############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methodical.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methodical_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/methodical.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methodical/DESCRIPTION’ ... OK * this is package ‘methodical’ version ‘1.6.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 34 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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: ..pdf .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 ‘methodical’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 dependencies in R code ... NOTE Namespaces in Imports field not imported from: ‘AnnotationHub’ ‘BSgenome.Hsapiens.UCSC.hg19’ ‘BSgenome.Hsapiens.UCSC.hg38’ ‘BiocCheck’ ‘BiocManager’ ‘BiocStyle’ ‘DelayedArray’ ‘HDF5Array’ ‘MatrixGenerics’ ‘TumourMethData’ ‘annotatr’ ‘devtools’ ‘knitr’ ‘rcmdcheck’ ‘remotes’ ‘rhdf5’ ‘tools’ ‘usethis’ All declared Imports should be used. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.chunk_regions’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .calculate_regions_intersections: no visible global function definition for ‘is’ .chunk_regions: no visible global function definition for ‘is’ .chunk_regions: no visible global function definition for ‘subsetByOverlaps’ .count_covered_bases: no visible global function definition for ‘is’ .find_tmrs_single: no visible global function definition for ‘is’ .summarize_chunk_methylation: no visible global function definition for ‘subsetByOverlaps’ .tss_correlations: no visible global function definition for ‘setNames’ annotateGRanges: no visible global function definition for ‘is’ annotatePlot: no visible global function definition for ‘is’ annotatePlot: no visible global function definition for ‘colorRampPalette’ annotatePlot: no visible global function definition for ‘subsetByOverlaps’ annotatePlot: no visible binding for global variable ‘region_type’ calculateMethSiteTranscriptCors: no visible global function definition for ‘is’ calculateMethSiteTranscriptCors: no visible binding for global variable ‘chunk’ calculateMethSiteTranscriptCors: no visible global function definition for ‘subsetByOverlaps’ calculateMethSiteTranscriptCors: no visible global function definition for ‘setNames’ calculateRegionMethylationTranscriptCors: no visible global function definition for ‘is’ calculateRegionMethylationTranscriptCors: no visible binding for global variable ‘p.adjust.methods’ calculateRegionMethylationTranscriptCors : : no visible global function definition for ‘setNames’ calculateRegionMethylationTranscriptCors: no visible global function definition for ‘p.adjust’ calculateSmoothedMethodicalScores: no visible global function definition for ‘is’ correct_correlation_pvalues: no visible binding for global variable ‘p.adjust.methods’ correct_correlation_pvalues: no visible global function definition for ‘p.adjust’ createRandomRegions: no visible global function definition for ‘is’ createRandomRegions: no visible global function definition for ‘seqlevels’ createRandomRegions: no visible global function definition for ‘seqlengths’ createRandomRegions: no visible global function definition for ‘overlapsAny’ createRandomRegions: no visible global function definition for ‘seqlevels<-’ expand_granges: no visible global function definition for ‘is’ expand_granges: no visible global function definition for ‘IRanges’ extractGRangesMethSiteValues: no visible global function definition for ‘is’ extractMethSitesFromGenome: no visible global function definition for ‘is’ kallistoIndex: no visible global function definition for ‘is’ kallistoQuantify: no visible global function definition for ‘is’ kallistoQuantify: no visible global function definition for ‘setNames’ liftoverMethRSE: no visible global function definition for ‘is’ maskRangesInRSE: no visible global function definition for ‘is’ maskRangesInRSE: no visible global function definition for ‘queryHits’ plotMethSiteCorCoefs: no visible global function definition for ‘is’ plotMethSiteCorCoefs: no visible global function definition for ‘col2rgb’ plotMethSiteCorCoefs: no visible binding for global variable ‘cor’ plotMethSiteCorCoefs: no visible global function definition for ‘complete.cases’ plotMethSiteCorCoefs: no visible binding for global variable ‘meth_cor_plot_position’ plotMethodicalScores: no visible global function definition for ‘is’ plotMethodicalScores: no visible global function definition for ‘seqlevels’ plotMethodicalScores: no visible binding for global variable ‘meth_site_start’ plotMethodicalScores: no visible binding for global variable ‘meth_site_plot_position’ plotMethodicalScores: no visible binding for global variable ‘methodical_score’ plotMethodicalScores: no visible binding for global variable ‘cor’ plotRegionValues: no visible global function definition for ‘is’ plotRegionValues: no visible global function definition for ‘col2rgb’ plotRegionValues: no visible global function definition for ‘complete.cases’ plotRegionValues: no visible global function definition for ‘modifyList’ plotRegionValues: no visible binding for global variable ‘meth_site_plot_position’ plotTMRs: no visible global function definition for ‘is’ plotTMRs: no visible binding for global variable ‘direction’ plotTMRs: no visible global function definition for ‘setNames’ rangesRelativeToTSS: no visible global function definition for ‘is’ rapidCorTest: no visible global function definition for ‘is’ rapidCorTest: no visible binding for global variable ‘p.adjust.methods’ rapidCorTest: no visible global function definition for ‘cor’ rapidCorTest: no visible global function definition for ‘pt’ rapidCorTest: no visible global function definition for ‘p.adjust’ sampleMethSites: no visible global function definition for ‘is’ strandedDistance: no visible global function definition for ‘is’ sumTranscriptValuesForGenes: no visible global function definition for ‘is’ sumTranscriptValuesForGenes : : no visible global function definition for ‘is’ sumTranscriptValuesForGenes: no visible binding for global variable ‘gene_transcripts’ summarizeRegionMethylation: no visible global function definition for ‘is’ summarizeRegionMethylation: no visible global function definition for ‘seqlevels’ Undefined global functions or variables: IRanges chunk col2rgb colorRampPalette complete.cases cor direction gene_transcripts is meth_cor_plot_position meth_site_plot_position meth_site_start methodical_score modifyList overlapsAny p.adjust p.adjust.methods pt queryHits region_type seqlengths seqlevels seqlevels<- setNames subsetByOverlaps Consider adding importFrom("grDevices", "col2rgb", "colorRampPalette") importFrom("methods", "is") importFrom("stats", "complete.cases", "cor", "p.adjust", "p.adjust.methods", "pt", "setNames") importFrom("utils", "modifyList") to your NAMESPACE file (and ensure that your DESCRIPTION Imports field contains 'methods'). * checking Rd files ... NOTE checkRd: (-1) kallistoQuantify.Rd:34: Lost braces; missing escapes or markup? 34 | {merged_output_prefix}_counts_merged.tsv.gz and {merged_output_prefix}_tpm_merged.tsv.gz. Default prefix is "kallisto_transcript" i.e. default output merged output files are | ^ checkRd: (-1) kallistoQuantify.Rd:34: Lost braces; missing escapes or markup? 34 | {merged_output_prefix}_counts_merged.tsv.gz and {merged_output_prefix}_tpm_merged.tsv.gz. Default prefix is "kallisto_transcript" i.e. default output merged output files are | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented data sets: ‘hg38_cpg_islands’ ‘infinium_450k_probe_granges_hg19’ 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 ... OK * checking Rd \usage sections ... WARNING Undocumented arguments in Rd file 'createRandomRegions.Rd' ‘sequence_names’ ‘all_sequence_names_equally_likely’ Documented arguments not in \usage in Rd file 'createRandomRegions.Rd': ‘sequences’ ‘all_sequences_equally_likely’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. 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 R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed extractMethSitesFromGenome 156.949 13.949 172.428 liftoverMethRSE 119.600 10.379 131.552 annotateGRanges 29.189 2.657 34.578 summarizeRegionMethylation 6.744 0.347 7.159 calculateRegionMethylationTranscriptCors 5.082 0.068 5.173 calculateMethSiteTranscriptCors 4.769 0.357 5.163 * 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: 2 WARNINGs, 5 NOTEs See ‘/Users/biocbuild/bbs-3.22-bioc/meat/methodical.Rcheck/00check.log’ for details.