RnBeads 1.3.7
Fabian Mueller
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RnBeads | | Last Changed Rev: 116535 / Revision: 116626 | | Last Changed Date: 2016-04-19 01:26:13 -0700 (Tue, 19 Apr 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | WARNINGS | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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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_1.3.7.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/RnBeads.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.3.7’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘GenomicRanges’ ‘MASS’ ‘RColorBrewer’
‘cluster’ ‘ff’ ‘fields’ ‘ggplot2’ ‘gplots’ ‘gridExtra’ ‘limma’
‘matrixStats’ ‘illuminaio’ ‘methylumi’ ‘plyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... [31s/32s] WARNING
Found the following significant warnings:
Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’
See ‘/Users/biocbuild/bbs-3.3-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 ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'GLAD'
'library' or 'require' calls not declared from:
'GLAD' 'IlluminaHumanMethylation450kanno.ilmn12.hg19' 'scales'
'library' or 'require' calls in package code:
'Category' 'GLAD' 'GOstats' 'Gviz'
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
'IlluminaHumanMethylation450kmanifest' 'RefFreeEWAS' 'annotate'
'biomaRt' 'doParallel' 'foreach' 'isva' 'minfi' 'nlme' 'quadprog'
'scales' 'sva' 'wateRmelon'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'GenomicRanges::unlist'
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'CONTROL.TARGETS.SAMPLE.INDEPENDENT'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
‘stopCluster’
BMIQ: no visible global function definition for ‘density’
BMIQ: no visible global function definition for ‘pbeta’
BMIQ: no visible global function definition for ‘qbeta’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘varLabels’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureData’
add.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.newpage’
add.snp.distances: no visible global function definition for
‘grid.draw’
add.snp.distances: no visible global function definition for ‘prcomp’
addReportPlots.diffMeth.bin.region.volcano: no visible binding for
global variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.diff’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.val’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.quot.log2’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.adj.fdr’
append.cpg.stats: no visible global function definition for ‘%dopar%’
append.cpg.stats: no visible global function definition for ‘foreach’
append.cpg.stats: no visible binding for global variable ‘chrom’
betaEst2: no visible global function definition for ‘optim’
blc2: no visible global function definition for ‘dbeta’
bootInferWBCbyLm: no visible global function definition for ‘rnorm’
bootInferWBCbyLm: no visible global function definition for ‘rt’
bootInferWBCbyLme: no visible global function definition for ‘rnorm’
bootInferWBCbyLme: no visible global function definition for ‘rt’
combineTestPvalsMeth: no visible global function definition for
‘pchisq’
complete.report: no visible global function definition for
‘packageVersion’
compute.sva.assoc: no visible global function definition for ‘prcomp’
computeDiffTab.default.region: no visible global function definition
for ‘%dopar%’
computeDiffTab.default.region: no visible global function definition
for ‘foreach’
computeDiffTab.default.region: no visible binding for global variable
‘i’
computeDiffTab.default.region: no visible global function definition
for ‘p.adjust’
computeDiffTab.extended.site: no visible global function definition for
‘p.adjust’
corrHeatmap: no visible global function definition for
‘colorRampPalette’
corrHeatmap : color.function: no visible global function definition for
‘rainbow’
create.densityScatter: no visible binding for global variable
‘..density..’
create.densityScatter: no visible global function definition for
‘densCols’
create.densityScatter: no visible global function definition for
‘colorRampPalette’
create.diffMeth.bin.dens.dmp.scatter: no visible global function
definition for ‘densCols’
create.diffMeth.bin.dens.dmp.scatter: no visible global function
definition for ‘colorRampPalette’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘mean.g1’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘mean.g2’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘color’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘plotOrder’
create.diffMeth.bin.dens.dmr.scatter: no visible global function
definition for ‘densCols’
create.diffMeth.bin.dens.dmr.scatter: no visible global function
definition for ‘colorRampPalette’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘mean.mean.g1’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘mean.mean.g2’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘color’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘plotOrder’
create.scatter.dens.points: no visible global function definition for
‘densCols’
create.scatter.dens.points: no visible global function definition for
‘colorRampPalette’
create.ucsc.track.hub: no visible global function definition for
‘samples’
data.frame2GRanges: no visible global function definition for
‘seqlevels<-’
data.frame2GRanges: no visible global function definition for
‘genome<-’
densRanks: no visible global function definition for ‘xy.coords’
deviation.plot: no visible global function definition for
‘split.screen’
deviation.plot: no visible global function definition for ‘screen’
deviation.plot: no visible global function definition for ‘par’
deviation.plot: no visible global function definition for ‘plot’
deviation.plot: no visible global function definition for ‘mtext’
deviation.plot: no visible global function definition for ‘polygon’
deviation.plot: no visible global function definition for ‘lines’
deviation.plot: no visible global function definition for
‘close.screen’
deviation.plot.beta.internal : get.fractions: no visible global
function definition for ‘ecdf’
dist.correlation: no visible global function definition for ‘as.dist’
estimateProportionsCP: no visible global function definition for
‘as.formula’
estimateProportionsCP: no visible global function definition for ‘lme’
estimateProportionsCP: no visible global function definition for ‘lm’
estimateProportionsCP: no visible global function definition for
‘getVarCov’
estimateProportionsCP: no visible global function definition for ‘vcov’
estimateProportionsCP: no visible global function definition for
‘residuals’
estimateProportionsCP: no visible global function definition for ‘pf’
exportDMRs2regionFile: no visible global function definition for
‘write.table’
get.adjustment.variables: no visible global function definition for
‘samples’
get.comparison.info : rm.na.from.adj.tab: no visible global function
definition for ‘samples’
get.comparison.info: no visible global function definition for ‘combn’
get.components.isva: no visible global function definition for ‘DoISVA’
get.components.sva: no visible global function definition for
‘model.matrix’
get.components.sva: no visible global function definition for
‘as.formula’
get.components.sva: no visible global function definition for ‘sva’
get.cpg.stats: no visible global function definition for
‘dinucleotideFrequency’
get.cpg.stats: no visible global function definition for
‘letterFrequency’
get.dataset.matrix: no visible global function definition for ‘samples’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘report’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘refText’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘diffmeth’
get.memory.usage: no visible global function definition for
‘memory.size’
get.rnb.version: no visible global function definition for
‘packageVersion’
get.subsegments: no visible global function definition for ‘dist’
get.subsegments: no visible global function definition for ‘hclust’
get.subsegments: no visible global function definition for ‘cutree’
getCGCounts : <anonymous>: no visible global function definition for
‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘as.profileCGH’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘daglad’
getMergeList: no visible global function definition for ‘samples’
groupPermutationP.site.parallel: no visible global function definition
for ‘%dopar%’
groupPermutationP.site.parallel: no visible global function definition
for ‘foreach’
heatmap.mod: no visible binding for global variable ‘dist’
heatmap.mod: no visible binding for global variable ‘hclust’
heatmap.mod : <anonymous>: no visible global function definition for
‘reorder’
heatmap.mod: no visible global function definition for ‘as.dendrogram’
heatmap.mod: no visible global function definition for
‘order.dendrogram’
heatmap.mod: no visible global function definition for ‘dev.flush’
heatmap.mod: no visible global function definition for ‘par’
heatmap.mod: no visible global function definition for ‘layout’
heatmap.mod: no visible global function definition for ‘image’
heatmap.mod: no visible global function definition for ‘axis’
heatmap.mod: no visible global function definition for ‘mtext’
heatmap.mod: no visible global function definition for ‘plot’
heatmap.mod: no visible global function definition for ‘frame’
heatmap.mod: no visible global function definition for ‘title’
inferWBCbyLm: no visible global function definition for ‘lm’
inferWBCbyLm: no visible global function definition for ‘predict’
inferWBCbyLm: no visible global function definition for ‘residuals’
inferWBCbyLm: no visible global function definition for ‘model.matrix’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘lm’
inferWBCbyLme: no visible global function definition for ‘predict’
inferWBCbyLme: no visible global function definition for ‘residuals’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
inferWBCbyLme: no visible global function definition for ‘model.matrix’
init.pipeline.report: no visible global function definition for
‘read.delim’
intensities.by.color: no visible global function definition for
‘samples’
intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
limmaP: no visible global function definition for ‘model.matrix’
limmaP: no visible global function definition for ‘as.formula’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
load.rnb.set: no visible global function definition for ‘unzip’
locus.profile.get.base.tracks: no visible global function definition
for ‘useMart’
locus.profile.get.base.tracks: no visible global function definition
for ‘IdeogramTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘GenomeAxisTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘BiomartGeneRegionTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘UcscTrack’
locus.profile.get.methylation.track.heatmap: no visible global function
definition for ‘DataTrack’
locus.profile.get.methylation.track.smooth: no visible global function
definition for ‘DataTrack’
mds: no visible global function definition for ‘dist’
methylumi.intensities.by.color: no visible global function definition
for ‘featureNames’
methylumi.intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
methylumi.intensities.by.color: no visible global function definition
for ‘assayDataElement’
parallel.setup: no visible global function definition for
‘registerDoParallel’
parallel.setup: no visible global function definition for
‘getDoParWorkers’
plot.heatmap.pc.correlations: no visible global function definition for
‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
‘grid.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’
plotCGHProfile: no visible global function definition for ‘par’
plotCGHProfile: no visible global function definition for ‘layout’
plotCGHProfile: no visible global function definition for ‘plot’
plotCGHProfile: no visible global function definition for ‘lines’
plotCGHProfile: no visible global function definition for ‘abline’
plotcdf: no visible global function definition for ‘ecdf’
plotcdf: no visible global function definition for ‘knots’
print.inferWBCsummary: no visible global function definition for
‘pnorm’
projectWBC: no visible global function definition for ‘solve.QP’
read.GS.report: no visible global function definition for
‘featureNames’
read.data.dir: no visible global function definition for ‘read.table’
read.idat.files: no visible global function definition for ‘ecdf’
read.idat.files: no visible binding for global variable ‘barcode’
read.sample.annotation: no visible global function definition for
‘read.table’
read.single.bed: no visible global function definition for ‘read.table’
read.single.bed: no visible global function definition for ‘read.delim’
refFreeEWASP: no visible global function definition for
‘packageVersion’
refFreeEWASP: no visible global function definition for ‘model.matrix’
refFreeEWASP: no visible global function definition for ‘as.formula’
refFreeEWASP: no visible global function definition for ‘EstDimRMT’
refFreeEWASP: no visible global function definition for
‘RefFreeEwasModel’
refFreeEWASP: no visible global function definition for
‘PairsBootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for
‘BootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for ‘pt’
rnb.RnBSet.to.GRangesList: no visible global function definition for
‘samples’
rnb.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bed: no visible global function definition for
‘write.table’
rnb.RnBSet.to.bedGraph: no visible global function definition for
‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
‘write.table’
rnb.build.index.internal: no visible global function definition for
‘read.delim’
rnb.color.legends : plotlegend: no visible global function definition
for ‘par’
rnb.color.legends : plotlegend: no visible global function definition
for ‘plot.new’
rnb.color.legends : plotlegend: no visible global function definition
for ‘legend’
rnb.diffmeth.to.EpiExplorer.file: no visible global function definition
for ‘write.table’
rnb.execute.clustering: no visible global function definition for
‘dist’
rnb.execute.clustering: no visible global function definition for
‘hclust’
rnb.execute.clustering: no visible global function definition for
‘cutree’
rnb.execute.dreduction: no visible global function definition for
‘samples’
rnb.execute.dreduction: no visible global function definition for
‘prcomp’
rnb.execute.filter.summary.internal: no visible global function
definition for ‘samples’
rnb.execute.normalization: no visible global function definition for
‘samples’
rnb.execute.normalization: no visible global function definition for
‘phenoData’
rnb.execute.normalization: no visible global function definition for
‘phenoData<-’
rnb.execute.normalization: no visible global function definition for
‘RGChannelSet’
rnb.execute.normalization: no visible global function definition for
‘preprocessSWAN’
rnb.execute.normalization: no visible global function definition for
‘getMeth’
rnb.execute.normalization: no visible global function definition for
‘getUnmeth’
rnb.execute.normalization: no visible global function definition for
‘featureNames’
rnb.execute.normalization: no visible global function definition for
‘%dopar%’
rnb.execute.normalization: no visible global function definition for
‘foreach’
rnb.execute.normalization: no visible global function definition for
‘mapToGenome’
rnb.execute.normalization: no visible global function definition for
‘addSex’
rnb.execute.normalization: no visible global function definition for
‘getSex’
rnb.execute.normalization: no visible global function definition for
‘getCN’
rnb.execute.quality: no visible global function definition for
‘samples’
rnb.execute.quality : <anonymous>: no visible global function
definition for ‘samples’
rnb.export.annotation: no visible global function definition for
‘write.table’
rnb.export.to.ewasher: no visible global function definition for
‘samples’
rnb.export.to.ewasher: no visible global function definition for
‘write.table’
rnb.export.to.ewasher: no visible global function definition for
‘model.matrix’
rnb.get.assemblies: no visible global function definition for
‘installed.packages’
rnb.get.chrom.sizes: no visible global function definition for
‘read.delim’
rnb.get.reliability.counts.per.sample: no visible global function
definition for ‘samples’
rnb.load.bed: no visible global function definition for ‘read.delim’
rnb.plot.GLAD.profile: no visible global function definition for ‘data’
rnb.plot.GLAD.profile: no visible binding for global variable
‘cytoband’
rnb.plot.beta.density.group: no visible binding for global variable
‘group’
rnb.plot.biseq.coverage: no visible global function definition for
‘samples’
rnb.plot.biseq.coverage.hist: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible binding for global variable
‘Target’
rnb.plot.control.barplot: no visible binding for global variable
‘Index’
rnb.plot.control.barplot: no visible binding for global variable ‘ID’
rnb.plot.control.barplot: no visible binding for global variable
‘Address’
rnb.plot.control.barplot: no visible global function definition for
‘grid.newpage’
rnb.plot.control.barplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.barplot: no visible global function definition for
‘grid.draw’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.newpage’
rnb.plot.control.boxplot: no visible binding for global variable
‘Probe’
rnb.plot.control.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.coverage.thresholds: no visible global function definition for
‘rgb’
rnb.plot.ct.heatmap: no visible binding for global variable ‘x’
rnb.plot.ct.heatmap: no visible binding for global variable ‘y’
rnb.plot.ct.heatmap: no visible binding for global variable ‘v’
rnb.plot.ct.heatmap: no visible global function definition for
‘grid.draw’
rnb.plot.dreduction: no visible global function definition for ‘prcomp’
rnb.plot.locus.profile: no visible global function definition for
‘plotTracks’
rnb.plot.marker.fstat: no visible binding for global variable ‘x’
rnb.plot.marker.fstat: no visible binding for global variable ‘y’
rnb.plot.marker.fstat: no visible global function definition for
‘muted’
rnb.plot.negative.boxplot: no visible global function definition for
‘samples’
rnb.plot.negative.boxplot: no visible binding for global variable
‘numeric.names’
rnb.plot.negative.boxplot: no visible binding for global variable
‘type’
rnb.plot.negative.boxplot: no visible binding for global variable
‘types’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.newpage’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Sample’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.num.sites.covg: no visible global function definition for
‘samples’
rnb.plot.num.sites.covg : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.num.sites.covg: no visible binding for global variable
‘numSites’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgMedian’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercLow’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercUp’
rnb.plot.num.sites.covg: no visible binding for global variable ‘comma’
rnb.plot.region.profile.density: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profile.density: no visible binding for global variable
‘..density..’
rnb.plot.region.profiles : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.region.profiles: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profiles: no visible binding for global variable
‘group’
rnb.plot.region.site.density: no visible binding for global variable
‘relative.coord’
rnb.plot.sentrix.distributions: no visible global function definition
for ‘samples’
rnb.plot.sentrix.distributions: no visible binding for global variable
‘Slide’
rnb.plot.snp.barplot: no visible global function definition for
‘samples’
rnb.plot.snp.boxplot: no visible global function definition for
‘samples’
rnb.plot.snp.boxplot: no visible binding for global variable ‘SNP’
rnb.plot.snp.boxplot: no visible binding for global variable
‘Beta.values’
rnb.plot.snp.heatmap: no visible global function definition for
‘samples’
rnb.run.example: no visible global function definition for
‘download.file’
rnb.run.example: no visible global function definition for ‘untar’
rnb.run.preprocessing : logger.completed.filtering: no visible global
function definition for ‘samples’
rnb.sample.summary.table: no visible global function definition for
‘samples’
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
function definition for ‘samples’
rnb.section.clustering: no visible global function definition for
‘samples’
rnb.section.clustering : add.legend: no visible global function
definition for ‘screen’
rnb.section.clustering : add.legend: no visible global function
definition for ‘par’
rnb.section.clustering : add.legend: no visible global function
definition for ‘plot.new’
rnb.section.clustering : add.legend: no visible global function
definition for ‘legend’
rnb.section.clustering: no visible global function definition for
‘split.screen’
rnb.section.clustering: no visible global function definition for
‘close.screen’
rnb.section.clustering.add.heatmap: no visible global function
definition for ‘as.dendrogram’
rnb.section.clustering.add.heatmap : distfun: no visible global
function definition for ‘dist’
rnb.section.clustering.add.heatmap: no visible global function
definition for ‘hclust’
rnb.section.diffMeth.region: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.region: no visible global function definition for
‘foreach’
rnb.section.diffMeth.region: no visible binding for global variable ‘k’
rnb.section.diffMeth.region : do.enrichment.table: no visible global
function definition for ‘sigCategories’
rnb.section.diffMeth.site: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
‘foreach’
rnb.section.gender.prediction: no visible global function definition
for ‘muted’
rnb.section.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
‘phenoData’
rnb.section.locus.profiles: no visible global function definition for
‘samples’
rnb.section.locus.profiles : do.plots: no visible global function
definition for ‘plotTracks’
rnb.section.locus.profiles: no visible global function definition for
‘%dopar%’
rnb.section.locus.profiles: no visible global function definition for
‘foreach’
rnb.section.normalization: no visible global function definition for
‘samples’
rnb.section.region.description: no visible binding for global variable
‘size’
rnb.section.region.description: no visible binding for global variable
‘n.sites’
rnb.section.region.profiles: no visible global function definition for
‘samples’
rnb.section.region.subsegmentation : get.summary.df.from.list: no
visible global function definition for ‘melt’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘region.size’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘is.subsegmentation’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘num.sites’
rnb.section.replicate.concordance: no visible global function
definition for ‘combn’
rnb.show.report: no visible global function definition for ‘browseURL’
rnb.step.betadistribution.internal: no visible global function
definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
definition for ‘foreach’
rnb.step.cell.types: no visible global function definition for
‘samples’
rnb.step.clustering.internal: no visible global function definition for
‘samples’
rnb.step.cnv: no visible binding for global variable ‘intensities’
rnb.step.dreduction: no visible global function definition for
‘%dopar%’
rnb.step.dreduction: no visible global function definition for
‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
for ‘percent_format’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.normalization: no visible global function definition for
‘phenoData’
rnb.write.table: no visible global function definition for
‘write.table’
robustHyperGResultSummary: no visible global function definition for
‘sigCategories’
robustHyperGResultSummary: no visible global function definition for
‘pvalues’
robustHyperGResultSummary: no visible global function definition for
‘oddsRatios’
robustHyperGResultSummary: no visible global function definition for
‘expectedCounts’
robustHyperGResultSummary: no visible global function definition for
‘geneCounts’
robustHyperGResultSummary: no visible global function definition for
‘universeCounts’
robustHyperGResultSummary: no visible binding for global variable
‘Term’
rowOneSampleTP: no visible global function definition for ‘pt’
rowPairedTP: no visible global function definition for ‘pt’
rowWelchP: no visible global function definition for ‘pt’
save.rnb.set: no visible global function definition for ‘zip’
set.covariates.ct: no visible global function definition for ‘samples’
symmetric.melt: no visible global function definition for ‘melt’
tTestP: no visible global function definition for ‘t.test’
test.traits: no visible global function definition for ‘fisher.test’
test.traits: no visible global function definition for ‘wilcox.test’
test.traits: no visible global function definition for ‘kruskal.test’
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
‘reg.type’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureData<-’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureNames<-’
combine,RnBSet-RnBSet: no visible global function definition for
‘samples’
initialize,ReportPlot: no visible global function definition for ‘pdf’
initialize,ReportPlot: no visible global function definition for ‘png’
initialize,ReportPlot: no visible global function definition for
‘dev.control’
initialize,ReportPlot: no visible global function definition for ‘par’
off,ReportPlot : convert.f : doerror: no visible global function
definition for ‘dev.off’
off,ReportPlot : convert.f: no visible global function definition for
‘dev2bitmap’
off,ReportPlot: no visible global function definition for ‘dev.off’
remove.samples,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
‘samples’
remove.samples,RnBeadSet: no visible global function definition for
‘samples’
sampleCovgApply,RnBSet: no visible global function definition for
‘samples’
sampleMethApply,RnBSet: no visible global function definition for
‘samples’
summarize.regions,RnBSet: no visible global function definition for
‘samples’
summarize.regions,RnBSet: multiple local function definitions for
‘aggr.f’ with different formal arguments
Undefined global functions or variables:
%dopar% ..density.. Address Beta.values BiomartGeneRegionTrack
BootRefFreeEwasModel ChrNumeric DataTrack DoISVA EstDimRMT
GenomeAxisTrack ID IdeogramTrack IlluminaHumanMethylation450kmanifest
Index Intensity PairsBootRefFreeEwasModel Probe RGChannelSet
RefFreeEwasModel SNP Sample Slide Target Term UcscTrack abline addSex
as.dendrogram as.dist as.formula as.profileCGH assayDataElement
assayDataElementNames axis barcode browseURL chrom close.screen color
colorRampPalette combinedRank combn comma covgMedian covgPercLow
covgPercUp cutree cytoband daglad data dbeta densCols density
dev.control dev.flush dev.off dev2bitmap diffmeth diffmeth.p.adj.fdr
diffmeth.p.val dinucleotideFrequency dist download.file ecdf
expectedCounts featureData featureData<- featureNames featureNames<-
fisher.test foreach frame geneCounts genome<- getCN getDoParWorkers
getMeth getSex getUnmeth getVarCov grid.draw grid.newpage group
group1 group2 hclust i image installed.packages intensities
is.subsegmentation k knots kruskal.test layout legend letterFrequency
lines lm lme mapToGenome mean.diff mean.g1 mean.g2 mean.mean.g1
mean.mean.g2 mean.quot.log2 melt memory.size model.matrix mtext muted
n.sites num.sites numSites numeric.names oddsRatios optim
order.dendrogram p.adjust packageVersion par pbeta pchisq pdf
percent_format pf phenoData phenoData<- plot plot.new plotOrder
plotTracks png pnorm polygon prcomp predict preprocessSWAN pt pvalues
qbeta rainbow read.delim read.table refText reg.type region.size
registerDoParallel relative.coord reorder report residuals rgb rnorm
rt samples screen seqlevels<- sigCategories size solve.QP
split.screen stopCluster sva t.test target title type types
universeCounts untar unzip useMart v varLabels vcov wilcox.test
write.table x xy.coords y zip
Consider adding
importFrom("grDevices", "colorRampPalette", "densCols", "dev.control",
"dev.flush", "dev.off", "dev2bitmap", "pdf", "png",
"rainbow", "rgb", "xy.coords")
importFrom("graphics", "abline", "axis", "close.screen", "frame",
"image", "layout", "legend", "lines", "mtext", "par",
"plot", "plot.new", "polygon", "screen", "split.screen",
"title")
importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "cutree",
"dbeta", "density", "dist", "ecdf", "fisher.test", "hclust",
"knots", "kruskal.test", "lm", "model.matrix", "optim",
"order.dendrogram", "p.adjust", "pbeta", "pchisq", "pf",
"pnorm", "prcomp", "predict", "pt", "qbeta", "reorder",
"residuals", "rnorm", "rt", "t.test", "vcov", "wilcox.test")
importFrom("utils", "browseURL", "combn", "data", "download.file",
"installed.packages", "memory.size", "packageVersion",
"read.delim", "read.table", "untar", "unzip", "write.table",
"zip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'BigFfMat,ANY,ANY,ANY'
generic '[<-' and siglist 'BigFfMat,ANY,ANY,ANY'
generic 'dim' and siglist 'BigFfMat'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... 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 ... [12s/13s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [98s/567s]
[98s/567s] 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/RnBeads.Rcheck/00check.log’
for details.