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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('UMI4Cats_1.23.0.tar.gz','quit-with-status'=TRUE)"
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── Installing UMI4Cats ─────────────────────────────────────────────────────────
✔ Package installed successfully
── UMI4Cats session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwCG8BL/file15111417b53443/UMI4Cats
→ BiocVersion: 3.24
→ Package: UMI4Cats
→ PackageVersion: 1.23.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/UMI4Cats.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpwCG8BL/file15111417b53443/UMI4Cats
→ installDir: /tmp/RtmpwCG8BL/file151114370b2e57
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on UMI4Cats ───────────────────────────────────────────────
* 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 4.1.0 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...
* 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 (50%).
* 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:
    • UMI4Cats.Rmd
* Checking package installation calls in R code...
* Checking for library/require of UMI4Cats...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/demultiplexFastq.R (line 52, column 54)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/callInteractions.R (line 130, column 22)
    • R/callInteractions.R (line 137, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/callInteractions.R (line 92, column 5)
    • ...
    • R/digestGenome.R (line 97, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/AllClasses.R (line 204, column 13)
    • R/plotUMI4C.R (line 302, column 35)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/contactsUMI4C.R (line 897, column 16)
  • suppressMessages() in R/contactsUMI4C.R (line 613, column 5)
  • suppressWarnings() in R/groupUMI4C.R (line 78, column 14)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 25
functions greater than 50 lines.
  The longest 5 functions are:
    • makeUMI4C() (R/AllClasses.R): 183 lines
    • ...
    • .singlePrepUMI4C() (R/contactsUMI4C.R): 112 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • demultiplexFastq.Rd
  • ...
  • plotInteractionsUMI4C.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 3% of man
pages use at least one of these tags.
  Found in files:
    • demultiplexFastq.Rd
    • differentialNbinomWaldTestUMI4C.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • demultiplexFastq.Rd
    • differentialNbinomWaldTestUMI4C.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; 279 lines (6%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L6 #' @note The \code{UMI4C} class extends ...
    • ...
    • vignettes/UMI4Cats.Rmd#L555 The `plotUMI4C` function is a wrapper fo ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 522 lines (10%) are
not.
  First few lines:
    • R/AllClasses.R#L164 stop("colData must contain 'co ...
    • ...
    • vignettes/UMI4Cats.Rmd#L527 ...
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 UMI4Cats.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.