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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('MethylAid_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing MethylAid ────────────────────────────────────────────────────────
✔ Package installed successfully
── MethylAid session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpoLBHBO/filed5b4a47e9ebe4/MethylAid
→ BiocVersion: 3.24
→ Package: MethylAid
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/MethylAid.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpoLBHBO/filed5b4a47e9ebe4/MethylAid
→ installDir: /tmp/RtmpoLBHBO/filed5b4a730f81b6
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on MethylAid ──────────────────────────────────────────────
* 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 3.4 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...
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 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (29%).
* 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:
    • MethylAid.Rnw
! WARNING: Evaluate more vignette chunks.
ℹ 11 out of 16 code chunks = 68% unevaluated
ℹ 
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • MethylAid.Rnw
* Checking package installation calls in R code...
* Checking for library/require of MethylAid...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • filterControlPlots.R (line 52, column 68)
    • ...
    • util.R (line 138, column 13)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/summarizedData.R (line 40, column 5)
    • print() in R/util.R (line 37, column 24)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/uitext.R (line 2, column 7)
    • ...
    • R/util.R (line 1, column 9)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/summarization.R (line 33, column 17)
    • ...
    • R/summarizedData.R (line 99, column 18)
* 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 5
functions greater than 50 lines.
  The longest 5 functions are:
    • ui() (R/ui.R): 158 lines
    • ...
    • summarizePerBatch() (R/summarization.R): 52 lines
* Checking man page documentation...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
  Found in files:
    • exampleData.Rd
    • visualize.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • exampleData.Rd
    • visualize.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; 168 lines (9%) are > 80 characters long.
  First few lines:
    • R/filterControlPlots.R#L11 ## smoothScatter(bg$x, bg$y, ...
    • ...
    • vignettes/MethylAid.Rnw#L233 tcga <- summarize(targets, batchSize = 1 ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 366 lines (19%) are
not.
  First few lines:
    • R/filterControlPlots.R#L5 col="grey90", ...
    • ...
    • vignettes/MethylAid.Rnw#L276 BS = 12.75, HC = 13.25, DP ...
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 ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the MethylAid.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.