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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('rBiopaxParser_2.52.0.tar.gz','quit-with-status'=TRUE)"
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── Installing rBiopaxParser ────────────────────────────────────────────────────
✔ Package installed successfully
── rBiopaxParser session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmpL6CTzP/file16747970b48bf8/rBiopaxParser
→ BiocVersion: 3.23
→ Package: rBiopaxParser
→ PackageVersion: 2.52.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/rBiopaxParser.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpL6CTzP/file16747970b48bf8/rBiopaxParser
→ installDir: /tmp/RtmpL6CTzP/file16747949b0d0a9
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on rBiopaxParser ──────────────────────────────────────────
* 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 4.0 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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* 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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • rBiopaxParserVignette.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 28 out of 37 code chunks = 75% unevaluated
ℹ 
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • rBiopaxParserVignette.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • rBiopaxParserVignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of rBiopaxParser...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/downloadBiopaxData.R (line 78, column 13)
    • ...
    • require() in R/visualizeBiopax.R (line 832, column 13)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/helperFunctions.R (line 169, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • biopax2Classes.R (line 500, column 18)
    • ...
    • writeBiopax.R (line 97, column 26)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/pathway2Graph.R (line 178, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/biopax2Classes.R (line 33, column 23)
    • ...
    • R/writeBiopax.R (line 111, column 31)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/downloadBiopaxData.R (line 79, column 25)
    • ...
    • R/writeBiopax.R (line 110, column 50)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/helperFunctions.R (line 20, column 51)
    • ...
    • R/writeBiopax.R (line 36, column 56)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 23 times:
    • T in R/biopax2Classes.R (line 34, column 37)
    • ...
    • T in R/visualizeBiopax.R (line 182, column 150)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • helperFunctions.R (line 23, column 35)
    • ...
    • helperFunctions.R (line 166, column 28)
* 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 10
functions greater than 50 lines.
  The longest 5 functions are:
    • getClassProperties() (R/biopax2Classes.R): 911 lines
    • ...
    • uniteGraphs() (R/visualizeBiopax.R): 106 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/getParticipants.Rd
    • man/print.biopax.Rd
    • man/removeDisconnectedParts.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • CLASS_INHERITANCE_BP2.Rd
  • ...
  • mergePathways.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
  Found in files:
    • downloadBiopaxData.Rd
    • ...
    • writeBiopax.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • downloadBiopaxData.Rd
    • ...
    • writeBiopax.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; 953 lines (17%) are > 80 characters long.
  First few lines:
    • R/biopax2Classes.R#L34 matrix(ncol=2,byrow=T, dimnames=list(l ...
    • ...
    • vignettes/rBiopaxParserVignette.Rnw#L642 or download and unzip the file
    directly ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2205 lines (40%) contain tabs.
  First few lines:
    • R/biopax2Classes.R#L4 # for the BioPax level 2 representat ...
    • ...
    • vignettes/rBiopaxParserVignette.Rnw#L601 splitComplexMolecules=TRUE,
    verbose=TRU ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 118 lines (2%) are
not.
  First few lines:
    • R/pathway2Graph.R#L30 ...
    • ...
    • vignettes/rBiopaxParserVignette.Rnw#L396 \label{table:exampledatatable}
    ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 7 WARNINGS | ℹ 18 NOTES
ℹ See the rBiopaxParser.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.