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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DOtools_1.3.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DOtools ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DOtools session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpcsWfX3/file84b1625f32e0a/DOtools
→ BiocVersion: 3.24
→ Package: DOtools
→ PackageVersion: 1.3.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DOtools.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpcsWfX3/file84b1625f32e0a/DOtools
→ installDir: /tmp/RtmpcsWfX3/file84b1649b86dcc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DOtools ────────────────────────────────────────────────
* 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 4.5.0 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:
MultipleComparison
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 (17%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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 DOtools...
* Checking coding practice...
! WARNING: Remove set.seed usage (found 2 times)
  • set.seed() in R/DO.FullRecluster.R (line 39, column 5)
  • set.seed() in R/DO.VlnPlot.R (line 567, 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 32
functions greater than 50 lines.
  The longest 5 functions are:
    • DO.Dotplot() (R/DO.Dotplot.R): 927 lines
    • ...
    • .annoSegment() (R/DO.Dotplot.R): 495 lines
* Checking man page documentation...
Registered S3 method overwritten by 'zellkonverter':
  method                                             from      
  py_to_r.pandas.core.arrays.categorical.Categorical reticulate
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • DO.CellBender.Rd
  • ...
  • DO.scVI.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
  Found in files:
    • DO.CellBender.Rd
    • ...
    • DO.scVI.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • DO.CellBender.Rd
    • ...
    • DO.scVI.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; 54 lines (0%) are > 80 characters long.
  First few lines:
    • R/DO.EvalIntegration.R#L367 stop("Input matrix and batch inf ...
    • ...
    • R/DO.VlnPlot.R#L483 p_val <- wilcox.te ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 74 lines (1%) are not.
  First few lines:
    • R/DO.BoxPlot.R#L443 degs <- FindMarkers(sc ...
    • ...
    • R/DO.VlnPlot.R#L497 ) ...
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 | ⚠ 1 WARNINGS | ℹ 9 NOTES
ℹ See the DOtools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.