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### Running command:
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###   /home/rapidbuild/bbs-3.24-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('scater_1.41.1.tar.gz','quit-with-status'=TRUE)"
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── Installing scater ───────────────────────────────────────────────────────────
✔ Package installed successfully
── scater session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpTV1sSW/file2ded406675825b/scater
→ BiocVersion: 3.24
→ Package: scater
→ PackageVersion: 1.41.1
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.24-bioc-rapid/meat/scater.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpTV1sSW/file2ded406675825b/scater
→ installDir: /tmp/RtmpTV1sSW/file2ded40119b6dd6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scater ─────────────────────────────────────────────────
* 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...
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 (44%).
* 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:
    • overview.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scater...
* Checking coding practice...
! WARNING: .Deprecated / .Defunct usage (found 6 times)
  • .Defunct() in R/defunct.R (line 31, column 5)
  • ...
  • .Defunct() in R/defunct.R (line 69, 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 15
functions greater than 50 lines.
  The longest 5 functions are:
    • .central_plotter() (R/plot_central.R): 207 lines
    • ...
    • plotHighestExprs() (R/plotHighestExprs.R): 92 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/scater-pkg.Rd
    • man/scater-plot-args.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • annotateBMFeatures.Rd
  • reexports.Rd
  • toSingleCellExperiment.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • annotateBMFeatures.Rd
    • plot_reddim.Rd
    • toSingleCellExperiment.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • annotateBMFeatures.Rd
    • plot_reddim.Rd
    • toSingleCellExperiment.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; 772 lines (13%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L18 #' \item{\code{logExprsOffset}:}{Scal ...
    • ...
    • vignettes/overview.Rmd#L265 Here, we examine the relationship betwee ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/plotPlatePosition.R#L97 other_fields = other_fields, ...
    • R/plotRLE.R#L73 assay_logged=exprs_logged, ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 64 lines (1%) are not.
  First few lines:
    • R/AllClasses.R#L46 contains = "ExpressionSet", ...
    • ...
    • R/utils_plotting.R#L117 x = data_matrix[, i]) ...
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 11 NOTES
ℹ See the scater.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.