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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('ClassifyR_3.17.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ClassifyR ────────────────────────────────────────────────────────
✔ Package installed successfully
── ClassifyR session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpfMAQEG/file6ba3469ce70fa/ClassifyR
→ BiocVersion: 3.24
→ Package: ClassifyR
→ PackageVersion: 3.17.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/ClassifyR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpfMAQEG/file6ba3469ce70fa/ClassifyR
→ installDir: /tmp/RtmpfMAQEG/file6ba3425b62772
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ClassifyR ──────────────────────────────────────────────
* 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 4.1.0 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:
GeneExpression, DifferentialExpression, GenePrediction
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...
ℹ NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* 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 (26%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • ClassifyR.Rmd
    • DevelopersGuide.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/ClassifyR.Rmd
    • vignettes/DevelopersGuide.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ClassifyR...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/calcPerformance.R (line 109, column 3)
    • ...
    • R/utilities.R (line 655, column 5)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • classes.R (line 250, column 31)
    • ...
    • utilities.R (line 498, column 27)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/crissCrossValidate.R (line 389, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/interfaceMerge.R (line 7, column 17)
    • ...
    • R/utilities.R (line 37, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/calcPerformance.R (line 490, column 13)
    • ...
    • R/samplesMetricMap.R (line 164, column 13)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/calcPerformance.R (line 106, column 10)
    • ...
    • R/runTests.R (line 150, column 39)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • edgesToHubNetworks.R (line 37, column 19)
    • ...
    • utilities.R (line 327, column 31)
* 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 42
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.101() (R/samplesMetricMap.R): 422 lines
    • ...
    • crissCrossValidate() (R/crissCrossValidate.R): 262 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/available.Rd
    • ...
    • man/precisionPathwaysEvaluations.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • crissCrossPlot.Rd
  • ...
  • prepareData.Rd
* Checking package NEWS...
* Checking unit tests...
ℹ NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider shorter lines; 2315 lines (21%) are > 80 characters long.
  First few lines:
    • R/available.R#L7 #' @param what Default: \code{"classifie ...
    • ...
    • vignettes/DevelopersGuide.Rmd#L101 * Follow the other [style requirements
    o ...
ℹ NOTE: Consider 4 spaces instead of tabs; 3 lines (0%) contain tabs.
  First few lines:
    • R/rankingCoxPH.R#L49 result<- .C("coxmat", regmat = as.doub ...
    • R/rankingCoxPH.R#L63 sctest3 = as.double(1), PA ...
    • R/rankingCoxPH.R#L64 return(result) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4276 lines (38%) are
not.
  First few lines:
    • R/available.R#L19 what <- match.arg(what) ...
    • ...
    • vignettes/DevelopersGuide.Rmd#L91 style = 'margin-left: aut ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 20 NOTES
ℹ See the ClassifyR.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.