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This page was generated on 2025-07-19 12:05 -0400 (Sat, 19 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4791
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4529
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4572
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4513
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4510
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 1233/2311HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methodical 1.5.0  (landing page)
Richard Heery
Snapshot Date: 2025-07-18 13:25 -0400 (Fri, 18 Jul 2025)
git_url: https://git.bioconductor.org/packages/methodical
git_branch: devel
git_last_commit: 071c5e5
git_last_commit_date: 2025-04-15 13:26:47 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64... NOT SUPPORTED ...
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


CHECK results for methodical on nebbiolo2

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.

raw results


Summary

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: 2025-07-18 23:55:51 -0400 (Fri, 18 Jul 2025)
EndedAt: 2025-07-19 00:19:16 -0400 (Sat, 19 Jul 2025)
EllapsedTime: 1404.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: methodical.Rcheck
Warnings: 1

Command output

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###
### 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
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/methodical.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 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’
.expand_transcript_ranges: no visible binding for global variable
  ‘transcript_name’
.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
  ‘seqlengths’
createRandomRegions: no visible global function definition for
  ‘overlapsAny’
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’
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 : <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 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
  transcript_name 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 ... WARNING
Documented arguments not in \usage in Rd file 'calculateMethSiteTranscriptCors.Rd':
  ‘expand_upstream’ ‘expand_downstream’

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               136.578 14.443 151.045
liftoverMethRSE                          108.288 10.499 119.248
annotateGRanges                           34.881  3.672  42.226
makeMethRSEFromBedgraphs                  10.619  6.634   8.145
makeMethRSEFromArrayFiles                 11.387  3.615  11.661
calculateMethSiteTranscriptCors           10.626  1.113  11.663
summarizeRegionMethylation                 8.354  1.747   9.926
calculateRegionMethylationTranscriptCors   7.363  1.836   9.158
* 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 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/methodical.Rcheck/00check.log’
for details.


Installation output

methodical.Rcheck/00install.out

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###
### 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)

Tests output


Example timings

methodical.Rcheck/methodical-Ex.timings

nameusersystemelapsed
annotateGRanges34.881 3.67242.226
annotatePlot2.6650.0303.174
calculateMethSiteTranscriptCors10.626 1.11311.663
calculateRegionMethylationTranscriptCors7.3631.8369.158
calculateSmoothedMethodicalScores0.0080.0040.012
createRandomRegions0.6650.1920.688
dot-find_tmrs_single0.6450.1040.749
expand_granges0.0240.0030.027
extractGRangesMethSiteValues0.1790.0320.210
extractMethSitesFromGenome136.578 14.443151.045
kallistoIndex000
liftoverMethRSE108.288 10.499119.248
makeMethRSEFromArrayFiles11.387 3.61511.661
makeMethRSEFromBedgraphs10.619 6.634 8.145
maskRangesInRSE0.2280.0170.245
methrixToRSE0.3620.0200.386
plotMethSiteCorCoefs0.8780.0760.953
plotMethodicalScores0.4440.0150.458
plotMethylationValues0.9240.0690.993
plotTMRs1.2090.5041.607
rangesRelativeToTSS0.1800.0220.203
rapidCorTest0.0560.0030.059
sampleMethSites0.3230.0490.372
strandedDistance0.2410.0250.266
summarizeRegionMethylation8.3541.7479.926