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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('KEGGgraph_1.72.0.tar.gz','quit-with-status'=TRUE)"
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── Installing KEGGgraph ────────────────────────────────────────────────────────
✔ Package installed successfully
── KEGGgraph session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph
→ BiocVersion: 3.23
→ Package: KEGGgraph
→ PackageVersion: 1.72.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/KEGGgraph.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph
→ installDir: /tmp/RtmpVXLDBu/file7dc256ffe33d2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on KEGGgraph ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking version number validity...
* Checking R version dependency...
ℹ NOTE: Update R version dependency from 3.5.0 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...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph/man/getNamedElement.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph/man/KEGGEdgeSubType-class.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph/man/parseGraphics.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph/man/parsePathwayInfo.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpVXLDBu/file7dc257c1e5a4e/KEGGgraph/man/subGraphByNodeType.Rd'
* 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...
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...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
  Rnw vignette(s) found:
    • KEGGgraph.Rnw
    • KEGGgraphApp.Rnw
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found in files:
    • vignettes/KEGGgraph.Rnw (chunk no. 11, line 79, column 45)
    • vignettes/KEGGgraph.Rnw (chunk no. 11, line 80, column 43)
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/KEGGgraphApp.Rnw
* Checking package installation calls in R code...
* Checking for library/require of KEGGgraph...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/graph.R (line 24, column 32)
    • ...
    • R/parse.R (line 540, column 13)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • graph.R (line 92, column 10)
    • ...
    • vis.R (line 65, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/parse.R (line 211, column 13)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/kgmlfile.R (line 46, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/parse.R (line 267, column 15)
    • R/parse.R (line 271, column 10)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Deprecated() in R/kgmlfile.R (line 55, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/kgmlfile.R (line 58, column 23)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 2
functions greater than 50 lines.
  The longest 5 functions are:
    • KEGGpathway2Graph() (R/parse.R): 56 lines
    • parseEntry() (R/parse.R): 55 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/expandKEGGNode.Rd
    • ...
    • man/subtypeDisplay-methods.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • getValue-methods.Rd
    • ...
    • subtypeDisplay-methods.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; 143 lines (3%) are > 80 characters long.
  First few lines:
    • R/annotation.R#L6 stop("This function so far supports ...
    • ...
    • vignettes/KEGGgraphApp.Rnw#L321 \bibitem[Aittokallio and Schwikowski, 20
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 28 lines (1%) contain tabs.
  First few lines:
    • man/KEGGEdge-class.Rd#L15 \describe{ ...
    • ...
    • man/plotKEGGgraph.Rd#L44 "hsa:5494","hsa:5609") ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1407 lines (32%) are
not.
  First few lines:
    • R/annotation.R#L5 if(organism!="hsa") { ...
    • ...
    • vignettes/KEGGgraphApp.Rnw#L333 of colorectal cancer cell carcinoids, ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 16 NOTES
ℹ See the KEGGgraph.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.