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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('RBGL_1.88.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RBGL ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── RBGL session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpMmkM0F/file8849d30cc40d4/RBGL
→ BiocVersion: 3.23
→ Package: RBGL
→ PackageVersion: 1.88.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/RBGL.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpMmkM0F/file8849d30cc40d4/RBGL
→ installDir: /tmp/RtmpMmkM0F/file8849d492c5024
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RBGL ───────────────────────────────────────────────────
* 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...
* 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 that Package field matches directory/tarball name...
* 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 (33%).
* 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:
    • RBGL.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/RBGL.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RBGL...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/interfaces.R (line 91, column 21)
    • ...
    • R/interfaces.R (line 1301, column 11)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/interfaces.R (line 274, column 13)
    • ...
    • R/separates.R (line 18, column 8)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/interfaces.R (line 37, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • sp.between() (R/interfaces.R): 72 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/RBGL.overview.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • bccluster.Rd
  • ...
  • sloanStartEndVertices.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:
    • layout.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • layout.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; 80 lines (1%) are > 80 characters long.
  First few lines:
    • R/interfaces.R#L84 warning("API is changing: checkConn is ...
    • ...
    • vignettes/RBGL.Rmd#L931 ```{r figkcliques, fig.small = TRUE, fig ...
ℹ NOTE: Consider 4 spaces instead of tabs; 118 lines (2%) contain tabs.
  First few lines:
    • R/interfaces.R#L8 as.integer(nv), as.integer(ne), as.inte ...
    • ...
    • R/kCores.R#L45 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 747 lines (13%) are
not.
  First few lines:
    • R/interfaces.R#L22 as.integer(nv), as.integer(ne), ...
    • ...
    • vignettes/RBGL.Rmd#L923 if for all nodes j in KC, D[v] ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the RBGL.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.