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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RCX_1.17.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RCX ──────────────────────────────────────────────────────────────
✔ Package installed successfully
── RCX session metadata ────────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAfp4JR/file10968246f74fc8/RCX
→ BiocVersion: 3.24
→ Package: RCX
→ PackageVersion: 1.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RCX.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAfp4JR/file10968246f74fc8/RCX
→ installDir: /tmp/RtmpAfp4JR/file1096823767eedc
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RCX ────────────────────────────────────────────────────
* 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 4.2.0 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...
! 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • Creating_RCX_from_scratch.Rmd
    • Extending_the_RCX_Data_Model.Rmd
    • RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RCX...
* Checking coding practice...
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/Json-fromJson.R (line 91, column 15)
    • ...
    • cat() in R/Visualize.R (line 228, column 15)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AspectDependencies.R (line 36, column 8)
    • ...
    • R/zzz.R (line 12, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Utils-error-handling.R (line 93, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 14
functions greater than 50 lines.
  The longest 5 functions are:
    • validate.RCX() (R/Validate.R): 353 lines
    • ...
    • processCX() (R/Json-fromJson.R): 100 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • setExtension.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:
    • setExtension.Rd
    • visualize.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; 1426 lines (12%) are > 80 characters long.
  First few lines:
    • R/AspectDependencies.R#L9 ######################################## ...
    • ...
    •
    vignettes/RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd#L460
    As igraph, graphNEL objects can not hold ...
ℹ NOTE: Consider 4 spaces instead of tabs; 55 lines (0%) contain tabs.
  First few lines:
    • vignettes/Appendix_The_RCX_and_CX_Data_Model.Rmd#L114 |RCX property |RCX
    specifics |CX p ...
    • ...
    • vignettes/Creating_RCX_from_scratch.Rmd#L256 95 # status:error ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1667 lines (14%) are
not.
  First few lines:
    • R/AspectDependencies.R#L37 UseMethod("hasIds", aspect) ...
    • ...
    •
    vignettes/RCX_an_R_package_implementing_the_Cytoscape_Exchange_format.Rmd#L308
    openExternal = TRUE) ...
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 13 NOTES
ℹ See the RCX.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.