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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('gemma.R_3.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing gemma.R ──────────────────────────────────────────────────────────
✔ Package installed successfully
── gemma.R session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpOdiLEx/filea2b7a7313f135/gemma.R
→ BiocVersion: 3.24
→ Package: gemma.R
→ PackageVersion: 3.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/gemma.R.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpOdiLEx/filea2b7a7313f135/gemma.R
→ installDir: /tmp/RtmpOdiLEx/filea2b7a4860673f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on gemma.R ────────────────────────────────────────────────
* 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...
* 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:
    • gemma.R.Rmd
    • metadata.Rmd
    • metanalysis.Rmd
* Checking package installation calls in R code...
* Checking for library/require of gemma.R...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/convenience.R (line 406, column 29)
    • R/processors.R (line 386, column 38)
    • R/processors.R (line 913, column 95)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/validators.R (line 3, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/body.R (line 83, column 14)
    • ...
    • R/validators.R (line 349, column 12)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/body.R (line 197, column 46)
    • R/convenience.R (line 782, column 46)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/convenience.R (line 919, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 29
functions greater than 50 lines.
  The longest 5 functions are:
    • get_dataset_object() (R/convenience.R): 271 lines
    • ...
    • _anonymous_.149() (R/processors.R): 131 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/gemma_kable.Rd
    • man/gemma_memoise.Rd
    • man/update_result.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • gemma_kable.Rd
  • ...
  • set_gemma_user.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
ℹ NOTE: skip_on_bioc() found in testthat files: testCaches.R testConvenience.R
testDatasetEndpoints.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 808 lines (10%) are > 80 characters long.
  First few lines:
    • R/aa_caching.R#L23 #' to save the cache files for memoisati ...
    • ...
    • vignettes/metanalysis.Rmd#L504 {expression_frame$e ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 219 lines (3%) are
not.
  First few lines:
    • R/aa_caching.R#L5 dir <- getOption(x = "gemma.cache", ...
    • ...
    • vignettes/metanalysis.Rmd#L519 x = 1.5, label = '*',size= ...
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 | ⚠ 2 WARNINGS | ℹ 12 NOTES
ℹ See the gemma.R.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.