############################################################################## ############################################################################## ### ### 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_1.1.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.5 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methodical/DESCRIPTION’ ... OK * this is package ‘methodical’ version ‘1.1.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * 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 Unexported object imported by a ':::' call: ‘HDF5Array:::.serialize_HDF5SummarizedExperiment’ See the note in ?`:::` about the use of this operator. There are ::: calls to the package's namespace in its code. A package almost never needs to use ::: for its own objects: ‘.chunk_regions’ ‘.tss_iterator’ * 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’ .create_meth_rse_from_hdf5: no visible global function definition for ‘setNames’ .split_bedgraph: no visible binding for global variable ‘meth_site_groups’ .split_bedgraph: no visible binding for global variable ‘total_files’ .split_bedgraph: no visible binding for global variable ‘meth_sites_df’ .split_bedgraph: no visible global function definition for ‘setNames’ .split_bedgraph: no visible binding for global variable ‘seqnames_column’ .split_bedgraph: no visible binding for global variable ‘start_column’ .split_bedgraph: no visible binding for global variable ‘end_column’ .split_bedgraph: no visible binding for global variable ‘value_column’ .split_bedgraph: no visible binding for global variable ‘dt_threads’ .split_bedgraph: no visible binding for global variable ‘zero_based’ .split_bedgraph: no visible binding for global variable ‘normalization_factor’ .split_bedgraph: no visible binding for global variable ‘decimal_places’ .split_bedgraph: no visible binding for global variable ‘mg’ .split_bedgraph: no visible binding for global variable ‘temp_chunk_dirs’ .split_meth_array_file: no visible binding for global variable ‘probe_groups’ .split_meth_array_file: no visible binding for global variable ‘total_files’ .split_meth_array_file: no visible binding for global variable ‘probe_sites_df’ .split_meth_array_file: no visible global function definition for ‘setNames’ .split_meth_array_file: no visible binding for global variable ‘probe_name_column’ .split_meth_array_file: no visible binding for global variable ‘beta_value_column’ .split_meth_array_file: no visible binding for global variable ‘normalization_factor’ .split_meth_array_file: no visible binding for global variable ‘decimal_places’ .split_meth_array_file: no visible binding for global variable ‘name’ .split_meth_array_file: no visible binding for global variable ‘pg’ .split_meth_array_file: no visible binding for global variable ‘temp_chunk_dirs’ .split_meth_array_file: no visible binding for global variable ‘dt_threads’ .split_meth_array_files_into_chunks: no visible binding for global variable ‘name’ .summarize_chunk_methylation: no visible global function definition for ‘subsetByOverlaps’ .tss_correlations: no visible global function definition for ‘setNames’ .write_chunks_to_hdf5: no visible binding for global variable ‘chunk’ 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’ createRandomRegions: no visible global function definition for ‘is’ createRandomRegions: no visible global function definition for ‘seqlengths’ createRandomRegions: no visible global function definition for ‘overlapsAny’ extractGRangesMethSiteValues: no visible global function definition for ‘is’ extractMethSitesFromGenome: no visible global function definition for ‘is’ findTMRs: 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’ makeMethRSEFromArrayFiles: no visible global function definition for ‘is’ makeMethRSEFromBedgraphs: no visible global function definition for ‘is’ maskRangesInRSE: no visible global function definition for ‘is’ maskRangesInRSE: no visible global function definition for ‘queryHits’ methrixToRSE: no visible global function definition for ‘is’ plotMethSiteCorCoefs: no visible global function definition for ‘is’ 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’ plotMethylationValues: no visible global function definition for ‘is’ plotMethylationValues: no visible global function definition for ‘complete.cases’ plotMethylationValues: 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: beta_value_column chunk colorRampPalette complete.cases cor decimal_places direction dt_threads end_column gene_transcripts is meth_cor_plot_position meth_site_groups meth_site_plot_position meth_site_start meth_sites_df methodical_score mg name normalization_factor overlapsAny p.adjust p.adjust.methods pg probe_groups probe_name_column probe_sites_df pt queryHits region_type seqlengths seqlevels seqnames_column setNames start_column subsetByOverlaps temp_chunk_dirs total_files value_column zero_based Consider adding importFrom("grDevices", "colorRampPalette") importFrom("methods", "is") importFrom("stats", "complete.cases", "cor", "p.adjust", "p.adjust.methods", "pt", "setNames") 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 ... 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 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 61.484 5.984 67.510 liftoverMethRSE 49.556 4.140 54.275 annotateGRanges 13.543 0.807 19.156 makeMethRSEFromBedgraphs 3.941 2.152 2.943 makeMethRSEFromArrayFiles 4.784 1.193 4.906 * 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: 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/methodical.Rcheck/00check.log’ for details.