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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RedeR_3.9.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RedeR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── RedeR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYE7SRe/file10e3845a5b9c8f/RedeR
→ BiocVersion: 3.24
→ Package: RedeR
→ PackageVersion: 3.9.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RedeR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYE7SRe/file10e3845a5b9c8f/RedeR
→ installDir: /tmp/RtmpYE7SRe/file10e3842366a389
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RedeR ──────────────────────────────────────────────────
* 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 4.4 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...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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...
* Checking for library/require of RedeR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/exportedCallMethods.R (line 595, column 16)
    • R/exportedCallMethods.R (line 640, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/AllClasses.R (line 39, column 14)
    • ...
    • print() in R/exportedAttributeSeters.R (line 274, column 5)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/exportedCallMethods.R (line 148, column 20)
    • system() in R/exportedCallMethods.R (line 162, column 13)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/exportedCallMethods.R (line 341, column 27)
  • suppressWarnings() in R/exportedCallMethods.R (line 346, column 30)
  • suppressWarnings() in R/exportedCallMethods.R (line 354, column 17)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 16
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.54() (R/exportedAddGraphMethods.R): 282 lines
    • ...
    • _anonymous_.42() (R/exportedGetGraphMethods.R): 89 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • subg.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 76% of man
pages use at least one of these tags.
  Found in files:
    • addEdges-methods.Rd
    • ...
    • version-methods.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • addGraph-methods.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; 55 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L49 setClassUnion("numeric_Or_integer_Or_mis ...
    • ...
    • vignettes/RedeR.Rmd#L507 The exact output will vary, but you need ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • vignettes/RedeR.Rmd#L452 tal <- att.setv(tal, from="Species", to= ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 94 lines (2%) are not.
  First few lines:
    • R/AllValidations.R#L273 atts[["nodeLabelColor"]]) ...
    • ...
    • vignettes/RedeR.Rmd#L405 title="Node color (logFC)", stretch = ...
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 15 NOTES
ℹ See the RedeR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.