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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DMRScan_1.35.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DMRScan ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DMRScan session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAleiqZ/file83c1857dadf9/DMRScan
→ BiocVersion: 3.24
→ Package: DMRScan
→ PackageVersion: 1.35.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DMRScan.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpAleiqZ/file83c1857dadf9/DMRScan
→ installDir: /tmp/RtmpAleiqZ/file83c185682173a
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DMRScan ────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
ℹ NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews: Clustering
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...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (30%).
* 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:
    • DMRScan_vignette.Rmd
* Checking package installation calls in R code...
* Checking for library/require of DMRScan...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/dmrscan_foo.R (line 79, column 28)
    • ...
    • R/varAR.R (line 10, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • importantSampling.R (line 42, column 17)
    • ...
    • windowTest.R (line 23, column 30)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/dmrscan_foo.R (line 78, column 9)
    • ...
    • cat() in R/makeCpGranges.R (line 182, column 7)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/estimateTgrid.R (line 97, column 15)
    • ...
    • R/importantSampling.R (line 56, column 22)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/dmrscan_foo.R (line 89, 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 7
functions greater than 50 lines.
  The longest 5 functions are:
    • dmrscan() (R/dmrscan_foo.R): 132 lines
    • ...
    • makeCpGgenes() (R/makeCpGranges.R): 52 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/DMRScan.methylationData.Rd
    • man/DMRScan.phenotypes.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; 100 lines (8%) are > 80 characters long.
  First few lines:
    • R/dmrscan_foo.R#L6 #' \code{\link{makeCpGregions}}, a vecto ...
    • ...
    • vignettes/DMRScan_vignette.Rmd#L230 [2] Peters TJ, Buckley MJ, Statham
    AL, P ...
ℹ NOTE: Consider 4 spaces instead of tabs; 40 lines (3%) contain tabs.
  First few lines:
    • R/dmrscan_foo.R#L79 nProbe <- sum(sapply(observati ...
    • ...
    • vignettes/DMRScan_vignette.Rmd#L199 |Chr22:23801059-23801111 |7 |0.000
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 137 lines (11%) are
not.
  First few lines:
    • R/dmrscan_foo.R#L86 windowSize ...
    • ...
    • vignettes/DMRScan_vignette.Rmd#L220 dmrscan.results <-
    dmrscan(observation ...
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 | ⚠ 1 WARNINGS | ℹ 17 NOTES
ℹ See the DMRScan.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.