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BioC 3.2: CHECK report for RnBeads on perceval

This page was generated on 2015-08-24 10:54:41 -0700 (Mon, 24 Aug 2015).

Package 873/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 1.1.6
Fabian Mueller
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RnBeads
Last Changed Rev: 107650 / Revision: 107696
Last Changed Date: 2015-08-21 01:02:35 -0700 (Fri, 21 Aug 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: RnBeads
Version: 1.1.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.1.6.tar.gz
StartedAt: 2015-08-24 04:42:13 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 04:51:59 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 586.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RnBeads.Rcheck
Warnings: 4

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.1.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘1.1.6’
* 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 ... [46s/47s] OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  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 ... OK
* 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:
  ‘annotate’ ‘biomaRt’ ‘Category’ ‘doParallel’ ‘foreach’ ‘GLAD’
  ‘GOstats’ ‘Gviz’ ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
  ‘IlluminaHumanMethylation450kmanifest’ ‘isva’ ‘minfi’ ‘nlme’
  ‘quadprog’ ‘RefFreeEWAS’ ‘scales’ ‘sva’ ‘wateRmelon’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘doParallel:::.options’ ‘grDevices:::.smoothScatterCalcDensity’
  ‘Gviz:::.getBMFeatureMap’ ‘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’
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’
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’
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’
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’
plotcdf: no visible global function definition for ‘unit’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
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.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.boxplot: no visible binding for global variable
  ‘Probe’
rnb.plot.control.boxplot: no visible binding for global variable
  ‘Intensity’
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.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.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
  ‘samples’
rnb.RnBSet.to.GRangesList: 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 : .local: 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 : .local: no visible global function definition
  for ‘samples’
mergeSamples,RnBSet : .local: 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.samples,RnBSet: no visible global function definition for
  ‘samples’
summarize.regions,RnBSet : .local: no visible global function
  definition for ‘samples’
* 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 'RnBiseqSet-class':
RnBiseqSet
  Code: function(pheno, sites, meth, covg = NULL, assembly = "hg19",
                 target = "CpG", summarize.regions = TRUE, region.types
                 = rnb.region.types.for.analysis(assembly), useff =
                 rnb.getOption("disk.dump.big.matrices"), usebigff =
                 rnb.getOption("disk.dump.bigff"), verbose = FALSE)
  Docs: function(pheno, sites, meth, covg = NULL, assembly = "hg19",
                 target = "CpG", summarize.regions = TRUE, region.types
                 = rnb.region.types.for.analysis(assembly), useff =
                 rnb.getOption("disk.dump.big.matrices"), verbose =
                 FALSE)
  Argument names in code not in docs:
    usebigff
  Mismatches in argument names:
    Position: 10 Code: usebigff Docs: verbose

Codoc mismatches from documentation object 'read.bed.files':
read.bed.files
  Code: function(base.dir = NULL, file.names = NULL, sample.sheet =
                 NULL, file.names.col = 0, assembly =
                 rnb.getOption("assembly"), region.types =
                 rnb.region.types.for.analysis(assembly),
                 pos.coord.shift = 1L, skip.lines = 1, sep.samples =
                 rnb.getOption("import.table.separator"),
                 merge.bed.files = TRUE, useff =
                 rnb.getOption("disk.dump.big.matrices"), usebigff =
                 rnb.getOption("disk.dump.bigff"), verbose = TRUE, ...)
  Docs: function(base.dir = NULL, file.names = NULL, sample.sheet =
                 NULL, file.names.col = 0, assembly =
                 rnb.getOption("assembly"), region.types =
                 rnb.region.types.for.analysis(assembly),
                 pos.coord.shift = 1L, skip.lines = 1, sep.samples =
                 rnb.getOption("import.table.separator"),
                 merge.bed.files = TRUE, useff =
                 rnb.getOption("disk.dump.big.matrices"), verbose =
                 TRUE, ...)
  Argument names in code not in docs:
    usebigff
  Mismatches in argument names:
    Position: 12 Code: usebigff Docs: verbose
    Position: 13 Code: verbose Docs: ...

Codoc mismatches from documentation object 'rnb.execute.computeDiffMeth':
rnb.execute.computeDiffMeth
  Code: function(x, pheno.cols, region.types =
                 rnb.region.types.for.analysis(x), covg.thres =
                 rnb.getOption("filtering.coverage.threshold"),
                 pheno.cols.all.pairwise =
                 rnb.getOption("differential.comparison.columns.all.pairwise"),
                 columns.pairs = rnb.getOption("columns.pairing"),
                 columns.adj =
                 rnb.getOption("covariate.adjustment.columns"),
                 adjust.sva =
                 rnb.getOption("differential.adjustment.sva"),
                 pheno.cols.adjust.sva =
                 rnb.getOption("inference.targets.sva"),
                 adjust.celltype =
                 rnb.getOption("differential.adjustment.celltype"),
                 skip.sites = !rnb.getOption("analyze.sites"),
                 disk.dump = rnb.getOption("disk.dump.big.matrices"),
                 disk.dump.dir = tempfile(pattern = "diffMethTables_"),
                 ...)
  Docs: function(x, pheno.cols, region.types =
                 rnb.region.types.for.analysis(x), covg.thres =
                 rnb.getOption("filtering.coverage.threshold"),
                 pheno.cols.all.pairwise =
                 rnb.getOption("differential.comparison.columns.all.pairwise"),
                 columns.pairs = rnb.getOption("columns.pairing"),
                 columns.adj =
                 rnb.getOption("covariate.adjustment.columns"),
                 adjust.sva =
                 rnb.getOption("differential.adjustment.sva"),
                 pheno.cols.adjust.sva =
                 rnb.getOption("inference.targets.sva"),
                 adjust.celltype =
                 rnb.getOption("differential.adjustment.celltype"),
                 disk.dump = rnb.getOption("disk.dump.big.matrices"),
                 disk.dump.dir = tempfile(pattern = "diffMethTables_"),
                 ...)
  Argument names in code not in docs:
    skip.sites
  Mismatches in argument names:
    Position: 11 Code: skip.sites Docs: disk.dump
    Position: 12 Code: disk.dump Docs: disk.dump.dir
    Position: 13 Code: disk.dump.dir Docs: ...

S4 class codoc mismatches from documentation object 'RnBDiffMeth-class':
Slots for class 'RnBDiffMeth'
  Code: comparison.grouplabels comparison.info comparisons covg.thres
        disk.dump disk.path includesSites region.types regions
        site.test.method sites
  Docs: comparison.grouplabels comparison.info comparisons covg.thres
        disk.dump disk.path region.types regions site.test.method sites

* 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 ... [19s/19s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [110s/113s]
 [111s/114s] 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: 4 WARNINGs, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck/00check.log’
for details.

RnBeads.Rcheck/00install.out:

* 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
** 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)

RnBeads.Rcheck/RnBeads-Ex.timings:

nameusersystemelapsed
M-methods0.0000.0000.001
U-methods0.0010.0000.001
addDiffMethTable-RnBDiffMeth-methods0.0000.0000.001
addPheno-RnBSet-methods0.0000.0000.001
addRegionSubsegments0.0010.0010.001
annotation-methods0.0000.0000.001
assembly-methods0.0000.0000.001
combine-methods0.0010.0000.001
combineTestPvalsMeth0.0000.0000.001
computeDiffTab.region000
computeDiffTab.site0.0010.0000.000
covg-methods000
create.densityScatter000
create.scatter.dens.points000
createReport0.0010.0000.000
createReportPlot0.0010.0000.000
dpval-methods000
exportDMRs2regionFile000
get.adjustment.variables0.0010.0000.000
get.comparison.grouplabels-RnBDiffMeth-methods0.0010.0000.000
get.comparison.groupsizes-RnBDiffMeth-methods000
get.comparison.info000
get.comparisons-RnBDiffMeth-methods0.0010.0000.000
get.covariates.sva0.0000.0000.001
get.covg.thres-RnBDiffMeth-methods0.0000.0000.001
get.files0.0010.0010.001
get.region.types-RnBDiffMeth-methods0.0000.0000.001
get.site.test.method-RnBDiffMeth-methods0.0000.0000.001
get.table-RnBDiffMeth-methods0.0010.0000.001
getSubCmdTokens-ClusterArchitectureSGE-methods000
has.covariates.sva000
is.valid-RnBDiffMeth-methods0.0010.0000.000
join.diffMeth-methods000
limmaP000
logger.argument0.0010.0010.001
logger.getfiles0.0000.0000.001
logger.isinitialized0.0000.0000.001
logger.validate.file0.0010.0000.001
loggerManagement0.0010.0000.001
loggerMessages0.0000.0000.001
mergeSamples-methods0.0010.0000.000
meth-methods0.0010.0000.000
mval-methods000
parallel.getNumWorkers0.0010.0000.000
parallel.isEnabled0.0010.0000.000
parallel.setup0.0000.0000.001
parallel.teardown0.0010.0000.001
performEnrichment.diffMeth0.0010.0010.001
performGOenrichment.diffMeth.entrez0.0000.0000.001
pheno-methods0.0000.0000.001
qc-methods0.0000.0000.001
read.sample.annotation0.0010.0010.001
regionMapping-methods0.0000.0000.001
regions-methods0.0000.0000.001
reload-RnBDiffMeth-methods000
remove.samples-methods0.0010.0000.000
remove.sites-methods0.0000.0000.001
rnb.RnBSet.to.GRangesList0.0000.0000.001
rnb.RnBSet.to.bed0.0010.0000.001
rnb.RnBSet.to.bedGraph0.0010.0010.001
rnb.add.list0.0000.0000.001
rnb.add.paragraph0.0000.0000.001
rnb.add.reference0.0010.0000.001
rnb.add.section0.0000.0010.001
rnb.annotation.size0.0000.0000.001
rnb.annotation2data.frame0.0000.0000.001
rnb.beta2mval0.0010.0000.001
rnb.execute.batcheffects0.0000.0010.001
rnb.execute.clustering000
rnb.execute.computeDiffMeth0.0010.0000.000
rnb.execute.context.removal000
rnb.execute.cross.reactive.removal000
rnb.execute.dreduction0.0010.0000.000
rnb.execute.export.csv0.0010.0000.000
rnb.execute.gender.prediction000
rnb.execute.greedycut000
rnb.execute.import0.0010.0000.000
rnb.execute.na.removal0.0010.0000.000
rnb.execute.normalization0.0010.0000.000
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva000
rnb.execute.tnt0.0010.0000.001
rnb.execute.variability.removal000
rnb.export.all.annotation0.0010.0000.000
rnb.export.annotation0.0010.0000.001
rnb.export.to.ewasher0.0000.0010.001
rnb.export.to.trackhub0.0000.0000.001
rnb.get.annotation0.0010.0000.000
rnb.get.assemblies000
rnb.get.chromosomes0.0000.0010.000
rnb.get.directory0.0010.0000.000
rnb.get.mapping0.0010.0000.000
rnb.get.reference000
rnb.get.reliability.matrix000
rnb.infinium.control.targets0.0010.0000.000
rnb.initialize.reports000
rnb.is.option0.0000.0010.000
rnb.message.plot0.0010.0000.000
rnb.mval2beta0.0010.0000.000
rnb.options000
rnb.options2xml000
rnb.plot.betadistribution.probeCategories0.0010.0000.000
rnb.plot.betadistribution.sampleGroups000
rnb.plot.control.barplot000
rnb.plot.control.boxplot0.0010.0000.000
rnb.plot.dreduction0.0010.0000.000
rnb.plot.locus.profile000
rnb.plot.negative.boxplot000
rnb.plot.region.profile.density0.0010.0000.000
rnb.plot.region.profiles000
rnb.plot.region.site.density000
rnb.plot.sentrix.distribution0.0010.0000.000
rnb.plot.snp.barplot0.0010.0000.001
rnb.plot.snp.boxplot0.0010.0000.001
rnb.plot.snp.heatmap0.0000.0000.001
rnb.region.types0.0000.0000.001
rnb.region.types.for.analysis0.0010.0000.000
rnb.remove.annotation000
rnb.run.example0.0000.0010.000
rnb.runs0.0010.0000.000
rnb.sample.groups0.0010.0000.000
rnb.sample.summary.table000
rnb.set.annotation000
rnb.write.table0.0010.0000.000
rnb.xml2options0.0010.0000.000
rowOneSampleTP0.0000.0000.001
rowWelchP0.0000.0000.001
run-RnBClusterRun-methods0.0000.0000.001
samples-methods0.0010.0000.001
save.tables-RnBDiffMeth-methods0.0000.0010.001
set.covariates.sva0.0000.0000.001
sites-methods0.0010.0000.001
summarize.regions-methods000
summarized.regions-methods000