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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('FlowSOM_2.21.0.tar.gz','quit-with-status'=TRUE)"
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── Installing FlowSOM ──────────────────────────────────────────────────────────
✔ Package installed successfully
── FlowSOM session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpsIWWRz/file9c7fb6478f960/FlowSOM
→ BiocVersion: 3.24
→ Package: FlowSOM
→ PackageVersion: 2.21.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/FlowSOM.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpsIWWRz/file9c7fb6478f960/FlowSOM
→ installDir: /tmp/RtmpsIWWRz/file9c7fb3ec1992b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on FlowSOM ────────────────────────────────────────────────
* 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 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...
* 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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (16%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • FlowSOM.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • FlowSOM.Rnw
* Checking package installation calls in R code...
* Checking for library/require of FlowSOM...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/2_buildSOM.R (line 71, column 7)
    • ...
    • R/6_deprecated.R (line 912, column 27)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • 2_buildSOM.R (line 205, column 22)
    • ...
    • 6_deprecated.R (line 714, column 33)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/3_buildMST.R (line 368, column 5)
    • ...
    • print() in R/6_deprecated.R (line 1055, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/5_plotFunctions.R (line 2131, column 26)
    • R/5_plotFunctions.R (line 2133, column 26)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/0_FlowSOM.R (line 442, column 38)
    • ...
    • R/5_plotFunctions.R (line 3040, column 12)
! WARNING: Remove set.seed usage (found 5 times)
  • set.seed() in R/0_FlowSOM.R (line 113, column 5)
  • ...
  • set.seed() in R/5_plotFunctions.R (line 780, column 23)
! WARNING: .Deprecated / .Defunct usage (found 15 times)
  • .Deprecated() in R/6_deprecated.R (line 22, column 3)
  • ...
  • .Deprecated() in R/6_deprecated.R (line 892, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/MetaclusterMFIs.Rd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
  • suppressWarnings() in R/1_readInput.R (line 121, column 26)
  • ...
  • suppressMessages() in R/5_plotFunctions.R (line 3165, column 8)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 26
functions greater than 50 lines.
  The longest 5 functions are:
    • FlowSOMmary() (R/5_plotFunctions.R): 247 lines
    • ...
    • PlotFileScatters() (R/6_deprecated.R): 188 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/PlotVariable.Rd
    • man/print.FlowSOM.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • AddBackground.Rd
  • ...
  • UpdateFlowSOM.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
  Found in files:
    • PlotClusters2D.Rd
    • PlotOverview2D.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 157 lines (2%) are > 80 characters long.
  First few lines:
    • R/0_FlowSOM.R#L27 #' @param colsToUse Markers, channel ...
    • ...
    • vignettes/FlowSOM.Rnw#L433 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 2801 lines (35%) are
not.
  First few lines:
    • R/0_FlowSOM.R#L101 # Method to run general FlowSOM workfl ...
    • ...
    • vignettes/FlowSOM.Rnw#L447 ggplot2::scale_size_manual(values =c(" ...
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 | ⚠ 4 WARNINGS | ℹ 19 NOTES
ℹ See the FlowSOM.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.