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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scAnnotatR_1.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scAnnotatR ───────────────────────────────────────────────────────
✔ Package installed successfully
── scAnnotatR session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDhG4nJ/file12901c122cb81d/scAnnotatR
→ BiocVersion: 3.24
→ Package: scAnnotatR
→ PackageVersion: 1.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scAnnotatR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpDhG4nJ/file12901c122cb81d/scAnnotatR
→ installDir: /tmp/RtmpDhG4nJ/file12901c7ce08376
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scAnnotatR ─────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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 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, ImmunoOncology, DataImport
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 (19%).
* 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:
    • classifying-cells.Rmd
    • training-basic-model.Rmd
    • training-child-model.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scAnnotatR...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/support.R (line 185, column 7)
    • print() in R/tree.R (line 137, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/classifier.R (line 365, column 7)
    • ...
    • R/tree.R (line 117, column 27)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/support.R (line 117, column 10)
    • R/support.R (line 123, column 10)
    • R/support.R (line 150, column 10)
* 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 8
functions greater than 50 lines.
  The longest 5 functions are:
    • classify_cells_sce() (R/classifier.R): 112 lines
    • ...
    • test_performance() (R/support.R): 66 lines
* Checking man page documentation...
Warning: replacing previous import ‘ape::where’ by ‘dplyr::where’ when loading ‘scAnnotatR’
Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘scAnnotatR’
Registered S3 method overwritten by 'spatstat.explore':
  method   from
  plot.roc pROC
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • cell_type-set.Rd
  • load_models.Rd
  • p_thres-set.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; 93 lines (3%) are > 80 characters long.
  First few lines:
    • R/class.R#L43 #' @param marker_genes vector/character ...
    • ...
    • vignettes/training-child-model.Rmd#L279 To have all plasma cells
    specified as pl ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 853 lines (25%) are
not.
  First few lines:
    • R/class.R#L33 slots = list(cell ...
    • ...
    • vignettes/training-child-model.Rmd#L284 ignore_ambi ...
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 13 NOTES
ℹ See the scAnnotatR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.