############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:RnBeads.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings RnBeads_2.25.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/RnBeads.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘RnBeads/DESCRIPTION’ ... OK * this is package ‘RnBeads’ version ‘2.25.0’ * checking package namespace information ... OK * checking package dependencies ... INFO 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/RnBeads.Rcheck/00install.out’ for details. * checking installed package size ... INFO installed size is 5.6Mb sub-directories of 1Mb or more: R 3.2Mb bin 1.0Mb * 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 code 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: program compiled against libxml 212 using older 211 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 Warning: program compiled against libxml 212 using older 211 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 ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 .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.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 ‘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’ computeDiffVar.bin.site: no visible binding for global variable ‘p.vals.t.na.adj’ 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.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.genesymbol.of.coordinate: no visible global function definition for ‘getBM’ get.platform.tokens: no visible global function definition for ‘setNames’ getCGCounts: no visible global function definition for ‘seqlengths’ getCGCounts : : no visible global function definition for ‘ChrNumeric’ getGLADProfiles: no visible global function definition for ‘samples’ getGLADProfiles: no visible global function definition for ‘mclapply’ getGLADProfiles : : no visible global function definition for ‘as.profileCGH’ getGLADProfiles : : 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.add.nv.heatmap: no visible binding for global variable ‘dataset’ 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 : : 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.biseq.coverage.hist: no visible binding for global variable ‘count’ 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 : : 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.nv.heatmap: no visible global function definition for ‘useMart’ rnb.plot.region.profile.density: no visible binding for global variable ‘relative.coord’ rnb.plot.region.profiles : : 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.exploratory: no visible global function definition for ‘useMart’ 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.beta.value.density.plot: no visible global function definition for ‘%dopar%’ rnb.section.beta.value.density.plot: no visible global function definition for ‘foreach’ rnb.section.clustering : : : 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.diffMeth.site: no visible global function definition for ‘useMart’ 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.na.removal.internal : : no visible binding for global variable ‘count’ rnb.section.normalization: no visible global function definition for ‘samples’ rnb.section.nv.probes.heatmap: 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% 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 count covgMedian covgPercLow covgPercUp cv.glmnet daglad dataset diffmeth diffmeth.p.adj.fdr diffmeth.p.val dinucleotideFrequency expectedCounts featureData featureData<- featureNames featureNames<- foreach geneCounts genome<- getBM 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 ... NOTE checkRd: (-1) as.RnBeadRawSet.Rd:9: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.RnBeadRawSet.Rd:10: Lost braces in \itemize; meant \describe ? checkRd: (-1) as.RnBeadRawSet.Rd:11: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:50-51: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:52-54: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:55-57: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:58-59: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReport.Rd:60-61: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReportPlot.Rd:48: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReportPlot.Rd:49: Lost braces in \itemize; meant \describe ? checkRd: (-1) createReportPlot.Rd:50: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:26-27: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:28: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:29: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.combine.seq.Rd:30: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:40: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:41-43: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:44: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:45: Lost braces in \itemize; meant \describe ? checkRd: (-1) rnb.execute.export.csv.Rd:46: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: coercion-methods.Rd: MethyLumiSet-class read.idat.files.Rd: MethyLumiSet-class, methylumIDAT read.idat.files2.Rd: MethyLumiSet-class, methylumIDAT rnb.execute.dreduction.Rd: isoMDS rnb.execute.import.Rd: MethyLumiSet-class rnb.execute.normalization.Rd: MethyLumiSet-class rnb.get.annotation.Rd: GRangesList, GRanges rnb.get.mapping.Rd: IRanges rnb.plot.biseq.coverage.Rd: ggplot rnb.plot.biseq.coverage.hist.Rd: ggplot rnb.plot.biseq.coverage.violin.Rd: ggplot rnb.plot.control.barplot.Rd: ggplot rnb.plot.control.boxplot.Rd: ggplot rnb.plot.negative.boxplot.Rd: ggplot rnb.plot.num.sites.covg.Rd: ggplot rnb.plot.sentrix.distribution.Rd: ggplot rnb.plot.snp.barplot.Rd: ggplot rnb.plot.snp.boxplot.Rd: ggplot save.rnb.set.Rd: ff Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. 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 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 ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 WARNINGs, 8 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/RnBeads.Rcheck/00check.log’ for details.