Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-13 12:03 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1252/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methodical 1.5.0 (landing page) Richard Heery
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
To the developers/maintainers of the methodical package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methodical.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: methodical |
Version: 1.5.0 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:methodical.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings methodical_1.5.0.tar.gz |
StartedAt: 2025-10-13 01:28:47 -0400 (Mon, 13 Oct 2025) |
EndedAt: 2025-10-13 01:53:25 -0400 (Mon, 13 Oct 2025) |
EllapsedTime: 1478.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: methodical.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:methodical.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings methodical_1.5.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/methodical.Rcheck’ * using R version 4.5.1 Patched (2025-08-23 r88802) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘methodical/DESCRIPTION’ ... OK * this is package ‘methodical’ version ‘1.5.0’ * 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: .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 loading without being on the library search path ... 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’ ‘MatrixGenerics’ ‘TumourMethData’ ‘annotatr’ ‘devtools’ ‘knitr’ ‘rcmdcheck’ ‘remotes’ ‘usethis’ All declared Imports should be used. 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’ * 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’ .find_tmrs_single: no visible global function definition for ‘is’ .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 : <anonymous>: 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’ makeMethRSEFromArrayFiles: no visible global function definition for ‘is’ makeMethRSEFrominput_files: 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 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 : <anonymous>: 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 beta_value_column chunk col2rgb 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 modifyList name normalization_factor overlapsAny p.adjust p.adjust.methods pg probe_groups probe_name_column probe_sites_df pt queryHits region_type seqlengths seqlevels seqlevels<- seqnames_column setNames start_column subsetByOverlaps temp_chunk_dirs total_files value_column zero_based 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 ... OK * 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 ... ERROR Running examples in ‘methodical-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: makeMethRSEFrominput_files > ### Title: Create a HDF5-backed RangedSummarizedExperiment for methylation > ### values in input_files > ### Aliases: makeMethRSEFrominput_files > > ### ** Examples > > > # Load CpGs within first million base pairs of chromosome 1 as a GRanges object > data("hg38_cpgs_subset", package = "methodical") > > # Get paths to input_files > input_files <- list.files(path = system.file('extdata', package = 'methodical'), + pattern = ".bg.gz", full.names = TRUE) > > # Create sample metadata > sample_metadata <- data.frame( + tcga_project = gsub("_.*", "", gsub("TCGA_", "", basename(input_files))), + sample_type = ifelse(grepl("N", basename(input_files)), "Normal", "Tumour"), + row.names = tools::file_path_sans_ext(basename(input_files)) + ) > > # Create a HDF5-backed RangedSummarizedExperiment from input_files > meth_rse <- makeMethRSEFrominput_files(input_files = input_files, + meth_sites = hg38_cpgs_subset, sample_metadata = sample_metadata, + hdf5_dir = paste0(tempdir(), "/bedgraph_hdf5_1")) Processing bedGraph 1 out of 4: /home/biocbuild/bbs-3.22-bioc/R/site-library/methodical/extdata/TCGA_BRCA_A0CE.bg.gz Error: BiocParallel errors 1 remote errors, element index: 1 3 unevaluated and other errors first remote error: Error in data.table::fread(bg_file, select = c(seqnames_column, start_column, : Column number 5 (select[4]) is too large for this table, which only has 4 columns. Execution halted Examples with CPU (user + system) or elapsed time > 5s user system elapsed extractMethSitesFromGenome 138.582 12.871 151.467 liftoverMethRSE 111.625 11.747 124.166 annotateGRanges 31.912 2.296 36.812 makeMethRSEFromArrayFiles 22.948 0.279 11.640 calculateRegionMethylationTranscriptCors 7.411 0.069 7.481 calculateMethSiteTranscriptCors 5.651 0.092 5.743 * 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: 1 ERROR, 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/methodical.Rcheck/00check.log’ for details.
methodical.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL methodical ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘methodical’ ... ** this is package ‘methodical’ version ‘1.5.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (methodical)
methodical.Rcheck/methodical-Ex.timings
name | user | system | elapsed | |
annotateGRanges | 31.912 | 2.296 | 36.812 | |
annotatePlot | 2.790 | 0.025 | 2.920 | |
calculateMethSiteTranscriptCors | 5.651 | 0.092 | 5.743 | |
calculateRegionMethylationTranscriptCors | 7.411 | 0.069 | 7.481 | |
calculateSmoothedMethodicalScores | 0.007 | 0.001 | 0.009 | |
createRandomRegions | 0.605 | 0.005 | 0.609 | |
dot-find_tmrs_single | 0.601 | 0.000 | 0.600 | |
expand_granges | 0.025 | 0.000 | 0.025 | |
extractGRangesMethSiteValues | 0.182 | 0.001 | 0.182 | |
extractMethSitesFromGenome | 138.582 | 12.871 | 151.467 | |
kallistoIndex | 0 | 0 | 0 | |
liftoverMethRSE | 111.625 | 11.747 | 124.166 | |
makeMethRSEFromArrayFiles | 22.948 | 0.279 | 11.640 | |