BioC 3.4: CHECK report for RnBeads on tokay1

Package: RnBeads

Version: 1.6.1

Command: rm -rf RnBeads.buildbin-libdir RnBeads.Rcheck && mkdir RnBeads.buildbin-libdir RnBeads.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RnBeads.buildbin-libdir RnBeads_1.6.1.tar.gz >RnBeads.Rcheck\00install.out 2>&1 && cp RnBeads.Rcheck\00install.out RnBeads-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RnBeads.buildbin-libdir --install="check:RnBeads-install.out" --force-multiarch --no-vignettes --timings RnBeads_1.6.1.tar.gz

StartedAt: 2017-04-15 00:35:03 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:46:01 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 657.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RnBeads.Rcheck

Warnings: 6

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### Running command:
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###   rm -rf RnBeads.buildbin-libdir RnBeads.Rcheck && mkdir RnBeads.buildbin-libdir RnBeads.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RnBeads.buildbin-libdir RnBeads_1.6.1.tar.gz >RnBeads.Rcheck\00install.out 2>&1 && cp RnBeads.Rcheck\00install.out RnBeads-install.out  && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=RnBeads.buildbin-libdir --install="check:RnBeads-install.out" --force-multiarch --no-vignettes --timings RnBeads_1.6.1.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/RnBeads.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RnBeads/DESCRIPTION' ... OK
* this is package 'RnBeads' version '1.6.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'BiocGenerics' 'S4Vectors' 'GenomicRanges' 'MASS' 'RColorBrewer'
  '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 ... OK
* checking for portable file names ... OK
* checking whether package 'RnBeads' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'gridExtra::combine' by 'methylumi::combine' when loading 'RnBeads'
See 'C:/Users/biocbuild/bbs-3.4-bioc/meat/RnBeads.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.2Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'data' contains no data sets.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'GLAD'
'library' or 'require' calls not declared from:
  'GLAD' 'IlluminaHumanMethylation450kanno.ilmn12.hg19' 'scales'
'library' or 'require' calls in package code:
  'Category' 'GLAD' 'GOstats' 'Gviz'
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'
  'IlluminaHumanMethylation450kmanifest' 'RefFreeEWAS' 'annotate'
  'biomaRt' 'doParallel' 'foreach' 'glmnet' 'impute' 'isva' 'minfi'
  'nlme' 'quadprog' 'scales' 'sva' 'wateRmelon'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'GenomicRanges::unlist'
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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'CONTROL.TARGETS.SAMPLE.INDEPENDENT'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add.combination.plot: warning in facet_grid(Set ˜ ., scale = "free",
  drop = TRUE): partial argument match of 'scale' to 'scales'
.stopImplicitCluster: no visible global function definition for
  'stopCluster'
BMIQ: no visible global function definition for 'density'
BMIQ: no visible global function definition for 'pbeta'
BMIQ: no visible global function definition for 'qbeta'
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 binding for global variable 'Sample'
add.combination.plot: no visible binding for global variable
  'Difference'
add.combination.plot: no visible binding for global variable 'Density'
add.combination.plot: no visible binding for global variable 'yint'
add.combination.plot: no visible binding for global variable 'Measure'
add.error.plot: no visible binding for global variable 'Value'
add.error.plot: no visible binding for global variable 'Sample'
add.error.plot: no visible binding for global variable 'Deviance'
add.error.plot: no visible binding for global variable 'yint'
add.error.plot: no visible binding for global variable 'Measure'
add.negative.control.boxplot: no visible global function definition for
  'samples'
add.qc.barplots: no visible global function definition for 'samples'
add.quantile.plot: no visible binding for global variable 'Difference'
add.quantile.plot: no visible binding for global variable '..density..'
add.quantile.plot: no visible binding for global variable 'Sample'
add.quantile.plot: no visible binding for global variable 'Density'
add.seq.coverage.histograms: no visible global function definition for
  'samples'
add.seq.coverage.plot: no visible global function definition for
  'samples'
add.seq.coverage.violins: no visible global function definition for
  'samples'
add.snp.barplot: no visible global function definition for 'samples'
add.snp.distances: no visible global function definition for
  'grid.newpage'
add.snp.distances: no visible global function definition for
  'grid.draw'
add.snp.distances: no visible global function definition for 'prcomp'
addReportPlots.diffMeth.bin.region.volcano: no visible binding for
  global variable 'combinedRank'
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'
agePredictor450: no visible global function definition for 'read.csv'
agePredictor450: no visible global function definition for
  'capture.output'
agePredictor450: no visible global function definition for 'impute.knn'
agePredictorRRBS: no visible global function definition for 'read.csv'
agePredictorRRBS: no visible global function definition for
  'capture.output'
agePredictorRRBS: no visible global function definition for
  'impute.knn'
agePredictorRRBS: no visible global function definition for 'samples'
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'
betaEst2: no visible global function definition for 'optim'
blc2: no visible global function definition for 'dbeta'
bootInferWBCbyLm: no visible global function definition for 'rnorm'
bootInferWBCbyLm: no visible global function definition for 'rt'
bootInferWBCbyLme: no visible global function definition for 'rnorm'
bootInferWBCbyLme: no visible global function definition for 'rt'
combineTestPvalsMeth: no visible global function definition for
  'pchisq'
complete.report: no visible global function definition for
  'packageVersion'
compute.sva.assoc: no visible global function definition for 'prcomp'
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.region: no visible global function definition
  for 'p.adjust'
computeDiffTab.extended.site: no visible global function definition for
  'p.adjust'
corrHeatmap: no visible global function definition for
  'colorRampPalette'
corrHeatmap : color.function: no visible global function definition for
  'rainbow'
create.densityScatter: no visible binding for global variable
  '..density..'
create.densityScatter: no visible global function definition for
  'densCols'
create.densityScatter: no visible global function definition for
  'colorRampPalette'
create.diffMeth.bin.dens.dmp.scatter: no visible global function
  definition for 'densCols'
create.diffMeth.bin.dens.dmp.scatter: no visible global function
  definition for 'colorRampPalette'
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
  variable 'mean.g1'
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
  variable 'mean.g2'
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
  variable 'color'
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
  variable 'plotOrder'
create.diffMeth.bin.dens.dmr.scatter: no visible global function
  definition for 'densCols'
create.diffMeth.bin.dens.dmr.scatter: no visible global function
  definition for 'colorRampPalette'
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
  variable 'mean.mean.g1'
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
  variable 'mean.mean.g2'
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
  variable 'color'
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
  variable 'plotOrder'
create.scatter.dens.points: no visible global function definition for
  'densCols'
create.scatter.dens.points: no visible global function definition for
  'colorRampPalette'
create.ucsc.track.hub: no visible global function definition for
  'samples'
createPredictor : ret: no visible global function definition for 'coef'
createPredictor : ret: no visible global function definition for
  'capture.output'
createPredictor : ret: no visible global function definition for
  'impute.knn'
createPredictor : ret: no visible global function definition for
  'predict'
cv.array: no visible global function definition for 'capture.output'
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<-'
densRanks: no visible global function definition for 'xy.coords'
deviation.plot: no visible global function definition for
  'split.screen'
deviation.plot: no visible global function definition for 'screen'
deviation.plot: no visible global function definition for 'par'
deviation.plot: no visible global function definition for 'plot'
deviation.plot: no visible global function definition for 'mtext'
deviation.plot: no visible global function definition for 'polygon'
deviation.plot: no visible global function definition for 'lines'
deviation.plot: no visible global function definition for
  'close.screen'
deviation.plot.beta.internal : get.fractions: no visible global
  function definition for 'ecdf'
dist.correlation: no visible global function definition for 'as.dist'
estimateProportionsCP: no visible global function definition for
  'as.formula'
estimateProportionsCP: no visible global function definition for 'lme'
estimateProportionsCP: no visible global function definition for 'lm'
estimateProportionsCP: no visible global function definition for
  'getVarCov'
estimateProportionsCP: no visible global function definition for 'vcov'
estimateProportionsCP: no visible global function definition for
  'residuals'
estimateProportionsCP: no visible global function definition for 'pf'
exportDMRs2regionFile: no visible global function definition for
  'write.table'
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.comparison.info: no visible global function definition for 'combn'
get.components.isva: no visible global function definition for 'DoISVA'
get.components.sva: no visible global function definition for
  'model.matrix'
get.components.sva: no visible global function definition for
  'as.formula'
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.memory.usage: no visible global function definition for
  'memory.size'
get.rnb.version: no visible global function definition for
  'packageVersion'
get.subsegments: no visible global function definition for 'dist'
get.subsegments: no visible global function definition for 'hclust'
get.subsegments: no visible global function definition for 'cutree'
getCGCounts : <anonymous>: no visible global function definition for
  'ChrNumeric'
getGLADProfiles: no visible global function definition for 'samples'
getGLADProfiles : <anonymous>: no visible global function definition
  for 'as.profileCGH'
getGLADProfiles : <anonymous>: no visible global function definition
  for 'daglad'
getMergeList: no visible global function definition for 'samples'
groupPermutationP.site.parallel: no visible global function definition
  for '%dopar%'
groupPermutationP.site.parallel: no visible global function definition
  for 'foreach'
heatmap.mod: no visible binding for global variable 'dist'
heatmap.mod: no visible binding for global variable 'hclust'
heatmap.mod : <anonymous>: no visible global function definition for
  'reorder'
heatmap.mod: no visible global function definition for 'as.dendrogram'
heatmap.mod: no visible global function definition for
  'order.dendrogram'
heatmap.mod: no visible global function definition for 'dev.flush'
heatmap.mod: no visible global function definition for 'par'
heatmap.mod: no visible global function definition for 'layout'
heatmap.mod: no visible global function definition for 'image'
heatmap.mod: no visible global function definition for 'axis'
heatmap.mod: no visible global function definition for 'mtext'
heatmap.mod: no visible global function definition for 'plot'
heatmap.mod: no visible global function definition for 'frame'
heatmap.mod: no visible global function definition for 'title'
inferWBCbyLm: no visible global function definition for 'lm'
inferWBCbyLm: no visible global function definition for 'predict'
inferWBCbyLm: no visible global function definition for 'residuals'
inferWBCbyLm: no visible global function definition for 'model.matrix'
inferWBCbyLme: no visible global function definition for 'lme'
inferWBCbyLme: no visible global function definition for 'lm'
inferWBCbyLme: no visible global function definition for 'predict'
inferWBCbyLme: no visible global function definition for 'residuals'
inferWBCbyLme: no visible global function definition for 'getVarCov'
inferWBCbyLme: no visible global function definition for 'model.matrix'
init.pipeline.report: no visible global function definition for
  'read.delim'
intensities.by.color: no visible global function definition for
  'samples'
intensities.by.color: no visible binding for global variable
  'IlluminaHumanMethylation450kmanifest'
limmaP: no visible global function definition for 'model.matrix'
limmaP: no visible global function definition for 'as.formula'
limmaP: no visible binding for global variable 'group1'
limmaP: no visible binding for global variable 'group2'
load.rnb.set: no visible global function definition for 'unzip'
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'
mds: no visible global function definition for 'dist'
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'
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'
plotCGHProfile: no visible global function definition for 'par'
plotCGHProfile: no visible global function definition for 'layout'
plotCGHProfile: no visible global function definition for 'plot'
plotCGHProfile: no visible global function definition for 'lines'
plotCGHProfile: no visible global function definition for 'abline'
plotcdf: no visible global function definition for 'ecdf'
plotcdf: no visible global function definition for 'knots'
print.inferWBCsummary: no visible global function definition for
  'pnorm'
projectWBC: no visible global function definition for 'solve.QP'
read.GS.report: no visible global function definition for
  'featureNames'
read.data.dir: no visible global function definition for 'read.table'
read.idat.files: no visible global function definition for 'ecdf'
read.idat.files: no visible binding for global variable 'barcode'
read.sample.annotation: no visible global function definition for
  'read.table'
read.single.bed: no visible global function definition for 'read.table'
read.single.bed: no visible global function definition for 'read.delim'
refFreeEWASP: no visible global function definition for
  'packageVersion'
refFreeEWASP: no visible global function definition for 'model.matrix'
refFreeEWASP: no visible global function definition for 'as.formula'
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'
refFreeEWASP: no visible global function definition for 'pt'
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.bed: no visible global function definition for
  'write.table'
rnb.RnBSet.to.bedGraph: no visible global function definition for
  'samples'
rnb.RnBSet.to.bedGraph: no visible global function definition for
  'write.table'
rnb.build.index.internal: no visible global function definition for
  'read.delim'
rnb.color.legends : plotlegend: no visible global function definition
  for 'par'
rnb.color.legends : plotlegend: no visible global function definition
  for 'plot.new'
rnb.color.legends : plotlegend: no visible global function definition
  for 'legend'
rnb.diffmeth.to.EpiExplorer.file: no visible global function definition
  for 'write.table'
rnb.execute.clustering: no visible global function definition for
  'dist'
rnb.execute.clustering: no visible global function definition for
  'hclust'
rnb.execute.clustering: no visible global function definition for
  'cutree'
rnb.execute.dreduction: no visible global function definition for
  'samples'
rnb.execute.dreduction: no visible global function definition for
  'prcomp'
rnb.execute.filter.summary.internal: no visible global function
  definition for 'samples'
rnb.execute.na.removal: no visible binding for global variable
  'filtered'
rnb.execute.na.removal.internal: no visible global function definition
  for 'samples'
rnb.execute.normalization: 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
  '%dopar%'
rnb.execute.normalization: no visible global function definition for
  'foreach'
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.quality: no visible global function definition for
  'samples'
rnb.execute.quality : <anonymous>: no visible global function
  definition for 'samples'
rnb.export.annotation: no visible global function definition for
  'write.table'
rnb.export.to.ewasher: no visible global function definition for
  'samples'
rnb.export.to.ewasher: no visible global function definition for
  'write.table'
rnb.export.to.ewasher: no visible global function definition for
  'model.matrix'
rnb.filter.dataset: no visible global function definition for 'samples'
rnb.get.assemblies: no visible global function definition for
  'installed.packages'
rnb.get.chrom.sizes: no visible global function definition for
  'read.delim'
rnb.get.reliability.counts.per.sample: no visible global function
  definition for 'samples'
rnb.load.bed: no visible global function definition for 'read.delim'
rnb.plot.GLAD.profile: no visible global function definition for 'data'
rnb.plot.GLAD.profile: no visible binding for global variable
  'cytoband'
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.coverage.thresholds: no visible global function definition for
  'rgb'
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 'prcomp'
rnb.plot.dreduction: no visible global function definition for 'tsne'
rnb.plot.dreduction: no visible global function definition for 'dist'
rnb.plot.locus.profile: no visible global function definition for
  'plotTracks'
rnb.plot.marker.fstat: no visible binding for global variable 'x'
rnb.plot.marker.fstat: no visible binding for global variable 'y'
rnb.plot.marker.fstat: no visible global function definition for
  'muted'
rnb.plot.negative.boxplot: no visible global function definition for
  'samples'
rnb.plot.negative.boxplot: no visible binding for global variable
  'numeric.names'
rnb.plot.negative.boxplot: no visible binding for global variable
  'type'
rnb.plot.negative.boxplot: no visible binding for global variable
  'types'
rnb.plot.negative.boxplot: no visible global function definition for
  'grid.newpage'
rnb.plot.negative.boxplot: no visible binding for global variable
  'Sample'
rnb.plot.negative.boxplot: no visible binding for global variable
  'Intensity'
rnb.plot.negative.boxplot: no visible global function definition for
  'grid.draw'
rnb.plot.num.sites.covg: no visible global function definition for
  'samples'
rnb.plot.num.sites.covg : <anonymous>: no visible global function
  definition for 'samples'
rnb.plot.num.sites.covg: no visible binding for global variable
  'numSites'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgMedian'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgPercLow'
rnb.plot.num.sites.covg: no visible binding for global variable
  'covgPercUp'
rnb.plot.num.sites.covg: no visible binding for global variable 'comma'
rnb.plot.region.profile.density: no visible binding for global variable
  'relative.coord'
rnb.plot.region.profile.density: no visible binding for global variable
  '..density..'
rnb.plot.region.profiles : <anonymous>: no visible global function
  definition for 'samples'
rnb.plot.region.profiles: no visible binding for global variable
  'relative.coord'
rnb.plot.region.profiles: no visible binding for global variable
  'group'
rnb.plot.region.site.density: no visible binding for global variable
  'relative.coord'
rnb.plot.sentrix.distributions: no visible global function definition
  for 'samples'
rnb.plot.sentrix.distributions: no visible binding for global variable
  'Slide'
rnb.plot.snp.barplot: no visible global function definition for
  'samples'
rnb.plot.snp.boxplot: no visible global function definition for
  'samples'
rnb.plot.snp.boxplot: no visible binding for global variable 'SNP'
rnb.plot.snp.boxplot: no visible binding for global variable
  'Beta.values'
rnb.plot.snp.heatmap: no visible global function definition for
  'samples'
rnb.run.example: no visible global function definition for
  'download.file'
rnb.run.example: no visible global function definition for 'untar'
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.clustering : add.legend: no visible global function
  definition for 'screen'
rnb.section.clustering : add.legend: no visible global function
  definition for 'par'
rnb.section.clustering : add.legend: no visible global function
  definition for 'plot.new'
rnb.section.clustering : add.legend: no visible global function
  definition for 'legend'
rnb.section.clustering: no visible global function definition for
  'split.screen'
rnb.section.clustering: no visible global function definition for
  'close.screen'
rnb.section.clustering.add.heatmap: no visible global function
  definition for 'as.dendrogram'
rnb.section.clustering.add.heatmap : distfun: no visible global
  function definition for 'dist'
rnb.section.clustering.add.heatmap: no visible global function
  definition for 'hclust'
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.site: no visible global function definition for
  '%dopar%'
rnb.section.diffMeth.site: no visible global function definition for
  'foreach'
rnb.section.gender.prediction: no visible global function definition
  for 'muted'
rnb.section.import: no visible global function definition for 'samples'
rnb.section.import: no visible global function definition for
  'phenoData'
rnb.section.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.replicate.concordance: no visible global function
  definition for 'combn'
rnb.show.report: no visible global function definition for 'browseURL'
rnb.step.betadistribution.internal: no visible global function
  definition for '%dopar%'
rnb.step.betadistribution.internal: no visible global function
  definition for 'foreach'
rnb.step.cell.types: no visible global function definition for
  'samples'
rnb.step.clustering.internal: no visible global function definition for
  'samples'
rnb.step.cnv: no visible binding for global variable 'intensities'
rnb.step.dreduction: no visible global function definition for
  '%dopar%'
rnb.step.dreduction: no visible global function definition for
  'foreach'
rnb.step.dreduction: no visible binding for global variable 'target'
rnb.step.filter.summary.internal: no visible global function definition
  for 'percent_format'
rnb.step.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'
rnb.write.table: no visible global function definition for
  'write.table'
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'
rowOneSampleTP: no visible global function definition for 'pt'
rowPairedTP: no visible global function definition for 'pt'
rowWelchP: no visible global function definition for 'pt'
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'
save.rnb.set: no visible global function definition for 'zip'
set.covariates.ct: no visible global function definition for 'samples'
simpleGlmnet: no visible global function definition for
  'capture.output'
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'
simpleGlmnet: no visible global function definition for 'coef'
simpleGlmnetEvaluate: no visible global function definition for
  'cv.glmnet'
simpleGlmnetEvaluate: no visible global function definition for
  'glmnet'
simpleGlmnetRRBS: no visible global function definition for 'cv.glmnet'
simpleGlmnetRRBS: no visible global function definition for 'glmnet'
simpleGlmnetRRBS: no visible global function definition for 'coef'
symmetric.melt: no visible global function definition for 'melt'
tTestP: no visible global function definition for 't.test'
test.traits: no visible global function definition for 'fisher.test'
test.traits: no visible global function definition for 'wilcox.test'
test.traits: no visible global function definition for 'kruskal.test'
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
  'reg.type'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for 'featureData<-'
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
  for 'featureNames<-'
combine,RnBSet-RnBSet: no visible global function definition for
  'samples'
initialize,ReportPlot: no visible global function definition for 'pdf'
initialize,ReportPlot: no visible global function definition for 'png'
initialize,ReportPlot: no visible global function definition for
  'dev.control'
initialize,ReportPlot: no visible global function definition for 'par'
mask.sites.meth,RnBSet: no visible global function definition for
  'samples'
off,ReportPlot : convert.f : doerror: no visible global function
  definition for 'dev.off'
off,ReportPlot : convert.f: no visible global function definition for
  'dev2bitmap'
off,ReportPlot: no visible global function definition for 'dev.off'
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
Undefined global functions or variables:
  %dopar% ..count.. ..density.. Address Age Beta.values
  BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
  Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack ID
  IdeogramTrack IlluminaHumanMethylation450kmanifest Index Intensity
  Measure PairsBootRefFreeEwasModel Probe RGChannelSet RefFreeEwasModel
  SNP Sample Slide Target Term UcscTrack Value abline addSex
  as.dendrogram as.dist as.formula as.profileCGH assayDataElement
  assayDataElementNames axis barcode browseURL capture.output chrom
  close.screen coef color colorRampPalette combinedRank combn comma
  covgMedian covgPercLow covgPercUp cutree cv.glmnet cytoband daglad
  data dbeta densCols density dev.control dev.flush dev.off dev2bitmap
  diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency dist
  download.file ecdf expectedCounts featureData featureData<-
  featureNames featureNames<- filtered fisher.test foreach frame
  geneCounts genome<- getCN getDoParWorkers getMeth getSex getUnmeth
  getVarCov glmnet grid.draw grid.newpage group group1 group2 hclust i
  image impute.knn installed.packages intensities is.subsegmentation k
  knots kruskal.test layout legend letterFrequency lines lm lme
  mapToGenome mean.diff mean.g1 mean.g2 mean.mean.g1 mean.mean.g2
  mean.quot.log2 melt memory.size model.matrix mtext muted n.sites
  num.sites numSites numeric.names oddsRatios optim order.dendrogram
  p.adjust packageVersion par pbeta pchisq pdf percent_format pf
  phenoData phenoData<- plot plot.new plotOrder plotTracks png pnorm
  polygon prcomp predict preprocessSWAN pt pvalues qbeta rainbow
  read.csv read.delim read.table refText reg.type region.size
  registerDoParallel relative.coord reorder report residuals rgb rnorm
  rt samples screen seqlevels<- sigCategories sites2ignore size
  solve.QP split.screen stopCluster sva t.test target title tsne type
  types universeCounts untar unzip useMart v varLabels vcov wilcox.test
  write.table x xy.coords y yint zip
Consider adding
  importFrom("grDevices", "colorRampPalette", "densCols", "dev.control",
             "dev.flush", "dev.off", "dev2bitmap", "pdf", "png",
             "rainbow", "rgb", "xy.coords")
  importFrom("graphics", "abline", "axis", "close.screen", "frame",
             "image", "layout", "legend", "lines", "mtext", "par",
             "plot", "plot.new", "polygon", "screen", "split.screen",
             "title")
  importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "coef",
             "cutree", "dbeta", "density", "dist", "ecdf", "fisher.test",
             "hclust", "knots", "kruskal.test", "lm", "model.matrix",
             "optim", "order.dendrogram", "p.adjust", "pbeta", "pchisq",
             "pf", "pnorm", "prcomp", "predict", "pt", "qbeta",
             "reorder", "residuals", "rnorm", "rt", "t.test", "vcov",
             "wilcox.test")
  importFrom("utils", "browseURL", "capture.output", "combn", "data",
             "download.file", "installed.packages", "memory.size",
             "packageVersion", "read.csv", "read.delim", "read.table",
             "untar", "unzip", "write.table", "zip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'BigFfMat,ANY,ANY,ANY'
  generic '[<-' and siglist 'BigFfMat,ANY,ANY,ANY'
  generic 'dim' and siglist 'BigFfMat'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'agePredictor':
agePredictor
  Code: function(rnbSet, path = "")
  Docs: function(rnbSet, path = system.file(file.path("extdata",
                 "predefined_predictor.csv"), package = "RnBeads"))
  Mismatches in argument default values:
    Name: 'path'
    Code: ""
    Docs: system.file(file.path("extdata", "predefined_predictor.csv"), 
          package = "RnBeads")

Codoc mismatches from documentation object 'createPredictor':
createPredictor
  Code: function(linearModel, lambda = NULL)
  Docs: function(linearModel)
  Argument names in code not in docs:
    lambda

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'read.single.bed'
  'chr.col' 'start.col' 'end.col' 'strand.col' 'c.col' 't.col'
  'is.epp.style' 'coord.shift' 'ffread' 'context' '...'

Undocumented arguments in documentation object 'sampleCovgApply,RnBSet-method'
  'object' 'type' '...'

Undocumented arguments in documentation object 'sampleMethApply,RnBSet-method'
  'object' 'type' '...'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 WARNINGs, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.4-bioc/meat/RnBeads.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'RnBeads' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'gridExtra::combine' by 'methylumi::combine' when loading 'RnBeads'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'gridExtra::combine' by 'methylumi::combine' when loading 'RnBeads'

install for x64

* installing *source* package 'RnBeads' ...
** testing if installed package can be loaded
Warning: replacing previous import 'gridExtra::combine' by 'methylumi::combine' when loading 'RnBeads'
* MD5 sums
packaged installation of 'RnBeads' as RnBeads_1.6.1.zip
* DONE (RnBeads)

name	user	system	elapsed
M-methods	0.01	0.00	0.01
U-methods	0	0	0
addDiffMethTable-RnBDiffMeth-methods	0	0	0
addPheno-RnBSet-methods	0	0	0
addRegionSubsegments	0	0	0
annotation-methods	0	0	0
assembly-methods	0	0	0
combine-methods	0	0	0
combineTestPvalsMeth	0	0	0
computeDiffTab.region	0	0	0
computeDiffTab.site	0.02	0.00	0.02
covg-methods	0	0	0
create.densityScatter	0	0	0
create.scatter.dens.points	0	0	0
createReport	0	0	0
createReportPlot	0	0	0
dpval-methods	0	0	0
exportDMRs2regionFile	0	0	0
get.adjustment.variables	0	0	0
get.comparison.grouplabels-RnBDiffMeth-methods	0	0	0
get.comparison.groupsizes-RnBDiffMeth-methods	0	0	0
get.comparison.info	0	0	0
get.comparisons-RnBDiffMeth-methods	0	0	0
get.covariates.sva	0	0	0
get.covg.thres-RnBDiffMeth-methods	0	0	0
get.files	0	0	0
get.region.types-RnBDiffMeth-methods	0	0	0
get.site.test.method-RnBDiffMeth-methods	0	0	0
get.table-RnBDiffMeth-methods	0	0	0
getSubCmdTokens-ClusterArchitectureSGE-methods	0	0	0
has.covariates.sva	0	0	0
hasCovg-methods	0	0	0
includes.sites-RnBDiffMeth-methods	0	0	0
is.valid-RnBDiffMeth-methods	0	0	0
join.diffMeth-methods	0	0	0
limmaP	0	0	0
logger.argument	0	0	0
logger.getfiles	0	0	0
logger.isinitialized	0	0	0
logger.validate.file	0	0	0
loggerManagement	0	0	0
loggerMessages	0	0	0
mergeSamples-methods	0	0	0
meth-methods	0	0	0
mval-methods	0	0	0
nsites-methods	0	0	0
parallel.getNumWorkers	0	0	0
parallel.isEnabled	0	0	0
parallel.setup	0	0	0
parallel.teardown	0	0	0
performEnrichment.diffMeth	0	0	0
performGOenrichment.diffMeth.entrez	0	0	0
pheno-methods	0	0	0
qc-methods	0	0	0
read.sample.annotation	0	0	0
regionMapping-methods	0	0	0
regions-methods	0	0	0
reload-RnBDiffMeth-methods	0	0	0
remove.regions-methods	0	0	0
remove.samples-methods	0	0	0
remove.sites-methods	0	0	0
rnb.RnBSet.to.GRangesList	0	0	0
rnb.RnBSet.to.bed	0	0	0
rnb.RnBSet.to.bedGraph	0	0	0
rnb.add.list	0	0	0
rnb.add.paragraph	0	0	0
rnb.add.reference	0	0	0
rnb.add.section	0	0	0
rnb.annotation.size	0	0	0
rnb.annotation2data.frame	0	0	0
rnb.beta2mval	0	0	0
rnb.execute.batcheffects	0	0	0
rnb.execute.clustering	0	0	0
rnb.execute.computeDiffMeth	0	0	0
rnb.execute.context.removal	0	0	0
rnb.execute.cross.reactive.removal	0	0	0
rnb.execute.dreduction	0	0	0
rnb.execute.export.csv	0	0	0
rnb.execute.gender.prediction	0	0	0
rnb.execute.greedycut	0	0	0
rnb.execute.import	0	0	0
rnb.execute.na.removal	0	0	0
rnb.execute.normalization	0	0	0
rnb.execute.sex.removal	0	0	0
rnb.execute.snp.removal	0	0	0
rnb.execute.sva	0	0	0
rnb.execute.tnt	0	0	0
rnb.execute.variability.removal	0	0	0
rnb.export.all.annotation	0	0	0
rnb.export.annotation	0	0	0
rnb.export.to.ewasher	0	0	0
rnb.export.to.trackhub	0	0	0
rnb.get.annotation	0	0	0
rnb.get.assemblies	0	0	0
rnb.get.chromosomes	0	0	0
rnb.get.directory	0	0	0
rnb.get.mapping	0	0	0
rnb.get.reference	0	0	0
rnb.get.reliability.matrix	0	0	0
rnb.infinium.control.targets	0	0	0
rnb.initialize.reports	0	0	0
rnb.is.option	0	0	0
rnb.message.plot	0	0	0
rnb.mval2beta	0	0	0
rnb.options	0	0	0
rnb.options2xml	0	0	0
rnb.plot.betadistribution.probeCategories	0	0	0
rnb.plot.betadistribution.sampleGroups	0	0	0
rnb.plot.control.barplot	0	0	0
rnb.plot.control.boxplot	0	0	0
rnb.plot.dreduction	0	0	0
rnb.plot.locus.profile	0	0	0
rnb.plot.negative.boxplot	0	0	0
rnb.plot.region.profile.density	0	0	0
rnb.plot.region.profiles	0	0	0
rnb.plot.region.site.density	0	0	0
rnb.plot.sentrix.distribution	0	0	0
rnb.plot.snp.barplot	0	0	0
rnb.plot.snp.boxplot	0	0	0
rnb.plot.snp.heatmap	0	0	0
rnb.region.types	0.02	0.00	0.01
rnb.region.types.for.analysis	0	0	0
rnb.remove.annotation	0	0	0
rnb.run.example	0	0	0
rnb.runs	0	0	0
rnb.sample.groups	0	0	0
rnb.sample.summary.table	0	0	0
rnb.set.annotation	0	0	0
rnb.write.table	0	0	0
rnb.xml2options	0	0	0
rowOneSampleTP	0	0	0
rowWelchP	0	0	0
run-RnBClusterRun-methods	0	0	0
samples-methods	0	0	0
save.tables-RnBDiffMeth-methods	0	0	0
set.covariates.sva	0	0	0
sites-methods	0	0	0
summarize.regions-methods	0	0	0
summarized.regions-methods	0	0	0

name	user	system	elapsed
M-methods	0	0	0
U-methods	0	0	0
addDiffMethTable-RnBDiffMeth-methods	0	0	0
addPheno-RnBSet-methods	0	0	0
addRegionSubsegments	0	0	0
annotation-methods	0	0	0
assembly-methods	0	0	0
combine-methods	0	0	0
combineTestPvalsMeth	0	0	0
computeDiffTab.region	0	0	0
computeDiffTab.site	0	0	0
covg-methods	0	0	0
create.densityScatter	0	0	0
create.scatter.dens.points	0	0	0
createReport	0	0	0
createReportPlot	0	0	0
dpval-methods	0	0	0
exportDMRs2regionFile	0	0	0
get.adjustment.variables	0	0	0
get.comparison.grouplabels-RnBDiffMeth-methods	0	0	0
get.comparison.groupsizes-RnBDiffMeth-methods	0	0	0
get.comparison.info	0	0	0
get.comparisons-RnBDiffMeth-methods	0	0	0
get.covariates.sva	0	0	0
get.covg.thres-RnBDiffMeth-methods	0	0	0
get.files	0	0	0
get.region.types-RnBDiffMeth-methods	0	0	0
get.site.test.method-RnBDiffMeth-methods	0	0	0
get.table-RnBDiffMeth-methods	0	0	0
getSubCmdTokens-ClusterArchitectureSGE-methods	0	0	0
has.covariates.sva	0	0	0
hasCovg-methods	0	0	0
includes.sites-RnBDiffMeth-methods	0	0	0
is.valid-RnBDiffMeth-methods	0	0	0
join.diffMeth-methods	0	0	0
limmaP	0	0	0
logger.argument	0	0	0
logger.getfiles	0	0	0
logger.isinitialized	0	0	0
logger.validate.file	0	0	0
loggerManagement	0	0	0
loggerMessages	0	0	0
mergeSamples-methods	0	0	0
meth-methods	0	0	0
mval-methods	0	0	0
nsites-methods	0	0	0
parallel.getNumWorkers	0	0	0
parallel.isEnabled	0	0	0
parallel.setup	0	0	0
parallel.teardown	0	0	0
performEnrichment.diffMeth	0	0	0
performGOenrichment.diffMeth.entrez	0	0	0
pheno-methods	0	0	0
qc-methods	0	0	0
read.sample.annotation	0	0	0
regionMapping-methods	0	0	0
regions-methods	0	0	0
reload-RnBDiffMeth-methods	0	0	0
remove.regions-methods	0	0	0
remove.samples-methods	0	0	0
remove.sites-methods	0	0	0
rnb.RnBSet.to.GRangesList	0	0	0
rnb.RnBSet.to.bed	0	0	0
rnb.RnBSet.to.bedGraph	0	0	0
rnb.add.list	0	0	0
rnb.add.paragraph	0	0	0
rnb.add.reference	0	0	0
rnb.add.section	0	0	0
rnb.annotation.size	0	0	0
rnb.annotation2data.frame	0	0	0
rnb.beta2mval	0	0	0
rnb.execute.batcheffects	0	0	0
rnb.execute.clustering	0	0	0
rnb.execute.computeDiffMeth	0	0	0
rnb.execute.context.removal	0	0	0
rnb.execute.cross.reactive.removal	0	0	0
rnb.execute.dreduction	0	0	0
rnb.execute.export.csv	0	0	0
rnb.execute.gender.prediction	0	0	0
rnb.execute.greedycut	0	0	0
rnb.execute.import	0.01	0.00	0.01
rnb.execute.na.removal	0	0	0
rnb.execute.normalization	0	0	0
rnb.execute.sex.removal	0	0	0
rnb.execute.snp.removal	0	0	0
rnb.execute.sva	0	0	0
rnb.execute.tnt	0	0	0
rnb.execute.variability.removal	0	0	0
rnb.export.all.annotation	0	0	0
rnb.export.annotation	0	0	0
rnb.export.to.ewasher	0	0	0
rnb.export.to.trackhub	0	0	0
rnb.get.annotation	0	0	0
rnb.get.assemblies	0.00	0.01	0.02
rnb.get.chromosomes	0	0	0
rnb.get.directory	0	0	0
rnb.get.mapping	0	0	0
rnb.get.reference	0	0	0
rnb.get.reliability.matrix	0	0	0
rnb.infinium.control.targets	0	0	0
rnb.initialize.reports	0	0	0
rnb.is.option	0	0	0
rnb.message.plot	0	0	0
rnb.mval2beta	0	0	0
rnb.options	0	0	0
rnb.options2xml	0	0	0
rnb.plot.betadistribution.probeCategories	0	0	0
rnb.plot.betadistribution.sampleGroups	0	0	0
rnb.plot.control.barplot	0	0	0
rnb.plot.control.boxplot	0	0	0
rnb.plot.dreduction	0	0	0
rnb.plot.locus.profile	0	0	0
rnb.plot.negative.boxplot	0	0	0
rnb.plot.region.profile.density	0	0	0
rnb.plot.region.profiles	0	0	0
rnb.plot.region.site.density	0	0	0
rnb.plot.sentrix.distribution	0	0	0
rnb.plot.snp.barplot	0	0	0
rnb.plot.snp.boxplot	0	0	0
rnb.plot.snp.heatmap	0	0	0
rnb.region.types	0	0	0
rnb.region.types.for.analysis	0	0	0
rnb.remove.annotation	0	0	0
rnb.run.example	0	0	0
rnb.runs	0	0	0
rnb.sample.groups	0	0	0
rnb.sample.summary.table	0	0	0
rnb.set.annotation	0	0	0
rnb.write.table	0	0	0
rnb.xml2options	0	0	0
rowOneSampleTP	0	0	0
rowWelchP	0	0	0
run-RnBClusterRun-methods	0	0	0
samples-methods	0	0	0
save.tables-RnBDiffMeth-methods	0	0	0
set.covariates.sva	0	0	0
sites-methods	0	0	0
summarize.regions-methods	0	0	0
summarized.regions-methods	0	0	0