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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('splatter_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing splatter ─────────────────────────────────────────────────────────
✔ Package installed successfully
── splatter session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvjqLzo/file14590b5058f8d3/splatter
→ BiocVersion: 3.24
→ Package: splatter
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/splatter.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvjqLzo/file14590b5058f8d3/splatter
→ installDir: /tmp/RtmpvjqLzo/file14590b2ad10d7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on splatter ───────────────────────────────────────────────
* Checking for deprecated package usage...
✖ ERROR: Package dependency in the DESCRIPTION is 'Deprecated'.
  Do not use the following package(s):
    • mfa
* 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: 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 (40%).
* 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...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
  Found in files:
    • install.packages() in R/utils.R (line 164, column 13)
    • install() in R/utils.R (line 170, column 18)
* Checking for library/require of splatter...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/listSims.R (line 156, column 9)
    • ...
    • print() in R/params-functions.R (line 217, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/splatPop-simulate.R (line 391, column 25)
    • R/splatPop-simulate.R (line 788, column 25)
! WARNING: .Deprecated / .Defunct usage (found 3 times)
  • deprecate_warn() in R/mfa-estimate.R (line 34, column 16)
  • deprecate_warn() in R/mfa-simulate.R (line 41, column 16)
  • deprecate_warn() in R/MFAParams-methods.R (line 5, column 16)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
  • suppressMessages() in R/BASiCS-estimate.R (line 135, column 20)
  • ...
  • suppressMessages() in R/scDD-simulate.R (line 80, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 54
functions greater than 50 lines.
  The longest 5 functions are:
    • diffSCEs() (R/compare.R): 342 lines
    • ...
    • BASiCSSimulate() (R/BASiCS-simulate.R): 167 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • BASiCSEstimate.Rd
    • ...
    • splatPopSimulateSC.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
  Found in files:
    • addGeneLengths.Rd
    • ...
    • splatSimulate.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addGeneLengths.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; 74 lines (1%) are > 80 characters long.
  First few lines:
    • R/mfa-estimate.R#L37 details = "The mfa package was d ...
    • ...
    • vignettes/splatter.Rmd#L574 [SCE-vignette]: https://bioconductor.org ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 155 lines (1%) are
not.
  First few lines:
    • R/BASiCS-estimate.R#L51 n = 20000, th ...
    • ...
    • vignettes/splatter.Rmd#L277 cells. ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 1 WARNINGS | ℹ 12 NOTES
ℹ See the splatter.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.