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This page was generated on 2017-04-23 14:40:02 -0400 (Sun, 23 Apr 2017).
| Package 1131/1377 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| RnBeads 1.7.5 Fabian Mueller
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK |  | |||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | |||||
| toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | ||||||
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: RnBeads |
| Version: 1.7.5 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RnBeads_1.7.5.tar.gz |
| StartedAt: 2017-04-23 09:17:19 -0400 (Sun, 23 Apr 2017) |
| EndedAt: 2017-04-23 09:33:50 -0400 (Sun, 23 Apr 2017) |
| EllapsedTime: 991.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RnBeads.Rcheck |
| Warnings: 0 |
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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_1.7.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RnBeads.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.7.5’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘GenomicRanges’ ‘MASS’ ‘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 ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
R 1.4Mb
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 ... OK
* 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 ... NOTE
Unexported objects imported by ':::' calls:
'Gviz:::.getBMFeatureMap' 'doParallel:::.options'
'grDevices:::.smoothScatterCalcDensity'
'minfi:::.default.450k.annotation' 'minfi:::.extractFromRGSet450k'
'minfi:::.normalizeFunnorm450k'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.stopImplicitCluster: no visible global function definition for
‘stopCluster’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘phenoData’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘assayDataElementNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureNames’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘varLabels’
MethyLumiSet2RnBeadSet: no visible global function definition for
‘featureData’
add.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 global function definition for
‘samples’
add.agecomparison.plot: no visible binding for global variable ‘Sample’
add.combination.plot: no visible global function definition for
‘samples’
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’
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’
agePredictorBiseq: no visible global function definition for
‘impute.knn’
agePredictorBiseq: no visible global function definition for ‘samples’
agePredictorChip: no visible global function definition for
‘impute.knn’
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’
createPredictor : ret: no visible global function definition for
‘impute.knn’
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<-’
estimateProportionsCP: no visible global function definition for ‘lme’
estimateProportionsCP: no visible global function definition for
‘getVarCov’
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.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 binding for global variable
‘IlluminaHumanMethylationEPICmanifest’
intensities.by.color: no visible binding for global variable
‘IlluminaHumanMethylation450kmanifest’
intensities.by.color: no visible global function definition for
‘samples’
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.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’
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.add.snp.distances: no visible global function definition for
‘grid.newpage’
rnb.add.snp.distances: no visible global function definition for
‘grid.draw’
rnb.chromosome.lengths: no visible global function definition for
‘seqlengths’
rnb.enmix.oob: no visible global function definition for ‘%dopar%’
rnb.enmix.oob: no visible global function definition for ‘foreach’
rnb.execute.dreduction: no visible global function definition for
‘samples’
rnb.execute.filter.summary.internal: no visible global function
definition for ‘samples’
rnb.execute.na.removal.internal: 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
‘samples’
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.normalization.bmiq: no visible global function definition
for ‘%dopar%’
rnb.execute.normalization.bmiq: no visible global function definition
for ‘foreach’
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.filter.dataset: 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 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.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 ‘tsne’
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.boxplot: no visible binding for global variable ‘SNP’
rnb.plot.snp.boxplot: no visible binding for global variable ‘bv’
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.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.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’
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’
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’
set.covariates.ct: no visible global function definition for ‘samples’
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’
simpleGlmnetBiseq: no visible global function definition for
‘cv.glmnet’
simpleGlmnetBiseq: no visible global function definition for ‘glmnet’
simpleGlmnetEvaluate: no visible global function definition for
‘cv.glmnet’
simpleGlmnetEvaluate: no visible global function definition for
‘glmnet’
symmetric.melt: no visible global function definition for ‘melt’
addDiffMethTable,RnBDiffMeth: no visible binding for global variable
‘reg.type’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘getManifest’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘getGreen’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘getRed’
coerce,RGChannelSet-RnBeadRawSet: no visible global function definition
for ‘pData’
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’
mask.sites.meth,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBSet: no visible global function definition for
‘samples’
remove.samples,RnBeadRawSet: no visible global function definition for
‘samples’
remove.samples,RnBeadSet: no visible global function definition for
‘samples’
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 BiomartGeneRegionTrack
BootRefFreeEwasModel ChrNumeric DataTrack Density Deviance Difference
DoISVA Error EstDimRMT GenomeAxisTrack ID IdeogramTrack
IlluminaHumanMethylation450kmanifest
IlluminaHumanMethylationEPICmanifest Index Intensity Measure
PairsBootRefFreeEwasModel Probe RGChannelSet RefFreeEwasModel SNP
Sample Slide Target Term UcscTrack Value addSex as.profileCGH
assayDataElement assayDataElementNames barcode bv chrom color
combinedRank comma covgMedian covgPercLow covgPercUp cv.glmnet daglad
diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency
expectedCounts featureData featureData<- featureNames featureNames<-
foreach geneCounts genome<- getCN getDoParWorkers getGreen
getManifest getMeth getRed getSex getUnmeth getVarCov glmnet
grid.draw grid.newpage group group1 group2 i impute.knn intensities
is.subsegmentation k letterFrequency lme mapToGenome mean.diff
mean.g1 mean.g2 mean.mean.g1 mean.mean.g2 mean.quot.log2 melt muted
n.sites num.sites numSites numeric.names oddsRatios pData
percent_format phenoData phenoData<- plotOrder plotTracks
preprocessSWAN pvalues refText reg.type region.size
registerDoParallel relative.coord report samples seqlengths
seqlevels<- sigCategories sites2ignore size solve.QP stopCluster sva
target tsne type types universeCounts useMart v varLabels x y yint
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... 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: 5 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/RnBeads.Rcheck/00check.log’
for details.
RnBeads.Rcheck/00install.out:
* installing *source* package ‘RnBeads’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (RnBeads)
RnBeads.Rcheck/RnBeads-Ex.timings:
| name | user | system | elapsed | |
| M-methods | 0.001 | 0.001 | 0.000 | |
| U-methods | 0.000 | 0.000 | 0.001 | |
| addDiffMethTable-RnBDiffMeth-methods | 0.001 | 0.000 | 0.001 | |
| addPheno-RnBSet-methods | 0 | 0 | 0 | |
| addRegionSubsegments | 0 | 0 | 0 | |
| annotation-methods | 0.000 | 0.000 | 0.001 | |
| assembly-methods | 0 | 0 | 0 | |
| combine-methods | 0.001 | 0.000 | 0.000 | |
| combineTestPvalsMeth | 0 | 0 | 0 | |
| computeDiffTab.region | 0.000 | 0.000 | 0.001 | |
| computeDiffTab.site | 0.000 | 0.000 | 0.001 | |
| covg-methods | 0.001 | 0.000 | 0.001 | |
| create.densityScatter | 0 | 0 | 0 | |
| create.scatter.dens.points | 0.001 | 0.000 | 0.000 | |
| createReport | 0 | 0 | 0 | |
| createReportPlot | 0 | 0 | 0 | |
| dpval-methods | 0.001 | 0.000 | 0.000 | |
| exportDMRs2regionFile | 0.001 | 0.000 | 0.000 | |
| get.adjustment.variables | 0.000 | 0.000 | 0.001 | |
| get.comparison.grouplabels-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.comparison.groupsizes-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.comparison.info | 0.000 | 0.000 | 0.001 | |
| get.comparisons-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| get.covariates.sva | 0 | 0 | 0 | |
| get.covg.thres-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.files | 0 | 0 | 0 | |
| get.region.types-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.site.test.method-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| get.table-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| getSubCmdTokens-ClusterArchitectureSGE-methods | 0 | 0 | 0 | |
| has.covariates.sva | 0.001 | 0.000 | 0.000 | |
| hasCovg-methods | 0.000 | 0.001 | 0.001 | |
| includes.sites-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| is.valid-RnBDiffMeth-methods | 0.001 | 0.000 | 0.001 | |
| join.diffMeth-methods | 0.001 | 0.000 | 0.001 | |
| limmaP | 0.001 | 0.000 | 0.001 | |
| logger.argument | 0 | 0 | 0 | |
| logger.getfiles | 0 | 0 | 0 | |
| logger.isinitialized | 0.000 | 0.000 | 0.001 | |
| logger.validate.file | 0.001 | 0.000 | 0.000 | |
| loggerManagement | 0 | 0 | 0 | |
| loggerMessages | 0.001 | 0.000 | 0.001 | |
| mergeSamples-methods | 0 | 0 | 0 | |
| meth-methods | 0.000 | 0.000 | 0.001 | |
| mval-methods | 0.001 | 0.000 | 0.001 | |
| nsites-methods | 0 | 0 | 0 | |
| parallel.getNumWorkers | 0.001 | 0.000 | 0.001 | |
| parallel.isEnabled | 0.000 | 0.000 | 0.001 | |
| parallel.setup | 0 | 0 | 0 | |
| parallel.teardown | 0 | 0 | 0 | |
| performEnrichment.diffMeth | 0 | 0 | 0 | |
| performGOenrichment.diffMeth.entrez | 0 | 0 | 0 | |
| pheno-methods | 0.001 | 0.000 | 0.000 | |
| qc-methods | 0.000 | 0.000 | 0.001 | |
| read.sample.annotation | 0.001 | 0.000 | 0.000 | |
| regionMapping-methods | 0.000 | 0.000 | 0.001 | |
| regions-methods | 0.001 | 0.000 | 0.000 | |
| reload-RnBDiffMeth-methods | 0 | 0 | 0 | |
| remove.regions-methods | 0 | 0 | 0 | |
| remove.samples-methods | 0.001 | 0.000 | 0.000 | |
| remove.sites-methods | 0.001 | 0.000 | 0.001 | |
| rnb.RnBSet.to.GRangesList | 0.001 | 0.000 | 0.001 | |
| rnb.RnBSet.to.bed | 0.000 | 0.000 | 0.001 | |
| rnb.RnBSet.to.bedGraph | 0 | 0 | 0 | |
| rnb.add.list | 0.001 | 0.000 | 0.001 | |
| rnb.add.paragraph | 0.001 | 0.000 | 0.001 | |
| rnb.add.reference | 0.001 | 0.000 | 0.000 | |
| rnb.add.section | 0.001 | 0.000 | 0.000 | |
| rnb.annotation.size | 0 | 0 | 0 | |
| rnb.annotation2data.frame | 0 | 0 | 0 | |
| rnb.beta2mval | 0 | 0 | 0 | |
| rnb.execute.batcheffects | 0.001 | 0.000 | 0.000 | |
| rnb.execute.clustering | 0 | 0 | 0 | |
| rnb.execute.computeDiffMeth | 0 | 0 | 0 | |
| rnb.execute.context.removal | 0.001 | 0.000 | 0.000 | |
| rnb.execute.cross.reactive.removal | 0.001 | 0.000 | 0.000 | |
| rnb.execute.dreduction | 0 | 0 | 0 | |
| rnb.execute.export.csv | 0.000 | 0.000 | 0.001 | |
| rnb.execute.gender.prediction | 0.001 | 0.000 | 0.001 | |
| rnb.execute.greedycut | 0.000 | 0.000 | 0.001 | |
| rnb.execute.import | 0.000 | 0.001 | 0.001 | |
| rnb.execute.na.removal | 0.001 | 0.000 | 0.001 | |
| rnb.execute.normalization | 0.001 | 0.000 | 0.001 | |
| rnb.execute.sex.removal | 0.000 | 0.000 | 0.001 | |
| rnb.execute.snp.removal | 0.000 | 0.000 | 0.001 | |
| rnb.execute.sva | 0 | 0 | 0 | |
| rnb.execute.tnt | 0.001 | 0.000 | 0.001 | |
| rnb.execute.variability.removal | 0 | 0 | 0 | |
| rnb.export.all.annotation | 0 | 0 | 0 | |
| rnb.export.annotation | 0.001 | 0.000 | 0.000 | |
| rnb.export.to.ewasher | 0.001 | 0.001 | 0.000 | |
| rnb.export.to.trackhub | 0 | 0 | 0 | |
| rnb.get.annotation | 0 | 0 | 0 | |
| rnb.get.assemblies | 0.001 | 0.000 | 0.001 | |
| rnb.get.chromosomes | 0.000 | 0.000 | 0.001 | |
| rnb.get.directory | 0.000 | 0.000 | 0.001 | |
| rnb.get.mapping | 0.001 | 0.000 | 0.001 | |
| rnb.get.reference | 0 | 0 | 0 | |
| rnb.get.reliability.matrix | 0.000 | 0.000 | 0.001 | |
| rnb.infinium.control.targets | 0.001 | 0.000 | 0.000 | |
| rnb.initialize.reports | 0.001 | 0.000 | 0.000 | |
| rnb.is.option | 0 | 0 | 0 | |
| rnb.message.plot | 0.000 | 0.000 | 0.001 | |
| rnb.mval2beta | 0.001 | 0.000 | 0.001 | |
| rnb.options | 0.000 | 0.000 | 0.001 | |
| rnb.options2xml | 0 | 0 | 0 | |
| rnb.plot.betadistribution.probeCategories | 0.000 | 0.000 | 0.001 | |
| rnb.plot.betadistribution.sampleGroups | 0.000 | 0.000 | 0.001 | |
| rnb.plot.control.barplot | 0.001 | 0.000 | 0.001 | |
| rnb.plot.control.boxplot | 0.000 | 0.000 | 0.001 | |
| rnb.plot.dreduction | 0.000 | 0.000 | 0.001 | |
| rnb.plot.locus.profile | 0.001 | 0.000 | 0.001 | |
| rnb.plot.negative.boxplot | 0.001 | 0.000 | 0.000 | |
| rnb.plot.region.profile.density | 0 | 0 | 0 | |
| rnb.plot.region.profiles | 0 | 0 | 0 | |
| rnb.plot.region.site.density | 0.001 | 0.000 | 0.000 | |
| rnb.plot.sentrix.distribution | 0 | 0 | 0 | |
| rnb.plot.snp.barplot | 0.000 | 0.000 | 0.001 | |
| rnb.plot.snp.boxplot | 0.001 | 0.000 | 0.001 | |
| rnb.plot.snp.heatmap | 0.001 | 0.000 | 0.001 | |
| rnb.region.types | 0 | 0 | 0 | |
| rnb.region.types.for.analysis | 0.000 | 0.000 | 0.001 | |
| rnb.remove.annotation | 0.001 | 0.000 | 0.001 | |
| rnb.run.example | 0.000 | 0.000 | 0.001 | |
| rnb.runs | 0.001 | 0.000 | 0.000 | |
| rnb.sample.groups | 0.001 | 0.000 | 0.000 | |
| rnb.sample.summary.table | 0.001 | 0.000 | 0.000 | |
| rnb.set.annotation | 0 | 0 | 0 | |
| rnb.write.table | 0.000 | 0.001 | 0.000 | |
| rnb.xml2options | 0 | 0 | 0 | |
| rowOneSampleTP | 0 | 0 | 0 | |
| rowWelchP | 0 | 0 | 0 | |
| run-RnBClusterRun-methods | 0 | 0 | 0 | |
| samples-methods | 0 | 0 | 0 | |
| save.tables-RnBDiffMeth-methods | 0 | 0 | 0 | |
| set.covariates.sva | 0.000 | 0.001 | 0.000 | |
| sites-methods | 0.001 | 0.000 | 0.000 | |
| summarize.regions-methods | 0.001 | 0.000 | 0.000 | |
| summarized.regions-methods | 0 | 0 | 0 | |