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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('limma_3.68.2.tar.gz','quit-with-status'=TRUE)"
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── Installing limma ────────────────────────────────────────────────────────────
✔ Package installed successfully
── limma session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpaOburp/file7de805e9268b0/limma
→ BiocVersion: 3.23
→ Package: limma
→ PackageVersion: 3.68.2
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/limma.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpaOburp/file7de805e9268b0/limma
→ installDir: /tmp/RtmpaOburp/file7de805419f059
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on limma ──────────────────────────────────────────────────
* 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 3.6.0 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 that Package field matches directory/tarball name...
* 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 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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:
    • usersguide.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 1 out of 2 code chunks = 50% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • intro.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/intro.Rmd
    • vignettes/usersguide.Rnw
* Checking package installation calls in R code...
* Checking for library/require of limma...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/plotExons.R (line 48, column 26)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • alias2Symbol.R (line 118, column 34)
    • ...
    • wsva.R (line 26, column 35)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/arrayWeightsGeneByGene.R (line 29, column 17)
    • ...
    • cat() in R/utility.R (line 86, column 17)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/background-kooperberg.R (line 45, column 10)
    • ...
    • R/write.R (line 82, column 53)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/modelmatrix.R (line 23, column 51)
    • ...
    • R/read.R (line 17, column 33)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 4 times:
    • F in R/beadCountWeights.R (line 104, column 9)
    • ...
    • F in R/beadCountWeights.R (line 117, column 17)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/utility.R (line 101, column 25)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8 times)
  • suppressWarnings() in R/dups.R (line 125, column 47)
  • ...
  • suppressWarnings() in R/zscoreHyper.R (line 9, column 9)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 95
functions greater than 50 lines.
  The longest 5 functions are:
    • barcodeplot() (R/barcodeplot.R): 427 lines
    • ...
    • fitFDistRobustly() (R/fitFDistRobustly.R): 255 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/02classes.Rd
    • ...
    • man/TestResults.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • anova-method.Rd
    • ...
    • wsva.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 18% of man
pages use at least one of these tags.
  Found in files:
    • arrayWeightsQuick.Rd
    • ...
    • writefit.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • arrayWeightsQuick.Rd
    • ...
    • writefit.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; 3802 lines (15%) are > 80 characters long.
  First few lines:
    • R/alias2Symbol.R#L12 suppressPackageStartupMessages(OK <- re ...
    • ...
    • vignettes/intro.Rmd#L53 [doi:10.12688/f1000research.27893.1](htt ...
ℹ NOTE: Consider 4 spaces instead of tabs; 11538 lines (44%) contain tabs.
  First few lines:
    • R/alias2Symbol.R#L9 alias <- as.character(alias) ...
    • ...
    • man/roast.Rd#L74 \item{FDR.Mixed}{non-directional false ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 1798 lines (7%) are
not.
  First few lines:
    • R/background-normexp.R#L115 mu <- theta[1] ...
    • ...
    • vignettes/intro.Rmd#L17 comment = NA ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 5 WARNINGS | ℹ 19 NOTES
ℹ See the limma.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.