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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('quantro_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing quantro ──────────────────────────────────────────────────────────
✔ Package installed successfully
── quantro session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpI8UAEq/file105da67ed4d277/quantro
→ BiocVersion: 3.24
→ Package: quantro
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/quantro.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpI8UAEq/file105da67ed4d277/quantro
→ installDir: /tmp/RtmpI8UAEq/file105da65291adce
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on quantro ────────────────────────────────────────────────
* 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 4.0 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...
* 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...
* 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 (25%).
* 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:
    • quantro.Rmd
✖ ERROR: Package installation calls found in vignette(s)
  Found in files:
    • vignettes/quantro.Rmd (chunk no. 3, line 86, column 5)
    • vignettes/quantro.Rmd (chunk no. 3, line 87, column 14)
! WARNING: Potential package installation calls found in vignette(s)
  Found in files:
    • vignettes/quantro.Rmd (chunk no. 3, line 86, column 5)
* Checking package installation calls in R code...
* Checking for library/require of quantro...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/AllClasses.R (line 211, column 14)
    • R/AllClasses.R (line 264, column 23)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/plots.R (line 196, column 26)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/AllClasses.R (line 206, column 14)
    • ...
    • R/plots.R (line 187, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressMessages() in R/plots.R (line 194, column 9)
  • suppressMessages() in R/plots.R (line 196, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
  The longest 5 functions are:
    • quantro() (R/AllClasses.R): 147 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/anova.Rd
    • ...
    • man/summary.Rd
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • quantroPlot.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
  Found in files:
    • quantroPlot.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; 12 lines (1%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L79 #' test was performed to assess the stat ...
    • ...
    • vignettes/quantro.Rmd#L236 `quantroPvalPerm` | If `B` is not equal ...
ℹ NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs.
  First few lines:
    • R/AllClasses.R#L225 MSe <- sum(withinDiff) / (nT - K) ...
    • R/AllClasses.R#L274 MSe <- sum(withinDiff) / (nT - K ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 25 lines (2%) are not.
  First few lines:
    • R/AllClasses.R#L10 representation = representation ...
    • ...
    • vignettes/quantro.Rmd#L151 main = "Beta Values", brewer. ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the quantro.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.