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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CATALYST_1.37.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CATALYST ─────────────────────────────────────────────────────────
✔ Package installed successfully
── CATALYST session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpvsgNFq/file61b8c223dbb51/CATALYST
→ BiocVersion: 3.24
→ Package: CATALYST
→ PackageVersion: 1.37.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CATALYST.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpvsgNFq/file61b8c223dbb51/CATALYST
→ installDir: /tmp/RtmpvsgNFq/file61b8c15a6570e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CATALYST ───────────────────────────────────────────────
* 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...
* 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • differential.Rmd
    • preprocessing.Rmd
* Checking package installation calls in R code...
* Checking for library/require of CATALYST...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print in R/plotYields.R (line 164, column 20)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/validityChecks.R (line 140, column 18)
    • R/validityChecks.R (line 144, column 18)
    • R/validityChecks.R (line 164, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/differential.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/cluster.R (line 127, column 11)
  • ...
  • suppressWarnings() in R/sce2fcs.R (line 91, column 20)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 27
functions greater than 50 lines.
  The longest 5 functions are:
    • prepData() (R/prepData.R): 204 lines
    • ...
    • plotDR() (R/plotDR.R): 123 lines
* Checking man page documentation...
* 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; 202 lines (3%) are > 80 characters long.
  First few lines:
    • R/plotMahal.R#L49 stopifnot(is.character(which), lengt ...
    • ...
    • vignettes/preprocessing.Rmd#L509 Besides writing out FCS files, conversio
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 15 lines (0%) are not.
  First few lines:
    • R/plotFreqHeatmap.R#L102 ...
    • ...
    • vignettes/preprocessing.Rmd#L460 facet_by = c("bc_id", "group_id")) ...
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 10 NOTES
ℹ See the CATALYST.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.