BioC 3.3: CHECK report for RnBeads on morelia

Package: RnBeads

Version: 1.3.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.3.0.tar.gz

StartedAt: 2015-10-22 10:43:22 -0400 (Thu, 22 Oct 2015)

EndedAt: 2015-10-22 10:57:54 -0400 (Thu, 22 Oct 2015)

EllapsedTime: 872.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: RnBeads.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RnBeads.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘1.3.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘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 for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... [26s/28s] OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
* 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
* 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 ... 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’ ‘isva’ ‘minfi’ ‘nlme’ ‘quadprog’
  ‘scales’ ‘sva’ ‘wateRmelon’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.negative.control.boxplot: no visible global function definition for
  ‘samples’
add.qc.barplots: no visible global function definition for ‘samples’
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 ‘unit’
add.snp.distances: no visible global function definition for
  ‘grid.draw’
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’
append.cpg.stats : cpg.stats: no visible global function definition for
  ‘DataFrame’
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’
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’
create.densityScatter: no visible binding for global variable
  ‘..density..’
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 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.ucsc.track.hub: no visible global function definition for
  ‘samples’
data.frame2GRanges: no visible global function definition for
  ‘seqlevels<-’
data.frame2GRanges: no visible global function definition for
  ‘genome<-’
estimateProportionsCP: no visible global function definition for ‘lme’
estimateProportionsCP: no visible global function definition for
  ‘getVarCov’
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’
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’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
intensities.by.color: no visible global function definition for
  ‘samples’
intensities.by.color: no visible binding for global variable
  ‘IlluminaHumanMethylation450kmanifest’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
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’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
  ‘unit’
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
  ‘unit’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘grid.draw’
plot.heatmap.rand: no visible global function definition for ‘melt’
plot.heatmap.rand: no visible global function definition for ‘unit’
plot.heatmap.symm: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for ‘unit’
plot.heatmap.symm: no visible global function definition for
  ‘grid.draw’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
plotcdf: no visible global function definition for ‘unit’
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.execute.dreduction: 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.to.ewasher: no visible global function definition for
  ‘samples’
rnb.plot.beta.comparison: no visible global function definition for
  ‘unit’
rnb.plot.beta.density.group: no visible binding for global variable
  ‘group’
rnb.plot.beta.density.group: no visible global function definition for
  ‘unit’
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.draw’
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
  ‘unit’
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 ‘unit’
rnb.plot.ct.heatmap: no visible global function definition for
  ‘grid.draw’
rnb.plot.dreduction: no visible global function definition for ‘unit’
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 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: 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.pheno.categories: no visible global function definition for
  ‘unit’
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.sample.summary.table: 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.site: no visible global function definition for
  ‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
  ‘foreach’
rnb.section.dreduction.internal : create.scatters: no visible global
  function definition for ‘unit’
rnb.section.dreduction.internal: no visible global function definition
  for ‘unit’
rnb.section.gender.prediction: no visible global function definition
  for ‘muted’
rnb.section.gender.prediction: no visible global function definition
  for ‘unit’
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.normalization: no visible global function definition for
  ‘samples’
rnb.section.normalization.shifts: no visible global function definition
  for ‘unit’
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.variability.removal: no visible global function definition
  for ‘unit’
rnb.step.betadistribution.internal: no visible global function
  definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
  definition for ‘foreach’
rnb.step.betadistribution.internal: no visible binding for global
  variable ‘params’
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.filter.summary.internal: no visible global function definition
  for ‘unit’
rnb.step.greedycut.internal : plotroc: no visible global function
  definition for ‘unit’
rnb.step.greedycut.internal : plotline: no visible global function
  definition for ‘unit’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.intersample.internal : scatter.var: no visible global function
  definition for ‘unit’
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’
set.covariates.ct: no visible global function definition for ‘samples’
symmetric.melt: no visible global function definition for ‘melt’
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’
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’
summarize.regions,RnBSet: no visible global function definition for
  ‘samples’
Undefined global functions or variables:
  %dopar% ..density.. Address Beta.values BiomartGeneRegionTrack
  BootRefFreeEwasModel ChrNumeric DataFrame DataTrack DoISVA EstDimRMT
  GenomeAxisTrack ID IdeogramTrack IlluminaHumanMethylation450kmanifest
  Index Intensity PairsBootRefFreeEwasModel Probe RGChannelSet
  RefFreeEwasModel SNP Sample Slide Target Term UcscTrack addSex
  as.profileCGH assayDataElement assayDataElementNames barcode chrom
  color combinedRank comma covgMedian covgPercLow covgPercUp daglad
  diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency
  expectedCounts featureData featureData<- featureNames featureNames<-
  foreach geneCounts genome<- getCN getDoParWorkers getMeth getSex
  getUnmeth getVarCov grid.draw group group1 group2 i intensities
  is.subsegmentation k letterFrequency lme mapToGenome mean.diff
  mean.g1 mean.g2 mean.mean.g1 mean.mean.g2 mean.quot.log2 melt muted
  n.sites num.sites numSites numeric.names oddsRatios params
  percent_format phenoData phenoData<- plotOrder plotTracks
  preprocessSWAN pvalues refText reg.type region.size
  registerDoParallel relative.coord report samples seqlevels<-
  sigCategories size solve.QP stopCluster sva target type types unit
  universeCounts useMart v varLabels x y
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [9s/9s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [121s/591s]
 [122s/591s] 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: 3 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/RnBeads.Rcheck/00check.log’
for details.

* installing *source* package ‘RnBeads’ ...
** R
** inst
** preparing package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
Creating a generic function for ‘vmode’ from package ‘ff’ in package ‘RnBeads’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : Error in 'rgl_init'
* DONE (RnBeads)

name	user	system	elapsed
M-methods	0.001	0.001	0.000
U-methods	0.000	0.000	0.001
addDiffMethTable-RnBDiffMeth-methods	0	0	0
addPheno-RnBSet-methods	0.001	0.000	0.000
addRegionSubsegments	0	0	0
annotation-methods	0	0	0
assembly-methods	0	0	0
combine-methods	0.000	0.001	0.001
combineTestPvalsMeth	0	0	0
computeDiffTab.region	0.001	0.000	0.000
computeDiffTab.site	0.001	0.000	0.000
covg-methods	0.000	0.000	0.001
create.densityScatter	0	0	0
create.scatter.dens.points	0	0	0
createReport	0	0	0
createReportPlot	0.000	0.000	0.001
dpval-methods	0	0	0
exportDMRs2regionFile	0	0	0
get.adjustment.variables	0	0	0
get.comparison.grouplabels-RnBDiffMeth-methods	0.001	0.000	0.001
get.comparison.groupsizes-RnBDiffMeth-methods	0.001	0.000	0.000
get.comparison.info	0	0	0
get.comparisons-RnBDiffMeth-methods	0	0	0
get.covariates.sva	0.000	0.000	0.001
get.covg.thres-RnBDiffMeth-methods	0.000	0.000	0.001
get.files	0	0	0
get.region.types-RnBDiffMeth-methods	0	0	0
get.site.test.method-RnBDiffMeth-methods	0.000	0.000	0.001
get.table-RnBDiffMeth-methods	0.001	0.000	0.000
getSubCmdTokens-ClusterArchitectureSGE-methods	0.001	0.001	0.000
has.covariates.sva	0	0	0
includes.sites-RnBDiffMeth-methods	0.000	0.000	0.001
is.valid-RnBDiffMeth-methods	0	0	0
join.diffMeth-methods	0	0	0
limmaP	0	0	0
logger.argument	0.001	0.000	0.000
logger.getfiles	0.000	0.000	0.001
logger.isinitialized	0.000	0.000	0.001
logger.validate.file	0	0	0
loggerManagement	0.001	0.000	0.001
loggerMessages	0.001	0.000	0.000
mergeSamples-methods	0	0	0
meth-methods	0.001	0.000	0.001
mval-methods	0	0	0
parallel.getNumWorkers	0.000	0.000	0.001
parallel.isEnabled	0.001	0.000	0.000
parallel.setup	0	0	0
parallel.teardown	0.000	0.000	0.001
performEnrichment.diffMeth	0	0	0
performGOenrichment.diffMeth.entrez	0.001	0.000	0.001
pheno-methods	0	0	0
qc-methods	0.000	0.000	0.001
read.sample.annotation	0	0	0
regionMapping-methods	0.001	0.000	0.000
regions-methods	0.001	0.000	0.001
reload-RnBDiffMeth-methods	0	0	0
remove.samples-methods	0	0	0
remove.sites-methods	0.001	0.001	0.000
rnb.RnBSet.to.GRangesList	0	0	0
rnb.RnBSet.to.bed	0.001	0.000	0.000
rnb.RnBSet.to.bedGraph	0.001	0.000	0.001
rnb.add.list	0	0	0
rnb.add.paragraph	0.000	0.000	0.001
rnb.add.reference	0.000	0.001	0.001
rnb.add.section	0.000	0.000	0.001
rnb.annotation.size	0	0	0
rnb.annotation2data.frame	0.000	0.000	0.001
rnb.beta2mval	0.001	0.000	0.000
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	0.001	0.000	0.001
rnb.execute.dreduction	0.001	0.000	0.000
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	0.001	0.000	0.000
rnb.execute.normalization	0.000	0.000	0.001
rnb.execute.sex.removal	0	0	0
rnb.execute.snp.removal	0	0	0
rnb.execute.sva	0.000	0.000	0.001
rnb.execute.tnt	0.001	0.000	0.000
rnb.execute.variability.removal	0.001	0.000	0.000
rnb.export.all.annotation	0.000	0.000	0.001
rnb.export.annotation	0	0	0
rnb.export.to.ewasher	0	0	0
rnb.export.to.trackhub	0.000	0.000	0.001
rnb.get.annotation	0.001	0.000	0.000
rnb.get.assemblies	0.001	0.001	0.000
rnb.get.chromosomes	0	0	0
rnb.get.directory	0.000	0.000	0.001
rnb.get.mapping	0	0	0
rnb.get.reference	0	0	0
rnb.get.reliability.matrix	0	0	0
rnb.infinium.control.targets	0.000	0.000	0.001
rnb.initialize.reports	0.001	0.000	0.000
rnb.is.option	0.001	0.000	0.000
rnb.message.plot	0.000	0.000	0.001
rnb.mval2beta	0.000	0.000	0.001
rnb.options	0	0	0
rnb.options2xml	0	0	0
rnb.plot.betadistribution.probeCategories	0.000	0.000	0.001
rnb.plot.betadistribution.sampleGroups	0	0	0
rnb.plot.control.barplot	0.000	0.000	0.001
rnb.plot.control.boxplot	0	0	0
rnb.plot.dreduction	0	0	0
rnb.plot.locus.profile	0	0	0
rnb.plot.negative.boxplot	0.000	0.000	0.001
rnb.plot.region.profile.density	0.001	0.000	0.000
rnb.plot.region.profiles	0.000	0.001	0.000
rnb.plot.region.site.density	0.000	0.000	0.001
rnb.plot.sentrix.distribution	0	0	0
rnb.plot.snp.barplot	0	0	0
rnb.plot.snp.boxplot	0.001	0.000	0.001
rnb.plot.snp.heatmap	0.001	0.000	0.000
rnb.region.types	0	0	0
rnb.region.types.for.analysis	0	0	0
rnb.remove.annotation	0.000	0.000	0.001
rnb.run.example	0	0	0
rnb.runs	0	0	0
rnb.sample.groups	0.001	0.000	0.000
rnb.sample.summary.table	0.001	0.000	0.001
rnb.set.annotation	0.001	0.000	0.000
rnb.write.table	0	0	0
rnb.xml2options	0.000	0.001	0.000
rowOneSampleTP	0.000	0.000	0.001
rowWelchP	0	0	0
run-RnBClusterRun-methods	0	0	0
samples-methods	0	0	0
save.tables-RnBDiffMeth-methods	0.000	0.000	0.001
set.covariates.sva	0.001	0.000	0.000
sites-methods	0.001	0.000	0.000
summarize.regions-methods	0	0	0
summarized.regions-methods	0.000	0.000	0.001