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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('clipper_1.53.0.tar.gz','quit-with-status'=TRUE)"
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── Installing clipper ──────────────────────────────────────────────────────────
✔ Package installed successfully
── clipper session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfNQpPF/file723606500f6dd/clipper
→ BiocVersion: 3.24
→ Package: clipper
→ PackageVersion: 1.53.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/clipper.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpfNQpPF/file723606500f6dd/clipper
→ installDir: /tmp/RtmpfNQpPF/file723605605f6c0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on clipper ────────────────────────────────────────────────
* 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 2.15.0 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
✖ ERROR: No biocViews terms found.
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...
* 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 (40%).
* 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:
    • clipper.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • clipper.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/clipper.Rnw
* Checking package installation calls in R code...
* Checking for library/require of clipper...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/clipper.R (line 24, column 3)
    • ...
    • R/pathwayTest.R (line 27, column 21)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • clipperBackbone.R (line 21, column 14)
    • ...
    • removeSelfLoops.R (line 20, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/clipperBackbone.R (line 36, column 6)
    • ...
    • R/permutation.R (line 34, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/deleteEdge.R (line 25, column 10)
    • R/deleteEdge.R (line 29, column 10)
    • R/deleteEdge.R (line 34, column 10)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • F in R/graph-theory.R (line 20, column 48)
    • ...
    • T in R/prunePaths.R (line 39, column 35)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in man/clipper.Rd
ℹ Found @ in man/clipperAllRoots.Rd
ℹ Found @ in man/cliqueMeanTest.Rd
ℹ Found @ in man/cliqueMixedTest.Rd
ℹ Found @ in man/cliquePairedTest.Rd
ℹ Found @ in man/cliqueVarianceTest.Rd
ℹ Found @ in man/easyClip.Rd
ℹ Found @ in man/pathwayTest.Rd
ℹ Found @ in vignettes/clipper.Rnw
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* 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:
    • clipperAllRoots() (R/clipper.R): 93 lines
    • ...
    • cliqueMixedTest() (R/cliqueMixedTest.R): 57 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotInCytoscape.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • easyLook.Rd
  • plotInCytoscape.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
  Found in files:
    • plotInCytoscape.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • plotInCytoscape.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 126 lines (5%) are > 80 characters long.
  First few lines:
    • R/clipper.R#L29 clipper <- function(expr, classes, graph ...
    • ...
    • vignettes/clipper.Rnw#L239 \bibitem{subramanian2005gene} Subramania ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 997 lines (38%) are
not.
  First few lines:
    • R/clipper.R#L19 cliques <- cliqueTest$cliques ...
    • ...
    • vignettes/clipper.Rnw#L238 ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 18 NOTES
ℹ See the clipper.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.