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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('staRgate_1.1.0.tar.gz','quit-with-status'=TRUE)"
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── Installing staRgate ─────────────────────────────────────────────────────────
✔ Package installed successfully
── staRgate session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp3jmEPF/file147a97ef7f40/staRgate
→ BiocVersion: 3.24
→ Package: staRgate
→ PackageVersion: 1.1.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/staRgate.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp3jmEPF/file147a97ef7f40/staRgate
→ installDir: /tmp/Rtmp3jmEPF/file147a9746561c9a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on staRgate ───────────────────────────────────────────────
* 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 4.3.0 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...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
Warning in person1(given = given[[i]], family = family[[i]], middle = middle[[i]],  :
  It is recommended to use ‘given’ instead of ‘middle’.
* 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:
    • vignette_run_pipeline.Rmd
* Checking package installation calls in R code...
* Checking for library/require of staRgate...
* Checking coding practice...
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • getPerc() (R/getPerc.R): 342 lines
    • ...
    • getDensityGates() (R/getDensityGates.R): 103 lines
* Checking man page documentation...
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 220 lines (9%) are > 80 characters long.
  First few lines:
    • R/getDensityGates.R#L120 # dplyr::add_row should add a row pe ...
    • ...
    • vignettes/vignette_run_pipeline.Rmd#L975 P. Van, W. Jiang, R. Gottardo
    and G. Fin ...
ℹ NOTE: Consider 4 spaces instead of tabs; 40 lines (2%) contain tabs.
  First few lines:
    • vignettes/vignette_run_pipeline.Rmd#L659 - Denominator: Combinations of
    positive ...
    • ...
    • vignettes/vignette_run_pipeline.Rmd#L714 - …" ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 818 lines (32%) are
not.
  First few lines:
    • R/getBiexpTransformGS.R#L51 ## Read in the table of parameters ...
    • ...
    • vignettes/vignette_run_pipeline.Rmd#L946 gating_args = list(min =
    current_gate, ...
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 8 NOTES
ℹ See the staRgate.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.