| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-27 02:34:42 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the RnBeads package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RnBeads.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1701/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RnBeads 2.17.0 (landing page) Fabian Mueller
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | TIMEOUT | |||||||||
| Package: RnBeads |
| Version: 2.17.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz |
| StartedAt: 2023-02-24 17:34:11 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 19:34:11 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 7200.5 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: RnBeads.Rcheck |
| Warnings: NA |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings RnBeads_2.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RnBeads.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RnBeads/DESCRIPTION’ ... OK
* this is package ‘RnBeads’ version ‘2.17.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'S4Vectors', 'GenomicRanges', 'MASS', 'cluster',
'ff', 'fields', 'ggplot2', 'gplots', 'grid', '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 ... NOTE
Found the following hidden files and directories:
.travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 5.5Mb
sub-directories of 1Mb or more:
R 3.1Mb
bin 1.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘qvalue’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'grid'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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.agecomparison.plot: no visible global function definition for
‘%dopar%’
add.agecomparison.plot: no visible global function definition for
‘foreach’
add.agecomparison.plot: no visible binding for global variable ‘i’
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.profile.plots: no visible global function definition for ‘mclapply’
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.stratification.plot: no visible global function definition for
‘%dopar%’
add.stratification.plot: no visible global function definition for
‘foreach’
add.stratification.plot: no visible binding for global variable ‘Group’
add.stratification.plot: no visible binding for global variable
‘Increase’
add.stratification.plot: no visible binding for global variable
‘Predicted’
add.stratification.plot: no visible binding for global variable
‘Annotated’
add.stratification.plot.immune: no visible global function definition
for ‘%dopar%’
add.stratification.plot.immune: no visible global function definition
for ‘foreach’
add.stratification.plot.immune: no visible binding for global variable
‘Group’
add.stratification.plot.immune: no visible binding for global variable
‘Immune’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘var.diff’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘log10P’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘combinedRank.var’
addReportPlot.diffVar.volcano: no visible binding for global variable
‘log10FDR’
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’
basic_combine: no visible global function definition for ‘samples’
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.site: no visible binding for global variable
‘p.vals.t.na.adj’
computeDiffTab.default.site : <anonymous>: no visible binding for
global variable ‘.inds.g2’
computeDiffVar.bin.site: no visible binding for global variable
‘p.vals.t.na.adj’
computeDiffVar.bin.site : <anonymous>: no visible binding for global
variable ‘eps’
computeDiffVar.bin.site : <anonymous>: no visible binding for global
variable ‘.inds.g2’
computeDiffVar.default.region: no visible global function definition
for ‘%dopar%’
computeDiffVar.default.region: no visible global function definition
for ‘foreach’
computeDiffVar.default.region: no visible binding for global variable
‘i’
create.densityScatter: no visible binding for global variable
‘..density..’
create.diffMeth.diffVar.subsample: no visible binding for global
variable ‘..density..’
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<-’
diffVar: no visible global function definition for ‘varFit’
diffVar: no visible binding for global variable ‘group1’
diffVar: no visible binding for global variable ‘group2’
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’
get.platform.tokens: no visible global function definition for
‘setNames’
getCGCounts: no visible global function definition for ‘seqlengths’
getCGCounts : <anonymous>: no visible global function definition for
‘ChrNumeric’
getGLADProfiles: no visible global function definition for ‘samples’
getGLADProfiles: no visible global function definition for ‘mclapply’
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’
iEVORA: no visible global function definition for ‘qvalue’
imputation.low.memory.cpgs: no visible global function definition for
‘samples’
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’
knn.imputation: no visible global function definition for ‘impute.knn’
limmaP: no visible binding for global variable ‘group1’
limmaP: no visible binding for global variable ‘group2’
loadLolaDbs: no visible global function definition for ‘loadRegionDB’
loadLolaDbs: no visible global function definition for ‘mergeRegionDBs’
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’
performLolaEnrichment.diffMeth: no visible global function definition
for ‘runLOLA’
performLolaEnrichment.diffVar: no visible global function definition
for ‘runLOLA’
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’
prepareGEOSampleInfoTemplate: no visible global function definition for
‘samples’
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’
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.bed.from.segmentation: no visible global function definition for
‘samples’
rnb.boxplot.from.segmentation: no visible global function definition
for ‘samples’
rnb.boxplot.from.segmentation: no visible binding for global variable
‘Segment’
rnb.boxplot.from.segmentation: no visible binding for global variable
‘AvgMeth’
rnb.chromosome.lengths: no visible global function definition for
‘seqlengths’
rnb.combine.seq: no visible global function definition for ‘samples’
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.high.coverage.removal.internal: no visible global function
definition for ‘samples’
rnb.execute.high.dpval.masking.internal: no visible global function
definition for ‘samples’
rnb.execute.imputation: no visible global function definition for
‘samples’
rnb.execute.low.coverage.masking.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.pOOBAH: no visible global function definition for ‘samples’
rnb.execute.pOOBAH: no visible global function definition for ‘SigDF’
rnb.execute.pOOBAH: no visible global function definition for ‘pOOBAH’
rnb.execute.pOOBAH: no visible binding for global variable ‘sigset.l’
rnb.execute.pOOBAH: no visible binding for global variable ‘pIG’
rnb.execute.pOOBAH: no visible binding for global variable ‘pII’
rnb.execute.pOOBAH: no visible binding for global variable ‘pIR’
rnb.execute.quality: no visible global function definition for
‘samples’
rnb.execute.quality : <anonymous>: no visible global function
definition for ‘samples’
rnb.execute.segmentation: no visible binding for global variable
‘Hsapiens’
rnb.execute.segmentation: no visible binding for global variable
‘Mmusculus’
rnb.execute.segmentation: no visible global function definition for
‘seqlengths’
rnb.execute.segmentation: no visible global function definition for
‘browserSession’
rnb.execute.segmentation: no visible global function definition for
‘genome<-’
rnb.execute.segmentation: no visible global function definition for
‘ucscTableQuery’
rnb.execute.segmentation: no visible global function definition for
‘getTable’
rnb.execute.segmentation: no visible global function definition for
‘samples’
rnb.execute.segmentation: no visible global function definition for
‘readMethylome’
rnb.execute.segmentation: no visible global function definition for
‘readSNPTable’
rnb.execute.segmentation: no visible global function definition for
‘removeSNPs’
rnb.execute.segmentation: no visible global function definition for
‘segmentPMDs’
rnb.execute.segmentation: no visible global function definition for
‘plotAlphaDistributionOneChr’
rnb.execute.segmentation: no visible global function definition for
‘calculateFDRs’
rnb.execute.segmentation: no visible global function definition for
‘segmentUMRsLMRs’
rnb.export.to.ewasher: no visible global function definition for
‘samples’
rnb.filter.dataset: no visible global function definition for ‘samples’
rnb.final.segmentation: no visible global function definition for
‘samples’
rnb.get.reliability.counts.per.sample: no visible global function
definition for ‘samples’
rnb.options.description.table.fromRd: no visible global function
definition for ‘Rd2HTML’
rnb.options.description.table.fromRd: no visible binding for global
variable ‘xmlValue’
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.segmentation.distributions: no visible binding for global
variable ‘x2’
rnb.plot.segmentation.distributions: no visible binding for global
variable ‘y2’
rnb.plot.segmentation.distributions: no visible binding for global
variable ‘texthere’
rnb.plot.segmentation.final: no visible global function definition for
‘plotFinalSegmentation’
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.example: no visible global function definition for ‘install’
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.region : do.enrichment.table.var: 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.diffVar: no visible global function definition for
‘%dopar%’
rnb.section.diffVar: no visible global function definition for
‘foreach’
rnb.section.diffVar.region: no visible global function definition for
‘%dopar%’
rnb.section.diffVar.region: no visible global function definition for
‘foreach’
rnb.section.diffVar.region: no visible binding for global variable ‘k’
rnb.section.import: no visible global function definition for ‘samples’
rnb.section.import: no visible global function definition for
‘phenoData’
rnb.section.imputation: no visible global function definition for
‘melt’
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.sex.prediction: no visible global function definition for
‘muted’
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.dreduction: no visible global function definition for
‘%dopar%’
rnb.step.dreduction: no visible global function definition for
‘foreach’
rnb.step.dreduction: no visible binding for global variable ‘target’
rnb.step.filter.summary.internal: no visible global function definition
for ‘percent_format’
rnb.step.filter.summary.internal: no visible global function definition
for ‘samples’
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’
sampleCovgApply: no visible global function definition for ‘samples’
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<-’
coerce,RnBeadRawSet-RGChannelSet: no visible global function definition
for ‘RGChannelSet’
join.diffMeth,RnBDiffMeth-RnBDiffMeth: no visible global function
definition for ‘clone’
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
updateMethylationSites,RnBSet: no visible global function definition
for ‘samples’
Undefined global functions or variables:
%dopar% ..count.. ..density.. .inds.g2 Address Age Annotated AvgMeth
BiomartGeneRegionTrack ChrNumeric DataTrack Density Deviance
Difference DoISVA Error GenomeAxisTrack Group Hsapiens ID
IdeogramTrack IlluminaHumanMethylation450kmanifest
IlluminaHumanMethylationEPICmanifest Immune Increase Index Intensity
Measure Mmusculus Predicted Probe RGChannelSet Rd2HTML SNP Sample
Segment SigDF Slide Target Term UcscTrack Value addSex as.profileCGH
assayDataElement assayDataElementNames barcode browserSession bv
calculateFDRs chrom clone combinedRank combinedRank.var comma
covgMedian covgPercLow covgPercUp cv.glmnet daglad diffmeth
diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency eps
expectedCounts featureData featureData<- featureNames featureNames<-
foreach geneCounts genome<- getCN getDoParWorkers getGreen
getManifest getMeth getRed getSex getTable getUnmeth getVarCov glmnet
grid.draw grid.newpage group group1 group2 i impute.knn install
is.subsegmentation k letterFrequency lme loadRegionDB log10FDR log10P
mapToGenome mclapply mean.diff mean.quot.log2 melt mergeRegionDBs
muted n.sites num.sites numSites numeric.names oddsRatios
p.vals.t.na.adj pData pIG pII pIR pOOBAH percent_format phenoData
phenoData<- plotAlphaDistributionOneChr plotFinalSegmentation
plotTracks preprocessSWAN pvalues qvalue readMethylome readSNPTable
refText reg.type region.size registerDoParallel relative.coord
removeSNPs report runLOLA samples segmentPMDs segmentUMRsLMRs
seqlengths seqlevels<- setNames sigCategories sigset.l sites2ignore
size solve.QP stopCluster sva target texthere tsne type types
ucscTableQuery universeCounts useMart v var.diff varFit varLabels x
x2 xmlValue y y2 yint
Consider adding
importFrom("stats", "setNames")
to your NAMESPACE file.
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...
RnBeads.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RnBeads ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘RnBeads’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (RnBeads)
RnBeads.Rcheck/RnBeads-Ex.timings
| name | user | system | elapsed | |
| M-methods | 0.000 | 0.001 | 0.000 | |
| U-methods | 0 | 0 | 0 | |
| addDiffMethTable-RnBDiffMeth-methods | 0.000 | 0.000 | 0.001 | |
| addPheno-RnBSet-methods | 0.001 | 0.000 | 0.000 | |
| addRegionSubsegments | 0 | 0 | 0 | |
| annotation-methods | 0 | 0 | 0 | |
| assembly-methods | 0 | 0 | 0 | |
| combine.rnb.sets-methods | 0 | 0 | 0 | |
| combineTestPvalsMeth | 0 | 0 | 0 | |
| computeDiffTab.region | 0 | 0 | 0 | |
| computeDiffTab.site | 0 | 0 | 0 | |
| covg-methods | 0 | 0 | 0 | |
| create.densityScatter | 0 | 0 | 0 | |
| create.scatter.dens.points | 0.000 | 0.000 | 0.001 | |
| createReport | 0.001 | 0.000 | 0.000 | |
| createReportPlot | 0 | 0 | 0 | |
| downloadLolaDbs | 0 | 0 | 0 | |
| dpval-methods | 0.000 | 0.000 | 0.001 | |
| exportDMRs2regionFile | 0 | 0 | 0 | |
| get.adjustment.variables | 0 | 0 | 0 | |
| get.comparison.grouplabels-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.comparison.groupsizes-RnBDiffMeth-methods | 0 | 0 | 0 | |
| get.comparison.info | 0 | 0 | 0 | |
| get.comparisons-RnBDiffMeth-methods | 0 | 0 | 0 | |
| 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 | 0.001 | 0.000 | 0.000 | |
| getCellTypesFromLolaDb | 0 | 0 | 0 | |
| getNamesFromLolaDb | 0 | 0 | 0 | |
| getSubCmdTokens-ClusterArchitectureSGE-methods | 0 | 0 | 0 | |
| getSubCmdTokens-ClusterArchitectureSLURM-methods | 0 | 0 | 0 | |
| getTargetFromLolaDb | 0 | 0 | 0 | |
| has.covariates.sva | 0 | 0 | 0 | |
| hasCovg-methods | 0 | 0 | 0 | |
| includes.sites-RnBDiffMeth-methods | 0 | 0 | 0 | |
| is.valid-RnBDiffMeth-methods | 0 | 0 | 0 | |
| join.diffMeth-methods | 0.000 | 0.000 | 0.001 | |
| limmaP | 0.001 | 0.000 | 0.000 | |
| loadLolaDbs | 0 | 0 | 0 | |
| logger.argument | 0 | 0 | 0 | |
| logger.getfiles | 0 | 0 | 0 | |
| logger.isinitialized | 0 | 0 | 0 | |
| logger.validate.file | 0 | 0 | 0 | |
| loggerManagement | 0 | 0 | 0 | |
| loggerMessages | 0.001 | 0.000 | 0.000 | |
| lolaBarPlot | 0 | 0 | 0 | |
| lolaBoxPlotPerTarget | 0 | 0 | 0 | |
| lolaVolcanoPlot | 0.000 | 0.000 | 0.001 | |
| mergeSamples-methods | 0 | 0 | 0 | |
| meth-methods | 0 | 0 | 0 | |
| mval-methods | 0 | 0 | 0 | |
| nsites-methods | 0 | 0 | 0 | |
| parallel.getNumWorkers | 0 | 0 | 0 | |
| parallel.isEnabled | 0 | 0 | 0 | |
| parallel.setup | 0.000 | 0.000 | 0.001 | |
| parallel.teardown | 0.001 | 0.000 | 0.000 | |
| performGOEnrichment.diffVar | 0 | 0 | 0 | |
| performGOenrichment.diffMeth.entrez | 0 | 0 | 0 | |
| performGoEnrichment.diffMeth | 0.000 | 0.000 | 0.001 | |
| performLolaEnrichment.diffMeth | 0 | 0 | 0 | |
| performLolaEnrichment.diffVar | 0 | 0 | 0 | |
| pheno-methods | 0.000 | 0.001 | 0.000 | |
| qc-methods | 0 | 0 | 0 | |
| read.sample.annotation | 0.001 | 0.000 | 0.000 | |
| regionMapping-methods | 0 | 0 | 0 | |
| regions-methods | 0 | 0 | 0 | |
| reload-RnBDiffMeth-methods | 0 | 0 | 0 | |
| remove.regions-methods | 0 | 0 | 0 | |
| remove.samples-methods | 0 | 0 | 0 | |
| remove.sites-methods | 0 | 0 | 0 | |
| rnb.RnBSet.to.GRangesList | 0 | 0 | 0 | |
| rnb.RnBSet.to.bed | 0 | 0 | 0 | |
| rnb.RnBSet.to.bedGraph | 0 | 0 | 0 | |
| rnb.add.list | 0.000 | 0.000 | 0.001 | |
| rnb.add.paragraph | 0.001 | 0.000 | 0.000 | |
| rnb.add.reference | 0 | 0 | 0 | |
| rnb.add.section | 0 | 0 | 0 | |
| rnb.annotation.size | 0.000 | 0.000 | 0.001 | |
| rnb.annotation2data.frame | 0 | 0 | 0 | |
| rnb.beta2mval | 0 | 0 | 0 | |
| rnb.execute.batcheffects | 0 | 0 | 0 | |
| rnb.execute.clustering | 0 | 0 | 0 | |
| rnb.execute.computeDiffMeth | 0 | 0 | 0 | |
| rnb.execute.context.removal | 0 | 0 | 0 | |
| rnb.execute.cross.reactive.removal | 0 | 0 | 0 | |
| rnb.execute.dreduction | 0 | 0 | 0 | |
| rnb.execute.export.csv | 0 | 0 | 0 | |
| rnb.execute.greedycut | 0 | 0 | 0 | |
| rnb.execute.import | 0 | 0 | 0 | |
| rnb.execute.na.removal | 0 | 0 | 0 | |
| rnb.execute.normalization | 0 | 0 | 0 | |