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BioC 3.2: CHECK report for RnBeads on oaxaca

This page was generated on 2016-04-23 10:29:14 -0700 (Sat, 23 Apr 2016).

Package 900/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RnBeads 1.2.2
Fabian Mueller
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/RnBeads
Last Changed Rev: 114168 / Revision: 116712
Last Changed Date: 2016-03-02 04:24:58 -0800 (Wed, 02 Mar 2016)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  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: 1.2.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.2.2.tar.gz
StartedAt: 2016-04-23 03:57:15 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 04:14:49 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 1054.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: RnBeads.Rcheck
Warnings: 5

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck’
* using R version 3.2.4 (2016-03-10)
* 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 ‘1.2.2’
* 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 ... [42s/50s] WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’
See ‘/Users/biocbuild/bbs-3.2-bioc/meat/RnBeads.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    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 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’ ‘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.
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
.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
  ‘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
  ‘grid.draw’
plot.heatmap.pc.pvalues: no visible global function definition for
  ‘melt’
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.draw’
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.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.filter.summary.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.to.ewasher: no visible global function definition for
  ‘samples’
rnb.get.reliability.counts.per.sample: no visible global function
  definition for ‘samples’
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 binding for global variable
  ‘Intensity’
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.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.draw’
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 : <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.preprocessing : logger.completed.filtering: 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.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.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.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.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
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’
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’
sampleCovgApply,RnBSet : .local: no visible global function definition
  for ‘samples’
sampleMethApply,RnBSet : .local: no visible global function definition
  for ‘samples’
summarize.regions,RnBSet : .local: no visible global function
  definition for ‘samples’
summarize.regions,RnBSet : .local: multiple local function definitions
  for ‘aggr.f’ with different formal arguments
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [2m/10m]
 [2m/10m] 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: 5 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’
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: 'rgl_init' failed, running with rgl.useNULL = TRUE
Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’
* DONE (RnBeads)

RnBeads.Rcheck/RnBeads-Ex.timings:

nameusersystemelapsed
M-methods0.0000.0000.001
U-methods0.0000.0000.001
addDiffMethTable-RnBDiffMeth-methods0.0010.0000.000
addPheno-RnBSet-methods0.0010.0000.000
addRegionSubsegments0.0010.0000.001
annotation-methods000
assembly-methods0.0000.0000.001
combine-methods000
combineTestPvalsMeth0.0010.0000.001
computeDiffTab.region000
computeDiffTab.site0.0000.0000.001
covg-methods000
create.densityScatter000
create.scatter.dens.points0.0000.0000.001
createReport0.0000.0000.001
createReportPlot0.0010.0000.001
dpval-methods0.0010.0000.000
exportDMRs2regionFile0.0000.0010.001
get.adjustment.variables000
get.comparison.grouplabels-RnBDiffMeth-methods000
get.comparison.groupsizes-RnBDiffMeth-methods0.0000.0000.001
get.comparison.info0.0010.0010.001
get.comparisons-RnBDiffMeth-methods000
get.covariates.sva0.0010.0000.001
get.covg.thres-RnBDiffMeth-methods0.0010.0000.001
get.files0.0010.0000.000
get.region.types-RnBDiffMeth-methods0.0000.0000.001
get.site.test.method-RnBDiffMeth-methods000
get.table-RnBDiffMeth-methods0.0010.0010.000
getSubCmdTokens-ClusterArchitectureSGE-methods0.0010.0000.000
has.covariates.sva0.0010.0000.001
hasCovg-methods0.0010.0000.000
includes.sites-RnBDiffMeth-methods0.0000.0000.001
is.valid-RnBDiffMeth-methods000
join.diffMeth-methods0.0000.0000.001
limmaP0.0000.0010.001
logger.argument000
logger.getfiles0.0010.0000.001
logger.isinitialized0.0010.0000.000
logger.validate.file0.0010.0000.001
loggerManagement0.0010.0000.001
loggerMessages000
mergeSamples-methods0.0000.0000.001
meth-methods0.0000.0000.001
mval-methods0.0000.0000.001
nsites-methods000
parallel.getNumWorkers0.0010.0000.000
parallel.isEnabled0.0000.0000.001
parallel.setup000
parallel.teardown0.0000.0010.001
performEnrichment.diffMeth0.0010.0000.000
performGOenrichment.diffMeth.entrez0.0010.0000.001
pheno-methods0.0010.0000.000
qc-methods0.0000.0000.001
read.sample.annotation000
regionMapping-methods0.0010.0000.001
regions-methods0.0010.0000.001
reload-RnBDiffMeth-methods000
remove.regions-methods0.0000.0000.001
remove.samples-methods0.0000.0000.001
remove.sites-methods0.0010.0000.001
rnb.RnBSet.to.GRangesList0.0010.0000.001
rnb.RnBSet.to.bed0.0010.0000.000
rnb.RnBSet.to.bedGraph0.0000.0000.001
rnb.add.list000
rnb.add.paragraph0.0010.0000.001
rnb.add.reference0.0010.0000.001
rnb.add.section0.0010.0000.000
rnb.annotation.size0.0000.0000.001
rnb.annotation2data.frame000
rnb.beta2mval000
rnb.execute.batcheffects0.0000.0010.001
rnb.execute.clustering000
rnb.execute.computeDiffMeth0.0010.0000.001
rnb.execute.context.removal0.0010.0000.000
rnb.execute.cross.reactive.removal0.0010.0000.000
rnb.execute.dreduction0.0010.0000.001
rnb.execute.export.csv0.0010.0000.000
rnb.execute.gender.prediction0.0000.0010.001
rnb.execute.greedycut000
rnb.execute.import0.0000.0000.001
rnb.execute.na.removal0.0010.0000.000
rnb.execute.normalization0.0010.0000.001
rnb.execute.sex.removal000
rnb.execute.snp.removal000
rnb.execute.sva0.0000.0000.001
rnb.execute.tnt000
rnb.execute.variability.removal0.0010.0000.001
rnb.export.all.annotation0.0000.0000.001
rnb.export.annotation0.0000.0000.001
rnb.export.to.ewasher000
rnb.export.to.trackhub0.0000.0000.001
rnb.get.annotation000
rnb.get.assemblies000
rnb.get.chromosomes0.0000.0000.001
rnb.get.directory0.0010.0000.000
rnb.get.mapping0.0010.0000.001
rnb.get.reference0.0010.0000.001
rnb.get.reliability.matrix0.0010.0000.000
rnb.infinium.control.targets0.0000.0000.001
rnb.initialize.reports000
rnb.is.option0.0010.0000.000
rnb.message.plot0.0010.0000.000
rnb.mval2beta0.0010.0000.001
rnb.options000
rnb.options2xml0.0000.0000.001
rnb.plot.betadistribution.probeCategories0.0000.0010.000
rnb.plot.betadistribution.sampleGroups0.0010.0000.001
rnb.plot.control.barplot0.0010.0000.001
rnb.plot.control.boxplot0.0010.0000.001
rnb.plot.dreduction0.0000.0000.001
rnb.plot.locus.profile000
rnb.plot.negative.boxplot0.0000.0000.001
rnb.plot.region.profile.density000
rnb.plot.region.profiles0.0000.0000.001
rnb.plot.region.site.density0.0010.0000.000
rnb.plot.sentrix.distribution000
rnb.plot.snp.barplot0.0010.0000.001
rnb.plot.snp.boxplot000
rnb.plot.snp.heatmap0.0010.0000.000
rnb.region.types0.0010.0000.001
rnb.region.types.for.analysis0.0000.0000.001
rnb.remove.annotation000
rnb.run.example000
rnb.runs000
rnb.sample.groups0.0010.0010.000
rnb.sample.summary.table000
rnb.set.annotation0.0010.0000.000
rnb.write.table0.0010.0000.000
rnb.xml2options0.0000.0010.001
rowOneSampleTP000
rowWelchP0.0000.0000.001
run-RnBClusterRun-methods0.0000.0000.001
samples-methods000
save.tables-RnBDiffMeth-methods0.0000.0000.001
set.covariates.sva0.0000.0000.001
sites-methods000
summarize.regions-methods000
summarized.regions-methods0.0000.0000.001