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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RCy3_2.33.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RCy3 ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── RCy3 session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9qlB2W/file10971e2446b7cf/RCy3
→ BiocVersion: 3.24
→ Package: RCy3
→ PackageVersion: 2.33.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RCy3.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp9qlB2W/file10971e2446b7cf/RCy3
→ installDir: /tmp/Rtmp9qlB2W/file10971e4fa30b5d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RCy3 ───────────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: GUI
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* 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...
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (11%).
* 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:
    • Cancer-networks-and-data.Rmd
    • ...
    • Upgrading-existing-scripts.Rmd
✖ ERROR: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/Cancer-networks-and-data.Rmd (chunk no. 2, line 28, column 5)
    • ...
    • vignettes/Upgrading-existing-scripts.Rmd (chunk no. 2, line 30, column
    18)
! WARNING: Potential package installation calls found in vignette(s)
  Found in files:
    • vignettes/Cancer-networks-and-data.Rmd (chunk no. 2, line 28, column 5)
    • ...
    • vignettes/Upgrading-existing-scripts.Rmd (chunk no. 2, line 29, column 5)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Cancer-networks-and-data.Rmd
    • ...
    • vignettes/Upgrading-existing-scripts.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/Rtmp9qlB2W/file10971e2446b7cf/RCy3/vignettes/Filtering-Networks.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
  More than one `opts_chunk$set()` in /tmp/Rtmp9qlB2W/file10971e2446b7cf/RCy3/vignettes/Phylogenetic-trees.Rmd
! WARNING: Vignette set global option 'eval=FALSE'
  Found in files:
    • vignettes/Cancer-networks-and-data.Rmd
    • ...
    • vignettes/Upgrading-existing-scripts.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RCy3...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Layouts.R (line 252, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/Commands.R (line 440, column 9)
    • ...
    • print() in R/Sandbox.R (line 251, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Annotations.R (line 55, column 12)
    • ...
    • R/Tables.R (line 346, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/Apps.R (line 188, column 14)
    • ...
    • R/StyleMappings.R (line 114, column 14)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/NetworkViews.R (line 96, column 17)
    • ...
    • R/Tables.R (line 422, column 22)
✖ ERROR: Avoid references to external hosting platforms
  Found in files:
    • RCy3-notebook.R (line 94, column 14)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/RCy3-notebook.R (line 6, column 15)
  • <<- in R/RCy3-notebook.R (line 7, column 19)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/Networks.R (line 820, column 13)
  • suppressWarnings() in R/Networks.R (line 826, column 13)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 19
functions greater than 50 lines.
  The longest 5 functions are:
    • createNetworkFromDataFrames() (R/Networks.R): 129 lines
    • ...
    • addAnnotationShape() (R/Annotations.R): 100 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • addAnnotationBoundedText.Rd
    • ...
    • updateStyleMapping.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 90% of man
pages use at least one of these tags.
  Found in files:
    • addAnnotationBoundedText.Rd
    • ...
    • updateStyleMapping.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; 1701 lines (9%) are > 80 characters long.
  First few lines:
    • R/Annotations.R#L48 fontSize = N ...
    • ...
    • vignettes/Upgrading-existing-scripts.Rmd#L272 *
    https://github.com/cytoscape/cytosca ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1607 lines (8%) are
not.
  First few lines:
    • R/Annotations.R#L53 cmd.string <- 'annotation add text' # ...
    • ...
    • vignettes/Upgrading-existing-scripts.Rmd#L272 *
    https://github.com/cytoscape/cytosca ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 4 ERRORS | ⚠ 2 WARNINGS | ℹ 17 NOTES
ℹ See the RCy3.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.