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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('singleCellTK_2.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing singleCellTK ─────────────────────────────────────────────────────
✔ Package installed successfully
── singleCellTK session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpmE4baW/file132f7433e0d242/singleCellTK
→ BiocVersion: 3.24
→ Package: singleCellTK
→ PackageVersion: 2.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/singleCellTK.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpmE4baW/file132f7433e0d242/singleCellTK
→ installDir: /tmp/RtmpmE4baW/file132f74394ac67e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on singleCellTK ───────────────────────────────────────────
* 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 4.0 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Sequencing,
Coverage
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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 (39%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of singleCellTK...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/scDblFinder_doubletDetection.R (line 99, column 44)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • getTopHVG.R (line 103, column 26)
    • ggPlotting.R (line 923, column 57)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/importAnnData.R (line 129, column 5)
    • ...
    • cat() in R/sctkQCUtils.R (line 624, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/decorate.R (line 3, column 7)
    • ...
    • R/seuratFunctions.R (line 943, column 18)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/combineSCE.R (line 282, column 10)
    • ...
    • R/singleCellTK.R (line 27, column 10)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • plotSCEHeatmap.R (line 334, column 29)
! WARNING: .Deprecated / .Defunct usage (found 6 times)
  • deprecate_warn() in R/ggPlotting.R (line 555, column 5)
  • ...
  • .Deprecated() in R/runUMAP.R (line 181, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 9 times)
  • <<- in R/reticulate_setup.R (line 19, column 12)
  • ...
  • <<- in R/reticulate_setup.R (line 27, column 6)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 11 times)
  • suppressMessages() in R/computeHeatmap.R (line 183, column 11)
  • ...
  • suppressWarnings() in R/seuratFunctions.R (line 1774, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 150
functions greater than 50 lines.
  The longest 5 functions are:
    • importMultipleSources() (R/importMultipleSources.R): 357 lines
    • ...
    • plotDoubletFinderResults() (R/ggPerQCWrapper.R): 303 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • computeHeatmap.Rd
  • ...
  • singleCellTK.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 25% of man
pages use at least one of these tags.
  Found in files:
    • exportSCE.Rd
    • ...
    • singleCellTK.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • exportSCE.Rd
    • ...
    • singleCellTK.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; 1329 lines (4%) are > 80 characters long.
  First few lines:
    • R/abundance.R#L31 #' ...
    • ...
    • vignettes/singleCellTK.Rmd#L96 vignettes to help you get started, which
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 10083 lines (32%) are
not.
  First few lines:
    • R/abundance.R#L33 analysisNam ...
    • ...
    • R/validityFunctions.R#L129 "' not found in the ...
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 17 NOTES
ℹ See the singleCellTK.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.