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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('memes_1.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing memes ────────────────────────────────────────────────────────────
✔ Package installed successfully
── memes session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpa5flvg/filed2abf243b097/memes
→ BiocVersion: 3.24
→ Package: memes
→ PackageVersion: 1.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/memes.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpa5flvg/filed2abf243b097/memes
→ installDir: /tmp/Rtmpa5flvg/filed2abf17b1e377
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on memes ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.1 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...
* 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 (14%).
* 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:
    • core_ame.Rmd
    • ...
    • tidy_motifs.Rmd
* Checking package installation calls in R code...
* Checking for library/require of memes...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/process_utils.R (line 56, column 5)
    • cat() in R/process_utils.R (line 67, column 5)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/ame.R (line 387, column 10)
    • ...
    • R/utils.R (line 238, column 10)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/fimo.R (line 276, column 20)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 6 times)
  • <<- in R/ame.R (line 266, column 16)
  • ...
  • <<- in R/motif_utils.R (line 67, column 13)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
  • suppressMessages() in R/dreme.R (line 156, column 3)
  • ...
  • suppressMessages() in R/tomtom.R (line 215, column 3)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_ame_heatmap() (R/ame_methods.R): 107 lines
    • ...
    • search_meme_database_path() (R/utils_internal.R): 73 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • runStreme.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • write_fasta.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; 337 lines (4%) are > 80 characters long.
  First few lines:
    • R/ame_methods.R#L220 # Couldn't come up with a clever way t ...
    • ...
    • vignettes/tidy_motifs.Rmd#L318 # extrainfo = FALSE drops the extra colu
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1897 lines (23%) are
not.
  First few lines:
    • R/ame_methods.R#L21 ame, ...
    • ...
    • vignettes/tidy_motifs.Rmd#L328 head(1) ...
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 | ⚠ 0 WARNINGS | ℹ 16 NOTES
ℹ See the memes.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.