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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('BiocGenerics_0.58.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BiocGenerics ─────────────────────────────────────────────────────
✔ Package installed successfully
── BiocGenerics session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjJmwTT/file736852dd47cbd/BiocGenerics
→ BiocVersion: 3.23
→ Package: BiocGenerics
→ PackageVersion: 0.58.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocGenerics.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpjJmwTT/file736852dd47cbd/BiocGenerics
→ installDir: /tmp/RtmpjJmwTT/file7368579a191e1
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BiocGenerics ───────────────────────────────────────────
* 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...
ℹ Package version 0.58.0; pre-release
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 4.0.0 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...
No vignettes found.
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of BiocGenerics...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/testPackage.R (line 59, column 5)
    • library() in R/testPackage.R (line 75, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/combine.R (line 43, column 15)
    • ...
    • R/updateObject.R (line 65, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/testPackage.R (line 88, column 5)
    • ...
    • cat() in R/testPackage.R (line 98, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotMA.R (line 7, column 10)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/path.Rd
ℹ Found @ in man/updateObject.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/updateObject.R (line 204, column 26)
  • suppressMessages() in R/updateObject.R (line 204, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.23() (R/combine.R): 110 lines
    • ...
    • _anonymous_.242() (R/updateObject.R): 58 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/annotation.Rd
    • ...
    • man/score.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • dge.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 1% of man
pages use at least one of these tags.
  Found in files:
    • testPackage.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • testPackage.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 18 lines (0%) are > 80 characters long.
  First few lines:
    • R/dge.R#L3 setGeneric("counts", function(obj ...
    • ...
    • man/organism_species.Rd#L56 \item \url{http://bioconductor.org/p ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2102 lines (25%) are
not.
  First few lines:
    • R/combine.R#L48 factor={ ...
    • ...
    • man/xtabs.Rd#L62 } ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the BiocGenerics.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.