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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ROntoTools_2.41.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ROntoTools ───────────────────────────────────────────────────────
✔ Package installed successfully
── ROntoTools session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpnKRBfF/file123a963b812ec2/ROntoTools
→ BiocVersion: 3.24
→ Package: ROntoTools
→ PackageVersion: 2.41.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ROntoTools.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpnKRBfF/file123a963b812ec2/ROntoTools
→ installDir: /tmp/RtmpnKRBfF/file123a9660d40757
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ROntoTools ─────────────────────────────────────────────
* 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...
! WARNING: Invalid BiocViews term(s):
  • 'NetworkAnalysis'
  • 'GraphsAndNetworks': Did you mean 'GraphAndNetwork'?
* Checking for recommended biocViews...
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmpnKRBfF/file123a963b812ec2/ROntoTools/vignettes/rontotools.Rnw'
ℹ NOTE: Consider adding these automatically suggested biocViews: Pathways,
KEGG, GraphAndNetwork, ThirdPartyClient
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
✖ ERROR: License 'CC BY-NC-ND 4.0 + file LICENSE' restricts 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 (67%).
* 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:
    • rontotools.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • rontotools.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/rontotools.Rnw
* Checking package installation calls in R code...
* Checking for library/require of ROntoTools...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/pathwayExpress.R (line 162, column 27)
    • library() in R/pDisExpress.R (line 158, column 27)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/graphWeights.R (line 139, column 36)
    • ...
    • R/utils.R (line 72, column 20)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • graphWeights.R (line 68, column 14)
    • ...
    • summary.peRes.R (line 103, column 16)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/pathwayExpress.R (line 219, column 10)
    • ...
    • R/pDisExpress.R (line 229, column 17)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/keggDataREST.R (line 42, column 13)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • T in R/keggDataREST.R (line 122, column 52)
    • ...
    • F in R/pDisExpress.R (line 184, column 53)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • keggDataREST.R (line 140, column 18)
    • renderInfo-methods.R (line 50, column 22)
    • renderInfo-methods.R (line 134, column 22)
! WARNING: Remove set.seed usage (found 6 times)
  • set.seed() in R/pathwayExpress.R (line 113, column 5)
  • ...
  • set.seed() in R/pDisExpress.R (line 162, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/peEdgeRenderInfo.Rd
ℹ Found @ in man/peNodeRenderInfo.Rd
ℹ Found @ in man/plot.pePathway-methods.Rd
ℹ Found @ in vignettes/rontotools.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
ℹ NOTE: Avoid '<<-' if possible (found 2 times)
  • <<- in R/summary.pDisRes.R (line 120, column 65)
  • <<- in R/summary.peRes.R (line 125, column 65)
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/graphWeights.R (line 150, column 25)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
  The longest 5 functions are:
    • keggPathwayGraphs() (R/keggDataREST.R): 104 lines
    • ...
    • _anonymous_.157() (R/plot-methods.R): 57 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/alpha1MR.Rd
    • ...
    • man/summary.peRes.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; 239 lines (9%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L3 #' This class is used to encode the resu ...
    • ...
    • vignettes/rontotools.Rnw#L379 The result object can be summarized in a
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • vignettes/rontotools.Rnw#L88 edgeWeightByType = list(activation = 1, ...
    • vignettes/rontotools.Rnw#L89 expression = 1, repression = -1), ...
    • vignettes/rontotools.Rnw#L90 defaultWeight = 0) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 694 lines (28%) are
not.
  First few lines:
    • R/AllClasses.R#L28 representation(pathways = "list ...
    • ...
    • vignettes/rontotools.Rnw#L384 pORA = FALSE, comb.pv = NU ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 7 WARNINGS | ℹ 17 NOTES
ℹ See the ROntoTools.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.