED Testing function: combineTestPvalsMeth
2021-10-15 04:57:11 2.4 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-10-15 04:57:11 2.4 STATUS STARTED Testing function: get.adjustment.variables
2021-10-15 04:57:12 2.4 STATUS COMPLETED Testing function: get.adjustment.variables
2021-10-15 04:57:12 2.4 STATUS STARTED Testing function: get.comparison.info
2021-10-15 04:57:12 2.4 STATUS COMPLETED Testing function: get.comparison.info
2021-10-15 04:57:12 2.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-10-15 04:57:12 2.4 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:12 2.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:12 2.4 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:13 2.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:13 2.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:13 2.4 INFO Conducting differential analysis using limma
2021-10-15 04:57:13 2.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:13 2.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:14 2.3 STATUS Computed table for tiling
2021-10-15 04:57:14 2.3 STATUS Computed table for genes
2021-10-15 04:57:15 2.3 STATUS Computed table for promoters
2021-10-15 04:57:15 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:15 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:15 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:15 2.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:15 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:16 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:16 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:16 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:16 2.3 STATUS Computed table for tiling
2021-10-15 04:57:17 2.3 STATUS Computed table for genes
2021-10-15 04:57:17 2.3 STATUS Computed table for promoters
2021-10-15 04:57:17 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:17 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:17 2.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:18 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:18 2.3 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-10-15 04:57:18 2.3 STATUS STARTED Testing function: diffVar
2021-10-15 04:57:18 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:18 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:18 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:18 2.3 WARNING Could not compute p-values with diffVar, returning NA
2021-10-15 04:57:18 2.3 INFO diffVar from missMethyl package not properly running
2021-10-15 04:57:19 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:19 2.3 STATUS STARTED Testing function: apply.iEVORA
2021-10-15 04:57:19 2.3 STATUS STARTED iEVORA method
2021-10-15 04:57:20 2.3 INFO No DVCs detected. All p-values set to 1.
2021-10-15 04:57:20 2.3 STATUS COMPLETED iEVORA method
2021-10-15 04:57:20 2.3 STATUS STARTED Testing function: rnb.execute.diffVar
2021-10-15 04:57:20 2.3 STATUS STARTED Differential Variability
2021-10-15 04:57:21 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:21 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:21 2.3 STATUS STARTED Imputation procedure knn
2021-10-15 04:57:21 2.3 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:57:21 2.3 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:21 2.3 INFO Conducting differential variability using diffVar
2021-10-15 04:57:21 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:21 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:21 2.3 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 04:57:22 2.3 STATUS Computed table for tiling
2021-10-15 04:57:22 2.3 STATUS Computed table for genes
2021-10-15 04:57:22 2.3 STATUS Computed table for promoters
2021-10-15 04:57:23 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:23 2.3 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 04:57:23 2.3 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:23 2.3 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:23 2.3 INFO Conducting differential variability using diffVar
2021-10-15 04:57:23 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:23 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:23 2.3 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 04:57:24 2.3 STATUS Computed table for tiling
2021-10-15 04:57:24 2.3 STATUS Computed table for genes
2021-10-15 04:57:24 2.3 STATUS Computed table for promoters
2021-10-15 04:57:24 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:25 2.3 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 04:57:25 2.3 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:25 2.3 STATUS COMPLETED Differential Variability
2021-10-15 04:57:25 2.3 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-10-15 04:57:25 2.3 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 04:57:25 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:25 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:25 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:25 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:26 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:26 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:26 2.4 STATUS STARTED Imputation procedure knn
2021-10-15 04:57:26 2.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:57:26 2.4 INFO Conducting differential variability using diffVar
2021-10-15 04:57:26 2.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:26 2.4 STATUS COMPLETED diffVar method
2021-10-15 04:57:26 2.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:27 2.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:28 2.3 STATUS Computed table for tiling
2021-10-15 04:57:28 2.3 STATUS Computed table for genes
2021-10-15 04:57:29 2.3 STATUS Computed table for promoters
2021-10-15 04:57:29 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:29 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:29 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:29 2.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:29 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:29 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:30 2.3 STATUS STARTED Imputation procedure knn
2021-10-15 04:57:30 2.3 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:57:30 2.3 INFO Conducting differential variability using diffVar
2021-10-15 04:57:30 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:30 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:30 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:30 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:31 2.3 STATUS Computed table for tiling
2021-10-15 04:57:31 2.4 STATUS Computed table for genes
2021-10-15 04:57:32 2.4 STATUS Computed table for promoters
2021-10-15 04:57:33 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:33 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:33 2.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:33 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:33 2.3 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 04:57:33 2.3 STATUS STARTED Testing class: RnBDiffMeth
2021-10-15 04:57:33 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:33 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:33 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:34 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:34 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:34 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:34 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:34 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:34 2.3 STATUS Computed table for tiling
2021-10-15 04:57:35 2.3 STATUS Computed table for genes
2021-10-15 04:57:35 2.3 STATUS Computed table for promoters
2021-10-15 04:57:35 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:35 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:36 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:36 2.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:36 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:36 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:36 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:36 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:36 2.3 STATUS Computed table for tiling
2021-10-15 04:57:37 2.3 STATUS Computed table for genes
2021-10-15 04:57:37 2.3 STATUS Computed table for promoters
2021-10-15 04:57:37 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:37 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:38 2.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:38 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:38 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:38 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:38 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:38 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:38 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:38 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:38 2.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:38 2.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:39 2.3 STATUS Computed table for genes
2021-10-15 04:57:40 2.3 STATUS Computed table for tiling
2021-10-15 04:57:40 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:40 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:40 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:40 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:40 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:40 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:40 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:40 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:41 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:41 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:41 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:41 2.3 STATUS Computed table for genes
2021-10-15 04:57:41 2.3 STATUS Computed table for tiling
2021-10-15 04:57:42 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:42 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:42 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:42 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:42 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:42 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:43 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:43 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:43 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:43 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:43 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:43 2.3 STATUS Computed table for promoters
2021-10-15 04:57:44 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:44 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:44 2.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:44 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:44 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:44 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:44 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:45 2.3 STATUS Computed table for promoters
2021-10-15 04:57:45 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:45 2.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:45 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:45 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:45 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:45 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:45 2.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:46 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:46 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:46 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:46 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:46 2.4 STATUS Computed table for genes
2021-10-15 04:57:47 2.4 STATUS Computed table for tiling
2021-10-15 04:57:47 2.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:47 2.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:47 2.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:47 2.4 STATUS STARTED Testing function: get.region.types
2021-10-15 04:57:47 2.4 STATUS COMPLETED Testing function: get.region.types
2021-10-15 04:57:47 2.4 STATUS STARTED Testing function: get.comparisons
2021-10-15 04:57:47 2.4 STATUS COMPLETED Testing function: get.comparisons
2021-10-15 04:57:47 2.4 STATUS STARTED Testing function: get.comparison.grouplabels
2021-10-15 04:57:47 2.4 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-10-15 04:57:48 2.4 STATUS STARTED Testing function: get.site.test.method
2021-10-15 04:57:48 2.4 STATUS COMPLETED Testing function: get.site.test.method
2021-10-15 04:57:48 2.4 STATUS STARTED Testing function: get.table
2021-10-15 04:57:48 2.4 STATUS COMPLETED Testing function: get.table
2021-10-15 04:57:48 2.4 STATUS STARTED Testing function: addDiffMethTable
2021-10-15 04:57:48 2.4 INFO Conducting differential analysis using limma
2021-10-15 04:57:48 2.4 STATUS COMPLETED Testing function: addDiffMethTable
2021-10-15 04:57:48 2.4 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-10-15 04:57:49 2.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-10-15 04:57:49 2.4 STATUS STARTED Destructor
2021-10-15 04:57:49 2.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:49 2.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 04:57:50 2.4 STATUS COMPLETED Destructor
2021-10-15 04:57:50 2.4 STATUS COMPLETED Testing class: RnBDiffMeth
2021-10-15 04:57:50 2.4 STATUS COMPLETED Testing function: apply.iEVORA
2021-10-15 04:57:50 2.4 STATUS STARTED iEVORA method
2021-10-15 04:57:52 2.3 INFO No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2
2021-10-15 04:57:52 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:52 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:52 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:52 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:52 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:52 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:53 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:53 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:53 2.3 STATUS Computed table for tiling
2021-10-15 04:57:53 2.3 STATUS Computed table for genes
2021-10-15 04:57:54 2.3 STATUS Computed table for promoters
2021-10-15 04:57:54 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:54 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:54 2.3 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:54 2.3 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:55 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:55 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:55 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:55 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:55 2.3 STATUS Computed table for tiling
2021-10-15 04:57:56 2.4 STATUS Computed table for genes
2021-10-15 04:57:56 2.4 STATUS Computed table for promoters
2021-10-15 04:57:57 2.3 STATUS Computed table for cpgislands
2021-10-15 04:57:57 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:57 2.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:57:57 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:57:57 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:57:57 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:57:57 2.3 STATUS STARTED Computing differential methylation tables
2021-10-15 04:57:58 2.3 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:57:58 2.3 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:57:58 2.3 INFO Conducting differential analysis using limma
2021-10-15 04:57:58 2.3 STATUS STARTED Imputation procedure knn
2021-10-15 04:57:58 2.3 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:57:58 2.3 INFO Conducting differential variability using diffVar
2021-10-15 04:57:58 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:57:58 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:57:58 2.3 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:57:59 2.3 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:57:59 2.3 STATUS Computed table for tiling
2021-10-15 04:58:00 2.3 STATUS Computed table for genes
2021-10-15 04:58:00 2.3 STATUS Computed table for promoters
2021-10-15 04:58:00 2.4 STATUS Computed table for cpgislands
2021-10-15 04:58:00 2.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:58:01 2.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:58:01 2.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:58:01 2.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:58:01 2.4 INFO Conducting differential analysis using limma
2021-10-15 04:58:01 2.4 STATUS STARTED Imputation procedure knn
2021-10-15 04:58:01 2.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:58:01 2.4 INFO Conducting differential variability using diffVar
2021-10-15 04:58:01 2.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:58:02 2.4 STATUS COMPLETED diffVar method
2021-10-15 04:58:02 2.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:58:02 2.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:58:03 2.3 STATUS Computed table for tiling
2021-10-15 04:58:04 2.3 STATUS Computed table for genes
2021-10-15 04:58:04 2.3 STATUS Computed table for promoters
2021-10-15 04:58:04 2.3 STATUS Computed table for cpgislands
2021-10-15 04:58:04 2.3 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:58:05 2.3 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:58:05 2.3 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:58:05 2.3 STATUS STARTED Differential Variability
2021-10-15 04:58:05 2.3 STATUS STARTED Retrieving comparison info
2021-10-15 04:58:05 2.3 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:58:05 2.3 STATUS STARTED Imputation procedure knn
2021-10-15 04:58:05 2.3 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:58:05 2.3 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:58:06 2.3 INFO Conducting differential variability using diffVar
2021-10-15 04:58:06 2.3 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:58:06 2.3 STATUS COMPLETED diffVar method
2021-10-15 04:58:06 2.3 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 04:58:06 2.3 STATUS Computed table for tiling
2021-10-15 04:58:07 2.4 STATUS Computed table for genes
2021-10-15 04:58:07 2.4 STATUS Computed table for promoters
2021-10-15 04:58:07 2.4 STATUS Computed table for cpgislands
2021-10-15 04:58:07 2.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 04:58:07 2.4 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:58:07 2.4 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 04:58:08 2.4 INFO Conducting differential variability using diffVar
2021-10-15 04:58:08 2.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 04:58:08 2.4 STATUS COMPLETED diffVar method
2021-10-15 04:58:08 2.4 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 04:58:09 2.4 STATUS Computed table for tiling
2021-10-15 04:58:09 2.4 STATUS Computed table for genes
2021-10-15 04:58:10 2.3 STATUS Computed table for promoters
2021-10-15 04:58:10 2.3 STATUS Computed table for cpgislands
2021-10-15 04:58:10 2.3 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 04:58:10 2.3 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 04:58:10 2.3 STATUS COMPLETED Differential Variability
2021-10-15 04:58:10 2.3 STATUS STARTED Analysis
2021-10-15 04:58:10 2.3 INFO Loaded information from data.RData
2021-10-15 04:58:11 2.3 STATUS STARTED Processing Detection P-values
2021-10-15 04:58:11 2.3 INFO Removed 3979 probes that overlap with SNPs
2021-10-15 04:58:11 2.3 INFO Completed Greedycut on 510 samples
2021-10-15 04:58:11 2.3 STATUS COMPLETED Processing Detection P-values
2021-10-15 04:58:11 2.3 WARNING File not found: data2.RData
2021-10-15 04:58:11 2.3 STATUS COMPLETED Analysis
2021-10-15 04:58:11 2.3 STATUS STARTED Testing imputation
2021-10-15 04:58:11 2.3 STATUS STARTED Imputation procedure knn
2021-10-15 04:58:12 2.3 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:58:12 2.3 STATUS STARTED Imputation procedure mean.samples
2021-10-15 04:58:13 2.3 STATUS COMPLETED Imputation procedure mean.samples
2021-10-15 04:58:13 2.3 STATUS STARTED Imputation procedure mean.cpgs
2021-10-15 04:58:13 2.4 STATUS COMPLETED Imputation procedure mean.cpgs
2021-10-15 04:58:13 2.4 STATUS STARTED Imputation procedure random
2021-10-15 04:58:14 2.4 STATUS COMPLETED Imputation procedure random
2021-10-15 04:58:14 2.4 STATUS COMPLETED Testing imputation
2021-10-15 04:58:14 2.4 STATUS STARTED Testing age prediction
2021-10-15 04:58:14 2.4 STATUS STARTED Performing Age Prediction
2021-10-15 04:58:18 2.5 STATUS COMPLETED Performing Age Prediction
2021-10-15 04:58:18 2.5 STATUS COMPLETED Testing age prediction
2021-10-15 04:58:18 2.5 STATUS STARTED Performing Age Prediction
2021-10-15 04:58:22 2.4 STATUS COMPLETED Performing Age Prediction
2021-10-15 04:58:23 2.5 STATUS STARTED Imputation procedure knn
2021-10-15 04:58:23 2.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:58:23 2.5 STATUS STARTED Imputation procedure mean.samples
2021-10-15 04:58:24 2.5 STATUS COMPLETED Imputation procedure mean.samples
2021-10-15 04:58:24 2.5 STATUS STARTED Imputation procedure mean.cpgs
2021-10-15 04:58:24 2.5 STATUS COMPLETED Imputation procedure mean.cpgs
2021-10-15 04:58:24 2.5 STATUS STARTED Imputation procedure random
2021-10-15 04:58:26 2.4 STATUS COMPLETED Imputation procedure random
2021-10-15 04:58:26 2.4 STATUS STARTED Testing imputation
2021-10-15 04:58:26 2.4 STATUS STARTED Imputation procedure knn
2021-10-15 04:58:26 2.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 04:58:26 2.4 STATUS STARTED Imputation procedure mean.samples
2021-10-15 04:58:27 2.4 STATUS COMPLETED Imputation procedure mean.samples
2021-10-15 04:58:27 2.4 STATUS STARTED Imputation procedure mean.cpgs
2021-10-15 04:58:28 2.4 STATUS COMPLETED Imputation procedure mean.cpgs
2021-10-15 04:58:28 2.4 STATUS STARTED Imputation procedure random
2021-10-15 04:58:28 2.4 STATUS COMPLETED Imputation procedure random
2021-10-15 04:58:28 2.4 STATUS COMPLETED Testing imputation
2021-10-15 04:58:28 2.4 STATUS STARTED Testing age prediction
2021-10-15 04:58:29 2.4 STATUS STARTED Performing Age Prediction
2021-10-15 04:58:32 2.6 STATUS COMPLETED Performing Age Prediction
2021-10-15 04:58:32 2.6 STATUS COMPLETED Testing age prediction
RUNIT TEST PROTOCOL -- Fri Oct 15 04:58:56 2021
***********************************************
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 25 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
215.15 16.92 257.48
|
RnBeads.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> BiocGenerics:::testPackage("RnBeads")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'bit'
The following object is masked from 'package:base':
xor
Attaching package ff
- getOption("fftempdir")=="C:/Users/biocbuild/bbs-3.13-bioc/tmpdir/RtmpQ3oZel/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")==685831618.56 -- consider a different value for tuning your system
- getOption("ffmaxbytes")==34291580928 -- consider a different value for tuning your system
Attaching package: 'ff'
The following objects are masked from 'package:utils':
write.csv, write.csv2
The following objects are masked from 'package:base':
is.factor, is.ordered
Attaching package: 'grid'
The following object is masked from 'package:ff':
pattern
Spam version 2.7-0 (2021-06-25) 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
See https://github.com/NCAR/Fields for
an extensive vignette, other supplements and source code
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Attaching package: 'gridExtra'
The following object is masked from 'package:BiocGenerics':
combine
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'scales'
The following object is masked from 'package:viridis':
viridis_pal
Attaching package: 'AnnotationDbi'
The following object is masked from 'package:MASS':
select
Attaching package: 'MatrixGenerics'
The following object is masked from 'package:Biobase':
rowMedians
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following objects are masked from 'package:ff':
mismatch, pattern
The following object is masked from 'package:base':
strsplit
locfit 1.5-9.4 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:matrixStats':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
2021-10-15 04:59:14 0.7 STATUS STARTED Unit testing: differential
2021-10-15 04:59:14 0.7 STATUS STARTED Testing function: rowWelchP
Loading required package: RnBeads.hg19
2021-10-15 04:59:14 0.8 STATUS COMPLETED Testing function: rowWelchP
2021-10-15 04:59:14 0.8 STATUS STARTED Testing function: limmaP
2021-10-15 04:59:14 0.8 STATUS COMPLETED Testing function: limmaP
2021-10-15 04:59:14 0.8 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-10-15 04:59:14 0.8 INFO Conducting differential analysis using limma
2021-10-15 04:59:14 0.8 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-10-15 04:59:14 0.8 STATUS STARTED Testing function: computeDiffTab.default.region
2021-10-15 04:59:14 0.8 INFO Conducting differential analysis using limma
2021-10-15 04:59:22 1.1 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-10-15 04:59:22 1.1 STATUS STARTED Testing function: combineTestPvalsMeth
2021-10-15 04:59:22 1.1 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-10-15 04:59:22 1.1 STATUS STARTED Testing function: get.adjustment.variables
2021-10-15 04:59:22 1.1 STATUS COMPLETED Testing function: get.adjustment.variables
2021-10-15 04:59:22 1.1 STATUS STARTED Testing function: get.comparison.info
2021-10-15 04:59:23 1.1 STATUS COMPLETED Testing function: get.comparison.info
2021-10-15 04:59:23 1.1 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-10-15 04:59:23 1.1 STATUS STARTED Retrieving comparison info
2021-10-15 04:59:23 1.1 STATUS COMPLETED Retrieving comparison info
2021-10-15 04:59:23 1.1 STATUS STARTED Computing differential methylation tables
2021-10-15 04:59:23 1.1 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:59:23 1.1 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:59:23 1.1 INFO Conducting differential analysis using limma
2021-10-15 04:59:23 1.1 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:59:23 1.1 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:59:23 1.1 STATUS Computed table for tiling
2021-10-15 04:59:24 1.1 STATUS Computed table for genes
2021-10-15 04:59:24 1.1 STATUS Computed table for promoters
2021-10-15 04:59:24 1.1 STATUS Computed table for cpgislands
2021-10-15 04:59:24 1.1 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:59:24 1.2 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 04:59:24 1.2 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:59:24 1.2 STATUS STARTED Computing Differential Methylation Table
2021-10-15 04:59:24 1.2 INFO Conducting differential analysis using limma
2021-10-15 04:59:24 1.2 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 04:59:24 1.2 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:59:26 1.0 STATUS Computed table for tiling
2021-10-15 04:59:26 1.0 STATUS Computed table for genes
2021-10-15 04:59:26 1.1 STATUS Computed table for promoters
2021-10-15 04:59:26 1.1 STATUS Computed table for cpgislands
2021-10-15 04:59:27 1.1 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 04:59:27 1.1 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 04:59:27 1.1 STATUS COMPLETED Computing differential methylation tables
2021-10-15 04:59:27 1.1 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-10-15 04:59:27 1.1 STATUS STARTED Testing function: diffVar
2021-10-15 04:59:27 1.1 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:00:24 3.8 STATUS COMPLETED diffVar method
2021-10-15 05:00:24 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:00:24 3.8 WARNING Could not compute p-values with diffVar, returning NA
2021-10-15 05:00:24 3.8 INFO diffVar from missMethyl package not properly running
2021-10-15 05:00:24 3.8 STATUS COMPLETED diffVar method
2021-10-15 05:00:24 3.8 STATUS STARTED Testing function: apply.iEVORA
2021-10-15 05:00:24 3.8 STATUS STARTED iEVORA method
2021-10-15 05:00:25 3.8 INFO No DVCs detected. All p-values set to 1.
2021-10-15 05:00:25 3.8 STATUS COMPLETED iEVORA method
2021-10-15 05:00:25 3.8 STATUS STARTED Testing function: rnb.execute.diffVar
2021-10-15 05:00:25 3.8 STATUS STARTED Differential Variability
2021-10-15 05:00:25 3.8 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:25 3.8 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:25 3.8 INFO No imputation method selected, 'knn' method used.
2021-10-15 05:00:25 3.8 STATUS STARTED Imputation procedure knn
2021-10-15 05:00:25 3.8 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:00:25 3.8 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:25 3.8 INFO Conducting differential variability using diffVar
2021-10-15 05:00:26 3.8 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:00:26 3.8 STATUS COMPLETED diffVar method
2021-10-15 05:00:26 3.9 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 05:00:26 3.9 STATUS Computed table for tiling
2021-10-15 05:00:27 3.7 STATUS Computed table for genes
2021-10-15 05:00:27 3.7 STATUS Computed table for promoters
2021-10-15 05:00:28 3.7 STATUS Computed table for cpgislands
2021-10-15 05:00:28 3.7 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 05:00:28 3.7 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:28 3.7 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:28 3.7 INFO Conducting differential variability using diffVar
2021-10-15 05:00:28 3.7 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:00:28 3.7 STATUS COMPLETED diffVar method
2021-10-15 05:00:28 3.7 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 05:00:29 3.7 STATUS Computed table for tiling
2021-10-15 05:00:29 3.7 STATUS Computed table for genes
2021-10-15 05:00:31 3.6 STATUS Computed table for promoters
2021-10-15 05:00:31 3.6 STATUS Computed table for cpgislands
2021-10-15 05:00:31 3.6 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 05:00:31 3.6 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:31 3.6 STATUS COMPLETED Differential Variability
2021-10-15 05:00:31 3.6 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-10-15 05:00:32 3.6 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 05:00:32 3.6 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:32 3.6 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:32 3.6 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:32 3.6 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:32 3.6 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:32 3.6 INFO Conducting differential analysis using limma
2021-10-15 05:00:32 3.6 STATUS STARTED Imputation procedure knn
2021-10-15 05:00:32 3.6 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:00:32 3.6 INFO Conducting differential variability using diffVar
2021-10-15 05:00:32 3.6 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:00:32 3.6 STATUS COMPLETED diffVar method
2021-10-15 05:00:32 3.6 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:32 3.6 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:33 3.6 STATUS Computed table for tiling
2021-10-15 05:00:37 2.9 STATUS Computed table for genes
2021-10-15 05:00:37 2.9 STATUS Computed table for promoters
2021-10-15 05:00:38 2.9 STATUS Computed table for cpgislands
2021-10-15 05:00:38 2.9 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:38 2.9 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:38 2.9 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:38 2.9 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:38 2.9 INFO Conducting differential analysis using limma
2021-10-15 05:00:38 2.9 STATUS STARTED Imputation procedure knn
2021-10-15 05:00:38 2.9 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:00:38 2.9 INFO Conducting differential variability using diffVar
2021-10-15 05:00:38 2.9 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:00:38 2.9 STATUS COMPLETED diffVar method
2021-10-15 05:00:38 2.9 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:38 2.9 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:39 3.1 STATUS Computed table for tiling
2021-10-15 05:00:40 3.2 STATUS Computed table for genes
2021-10-15 05:00:40 3.3 STATUS Computed table for promoters
2021-10-15 05:00:40 3.4 STATUS Computed table for cpgislands
2021-10-15 05:00:40 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:40 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:40 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:40 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 05:00:41 3.4 STATUS STARTED Testing class: RnBDiffMeth
2021-10-15 05:00:41 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:41 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:41 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:41 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:41 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:41 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:41 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:41 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:42 3.4 STATUS Computed table for tiling
2021-10-15 05:00:42 3.4 STATUS Computed table for genes
2021-10-15 05:00:42 3.4 STATUS Computed table for promoters
2021-10-15 05:00:43 3.4 STATUS Computed table for cpgislands
2021-10-15 05:00:43 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:43 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:43 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:43 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:43 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:43 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:43 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:44 3.4 STATUS Computed table for tiling
2021-10-15 05:00:44 3.4 STATUS Computed table for genes
2021-10-15 05:00:45 3.4 STATUS Computed table for promoters
2021-10-15 05:00:45 3.4 STATUS Computed table for cpgislands
2021-10-15 05:00:45 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:45 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:45 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:45 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:45 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:45 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:45 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:45 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:45 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:45 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:45 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:46 3.4 STATUS Computed table for genes
2021-10-15 05:00:47 3.4 STATUS Computed table for tiling
2021-10-15 05:00:47 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:47 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:47 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:47 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:47 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:47 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:47 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:47 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:47 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:47 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:47 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:48 3.4 STATUS Computed table for genes
2021-10-15 05:00:48 3.4 STATUS Computed table for tiling
2021-10-15 05:00:48 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:48 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:48 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:48 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:48 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:48 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:48 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:49 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:49 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:49 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:49 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:49 3.4 STATUS Computed table for promoters
2021-10-15 05:00:49 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:49 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:49 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:49 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:49 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:49 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:49 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:50 3.4 STATUS Computed table for promoters
2021-10-15 05:00:50 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:50 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:50 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:50 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:50 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:50 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:50 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:50 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:50 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:50 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:50 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:51 3.4 STATUS Computed table for genes
2021-10-15 05:00:51 3.5 STATUS Computed table for tiling
2021-10-15 05:00:51 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:51 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:51 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:51 3.5 STATUS STARTED Testing function: get.region.types
2021-10-15 05:00:51 3.5 STATUS COMPLETED Testing function: get.region.types
2021-10-15 05:00:51 3.5 STATUS STARTED Testing function: get.comparisons
2021-10-15 05:00:51 3.5 STATUS COMPLETED Testing function: get.comparisons
2021-10-15 05:00:52 3.5 STATUS STARTED Testing function: get.comparison.grouplabels
2021-10-15 05:00:52 3.5 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-10-15 05:00:52 3.5 STATUS STARTED Testing function: get.site.test.method
2021-10-15 05:00:52 3.5 STATUS COMPLETED Testing function: get.site.test.method
2021-10-15 05:00:52 3.5 STATUS STARTED Testing function: get.table
2021-10-15 05:00:52 3.5 STATUS COMPLETED Testing function: get.table
2021-10-15 05:00:52 3.5 STATUS STARTED Testing function: addDiffMethTable
2021-10-15 05:00:52 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:00:52 3.5 STATUS COMPLETED Testing function: addDiffMethTable
2021-10-15 05:00:52 3.5 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-10-15 05:00:52 3.5 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-10-15 05:00:53 3.5 STATUS STARTED Destructor
2021-10-15 05:00:53 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:00:53 3.5 STATUS COMPLETED Destructor
2021-10-15 05:00:53 3.5 STATUS COMPLETED Testing class: RnBDiffMeth
2021-10-15 05:00:53 3.5 STATUS COMPLETED Testing function: apply.iEVORA
2021-10-15 05:00:53 3.5 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:53 3.5 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:53 3.5 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:54 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:54 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:54 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:00:54 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:54 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:55 3.4 STATUS Computed table for tiling
2021-10-15 05:00:55 3.4 STATUS Computed table for genes
2021-10-15 05:00:55 3.4 STATUS Computed table for promoters
2021-10-15 05:00:55 3.4 STATUS Computed table for cpgislands
2021-10-15 05:00:56 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:56 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:56 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:56 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:56 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:56 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:56 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:56 3.4 STATUS Computed table for tiling
2021-10-15 05:00:57 3.4 STATUS Computed table for genes
2021-10-15 05:00:57 3.4 STATUS Computed table for promoters
2021-10-15 05:00:57 3.4 STATUS Computed table for cpgislands
2021-10-15 05:00:57 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:57 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:00:57 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:57 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:57 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:58 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:00:58 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:58 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:00:58 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:00:58 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:00:58 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:58 3.4 STATUS Computed table for genes
2021-10-15 05:00:59 3.4 STATUS Computed table for tiling
2021-10-15 05:00:59 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:00:59 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:00:59 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:00:59 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:00:59 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:00:59 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:00 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:00 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:00 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:00 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:00 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:00 3.4 STATUS Computed table for genes
2021-10-15 05:01:00 3.4 STATUS Computed table for tiling
2021-10-15 05:01:01 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:01 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:01 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:01 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:01 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:01 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:01 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:01 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:01 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:01 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:01 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:01 3.4 STATUS Computed table for promoters
2021-10-15 05:01:01 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:01 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:02 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:02 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:02 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:02 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:02 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:02 3.4 STATUS Computed table for promoters
2021-10-15 05:01:02 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:02 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:02 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:02 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:02 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:02 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:02 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:02 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:03 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:03 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:03 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:03 3.4 STATUS Computed table for genes
2021-10-15 05:01:03 3.5 STATUS Computed table for tiling
2021-10-15 05:01:03 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:03 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:04 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:04 3.5 STATUS STARTED Testing function: get.region.types
2021-10-15 05:01:04 3.5 STATUS COMPLETED Testing function: get.region.types
2021-10-15 05:01:04 3.5 STATUS STARTED Testing function: get.comparisons
2021-10-15 05:01:04 3.5 STATUS COMPLETED Testing function: get.comparisons
2021-10-15 05:01:04 3.5 STATUS STARTED Testing function: get.comparison.grouplabels
2021-10-15 05:01:04 3.5 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-10-15 05:01:04 3.5 STATUS STARTED Testing function: get.site.test.method
2021-10-15 05:01:04 3.5 STATUS COMPLETED Testing function: get.site.test.method
2021-10-15 05:01:04 3.5 STATUS STARTED Testing function: get.table
2021-10-15 05:01:04 3.5 STATUS COMPLETED Testing function: get.table
2021-10-15 05:01:04 3.5 STATUS STARTED Testing function: addDiffMethTable
2021-10-15 05:01:04 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:04 3.5 STATUS COMPLETED Testing function: addDiffMethTable
2021-10-15 05:01:04 3.5 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-10-15 05:01:05 3.5 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-10-15 05:01:05 3.5 STATUS STARTED Destructor
2021-10-15 05:01:05 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:05 3.5 STATUS COMPLETED Destructor
2021-10-15 05:01:05 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:06 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:06 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:06 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:06 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:06 3.5 WARNING Could not compute p-values with diffVar, returning NA
2021-10-15 05:01:06 3.5 INFO diffVar from missMethyl package not properly running
2021-10-15 05:01:06 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:06 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:06 3.5 STATUS STARTED Unit testing: differential
2021-10-15 05:01:06 3.5 STATUS STARTED Testing function: rowWelchP
2021-10-15 05:01:07 3.5 STATUS COMPLETED Testing function: rowWelchP
2021-10-15 05:01:07 3.5 STATUS STARTED Testing function: limmaP
2021-10-15 05:01:07 3.5 STATUS COMPLETED Testing function: limmaP
2021-10-15 05:01:07 3.5 STATUS STARTED Testing function: computeDiffTab.extended.site
2021-10-15 05:01:07 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:07 3.5 STATUS COMPLETED Testing function: computeDiffTab.extended.site
2021-10-15 05:01:07 3.5 STATUS STARTED Testing function: computeDiffTab.default.region
2021-10-15 05:01:07 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:08 3.4 STATUS COMPLETED Testing function: computeDiffTab.default.region
2021-10-15 05:01:08 3.4 STATUS STARTED Testing function: combineTestPvalsMeth
2021-10-15 05:01:08 3.4 STATUS COMPLETED Testing function: combineTestPvalsMeth
2021-10-15 05:01:08 3.4 STATUS STARTED Testing function: get.adjustment.variables
2021-10-15 05:01:08 3.4 STATUS COMPLETED Testing function: get.adjustment.variables
2021-10-15 05:01:08 3.4 STATUS STARTED Testing function: get.comparison.info
2021-10-15 05:01:08 3.4 STATUS COMPLETED Testing function: get.comparison.info
2021-10-15 05:01:08 3.4 STATUS STARTED Testing function: rnb.execute.computeDiffMeth
2021-10-15 05:01:09 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:09 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:09 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:09 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:09 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:09 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:09 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:09 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:09 3.4 STATUS Computed table for tiling
2021-10-15 05:01:10 3.4 STATUS Computed table for genes
2021-10-15 05:01:10 3.4 STATUS Computed table for promoters
2021-10-15 05:01:10 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:10 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:10 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:10 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:10 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:11 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:11 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:11 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:11 3.4 STATUS Computed table for tiling
2021-10-15 05:01:11 3.4 STATUS Computed table for genes
2021-10-15 05:01:12 3.5 STATUS Computed table for promoters
2021-10-15 05:01:12 3.5 STATUS Computed table for cpgislands
2021-10-15 05:01:12 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:12 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:12 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:12 3.5 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth
2021-10-15 05:01:12 3.5 STATUS STARTED Testing function: diffVar
2021-10-15 05:01:12 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:12 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:13 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:13 3.5 WARNING Could not compute p-values with diffVar, returning NA
2021-10-15 05:01:13 3.5 INFO diffVar from missMethyl package not properly running
2021-10-15 05:01:13 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:13 3.5 STATUS STARTED Testing function: apply.iEVORA
2021-10-15 05:01:13 3.5 STATUS STARTED iEVORA method
2021-10-15 05:01:14 3.4 INFO No DVCs detected. All p-values set to 1.
2021-10-15 05:01:14 3.4 STATUS COMPLETED iEVORA method
2021-10-15 05:01:14 3.4 STATUS STARTED Testing function: rnb.execute.diffVar
2021-10-15 05:01:15 3.4 STATUS STARTED Differential Variability
2021-10-15 05:01:15 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:15 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:15 3.4 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:15 3.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:15 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:15 3.4 INFO Conducting differential variability using diffVar
2021-10-15 05:01:15 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:15 3.4 STATUS COMPLETED diffVar method
2021-10-15 05:01:15 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:16 3.4 STATUS Computed table for tiling
2021-10-15 05:01:16 3.4 STATUS Computed table for genes
2021-10-15 05:01:16 3.4 STATUS Computed table for promoters
2021-10-15 05:01:16 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:16 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:16 3.4 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:17 3.4 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:17 3.4 INFO Conducting differential variability using diffVar
2021-10-15 05:01:17 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:17 3.4 STATUS COMPLETED diffVar method
2021-10-15 05:01:17 3.4 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:17 3.5 STATUS Computed table for tiling
2021-10-15 05:01:17 3.5 STATUS Computed table for genes
2021-10-15 05:01:18 3.5 STATUS Computed table for promoters
2021-10-15 05:01:18 3.5 STATUS Computed table for cpgislands
2021-10-15 05:01:18 3.5 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:18 3.5 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:18 3.5 STATUS COMPLETED Differential Variability
2021-10-15 05:01:18 3.5 STATUS COMPLETED Testing function: rnb.execute.diffVar
2021-10-15 05:01:18 3.5 STATUS STARTED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 05:01:18 3.5 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:18 3.5 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:19 3.5 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:19 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:19 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:19 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:19 3.5 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:19 3.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:19 3.5 INFO Conducting differential variability using diffVar
2021-10-15 05:01:19 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:19 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:19 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:19 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:20 3.4 STATUS Computed table for tiling
2021-10-15 05:01:21 3.4 STATUS Computed table for genes
2021-10-15 05:01:21 3.4 STATUS Computed table for promoters
2021-10-15 05:01:22 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:22 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:22 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:22 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:22 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:22 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:22 3.4 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:22 3.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:22 3.4 INFO Conducting differential variability using diffVar
2021-10-15 05:01:22 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:22 3.4 STATUS COMPLETED diffVar method
2021-10-15 05:01:23 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:23 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:23 3.5 STATUS Computed table for tiling
2021-10-15 05:01:24 3.5 STATUS Computed table for genes
2021-10-15 05:01:25 3.4 STATUS Computed table for promoters
2021-10-15 05:01:25 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:25 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:25 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:25 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:25 3.4 STATUS COMPLETED Testing function: rnb.execute.computeDiffMeth and Variability
2021-10-15 05:01:25 3.4 STATUS STARTED Testing class: RnBDiffMeth
2021-10-15 05:01:26 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:26 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:26 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:26 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:26 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:26 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:26 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:26 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:26 3.4 STATUS Computed table for tiling
2021-10-15 05:01:27 3.4 STATUS Computed table for genes
2021-10-15 05:01:27 3.4 STATUS Computed table for promoters
2021-10-15 05:01:27 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:27 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:27 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:27 3.4 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:27 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:28 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:28 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:28 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:28 3.5 STATUS Computed table for tiling
2021-10-15 05:01:28 3.5 STATUS Computed table for genes
2021-10-15 05:01:29 3.5 STATUS Computed table for promoters
2021-10-15 05:01:29 3.5 STATUS Computed table for cpgislands
2021-10-15 05:01:29 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:29 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:29 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:29 3.5 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:29 3.5 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:29 3.5 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:29 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:29 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:30 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:30 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:30 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:30 3.4 STATUS Computed table for genes
2021-10-15 05:01:31 3.4 STATUS Computed table for tiling
2021-10-15 05:01:31 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:31 3.4 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:31 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:31 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:31 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:31 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:31 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:31 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:32 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:32 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:32 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:32 3.4 STATUS Computed table for genes
2021-10-15 05:01:32 3.4 STATUS Computed table for tiling
2021-10-15 05:01:33 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:33 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:33 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:33 3.5 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:33 3.5 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:33 3.5 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:33 3.5 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:33 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:33 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:33 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:33 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:34 3.5 STATUS Computed table for promoters
2021-10-15 05:01:34 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:34 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:34 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:34 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:34 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:34 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:34 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:34 3.5 STATUS Computed table for promoters
2021-10-15 05:01:34 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:34 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:34 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:35 3.5 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:35 3.5 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:35 3.5 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:35 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:35 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:35 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:35 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:35 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:35 3.5 STATUS Computed table for genes
2021-10-15 05:01:36 3.5 STATUS Computed table for tiling
2021-10-15 05:01:36 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:36 3.5 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:36 3.5 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:36 3.5 STATUS STARTED Testing function: get.region.types
2021-10-15 05:01:36 3.5 STATUS COMPLETED Testing function: get.region.types
2021-10-15 05:01:36 3.5 STATUS STARTED Testing function: get.comparisons
2021-10-15 05:01:36 3.5 STATUS COMPLETED Testing function: get.comparisons
2021-10-15 05:01:36 3.5 STATUS STARTED Testing function: get.comparison.grouplabels
2021-10-15 05:01:36 3.5 STATUS COMPLETED Testing function: get.comparison.grouplabels
2021-10-15 05:01:36 3.5 STATUS STARTED Testing function: get.site.test.method
2021-10-15 05:01:36 3.5 STATUS COMPLETED Testing function: get.site.test.method
2021-10-15 05:01:36 3.5 STATUS STARTED Testing function: get.table
2021-10-15 05:01:36 3.5 STATUS COMPLETED Testing function: get.table
2021-10-15 05:01:37 3.5 STATUS STARTED Testing function: addDiffMethTable
2021-10-15 05:01:37 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:37 3.4 STATUS COMPLETED Testing function: addDiffMethTable
2021-10-15 05:01:37 3.4 STATUS STARTED Testing functions: join.diffMeth, is.valid
2021-10-15 05:01:38 3.4 STATUS COMPLETED Testing functions: join.diffMeth, is.valid
2021-10-15 05:01:38 3.4 STATUS STARTED Destructor
2021-10-15 05:01:38 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS STARTED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS COMPLETED Deleting RnBDiffMeth disk dump files from disk
2021-10-15 05:01:38 3.4 STATUS COMPLETED Destructor
2021-10-15 05:01:38 3.4 STATUS COMPLETED Testing class: RnBDiffMeth
2021-10-15 05:01:38 3.4 STATUS COMPLETED Testing function: apply.iEVORA
2021-10-15 05:01:39 3.4 STATUS STARTED iEVORA method
2021-10-15 05:01:40 3.4 INFO No DVCs detected. All p-values set to 1.
Coefficients not estimable: x2x2
2021-10-15 05:01:40 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:40 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:40 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:40 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:40 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:40 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:40 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:40 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:41 3.4 STATUS Computed table for tiling
2021-10-15 05:01:41 3.5 STATUS Computed table for genes
2021-10-15 05:01:41 3.5 STATUS Computed table for promoters
2021-10-15 05:01:42 3.5 STATUS Computed table for cpgislands
2021-10-15 05:01:42 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:42 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:42 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:42 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:42 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:42 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:42 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:43 3.5 STATUS Computed table for tiling
2021-10-15 05:01:43 3.5 STATUS Computed table for genes
2021-10-15 05:01:44 3.4 STATUS Computed table for promoters
2021-10-15 05:01:44 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:44 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:44 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:44 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:44 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:44 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:44 3.4 STATUS STARTED Computing differential methylation tables
2021-10-15 05:01:44 3.4 STATUS STARTED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:44 3.4 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:45 3.4 INFO Conducting differential analysis using limma
2021-10-15 05:01:45 3.4 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:45 3.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:45 3.4 INFO Conducting differential variability using diffVar
2021-10-15 05:01:45 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:45 3.4 STATUS COMPLETED diffVar method
2021-10-15 05:01:45 3.4 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:45 3.4 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:46 3.4 STATUS Computed table for tiling
2021-10-15 05:01:46 3.5 STATUS Computed table for genes
2021-10-15 05:01:46 3.5 STATUS Computed table for promoters
2021-10-15 05:01:47 3.5 STATUS Computed table for cpgislands
2021-10-15 05:01:47 3.5 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:47 3.5 STATUS COMPLETED Comparing: hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:47 3.5 STATUS STARTED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:47 3.5 STATUS STARTED Computing Differential Methylation Table
2021-10-15 05:01:47 3.5 INFO Conducting differential analysis using limma
2021-10-15 05:01:47 3.5 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:47 3.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:47 3.5 INFO Conducting differential variability using diffVar
2021-10-15 05:01:47 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:47 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:48 3.5 STATUS COMPLETED Computing Differential Methylation Table
2021-10-15 05:01:48 3.5 STATUS STARTED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:49 3.4 STATUS Computed table for tiling
2021-10-15 05:01:49 3.4 STATUS Computed table for genes
2021-10-15 05:01:50 3.4 STATUS Computed table for promoters
2021-10-15 05:01:50 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:50 3.4 STATUS COMPLETED Computing Differential Methylation Tables (Region Level)
2021-10-15 05:01:50 3.4 STATUS COMPLETED Comparing: KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:50 3.4 STATUS COMPLETED Computing differential methylation tables
2021-10-15 05:01:50 3.4 STATUS STARTED Differential Variability
2021-10-15 05:01:50 3.4 STATUS STARTED Retrieving comparison info
2021-10-15 05:01:50 3.4 STATUS COMPLETED Retrieving comparison info
2021-10-15 05:01:50 3.4 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:50 3.4 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:51 3.4 STATUS STARTED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:51 3.4 INFO Conducting differential variability using diffVar
2021-10-15 05:01:51 3.4 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:51 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:51 3.5 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:51 3.5 STATUS Computed table for tiling
2021-10-15 05:01:51 3.5 STATUS Computed table for genes
2021-10-15 05:01:52 3.5 STATUS Computed table for promoters
2021-10-15 05:01:52 3.5 STATUS Computed table for cpgislands
2021-10-15 05:01:52 3.5 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:52 3.5 STATUS COMPLETED Comparing hESC vs. hiPSC (based on Sample_Group)
2021-10-15 05:01:52 3.5 STATUS STARTED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:52 3.5 INFO Conducting differential variability using diffVar
2021-10-15 05:01:52 3.5 STATUS STARTED diffVar method
coef not specified. Using all columns of design matrix.
2021-10-15 05:01:52 3.5 STATUS COMPLETED diffVar method
2021-10-15 05:01:52 3.5 STATUS STARTED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:53 3.5 STATUS Computed table for tiling
2021-10-15 05:01:54 3.4 STATUS Computed table for genes
2021-10-15 05:01:54 3.4 STATUS Computed table for promoters
2021-10-15 05:01:54 3.4 STATUS Computed table for cpgislands
2021-10-15 05:01:54 3.4 STATUS COMPLETED Computing Differential Variability Tables (Region Level)
2021-10-15 05:01:54 3.4 STATUS COMPLETED Comparing KOSR vs. TeSR (based on Treatment)
2021-10-15 05:01:54 3.4 STATUS COMPLETED Differential Variability
2021-10-15 05:01:54 3.4 STATUS STARTED Analysis
2021-10-15 05:01:54 3.4 INFO Loaded information from data.RData
2021-10-15 05:01:54 3.4 STATUS STARTED Processing Detection P-values
2021-10-15 05:01:54 3.4 INFO Removed 3979 probes that overlap with SNPs
2021-10-15 05:01:55 3.4 INFO Completed Greedycut on 510 samples
2021-10-15 05:01:55 3.4 STATUS COMPLETED Processing Detection P-values
2021-10-15 05:01:55 3.4 WARNING File not found: data2.RData
2021-10-15 05:01:55 3.4 STATUS COMPLETED Analysis
2021-10-15 05:01:55 3.4 STATUS STARTED Testing imputation
2021-10-15 05:01:55 3.4 STATUS STARTED Imputation procedure knn
2021-10-15 05:01:56 3.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:01:56 3.5 STATUS STARTED Imputation procedure mean.samples
2021-10-15 05:01:56 3.5 STATUS COMPLETED Imputation procedure mean.samples
2021-10-15 05:01:56 3.5 STATUS STARTED Imputation procedure mean.cpgs
2021-10-15 05:01:57 3.5 STATUS COMPLETED Imputation procedure mean.cpgs
2021-10-15 05:01:57 3.5 STATUS STARTED Imputation procedure random
2021-10-15 05:01:58 3.4 STATUS COMPLETED Imputation procedure random
2021-10-15 05:01:58 3.4 STATUS COMPLETED Testing imputation
2021-10-15 05:01:58 3.4 STATUS STARTED Testing age prediction
2021-10-15 05:01:58 3.4 STATUS STARTED Performing Age Prediction
2021-10-15 05:02:01 3.7 STATUS COMPLETED Performing Age Prediction
2021-10-15 05:02:01 3.7 STATUS COMPLETED Testing age prediction
2021-10-15 05:02:01 3.7 STATUS STARTED Performing Age Prediction
2021-10-15 05:02:05 3.6 STATUS COMPLETED Performing Age Prediction
2021-10-15 05:02:05 3.6 STATUS STARTED Imputation procedure knn
2021-10-15 05:02:06 3.6 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:02:06 3.6 STATUS STARTED Imputation procedure mean.samples
2021-10-15 05:02:07 3.7 STATUS COMPLETED Imputation procedure mean.samples
2021-10-15 05:02:07 3.7 STATUS STARTED Imputation procedure mean.cpgs
2021-10-15 05:02:07 3.7 STATUS COMPLETED Imputation procedure mean.cpgs
2021-10-15 05:02:07 3.7 STATUS STARTED Imputation procedure random
2021-10-15 05:02:09 3.5 STATUS COMPLETED Imputation procedure random
2021-10-15 05:02:09 3.5 STATUS STARTED Testing imputation
2021-10-15 05:02:09 3.5 STATUS STARTED Imputation procedure knn
2021-10-15 05:02:09 3.5 STATUS COMPLETED Imputation procedure knn
2021-10-15 05:02:09 3.5 STATUS STARTED Imputation procedure mean.samples
2021-10-15 05:02:10 3.5 STATUS COMPLETED Imputation procedure mean.samples
2021-10-15 05:02:10 3.5 STATUS STARTED Imputation procedure mean.cpgs
2021-10-15 05:02:10 3.6 STATUS COMPLETED Imputation procedure mean.cpgs
2021-10-15 05:02:11 3.6 STATUS STARTED Imputation procedure random
2021-10-15 05:02:12 3.5 STATUS COMPLETED Imputation procedure random
2021-10-15 05:02:12 3.5 STATUS COMPLETED Testing imputation
2021-10-15 05:02:12 3.5 STATUS STARTED Testing age prediction
2021-10-15 05:02:12 3.5 STATUS STARTED Performing Age Prediction
2021-10-15 05:02:15 3.8 STATUS COMPLETED Performing Age Prediction
2021-10-15 05:02:15 3.8 STATUS COMPLETED Testing age prediction
RUNIT TEST PROTOCOL -- Fri Oct 15 05:02:37 2021
***********************************************
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 25 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
195.21 5.32 219.31
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RnBeads.Rcheck/examples_i386/RnBeads-Ex.timings
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RnBeads.Rcheck/examples_x64/RnBeads-Ex.timings
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