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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('VariantAnnotation_1.51.0.tar.gz')"
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─ BiocCheckVersion: 1.41.0
─ BiocVersion: 3.20
─ Package: VariantAnnotation
─ PackageVersion: 1.51.0
─ sourceDir: /tmp/RtmpxxZFjd/file36599f3aaa96bb/VariantAnnotation
─ installDir: /tmp/RtmpxxZFjd/file36599f20c673c5
─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/VariantAnnotation.BiocCheck
─ platform: unix
─ isTarBall: TRUE

* Installing package...
* 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...
    * NOTE: Update R version dependency from 4.0.0 to 4.4.0.
* 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...
    * NOTE: Consider adding these automatically suggested biocViews:
      Coverage
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
    * WARNING: Description field in the DESCRIPTION file is too concise
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
    * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
      with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
    * NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
    Bioconductor dependencies found in Imports & Depends (84%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
    * NOTE: 'sessionInfo' not found in vignette(s)
* Checking package installation calls in R code...
* Checking for library/require of VariantAnnotation...
    * WARNING: Avoid the use of 'library' or 'require' in R code
* Checking coding practice...
    * NOTE: Avoid sapply(); use vapply()
    * NOTE: Avoid 1:...; use seq_len() or seq_along()
    * NOTE: Avoid 'cat' and 'print' outside of 'show' methods
    * NOTE: Avoid using '=' for assignment and use '<-' instead
    * NOTE: Avoid the use of 'paste' in condition signals
    * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
    * WARNING: .Deprecated / .Defunct usage (found 1 times)
* Checking parsed R code in R directory, examples, vignettes...
    * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5
      times)
* Checking function lengths...
    * NOTE: The recommended function length is 50 lines or less. There
      are 11 functions greater than 50 lines.
* Checking man page documentation...
    * WARNING: Empty or missing \value sections found in man page(s).
    * NOTE: Consider adding runnable examples to man pages that
      document exported objects.
    * NOTE: Usage of dontrun{} / donttest{} tags found in man page
      examples. 10% of man pages use at least one of these tags.
    * NOTE: Use donttest{} instead of dontrun{}.
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
  and vignette source...
    * NOTE: Consider shorter lines; 22 lines (0%) are > 80 characters
      long.
    * NOTE: Consider 4 spaces instead of tabs; 28 lines (0%) contain
      tabs.
    * NOTE: Consider multiples of 4 spaces for line indents; 819 lines
      (12%) are not.
    See https://contributions.bioconductor.org/r-code.html
    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...
    * 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...
    Maintainer email is ok.

─ BiocCheck results ──
0 ERRORS | 4 WARNINGS | 20 NOTES

See the VariantAnnotation.BiocCheck folder and run
    browseVignettes(package = 'BiocCheck')
for details.