############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:methyAnalysis.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings methyAnalysis_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/methyAnalysis.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methyAnalysis/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methyAnalysis’ version ‘1.34.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'grid', 'BiocGenerics', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'Biobase', 'org.Hs.eg.db' 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: .BBSoptions 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 ‘methyAnalysis’ can be installed ... WARNING Found the following significant warnings: Warning: Package 'methyAnalysis' is deprecated and will be removed from See ‘/home/biocbuild/bbs-3.13-bioc/meat/methyAnalysis.Rcheck/00install.out’ for details. * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘IRanges’ ‘GenomicRanges’ ‘Biobase’ 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 ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... WARNING Packages in Depends field not imported from: 'grid' 'org.Hs.eg.db' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Missing or unexported objects: 'GenomicRanges::overlapsAny' 'bigmemoryExtras::attachAssayDataElements' Unexported objects imported by ':::' calls: 'Gviz:::.parMappings' 'Gviz:::.setupTextSize' 'Gviz:::.z2icol' 'Gviz:::setStacks' See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... WARNING 'assayElement<-' '\S4method{assayElement<-}{SummarizedExperiment}' The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .estimateTrackHeight: no visible global function definition for 'convertY' .estimateTrackHeight: no visible global function definition for 'unit' .identifySigProbe: no visible global function definition for 'rowMax' MethyLumiM2GenoSet: no visible global function definition for 'fData' MethyLumiM2GenoSet: no visible global function definition for 'metadata' MethyLumiM2GenoSet: no visible global function definition for 'mcols<-' annotateDMRInfo: no visible global function definition for 'elementNROWS' annotateDMRInfo: no visible global function definition for 'values' annotateGRanges: no visible global function definition for 'elementNROWS' annotateGRanges: no visible global function definition for 'values' annotateGRanges: no visible global function definition for 'resize' annotateGRanges: no visible global function definition for 'values<-' annotateGRanges: no visible global function definition for 'flank' annotateGRanges: no visible global function definition for 'nearest' annotateGRanges: no visible global function definition for 'findOverlaps' annotateGRanges: no visible global function definition for 'queryHits' annotateGRanges: no visible global function definition for 'subjectHits' buildAnnotationTracks: no visible global function definition for 'values<-' buildAnnotationTracks: no visible global function definition for 'DataFrame' buildAnnotationTracks: no visible global function definition for 'values' checkChrName: no visible global function definition for 'ranges<-' createTranscriptTrack: no visible global function definition for 'values' detectDMR.slideWin: no visible global function definition for 'values<-' estimateCMR.methylation: no visible global function definition for 'findOverlaps' estimateCMR.methylation: no visible global function definition for 'mcols' estimateCMR.methylation: no visible global function definition for 'values' estimateMethySeq: no visible global function definition for 'slice' estimateMethySeq: no visible global function definition for 'DataFrame' estimateMethySeq: no visible global function definition for 'findOverlaps' estimateMethySeq: no visible global function definition for 'values<-' estimateMethySeq: no visible global function definition for 'values' filterBisulfiteVariant: no visible global function definition for 'slice' filterBisulfiteVariant: no visible global function definition for 'findOverlaps' getContinuousRegion: no visible global function definition for 'values<-' getContinuousRegion: no visible global function definition for 'values' getContinuousRegion: no visible global function definition for 'reduce' getCoverage: no visible global function definition for 'values<-' getCoverage: no visible global function definition for 'DataFrame' getCoverage: no visible global function definition for 'values' getMethyProbeLocation: no visible global function definition for 'features' getMethyProbeLocation: no visible global function definition for 'values<-' getMethyProbeLocation: no visible global function definition for 'DataFrame' getMethyProbeLocation: no visible global function definition for 'keys' heatmapByChromosome: no visible global function definition for 'pushViewport' heatmapByChromosome: no visible global function definition for 'viewport' heatmapByChromosome: no visible global function definition for 'grid.layout' heatmapByChromosome: no visible global function definition for 'popViewport' heatmapByChromosome: no visible global function definition for 'convertX' heatmapByChromosome: no visible global function definition for 'unit' heatmapByChromosome: no visible global function definition for 'convertY' heatmapByChromosome: no visible global function definition for 'grid.rect' heatmapByChromosome: no visible global function definition for 'gpar' heatmapByChromosome: no visible global function definition for 'grid.lines' identifyCpG: no visible global function definition for 'matchPattern' identifySigDMR: no visible global function definition for 'values' identifySigDMR: no visible global function definition for 'values<-' identifySigDMR: no visible global function definition for 'subsetByOverlaps' plotHeatmapByGene: no visible global function definition for 'grid.newpage' plotHeatmapByGene: no visible global function definition for 'pushViewport' plotHeatmapByGene: no visible global function definition for 'viewport' plotHeatmapByGene: no visible global function definition for 'grid.layout' plotHeatmapByGene: no visible global function definition for 'popViewport' plotHeatmapByGene: no visible global function definition for 'grid.rect' plotHeatmapByGene: no visible global function definition for 'gpar' plotHeatmapByGene: no visible global function definition for 'grid.segments' plotHeatmapByGene: no visible global function definition for 'convertX' plotHeatmapByGene: no visible global function definition for 'unit' plotHeatmapByGene: no visible global function definition for 'grid.text' plotHeatmapByGene: no visible global function definition for 'convertY' plotMethylationHeatmapByGene : : no visible global function definition for 'grid.newpage' plotMethylationHeatmapByGene : : no visible global function definition for 'pushViewport' plotMethylationHeatmapByGene : : no visible global function definition for 'viewport' plotMethylationHeatmapByGene : : no visible global function definition for 'grid.layout' plotMethylationHeatmapByGene : : no visible global function definition for 'popViewport' plotMethylationHeatmapByGene : : no visible global function definition for 'grid.rect' plotMethylationHeatmapByGene : : no visible global function definition for 'gpar' plotMethylationHeatmapByGene : : no visible global function definition for 'grid.segments' plotMethylationHeatmapByGene : : no visible global function definition for 'convertX' plotMethylationHeatmapByGene : : no visible global function definition for 'unit' plotMethylationHeatmapByGene : : no visible global function definition for 'grid.text' plotMethylationHeatmapByGene : : no visible global function definition for 'convertY' plotTracksWithDataTrackInfo : : no visible global function definition for 'values' plotTracksWithDataTrackInfo: no visible global function definition for 'grid.newpage' plotTracksWithDataTrackInfo: no visible global function definition for 'pushViewport' plotTracksWithDataTrackInfo: no visible global function definition for 'viewport' plotTracksWithDataTrackInfo: no visible global function definition for 'grid.layout' plotTracksWithDataTrackInfo: no visible global function definition for 'convertX' plotTracksWithDataTrackInfo: no visible global function definition for 'unit' plotTracksWithDataTrackInfo : : no visible global function definition for 'convertX' plotTracksWithDataTrackInfo : : no visible global function definition for 'unit' plotTracksWithDataTrackInfo: no visible global function definition for 'popViewport' plotTracksWithDataTrackInfo: no visible global function definition for 'convertY' plotTracksWithDataTrackInfo: no visible global function definition for 'grid.text' plotTracksWithDataTrackInfo: no visible global function definition for 'gpar' plotTracksWithDataTrackInfo: no visible global function definition for 'grid.rect' transcriptDb2GeneRegionTrackByGene: no visible global function definition for 'values' updateMethyGenoSet: no visible global function definition for 'mcols<-' coerce,MethyGenoSet-MethyLumiM: no visible global function definition for 'mcols' coerce,MethyGenoSet-MethyLumiM: no visible global function definition for 'fData<-' Undefined global functions or variables: DataFrame convertX convertY elementNROWS fData fData<- features findOverlaps flank gpar grid.layout grid.lines grid.newpage grid.rect grid.segments grid.text keys matchPattern mcols mcols<- metadata nearest popViewport pushViewport queryHits ranges<- reduce resize rowMax slice subjectHits subsetByOverlaps unit values values<- viewport * checking Rd files ... NOTE prepare_Rd: estimateCMR.methylation.Rd:35-36: Dropping empty section \details prepare_Rd: estimateCMR.methylation.Rd:45-47: Dropping empty section \examples prepare_Rd: estimateMethySeq.Rd:33-35: Dropping empty section \details prepare_Rd: estimateMethySeq.Rd:44-46: Dropping empty section \seealso prepare_Rd: estimateMethySeq.Rd:47-49: Dropping empty section \examples prepare_Rd: filterBisulfiteVariant.Rd:51-52: Dropping empty section \examples prepare_Rd: getCoverage.Rd:35-36: Dropping empty section \examples * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMethylationHeatmapByGene 34.933 0.168 60.536 MethyLumiM2GenoSet 21.249 2.267 23.521 buildAnnotationTracks 21.756 0.499 45.714 heatmapByChromosome 17.778 0.051 18.230 plotHeatmapByGene 17.514 0.044 30.741 plotTracksWithDataTrackInfo 13.877 0.032 14.509 createTranscriptTrack 11.497 0.068 11.565 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 WARNINGs, 5 NOTEs See ‘/home/biocbuild/bbs-3.13-bioc/meat/methyAnalysis.Rcheck/00check.log’ for details.