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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('scDblFinder_1.27.0.tar.gz','quit-with-status'=TRUE)"
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── Installing scDblFinder ──────────────────────────────────────────────────────
✔ Package installed successfully
── scDblFinder session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpGGEH3d/file12a4d23dd3c891/scDblFinder
→ BiocVersion: 3.24
→ Package: scDblFinder
→ PackageVersion: 1.27.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/scDblFinder.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpGGEH3d/file12a4d23dd3c891/scDblFinder
→ installDir: /tmp/RtmpGGEH3d/file12a4d24ef0b552
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDblFinder ────────────────────────────────────────────
* 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,
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 (71%).
* 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:
    • computeDoubletDensity.Rmd
    • ...
    • scDblFinder.Rmd
* Checking package installation calls in R code...
* Checking for library/require of scDblFinder...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/atac.R (line 221, column 6)
    • ...
    • R/scDblFinder.R (line 812, column 10)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • enrichment.R (line 143, column 22)
    • ...
    • scDblFinder.R (line 424, column 22)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/getFragmentOverlaps.R (line 88, column 21)
    • cat() in R/getFragmentOverlaps.R (line 98, column 9)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/misc.R (line 420, column 15)
    • R/misc.R (line 455, column 13)
    • R/scDblFinder.R (line 309, column 23)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/atac.R (line 200, column 5)
  • ...
  • suppressWarnings() in R/scDblFinder.R (line 529, column 10)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
  The longest 5 functions are:
    • scDblFinder() (R/scDblFinder.R): 325 lines
    • ...
    • .doublet_cluster() (R/findDoubletClusters.R): 84 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • aggregateFeatures.Rd
  • ...
  • plotThresholds.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; 455 lines (9%) are > 80 characters long.
  First few lines:
    • R/atac_processing.R#L92 cellclust <- kmeans(scale(x), min(10 ...
    • ...
    • vignettes/scDblFinder.Rmd#L341 The simplest way is to do an average of
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 9 lines (0%) contain tabs.
  First few lines:
    • R/misc.R#L142 mm <- dplyr::bind_rows(lapply(mm, FUN=f ...
    • ...
    • R/misc.R#L150 return(head(g,nfeatures)) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1310 lines (27%) are
not.
  First few lines:
    • R/atac_processing.R#L17 if(!is(x,"sparseMatrix")) x <- as(x, " ...
    • ...
    • vignettes/scDblFinder.Rmd#L311 colData(res)[,grep("scDblFi ...
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 15 NOTES
ℹ See the scDblFinder.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.