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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('RUVcorr_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing RUVcorr ──────────────────────────────────────────────────────────
✔ Package installed successfully
── RUVcorr session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp7wWRCR/file1274ac29d98395/RUVcorr
→ BiocVersion: 3.24
→ Package: RUVcorr
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/RUVcorr.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmp7wWRCR/file1274ac29d98395/RUVcorr
→ installDir: /tmp/Rtmp7wWRCR/file1274ac71777ca6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on RUVcorr ────────────────────────────────────────────────
* 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...
* 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...
✖ 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 (8%).
* 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:
    • Vignette.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of RUVcorr...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotThreshold.R (line 41, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • plotThreshold.R (line 49, column 12)
    • plotThreshold.R (line 52, column 43)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/PCAPlot.R (line 83, column 3)
    • print() in R/plot.optimizeParameters.r (line 61, column 7)
    • print() in R/simulateGEdata.R (line 137, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/correlationPlot.R (line 43, column 10)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • is.optimizeParameters.R (line 24, column 18)
    • ...
    • plotThreshold.R (line 41, column 42)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
  • suppressWarnings() in R/simulateGEdata.R (line 167, column 5)
  • suppressWarnings() in R/simulateGEdata.R (line 168, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 5
functions greater than 50 lines.
  The longest 5 functions are:
    • simulateGEdata() (R/simulateGEdata.R): 114 lines
    • ...
    • ECDFPlot() (R/ECDFPlot.R): 61 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • is.optimizeParameters.Rd
  • ...
  • is.Weights.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
  Found in files:
    • is.optimizeParameters.Rd
    • is.simulateGEdata.Rd
    • print.simulateGEdata.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; 204 lines (9%) are > 80 characters long.
  First few lines:
    • R/assessQuality.R#L3 #' \code{assessQuality} allows to assess ...
    • ...
    • vignettes/Vignette.Rmd#L246 prior<-prioritise(CleanData, na_index, c ...
ℹ NOTE: Consider 4 spaces instead of tabs; 10 lines (0%) contain tabs.
  First few lines:
    • R/background.R#L28 colnames(Y)<-seq_len(dim(Y)[2]) ...
    • ...
    • vignettes/Vignette.Rmd#L37 * $\alpha$ is a $k \times n$ matrix of r ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 699 lines (30%) are
not.
  First few lines:
    • R/assessQuality.R#L30 est, # estimated expression values ...
    • ...
    • vignettes/Vignette.Rmd#L235 Weights=NULL) ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the RUVcorr.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.