##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('Rgraphviz_2.56.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################


── Installing Rgraphviz ────────────────────────────────────────────────────────
✔ Package installed successfully
── Rgraphviz session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRlSfwZ/file891517b64b9ae/Rgraphviz
→ BiocVersion: 3.23
→ Package: Rgraphviz
→ PackageVersion: 2.56.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/Rgraphviz.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpRlSfwZ/file891517b64b9ae/Rgraphviz
→ installDir: /tmp/RtmpRlSfwZ/file891515b6b5cb2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on Rgraphviz ──────────────────────────────────────────────
* 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 2.6.0 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 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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (14%).
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • newRgraphvizInterface.Rnw
    • Rgraphviz.Rnw
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • newRgraphvizInterface.Rnw
    • Rgraphviz.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • newRgraphvizInterface.Rnw
    • Rgraphviz.Rnw
* Checking package installation calls in R code...
* Checking for library/require of Rgraphviz...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/layoutGraph.R (line 41, column 11)
    • ...
    • R/SimpleMethods.R (line 170, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • agfunctions.R (line 120, column 20)
    • ...
    • SimpleMethods.R (line 175, column 19)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/agfunctions.R (line 114, column 11)
    • ...
    • R/SimpleMethods.R (line 223, column 19)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/agfunctions.R (line 45, column 29)
    • ...
    • R/plotGraph.R (line 94, column 20)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 1 times:
    • T in R/layoutGraph.R (line 139, column 33)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/SimpleMethods.R (line 82, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/Rgraphviz.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/renderGraph.R (line 354, column 24)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
  The longest 5 functions are:
    • renderNodes() (R/renderGraph.R): 130 lines
    • ...
    • _anonymous_.28() (R/plotGraph.R): 80 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/agwrite.Rd
    • ...
    • man/toDot-methods.Rd
.onUnload()
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • graphData-methods.Rd
  • graphDataDefaults-methods.Rd
* Checking package NEWS...
ℹ NOTE: More than one NEWS file found.See ?news for recognition ordering.
  Please remove one of the following:
    • inst/NEWS.Rd
    • graphviz/NEWS
    • doc/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; 58 lines (1%) are > 80 characters long.
  First few lines:
    • R/agfunctions.R#L28 edges <- buildEdgeList(graph, re ...
    • ...
    • vignettes/Rgraphviz.Rnw#L786 Currently, only the 1st call to set defa ...
ℹ NOTE: Consider 4 spaces instead of tabs; 86 lines (1%) contain tabs.
  First few lines:
    • R/agfunctions.R#L2 layout=TRUE, layoutTy ...
    • ...
    • man/GraphvizAttributes.Rd#L200 margin.  Default is \code{FALSE}} ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1767 lines (28%) are
not.
  First few lines:
    • R/agfunctions.R#L2 layout=TRUE, layoutTy ...
    • ...
    • vignettes/Rgraphviz.Rnw#L579 } ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 4 WARNINGS | ℹ 18 NOTES
ℹ See the Rgraphviz.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.