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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methodical_1.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing methodical ───────────────────────────────────────────────────────
✔ Package installed successfully
── methodical session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpA4quTh/filed57823d0720f4/methodical
→ BiocVersion: 3.24
→ Package: methodical
→ PackageVersion: 1.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methodical.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpA4quTh/filed57823d0720f4/methodical
→ installDir: /tmp/RtmpA4quTh/filed57825b69a2e1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methodical ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
→ Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (51%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • calculating_methylation_transcription_correlations.Rmd
    • working_with_meth_rses.Rmd
* Checking package installation calls in R code...
* Checking for library/require of methodical...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/make_meth_rse_accessory_functions.R (line 103, column 22)
    • ...
    • R/tmr_functions.R (line 75, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • tmr_functions.R (line 28, column 12)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/granges_accessory_functions.R (line 39, column 18)
    • ...
    • R/summarize_region_methylation.R (line 94, column 24)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/calculate_meth_site_transcript_cors.R (line 152, column 10)
    • ...
    • R/plotting_functions.R (line 140, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 5 times:
    • T in R/granges_accessory_functions.R (line 42, column 58)
    • ...
    • T in R/make_meth_rse.R (line 136, column 58)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/calculate_meth_site_transcript_cors.R (line 21, column 9)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/calculate_meth_site_transcript_cors.R (line 272,
  column 5)
  • suppressWarnings() in R/calculate_region_methylation_transcript_cors.R
  (line 165, column 42)
  • suppressWarnings() in R/plotting_functions.R (line 662, column 28)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 15
functions greater than 50 lines.
  The longest 5 functions are:
    • calculateMethSiteTranscriptCors()
    (R/calculate_meth_site_transcript_cors.R): 150 lines
    • ...
    • plotRegionValues() (R/plotting_functions.R): 116 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/dot-check_input_files.Rd
    • man/dot-collapse_strands.Rd
    • man/dot-set_meth_df_columns.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • convert_rse_to_bsseq.Rd
  • ...
  • findTMRs.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 834 lines (23%) are > 80 characters long.
  First few lines:
    • R/calculate_meth_site_transcript_cors.R#L4 #' @param
    tss_region_indices_list A list ...
    • ...
    • vignettes/working_with_meth_rses.Rmd#L244
    extractGRangesMethSiteValues(mcrpc_wgbs_ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1449 lines (41%) are
not.
  First few lines:
    • R/calculate_meth_site_transcript_cors.R#L13 cor_method,
    add_distance_to_region, mi ...
    • ...
    • vignettes/working_with_meth_rses.Rmd#L233 remove_one_to_many_mapping =
    TRUE, per ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking for bioc-devel mailing list subscription...
ℹ NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel
mailing list (requires admin credentials). Subscribe here:
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 16 NOTES
ℹ See the methodical.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.