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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicDataCommons_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GenomicDataCommons ───────────────────────────────────────────────
✔ Package installed successfully
── GenomicDataCommons session metadata ─────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8iTIFO/filea465b46d5abac/GenomicDataCommons
→ BiocVersion: 3.24
→ Package: GenomicDataCommons
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GenomicDataCommons.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp8iTIFO/filea465b46d5abac/GenomicDataCommons
→ installDir: /tmp/Rtmp8iTIFO/filea465b6be73197
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenomicDataCommons ─────────────────────────────────────
* 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 if 'Package:' field matches directory / tarball...
* 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 (15%).
* 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:
    • questions-and-answers.Rmd
    • somatic_mutations.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/questions-and-answers.Rmd
    • vignettes/somatic_mutations.Rmd
* Checking package installation calls in R code...
* Checking for library/require of GenomicDataCommons...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/clinical.R (line 92, column 69)
    • R/mapping.R (line 48, column 41)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/REST.R (line 105, column 19)
    • cat() in R/slicing.R (line 99, column 9)
    • cat() in R/utilities.R (line 2, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/bulk_transfer.R (line 55, column 18)
    • ...
    • R/REST.R (line 99, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/response.R (line 249, column 32)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/REST.R (line 27, column 16)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/clinical.R (line 77, column 18)
  • suppressWarnings() in R/gdc_token.R (line 47, column 13)
* Checking function lengths...
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • make_filter.Rd
  • slicing.Rd
  • transfer.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • gdc_cache.Rd
    • slicing.Rd
    • transfer.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • gdc_cache.Rd
    • slicing.Rd
    • transfer.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; 58 lines (2%) are > 80 characters long.
  First few lines:
    • R/bulk_transfer.R#L4 #' \href{the GDC Data Transfer Tool}{htt ...
    • ...
    • vignettes/questions-and-answers.Rmd#L85 I would like to get the number of
    cases ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 129 lines (4%) are
not.
  First few lines:
    • R/bulk_transfer.R#L78 as.charac ...
    • ...
    • vignettes/somatic_mutations.Rmd#L117 gdcdata() ...
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 17 NOTES
ℹ See the GenomicDataCommons.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.