RnBeads 1.6.1
Fabian Mueller
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/RnBeads | | Last Changed Rev: 123052 / Revision: 128728 | | Last Changed Date: 2016-10-26 09:03:47 -0400 (Wed, 26 Oct 2016) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ WARNINGS ] | |  |
| tokay1 | Windows Server 2012 R2 Standard / 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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### /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RnBeads_1.6.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RnBeads.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘1.6.1’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘GenomicRanges’ ‘MASS’ ‘RColorBrewer’
‘cluster’ ‘ff’ ‘fields’ ‘ggplot2’ ‘gplots’ ‘gridExtra’ ‘limma’
‘matrixStats’ ‘illuminaio’ ‘methylumi’ ‘plyr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RnBeads’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘gridExtra::combine’ by ‘methylumi::combine’ when loading ‘RnBeads’
See ‘/home/biocbuild/bbs-3.4-bioc/meat/RnBeads.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 6.3Mb
sub-directories of 1Mb or more:
R 1.2Mb
bin 1.0Mb
doc 3.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory ‘data’ contains no data sets.
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... NOTE
Warning: no function found corresponding to methods exports from ‘RnBeads’ for: ‘samples’
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: 'GLAD'
'library' or 'require' calls not declared from:
'GLAD' 'IlluminaHumanMethylation450kanno.ilmn12.hg19' 'scales'
'library' or 'require' calls in package code:
'Category' 'GLAD' 'GOstats' 'Gviz'
'IlluminaHumanMethylation450kanno.ilmn12.hg19'
'IlluminaHumanMethylation450kmanifest' 'RefFreeEWAS' 'annotate'
'biomaRt' 'doParallel' 'foreach' 'glmnet' 'impute' 'isva' 'minfi'
'nlme' 'quadprog' 'scales' 'sva' 'wateRmelon'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'GenomicRanges::unlist'
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'CONTROL.TARGETS.SAMPLE.INDEPENDENT'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
add.combination.plot: warning in facet_grid(Set ˜ ., scale = "free",
drop = TRUE): partial argument match of 'scale' to 'scales'
.stopImplicitCluster: no visible global function definition for
‘stopCluster’
BMIQ: no visible global function definition for ‘density’
BMIQ: no visible global function definition for ‘pbeta’
BMIQ: no visible global function definition for ‘qbeta’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘varLabels’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureData’
add.age.histogram: no visible binding for global variable ‘Age’
add.age.histogram: no visible binding for global variable ‘..count..’
add.age.histogram: no visible binding for global variable ‘..density..’
add.agecomparison.plot: no visible binding for global variable ‘Sample’
add.combination.plot: no visible binding for global variable
‘Difference’
add.combination.plot: no visible binding for global variable ‘Density’
add.combination.plot: no visible binding for global variable ‘yint’
add.combination.plot: no visible binding for global variable ‘Measure’
add.error.plot: no visible binding for global variable ‘Value’
add.error.plot: no visible binding for global variable ‘Sample’
add.error.plot: no visible binding for global variable ‘Deviance’
add.error.plot: no visible binding for global variable ‘yint’
add.error.plot: no visible binding for global variable ‘Measure’
add.negative.control.boxplot: no visible global function definition for
‘samples’
add.qc.barplots: no visible global function definition for ‘samples’
add.quantile.plot: no visible binding for global variable ‘Difference’
add.quantile.plot: no visible binding for global variable ‘..density..’
add.quantile.plot: no visible binding for global variable ‘Sample’
add.quantile.plot: no visible binding for global variable ‘Density’
add.seq.coverage.histograms: no visible global function definition for
‘samples’
add.seq.coverage.plot: no visible global function definition for
‘samples’
add.seq.coverage.violins: no visible global function definition for
‘samples’
add.snp.barplot: no visible global function definition for ‘samples’
add.snp.distances: no visible global function definition for
‘grid.newpage’
add.snp.distances: no visible global function definition for
‘grid.draw’
add.snp.distances: no visible global function definition for ‘prcomp’
addReportPlots.diffMeth.bin.region.volcano: no visible binding for
global variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.diff’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.val’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘combinedRank’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘mean.quot.log2’
addReportPlots.diffMeth.bin.site.volcano: no visible binding for global
variable ‘diffmeth.p.adj.fdr’
agePredictor450: no visible global function definition for ‘read.csv’
agePredictor450: no visible global function definition for
‘capture.output’
agePredictor450: no visible global function definition for ‘impute.knn’
agePredictorRRBS: no visible global function definition for ‘read.csv’
agePredictorRRBS: no visible global function definition for
‘capture.output’
agePredictorRRBS: no visible global function definition for
‘impute.knn’
agePredictorRRBS: no visible global function definition for ‘samples’
append.cpg.stats: no visible global function definition for ‘%dopar%’
append.cpg.stats: no visible global function definition for ‘foreach’
append.cpg.stats: no visible binding for global variable ‘chrom’
betaEst2: no visible global function definition for ‘optim’
blc2: no visible global function definition for ‘dbeta’
bootInferWBCbyLm: no visible global function definition for ‘rnorm’
bootInferWBCbyLm: no visible global function definition for ‘rt’
bootInferWBCbyLme: no visible global function definition for ‘rnorm’
bootInferWBCbyLme: no visible global function definition for ‘rt’
combineTestPvalsMeth: no visible global function definition for
‘pchisq’
complete.report: no visible global function definition for
‘packageVersion’
compute.sva.assoc: no visible global function definition for ‘prcomp’
computeDiffTab.default.region: no visible global function definition
for ‘%dopar%’
computeDiffTab.default.region: no visible global function definition
for ‘foreach’
computeDiffTab.default.region: no visible binding for global variable
‘i’
computeDiffTab.default.region: no visible global function definition
for ‘p.adjust’
computeDiffTab.extended.site: no visible global function definition for
‘p.adjust’
corrHeatmap: no visible global function definition for
‘colorRampPalette’
corrHeatmap : color.function: no visible global function definition for
‘rainbow’
create.densityScatter: no visible binding for global variable
‘..density..’
create.densityScatter: no visible global function definition for
‘densCols’
create.densityScatter: no visible global function definition for
‘colorRampPalette’
create.diffMeth.bin.dens.dmp.scatter: no visible global function
definition for ‘densCols’
create.diffMeth.bin.dens.dmp.scatter: no visible global function
definition for ‘colorRampPalette’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘mean.g1’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘mean.g2’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘color’
create.diffMeth.bin.dens.dmp.scatter: no visible binding for global
variable ‘plotOrder’
create.diffMeth.bin.dens.dmr.scatter: no visible global function
definition for ‘densCols’
create.diffMeth.bin.dens.dmr.scatter: no visible global function
definition for ‘colorRampPalette’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘mean.mean.g1’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘mean.mean.g2’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘color’
create.diffMeth.bin.dens.dmr.scatter: no visible binding for global
variable ‘plotOrder’
create.scatter.dens.points: no visible global function definition for
‘densCols’
create.scatter.dens.points: no visible global function definition for
‘colorRampPalette’
create.ucsc.track.hub: no visible global function definition for
‘samples’
createPredictor : ret: no visible global function definition for ‘coef’
createPredictor : ret: no visible global function definition for
‘capture.output’
createPredictor : ret: no visible global function definition for
‘impute.knn’
createPredictor : ret: no visible global function definition for
‘predict’
cv.array: no visible global function definition for ‘capture.output’
cv.array: no visible global function definition for ‘impute.knn’
data.frame2GRanges: no visible global function definition for
‘seqlevels<-’
data.frame2GRanges: no visible global function definition for
‘genome<-’
densRanks: no visible global function definition for ‘xy.coords’
deviation.plot: no visible global function definition for
‘split.screen’
deviation.plot: no visible global function definition for ‘screen’
deviation.plot: no visible global function definition for ‘par’
deviation.plot: no visible global function definition for ‘plot’
deviation.plot: no visible global function definition for ‘mtext’
deviation.plot: no visible global function definition for ‘polygon’
deviation.plot: no visible global function definition for ‘lines’
deviation.plot: no visible global function definition for
‘close.screen’
deviation.plot.beta.internal : get.fractions: no visible global
function definition for ‘ecdf’
dist.correlation: no visible global function definition for ‘as.dist’
estimateProportionsCP: no visible global function definition for
‘as.formula’
estimateProportionsCP: no visible global function definition for ‘lme’
estimateProportionsCP: no visible global function definition for ‘lm’
estimateProportionsCP: no visible global function definition for
‘getVarCov’
estimateProportionsCP: no visible global function definition for ‘vcov’
estimateProportionsCP: no visible global function definition for
‘residuals’
estimateProportionsCP: no visible global function definition for ‘pf’
exportDMRs2regionFile: no visible global function definition for
‘write.table’
general.cv: no visible global function definition for ‘%dopar%’
general.cv: no visible global function definition for ‘foreach’
general.cv: no visible binding for global variable ‘i’
get.adjustment.variables: no visible global function definition for
‘samples’
get.comparison.info : rm.na.from.adj.tab: no visible global function
definition for ‘samples’
get.comparison.info: no visible global function definition for ‘combn’
get.components.isva: no visible global function definition for ‘DoISVA’
get.components.sva: no visible global function definition for
‘model.matrix’
get.components.sva: no visible global function definition for
‘as.formula’
get.components.sva: no visible global function definition for ‘sva’
get.cpg.stats: no visible global function definition for
‘dinucleotideFrequency’
get.cpg.stats: no visible global function definition for
‘letterFrequency’
get.dataset.matrix: no visible global function definition for ‘samples’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘report’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘refText’
get.diffmeth.tab.col.desc.list.txt: no visible binding for global
variable ‘diffmeth’
get.memory.usage: no visible global function definition for
‘memory.size’
get.rnb.version: no visible global function definition for
‘packageVersion’
get.subsegments: no visible global function definition for ‘dist’
get.subsegments: no visible global function definition for ‘hclust’
get.subsegments: no visible global function definition for ‘cutree’
getCGCounts : <anonymous>: no visible global function definition for
‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘as.profileCGH’
getGLADProfiles : <anonymous>: no visible global function definition
for ‘daglad’
getMergeList: no visible global function definition for ‘samples’
groupPermutationP.site.parallel: no visible global function definition
for ‘%dopar%’
groupPermutationP.site.parallel: no visible global function definition
for ‘foreach’
heatmap.mod: no visible binding for global variable ‘dist’
heatmap.mod: no visible binding for global variable ‘hclust’
heatmap.mod : <anonymous>: no visible global function definition for
‘reorder’
heatmap.mod: no visible global function definition for ‘as.dendrogram’
heatmap.mod: no visible global function definition for
‘order.dendrogram’
heatmap.mod: no visible global function definition for ‘dev.flush’
heatmap.mod: no visible global function definition for ‘par’
heatmap.mod: no visible global function definition for ‘layout’
heatmap.mod: no visible global function definition for ‘image’
heatmap.mod: no visible global function definition for ‘axis’
heatmap.mod: no visible global function definition for ‘mtext’
heatmap.mod: no visible global function definition for ‘plot’
heatmap.mod: no visible global function definition for ‘frame’
heatmap.mod: no visible global function definition for ‘title’
inferWBCbyLm: no visible global function definition for ‘lm’
inferWBCbyLm: no visible global function definition for ‘predict’
inferWBCbyLm: no visible global function definition for ‘residuals’
inferWBCbyLm: no visible global function definition for ‘model.matrix’
inferWBCbyLme: no visible global function definition for ‘lme’
inferWBCbyLme: no visible global function definition for ‘lm’
inferWBCbyLme: no visible global function definition for ‘predict’
inferWBCbyLme: no visible global function definition for ‘residuals’
inferWBCbyLme: no visible global function definition for ‘getVarCov’
inferWBCbyLme: no visible global function definition for ‘model.matrix’
init.pipeline.report: no visible global function definition for
‘read.delim’
intensities.by.color: no visible global function definition for
‘samples’
intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
limmaP: no visible global function definition for ‘model.matrix’
limmaP: no visible global function definition for ‘as.formula’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
load.rnb.set: no visible global function definition for ‘unzip’
locus.profile.get.base.tracks: no visible global function definition
for ‘useMart’
locus.profile.get.base.tracks: no visible global function definition
for ‘IdeogramTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘GenomeAxisTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘BiomartGeneRegionTrack’
locus.profile.get.base.tracks: no visible global function definition
for ‘UcscTrack’
locus.profile.get.methylation.track.heatmap: no visible global function
definition for ‘DataTrack’
locus.profile.get.methylation.track.smooth: no visible global function
definition for ‘DataTrack’
mds: no visible global function definition for ‘dist’
methylumi.intensities.by.color: no visible global function definition
for ‘featureNames’
methylumi.intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
methylumi.intensities.by.color: no visible global function definition
for ‘assayDataElement’
parallel.setup: no visible global function definition for
‘registerDoParallel’
parallel.setup: no visible global function definition for
‘getDoParWorkers’
plot.heatmap.pc.correlations: no visible global function definition for
‘melt’
plot.heatmap.pc.correlations: no visible global function definition for
‘grid.newpage’
plot.heatmap.pc.correlations: no visible global function definition for
‘grid.draw’
plot.heatmap.pc.pvalues: no visible global function definition for
‘melt’
plot.heatmap.pc.pvalues: no visible global function definition for
‘grid.newpage’
plot.heatmap.pc.pvalues: no visible global function definition for
‘grid.draw’
plot.heatmap.rand: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for ‘melt’
plot.heatmap.symm: no visible global function definition for
‘grid.newpage’
plot.heatmap.symm: no visible global function definition for
‘grid.draw’
plotCGHProfile: no visible global function definition for ‘ChrNumeric’
plotCGHProfile: no visible global function definition for ‘par’
plotCGHProfile: no visible global function definition for ‘layout’
plotCGHProfile: no visible global function definition for ‘plot’
plotCGHProfile: no visible global function definition for ‘lines’
plotCGHProfile: no visible global function definition for ‘abline’
plotcdf: no visible global function definition for ‘ecdf’
plotcdf: no visible global function definition for ‘knots’
print.inferWBCsummary: no visible global function definition for
‘pnorm’
projectWBC: no visible global function definition for ‘solve.QP’
read.GS.report: no visible global function definition for
‘featureNames’
read.data.dir: no visible global function definition for ‘read.table’
read.idat.files: no visible global function definition for ‘ecdf’
read.idat.files: no visible binding for global variable ‘barcode’
read.sample.annotation: no visible global function definition for
‘read.table’
read.single.bed: no visible global function definition for ‘read.table’
read.single.bed: no visible global function definition for ‘read.delim’
refFreeEWASP: no visible global function definition for
‘packageVersion’
refFreeEWASP: no visible global function definition for ‘model.matrix’
refFreeEWASP: no visible global function definition for ‘as.formula’
refFreeEWASP: no visible global function definition for ‘EstDimRMT’
refFreeEWASP: no visible global function definition for
‘RefFreeEwasModel’
refFreeEWASP: no visible global function definition for
‘PairsBootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for
‘BootRefFreeEwasModel’
refFreeEWASP: no visible global function definition for ‘pt’
rnb.RnBSet.to.GRangesList: no visible global function definition for
‘samples’
rnb.RnBSet.to.bed: no visible global function definition for ‘samples’
rnb.RnBSet.to.bed: no visible global function definition for
‘write.table’
rnb.RnBSet.to.bedGraph: no visible global function definition for
‘samples’
rnb.RnBSet.to.bedGraph: no visible global function definition for
‘write.table’
rnb.build.index.internal: no visible global function definition for
‘read.delim’
rnb.color.legends : plotlegend: no visible global function definition
for ‘par’
rnb.color.legends : plotlegend: no visible global function definition
for ‘plot.new’
rnb.color.legends : plotlegend: no visible global function definition
for ‘legend’
rnb.diffmeth.to.EpiExplorer.file: no visible global function definition
for ‘write.table’
rnb.execute.clustering: no visible global function definition for
‘dist’
rnb.execute.clustering: no visible global function definition for
‘hclust’
rnb.execute.clustering: no visible global function definition for
‘cutree’
rnb.execute.dreduction: no visible global function definition for
‘samples’
rnb.execute.dreduction: no visible global function definition for
‘prcomp’
rnb.execute.filter.summary.internal: no visible global function
definition for ‘samples’
rnb.execute.na.removal: no visible binding for global variable
‘filtered’
rnb.execute.na.removal.internal: no visible global function definition
for ‘samples’
rnb.execute.normalization: no visible global function definition for
‘samples’
rnb.execute.normalization: no visible global function definition for
‘phenoData’
rnb.execute.normalization: no visible global function definition for
‘phenoData<-’
rnb.execute.normalization: no visible global function definition for
‘RGChannelSet’
rnb.execute.normalization: no visible global function definition for
‘preprocessSWAN’
rnb.execute.normalization: no visible global function definition for
‘getMeth’
rnb.execute.normalization: no visible global function definition for
‘getUnmeth’
rnb.execute.normalization: no visible global function definition for
‘featureNames’
rnb.execute.normalization: no visible global function definition for
‘%dopar%’
rnb.execute.normalization: no visible global function definition for
‘foreach’
rnb.execute.normalization: no visible global function definition for
‘mapToGenome’
rnb.execute.normalization: no visible global function definition for
‘addSex’
rnb.execute.normalization: no visible global function definition for
‘getSex’
rnb.execute.normalization: no visible global function definition for
‘getCN’
rnb.execute.quality: no visible global function definition for
‘samples’
rnb.execute.quality : <anonymous>: no visible global function
definition for ‘samples’
rnb.export.annotation: no visible global function definition for
‘write.table’
rnb.export.to.ewasher: no visible global function definition for
‘samples’
rnb.export.to.ewasher: no visible global function definition for
‘write.table’
rnb.export.to.ewasher: no visible global function definition for
‘model.matrix’
rnb.filter.dataset: no visible global function definition for ‘samples’
rnb.get.assemblies: no visible global function definition for
‘installed.packages’
rnb.get.chrom.sizes: no visible global function definition for
‘read.delim’
rnb.get.reliability.counts.per.sample: no visible global function
definition for ‘samples’
rnb.load.bed: no visible global function definition for ‘read.delim’
rnb.plot.GLAD.profile: no visible global function definition for ‘data’
rnb.plot.GLAD.profile: no visible binding for global variable
‘cytoband’
rnb.plot.beta.density.group: no visible binding for global variable
‘group’
rnb.plot.biseq.coverage: no visible global function definition for
‘samples’
rnb.plot.biseq.coverage.hist: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible global function definition for
‘samples’
rnb.plot.control.barplot: no visible binding for global variable
‘Target’
rnb.plot.control.barplot: no visible binding for global variable
‘Index’
rnb.plot.control.barplot: no visible binding for global variable ‘ID’
rnb.plot.control.barplot: no visible binding for global variable
‘Address’
rnb.plot.control.barplot: no visible global function definition for
‘grid.newpage’
rnb.plot.control.barplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.barplot: no visible global function definition for
‘grid.draw’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.newpage’
rnb.plot.control.boxplot: no visible binding for global variable
‘Probe’
rnb.plot.control.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.control.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.coverage.thresholds: no visible global function definition for
‘rgb’
rnb.plot.ct.heatmap: no visible binding for global variable ‘x’
rnb.plot.ct.heatmap: no visible binding for global variable ‘y’
rnb.plot.ct.heatmap: no visible binding for global variable ‘v’
rnb.plot.ct.heatmap: no visible global function definition for
‘grid.newpage’
rnb.plot.ct.heatmap: no visible global function definition for
‘grid.draw’
rnb.plot.dreduction: no visible global function definition for ‘prcomp’
rnb.plot.dreduction: no visible global function definition for ‘tsne’
rnb.plot.dreduction: no visible global function definition for ‘dist’
rnb.plot.locus.profile: no visible global function definition for
‘plotTracks’
rnb.plot.marker.fstat: no visible binding for global variable ‘x’
rnb.plot.marker.fstat: no visible binding for global variable ‘y’
rnb.plot.marker.fstat: no visible global function definition for
‘muted’
rnb.plot.negative.boxplot: no visible global function definition for
‘samples’
rnb.plot.negative.boxplot: no visible binding for global variable
‘numeric.names’
rnb.plot.negative.boxplot: no visible binding for global variable
‘type’
rnb.plot.negative.boxplot: no visible binding for global variable
‘types’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.newpage’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Sample’
rnb.plot.negative.boxplot: no visible binding for global variable
‘Intensity’
rnb.plot.negative.boxplot: no visible global function definition for
‘grid.draw’
rnb.plot.num.sites.covg: no visible global function definition for
‘samples’
rnb.plot.num.sites.covg : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.num.sites.covg: no visible binding for global variable
‘numSites’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgMedian’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercLow’
rnb.plot.num.sites.covg: no visible binding for global variable
‘covgPercUp’
rnb.plot.num.sites.covg: no visible binding for global variable ‘comma’
rnb.plot.region.profile.density: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profile.density: no visible binding for global variable
‘..density..’
rnb.plot.region.profiles : <anonymous>: no visible global function
definition for ‘samples’
rnb.plot.region.profiles: no visible binding for global variable
‘relative.coord’
rnb.plot.region.profiles: no visible binding for global variable
‘group’
rnb.plot.region.site.density: no visible binding for global variable
‘relative.coord’
rnb.plot.sentrix.distributions: no visible global function definition
for ‘samples’
rnb.plot.sentrix.distributions: no visible binding for global variable
‘Slide’
rnb.plot.snp.barplot: no visible global function definition for
‘samples’
rnb.plot.snp.boxplot: no visible global function definition for
‘samples’
rnb.plot.snp.boxplot: no visible binding for global variable ‘SNP’
rnb.plot.snp.boxplot: no visible binding for global variable
‘Beta.values’
rnb.plot.snp.heatmap: no visible global function definition for
‘samples’
rnb.run.example: no visible global function definition for
‘download.file’
rnb.run.example: no visible global function definition for ‘untar’
rnb.run.preprocessing : logger.completed.filtering: no visible global
function definition for ‘samples’
rnb.sample.summary.table: no visible global function definition for
‘samples’
rnb.section.ageprediction: no visible global function definition for
‘samples’
rnb.section.clustering : <anonymous> : <anonymous>: no visible global
function definition for ‘samples’
rnb.section.clustering: no visible global function definition for
‘samples’
rnb.section.clustering : add.legend: no visible global function
definition for ‘screen’
rnb.section.clustering : add.legend: no visible global function
definition for ‘par’
rnb.section.clustering : add.legend: no visible global function
definition for ‘plot.new’
rnb.section.clustering : add.legend: no visible global function
definition for ‘legend’
rnb.section.clustering: no visible global function definition for
‘split.screen’
rnb.section.clustering: no visible global function definition for
‘close.screen’
rnb.section.clustering.add.heatmap: no visible global function
definition for ‘as.dendrogram’
rnb.section.clustering.add.heatmap : distfun: no visible global
function definition for ‘dist’
rnb.section.clustering.add.heatmap: no visible global function
definition for ‘hclust’
rnb.section.diffMeth.region: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.region: no visible global function definition for
‘foreach’
rnb.section.diffMeth.region: no visible binding for global variable ‘k’
rnb.section.diffMeth.region : do.enrichment.table: no visible global
function definition for ‘sigCategories’
rnb.section.diffMeth.site: no visible global function definition for
‘%dopar%’
rnb.section.diffMeth.site: no visible global function definition for
‘foreach’
rnb.section.gender.prediction: no visible global function definition
for ‘muted’
rnb.section.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
‘phenoData’
rnb.section.locus.profiles: no visible global function definition for
‘samples’
rnb.section.locus.profiles : do.plots: no visible global function
definition for ‘plotTracks’
rnb.section.locus.profiles: no visible global function definition for
‘%dopar%’
rnb.section.locus.profiles: no visible global function definition for
‘foreach’
rnb.section.na.removal: no visible global function definition for
‘samples’
rnb.section.normalization: no visible global function definition for
‘samples’
rnb.section.region.description: no visible binding for global variable
‘size’
rnb.section.region.description: no visible binding for global variable
‘n.sites’
rnb.section.region.profiles: no visible global function definition for
‘samples’
rnb.section.region.subsegmentation : get.summary.df.from.list: no
visible global function definition for ‘melt’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘region.size’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘is.subsegmentation’
rnb.section.region.subsegmentation: no visible binding for global
variable ‘num.sites’
rnb.section.replicate.concordance: no visible global function
definition for ‘combn’
rnb.show.report: no visible global function definition for ‘browseURL’
rnb.step.betadistribution.internal: no visible global function
definition for ‘%dopar%’
rnb.step.betadistribution.internal: no visible global function
definition for ‘foreach’
rnb.step.cell.types: no visible global function definition for
‘samples’
rnb.step.clustering.internal: no visible global function definition for
‘samples’
rnb.step.cnv: no visible binding for global variable ‘intensities’
rnb.step.dreduction: no visible global function definition for
‘%dopar%’
rnb.step.dreduction: no visible global function definition for
‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
for ‘percent_format’
rnb.step.import: no visible global function definition for ‘samples’
rnb.step.import: no visible global function definition for ‘phenoData’
rnb.step.na.removal: no visible binding for global variable
‘sites2ignore’
rnb.step.na.removal.internal: no visible global function definition for
‘samples’
rnb.step.normalization: no visible global function definition for
‘phenoData’
rnb.write.table: no visible global function definition for
‘write.table’
robustHyperGResultSummary: no visible global function definition for
‘sigCategories’
robustHyperGResultSummary: no visible global function definition for
‘pvalues’
robustHyperGResultSummary: no visible global function definition for
‘oddsRatios’
robustHyperGResultSummary: no visible global function definition for
‘expectedCounts’
robustHyperGResultSummary: no visible global function definition for
‘geneCounts’
robustHyperGResultSummary: no visible global function definition for
‘universeCounts’
robustHyperGResultSummary: no visible binding for global variable
‘Term’
rowOneSampleTP: no visible global function definition for ‘pt’
rowPairedTP: no visible global function definition for ‘pt’
rowWelchP: no visible global function definition for ‘pt’
run.cross.validation: no visible global function definition for
‘samples’
run.cross.validation: no visible global function definition for ‘melt’
run.cross.validation: no visible binding for global variable ‘Measure’
run.cross.validation: no visible binding for global variable ‘Error’
save.rnb.set: no visible global function definition for ‘zip’
set.covariates.ct: no visible global function definition for ‘samples’
simpleGlmnet: no visible global function definition for
‘capture.output’
simpleGlmnet: no visible global function definition for ‘impute.knn’
simpleGlmnet: no visible global function definition for ‘cv.glmnet’
simpleGlmnet: no visible global function definition for ‘glmnet’
simpleGlmnet: no visible global function definition for ‘coef’
simpleGlmnetEvaluate: no visible global function definition for
‘cv.glmnet’
simpleGlmnetEvaluate: no visible global function definition for
‘glmnet’
simpleGlmnetRRBS: no visible global function definition for ‘cv.glmnet’
simpleGlmnetRRBS: no visible global function definition for ‘glmnet’
simpleGlmnetRRBS: no visible global function definition for ‘coef’
symmetric.melt: no visible global function definition for ‘melt’
tTestP: no visible global function definition for ‘t.test’
test.traits: no visible global function definition for ‘fisher.test’
test.traits: no visible global function definition for ‘wilcox.test’
test.traits: no visible global function definition for ‘kruskal.test’
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
‘reg.type’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureData<-’
coerce,RnBeadRawSet-MethyLumiSet: no visible global function definition
for ‘featureNames<-’
combine,RnBSet-RnBSet: no visible global function definition for
‘samples’
initialize,ReportPlot: no visible global function definition for ‘pdf’
initialize,ReportPlot: no visible global function definition for ‘png’
initialize,ReportPlot: no visible global function definition for
‘dev.control’
initialize,ReportPlot: no visible global function definition for ‘par’
mask.sites.meth,RnBSet: no visible global function definition for
‘samples’
off,ReportPlot : convert.f : doerror: no visible global function
definition for ‘dev.off’
off,ReportPlot : convert.f: no visible global function definition for
‘dev2bitmap’
off,ReportPlot: no visible global function definition for ‘dev.off’
remove.samples,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
‘samples’
remove.samples,RnBeadSet: no visible global function definition for
‘samples’
remove.sites,RnBSet: no visible global function definition for
‘samples’
sampleCovgApply,RnBSet: no visible global function definition for
‘samples’
sampleMethApply,RnBSet: no visible global function definition for
‘samples’
summarize.regions,RnBSet: no visible global function definition for
‘samples’
summarize.regions,RnBSet: multiple local function definitions for
‘aggr.f’ with different formal arguments
Undefined global functions or variables:
%dopar% ..count.. ..density.. Address Age Beta.values
BiomartGeneRegionTrack BootRefFreeEwasModel ChrNumeric DataTrack
Density Deviance Difference DoISVA Error EstDimRMT GenomeAxisTrack ID
IdeogramTrack IlluminaHumanMethylation450kmanifest Index Intensity
Measure PairsBootRefFreeEwasModel Probe RGChannelSet RefFreeEwasModel
SNP Sample Slide Target Term UcscTrack Value abline addSex
as.dendrogram as.dist as.formula as.profileCGH assayDataElement
assayDataElementNames axis barcode browseURL capture.output chrom
close.screen coef color colorRampPalette combinedRank combn comma
covgMedian covgPercLow covgPercUp cutree cv.glmnet cytoband daglad
data dbeta densCols density dev.control dev.flush dev.off dev2bitmap
diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency dist
download.file ecdf expectedCounts featureData featureData<-
featureNames featureNames<- filtered fisher.test foreach frame
geneCounts genome<- getCN getDoParWorkers getMeth getSex getUnmeth
getVarCov glmnet grid.draw grid.newpage group group1 group2 hclust i
image impute.knn installed.packages intensities is.subsegmentation k
knots kruskal.test layout legend letterFrequency lines lm lme
mapToGenome mean.diff mean.g1 mean.g2 mean.mean.g1 mean.mean.g2
mean.quot.log2 melt memory.size model.matrix mtext muted n.sites
num.sites numSites numeric.names oddsRatios optim order.dendrogram
p.adjust packageVersion par pbeta pchisq pdf percent_format pf
phenoData phenoData<- plot plot.new plotOrder plotTracks png pnorm
polygon prcomp predict preprocessSWAN pt pvalues qbeta rainbow
read.csv read.delim read.table refText reg.type region.size
registerDoParallel relative.coord reorder report residuals rgb rnorm
rt samples screen seqlevels<- sigCategories sites2ignore size
solve.QP split.screen stopCluster sva t.test target title tsne type
types universeCounts untar unzip useMart v varLabels vcov wilcox.test
write.table x xy.coords y yint zip
Consider adding
importFrom("grDevices", "colorRampPalette", "densCols", "dev.control",
"dev.flush", "dev.off", "dev2bitmap", "pdf", "png",
"rainbow", "rgb", "xy.coords")
importFrom("graphics", "abline", "axis", "close.screen", "frame",
"image", "layout", "legend", "lines", "mtext", "par",
"plot", "plot.new", "polygon", "screen", "split.screen",
"title")
importFrom("stats", "as.dendrogram", "as.dist", "as.formula", "coef",
"cutree", "dbeta", "density", "dist", "ecdf", "fisher.test",
"hclust", "knots", "kruskal.test", "lm", "model.matrix",
"optim", "order.dendrogram", "p.adjust", "pbeta", "pchisq",
"pf", "pnorm", "prcomp", "predict", "pt", "qbeta",
"reorder", "residuals", "rnorm", "rt", "t.test", "vcov",
"wilcox.test")
importFrom("utils", "browseURL", "capture.output", "combn", "data",
"download.file", "installed.packages", "memory.size",
"packageVersion", "read.csv", "read.delim", "read.table",
"untar", "unzip", "write.table", "zip")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
generic '[' and siglist 'BigFfMat,ANY,ANY,ANY'
generic '[<-' and siglist 'BigFfMat,ANY,ANY,ANY'
generic 'dim' and siglist 'BigFfMat'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'agePredictor':
agePredictor
Code: function(rnbSet, path = "")
Docs: function(rnbSet, path = system.file(file.path("extdata",
"predefined_predictor.csv"), package = "RnBeads"))
Mismatches in argument default values:
Name: 'path'
Code: ""
Docs: system.file(file.path("extdata", "predefined_predictor.csv"),
package = "RnBeads")
Codoc mismatches from documentation object 'createPredictor':
createPredictor
Code: function(linearModel, lambda = NULL)
Docs: function(linearModel)
Argument names in code not in docs:
lambda
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'read.single.bed'
‘chr.col’ ‘start.col’ ‘end.col’ ‘strand.col’ ‘c.col’ ‘t.col’
‘is.epp.style’ ‘coord.shift’ ‘ffread’ ‘context’ ‘...’
Undocumented arguments in documentation object 'sampleCovgApply,RnBSet-method'
‘object’ ‘type’ ‘...’
Undocumented arguments in documentation object 'sampleMethApply,RnBSet-method'
‘object’ ‘type’ ‘...’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.4-bioc/meat/RnBeads.Rcheck/00check.log’
for details.