############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:methylumi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings methylumi_2.52.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/methylumi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘methylumi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylumi’ version ‘2.52.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' NOTE Depends: includes the non-default packages: 'Biobase', 'scales', 'reshape2', 'ggplot2', 'matrixStats', 'FDb.InfiniumMethylation.hg19', 'minfi' 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 ‘methylumi’ can be installed ... OK * checking installed package size ... NOTE installed size is 10.0Mb sub-directories of 1Mb or more: R 1.3Mb data 2.7Mb extdata 5.8Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biobase’ ‘minfi’ ‘lattice’ ‘matrixStats’ 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 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 ... OK * 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 'library' or 'require' calls to packages already attached by Depends: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘minfi’ ‘reshape2’ ‘scales’ Please remove these calls from your code. 'library' or 'require' calls in package code: ‘Biostrings’ ‘MASS’ ‘lumi’ ‘parallel’ ‘rtracklayer’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Namespace in Imports field not imported from: ‘graphics’ All declared Imports should be used. Packages in Depends field not imported from: ‘FDb.InfiniumMethylation.hg19’ ‘ggplot2’ ‘matrixStats’ ‘methods’ ‘reshape2’ ‘scales’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. ':::' call which should be '::': ‘lumi:::produceMethylationGEOSubmissionFile’ See the note in ?`:::` about the use of this operator. Unexported objects imported by ':::' calls: ‘Biobase:::unsafeSetSlot’ ‘genefilter:::.findCentralMap’ 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 getBarcodes: warning in list.files(path = path, patt = "idat"): partial argument match of 'patt' to 'pattern' coerce,RangedSummarizedExperiment-GenomicMethylSet: warning in assays(from, withDim = F): partial argument match of 'withDim' to 'withDimnames' .getFinalReportBlock: no visible global function definition for ‘read.table’ .mclapply: no visible global function definition for ‘mclapply’ .parallel : : no visible global function definition for ‘ecdf’ .readOldMethylationFile: no visible global function definition for ‘read.delim’ CSVtoDF: no visible global function definition for ‘read.csv’ SEtoGRset: no visible global function definition for ‘GenomicRatioSet’ beta.mme: no visible global function definition for ‘weighted.mean’ beta.transform: no visible global function definition for ‘weighted.mean’ cy3: no visible global function definition for ‘addColorChannelInfo’ cy5: no visible global function definition for ‘addColorChannelInfo’ gamma.get.xcs: no visible global function definition for ‘gamma.integral’ gamma.get.xs : : no visible global function definition for ‘gamma.mle’ gamma.get.xs : : no visible global function definition for ‘gamma.integral’ gamma.signal: no visible global function definition for ‘gamma.integral’ gammaM.get.xcs : : no visible binding for global variable ‘offset’ gammaM.get.xs : : no visible global function definition for ‘gamma.mode’ gammaM.get.xs : : no visible global function definition for ‘gamma.mle’ getAssayDataNameSubstitutions: no visible global function definition for ‘read.table’ getMethylationBeadMappers : : no visible global function definition for ‘data’ getMethylationBeadMappers : : no visible binding for global variable ‘hm27.controls’ getMethylationBeadMappers : : no visible binding for global variable ‘hm450.controls’ getMethylationBeadMappers : : no visible binding for global variable ‘hm27.ordering’ getMethylationBeadMappers : : no visible binding for global variable ‘hm450.ordering’ getPlatform: no visible binding for global variable ‘FDb.InfiniumMethylation.hg19’ getPlatform: no visible global function definition for ‘data’ getPlatform: no visible global function definition for ‘DNAStringSet’ illumina.get.xs: no visible global function definition for ‘colQuantiles’ median.get.xs: no visible global function definition for ‘colMedians’ methylumi.bgcorr: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ methylumi.bgcorr: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ methylumi.diagnostics: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ methylumi.diagnostics: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ methylumi.diagnostics: no visible global function definition for ‘par’ methylumi.diagnostics: no visible global function definition for ‘colorRampPalette’ methylumi.diagnostics: no visible global function definition for ‘lines’ methylumi.diagnostics: no visible global function definition for ‘title’ methylumi.diagnostics: no visible global function definition for ‘plot.density’ methylumi.diagnostics: no visible global function definition for ‘abline’ methylumiCSV: no visible global function definition for ‘DFsToNChannelSet’ methylumiR: no visible global function definition for ‘capture.output’ methylumiToMinfi: no visible global function definition for ‘RGChannelSet’ normalizeMethyLumiSet: no visible global function definition for ‘capture.output’ normexp.get.xs: no visible global function definition for ‘huber’ normexp.get.xs: no visible global function definition for ‘colSds’ normexp.signal: no visible global function definition for ‘dnorm’ normexp.signal: no visible global function definition for ‘pnorm’ plotNegOob: no visible global function definition for ‘par’ plotNegOob : : no visible global function definition for ‘melt’ plotNegOob: no visible global function definition for ‘ggplot’ plotNegOob: no visible global function definition for ‘aes’ plotNegOob: no visible binding for global variable ‘intensity’ plotNegOob: no visible binding for global variable ‘channel.probes’ plotNegOob: no visible global function definition for ‘geom_histogram’ plotNegOob: no visible binding for global variable ‘..density..’ plotNegOob: no visible global function definition for ‘position_identity’ plotNegOob: no visible global function definition for ‘facet_grid’ plotNegOob: no visible global function definition for ‘scale_x_continuous’ plotNegOob: no visible global function definition for ‘scale_y_continuous’ plotNegOob: no visible global function definition for ‘scale_fill_manual’ plotNegOob: no visible global function definition for ‘opts’ plotNegOob: no visible global function definition for ‘theme_bw’ psummary: no visible global function definition for ‘p.adjust’ qc.probe.plot: no visible global function definition for ‘log_trans’ qc.probe.plot: no visible global function definition for ‘melt’ qc.probe.plot: no visible binding for global variable ‘variable’ qc.probe.plot: no visible binding for global variable ‘value’ qc.probe.plot: no visible global function definition for ‘coord_flip’ qc.probe.plot: no visible global function definition for ‘scale_x_continuous’ qc.probe.plot: no visible global function definition for ‘scale_y_discrete’ qc.probe.plot: no visible global function definition for ‘facet_grid’ qc.probe.plot: no visible global function definition for ‘scale_colour_manual’ qc.probe.plot: no visible global function definition for ‘scale_shape_manual’ qc.probe.plot: no visible global function definition for ‘theme_bw’ [,MethyLumiM-ANY-ANY-ANY: no visible global function definition for ‘packageDescription’ coerce,MethyLumiM-MethylSet: no visible global function definition for ‘MethylSet’ coerce,MethyLumiM-MethylSet: no visible global function definition for ‘packageVersion’ coerce,MethyLumiSet-MethylSet: no visible global function definition for ‘MethylSet’ coerce,MethyLumiSet-MethylSet: no visible global function definition for ‘packageVersion’ coerce,RangedSummarizedExperiment-GenomicMethylSet: no visible global function definition for ‘GenomicMethylSet’ coerce,eSet-MethyLumiM: no visible global function definition for ‘capture.output’ coerce,eSet-MethyLumiM: no visible global function definition for ‘packageDescription’ combine27k450k,MethyLumiSet-MethyLumiSet: no visible global function definition for ‘subsetCommonProbes’ combine,MethyLumiM-MethyLumiM: no visible global function definition for ‘capture.output’ combine,MethyLumiM-MethyLumiM: no visible global function definition for ‘packageDescription’ corplot,MethyLumiSet: no visible global function definition for ‘hclust’ corplot,MethyLumiSet: no visible global function definition for ‘as.dist’ getProbesByChannel,methylData : : no visible binding for global variable ‘allele’ hist,MethyLumiQC: no visible global function definition for ‘par’ hist,MethyLumiSet: no visible global function definition for ‘par’ initialize,MethyLumiQC: ... may be used in an incorrect context: ‘assayDataNew(...)’ intensities.IB,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ intensities.IB,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ intensities.M,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ intensities.M,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ intensities.OOB.allelic,MethyLumiSet-character-character: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ intensities.OOB.allelic,MethyLumiSet-character-character: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ intensities.OOB,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ intensities.OOB,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ intensities.U,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation27kCOLORCHANNEL’ intensities.U,MethyLumiSet-character: no visible binding for global variable ‘IlluminaHumanMethylation450kCOLORCHANNEL’ pairs,MethyLumiSet : upperPanel: no visible global function definition for ‘points’ pairs,MethyLumiSet : upperPanel: no visible global function definition for ‘abline’ pairs,MethyLumiSet : lowerPanel: no visible global function definition for ‘par’ pairs,MethyLumiSet : lowerPanel: no visible global function definition for ‘text’ pairs,MethyLumiSet : diagPanel: no visible global function definition for ‘par’ pairs,MethyLumiSet : diagPanel: no visible global function definition for ‘rect’ pairs,MethyLumiSet: no visible global function definition for ‘par’ plotNAs,methylData: no visible binding for global variable ‘index’ plotNAs,methylData: no visible binding for global variable ‘dropouts’ plotProbeNAs,methylData: no visible binding for global variable ‘mu’ plotProbeNAs,methylData: no visible binding for global variable ‘drops’ plotSampleIntensities,MethyLumiSet: no visible global function definition for ‘lines’ plotSampleIntensities,MethyLumiSet: no visible global function definition for ‘box’ plotSampleIntensities,MethyLumiSet: no visible global function definition for ‘axis’ pval.detect<-,methylData-numeric : : : no visible global function definition for ‘ecdf’ pval.detect<-,methylData-numeric: no visible global function definition for ‘rowMins’ Undefined global functions or variables: ..density.. DFsToNChannelSet DNAStringSet FDb.InfiniumMethylation.hg19 GenomicMethylSet GenomicRatioSet IlluminaHumanMethylation27kCOLORCHANNEL IlluminaHumanMethylation450kCOLORCHANNEL MethylSet RGChannelSet abline addColorChannelInfo aes allele as.dist axis box capture.output channel.probes colMedians colQuantiles colSds colorRampPalette coord_flip data dnorm dropouts drops ecdf facet_grid gamma.integral gamma.mle gamma.mode geom_histogram ggplot hclust hm27.controls hm27.ordering hm450.controls hm450.ordering huber index intensity lines log_trans mclapply melt mu offset opts p.adjust packageDescription packageVersion par plot.density pnorm points position_identity read.csv read.delim read.table rect rowMins scale_colour_manual scale_fill_manual scale_shape_manual scale_x_continuous scale_y_continuous scale_y_discrete subsetCommonProbes text theme_bw title value variable weighted.mean Consider adding importFrom("grDevices", "colorRampPalette") importFrom("graphics", "abline", "axis", "box", "lines", "par", "points", "rect", "text", "title") importFrom("stats", "as.dist", "dnorm", "ecdf", "hclust", "offset", "p.adjust", "pnorm", "weighted.mean") importFrom("utils", "capture.output", "data", "packageDescription", "packageVersion", "read.csv", "read.delim", "read.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: estimateM.Rd:34-36: Dropping empty section \seealso prepare_Rd: estimateM.Rd:37-39: Dropping empty section \examples checkRd: (-1) extractBarcodeAndPosition.Rd:14: Escaped LaTeX specials: \_ \_ * 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 ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 7 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/methylumi.Rcheck/00check.log’ for details.