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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CNORfuzzy_1.55.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CNORfuzzy ────────────────────────────────────────────────────────
✔ Package installed successfully
── CNORfuzzy session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpYAsIxH/file770e2164e9301/CNORfuzzy
→ BiocVersion: 3.24
→ Package: CNORfuzzy
→ PackageVersion: 1.55.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CNORfuzzy.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpYAsIxH/file770e2164e9301/CNORfuzzy
→ installDir: /tmp/RtmpYAsIxH/file770e22dd7fca4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CNORfuzzy ──────────────────────────────────────────────
* 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...
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: CellBiology,
Proteomics, SystemsBiology, Pathways, CellBasedAssays, ImmunoOncology,
TimeCourse
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: 'Date:' field format is not 'YYYY-MM-DD': 2013-8-28
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (50%).
* 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:
    • CNORfuzzy-vignette.Rnw
Warning: ! in callr subprocess.
Caused by error in `parse(text = code, keep.source = FALSE)`:
! <text>:1:26: unexpected symbol
1: alist( defaultParameters echo
                             ^
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • CNORfuzzy-vignette.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/CNORfuzzy-vignette.Rnw
* Checking package installation calls in R code...
* Checking for library/require of CNORfuzzy...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • CNORwrapFuzzy.R (line 170, column 23)
    • ...
    • writeFuzzyNetwork.R (line 438, column 18)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/CNORwrapFuzzy.R (line 47, column 9)
    • ...
    • print() in R/writeFuzzyNetwork.R (line 250, column 29)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/CNORwrapFuzzy.R (line 39, column 14)
    • ...
    • R/writeFuzzyNetwork.R (line 353, column 37)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • CNORwrapFuzzy.R (line 35, column 21)
    • ...
    • writeFuzzyNetwork.R (line 291, column 33)
* 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 17
functions greater than 50 lines.
  The longest 5 functions are:
    • getNetworkInfoFuzzy() (R/writeFuzzyNetwork.R): 360 lines
    • ...
    • CNORwrapFuzzy() (R/CNORwrapFuzzy.R): 197 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/compileMultiRes.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • computeScoreFuzzy.Rd
    • getRefinedModel.Rd
    • reduceFuzzy.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 38% of man
pages use at least one of these tags.
  Found in files:
    • CNORfuzzy-package.Rd
    • ...
    • writeFuzzyNetwork.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • CNORfuzzy-package.Rd
    • ...
    • writeFuzzyNetwork.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; 360 lines (8%) are > 80 characters long.
  First few lines:
    • R/CNORwrapFuzzy.R#L17 #This function is a wrapper around the w ...
    • ...
    • vignettes/CNORfuzzy-vignette.Rnw#L736 maxtime &positive integer &5*60 &
    stop c ...
ℹ NOTE: Consider 4 spaces instead of tabs; 73 lines (2%) contain tabs.
  First few lines:
    • R/cSimulator.R#L22 # ...
    • ...
    • man/writeFuzzyNetwork.Rd#L17 \item{verbose}{If extra warnings should ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 154 lines (3%) are
not.
  First few lines:
    • R/CNORwrapFuzzy.R#L112 CNOlist=paramsList$data, ...
    • ...
    • vignettes/CNORfuzzy-vignette.Rnw#L628 \bibitem{MMB} ...
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 v1.49.4 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 3 WARNINGS | ℹ 17 NOTES
ℹ See the CNORfuzzy.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.