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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('BiocPkgTools_1.30.0.tar.gz','quit-with-status'=TRUE)"
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── Installing BiocPkgTools ─────────────────────────────────────────────────────
✔ Package installed successfully
── BiocPkgTools session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpW08mtY/file73ee57a0747dc/BiocPkgTools
→ BiocVersion: 3.23
→ Package: BiocPkgTools
→ PackageVersion: 1.30.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/BiocPkgTools.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpW08mtY/file73ee57a0747dc/BiocPkgTools
→ installDir: /tmp/RtmpW08mtY/file73ee52a648b7c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on BiocPkgTools ───────────────────────────────────────────
* 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 4.1.0 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...
* 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...
ℹ 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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (13%).
* 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:
    • BiocPkgTools.Rmd
* Checking package installation calls in R code...
* Checking for library/require of BiocPkgTools...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/biocPkgList.R (line 48, column 57)
    • ...
    • R/pkgDependencyMetrics.R (line 376, column 9)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • biocBuildReport.R (line 126, column 23)
    • ...
    • utilities.R (line 68, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/cache.R (line 10, column 13)
    • ...
    • cat() in R/pkgBiocDeps.R (line 142, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/biocBuildReport.R (line 154, column 20)
    • ...
    • R/vignetteTools.R (line 42, column 7)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/biocBuildEmail.R (line 273, column 17)
    • ...
    • R/biocVIEWSdb.R (line 13, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/classDependencies.R (line 260, column 67)
! WARNING: .Deprecated / .Defunct usage (found 2 times)
  • .Defunct() in R/biocDownloadStats.R (line 94, column 9)
  • .Defunct() in R/biocRevDepEmail.R (line 90, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/biocBuildReport.R (line 146, column 9)
  • suppressMessages() in R/repositoryStats.R (line 82, column 24)
* 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:
    • biocBuildReport() (R/biocBuildReport.R): 112 lines
    • ...
    • .formatBiocYearsDF() (R/getYearsInBioc.R): 73 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/biocBuildReportDB.Rd
    • ...
    • man/templatePath.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • biocBuildEmail.Rd
    • ...
    • templatePath.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
  Found in files:
    • biocPkgRanges.Rd
    • ...
    • getPkgYearsInBioc.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • biocPkgRanges.Rd
    • ...
    • getPkgYearsInBioc.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; 69 lines (1%) are > 80 characters long.
  First few lines:
    • R/biocBuildEmail.R#L140 #' @param version `character()` A vector ...
    • ...
    • vignettes/BiocPkgTools.Rmd#L373 [relations vocabulary of the Library of
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 399 lines (8%) are
not.
  First few lines:
    • R/biocBuildReport.R#L52 stopifnot(is.logical(stage.timings), i ...
    • ...
    • vignettes/BiocPkgTools.Rmd#L415 city region country ...
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 | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the BiocPkgTools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.