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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('DMRcaller_1.45.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DMRcaller ────────────────────────────────────────────────────────
✔ Package installed successfully
── DMRcaller session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpQFmzSN/file83b5f41dae2f0/DMRcaller
→ BiocVersion: 3.24
→ Package: DMRcaller
→ PackageVersion: 1.45.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/DMRcaller.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpQFmzSN/file83b5f41dae2f0/DMRcaller
→ installDir: /tmp/RtmpQFmzSN/file83b5f314f4734
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DMRcaller ──────────────────────────────────────────────
* 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 3.5 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 (54%).
* 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...
* Checking package installation calls in R code...
* Checking for library/require of DMRcaller...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/computeVMDs.R (line 344, column 12)
    • ...
    • R/spatialCorrelation.R (line 85, column 23)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • computeDMRs.R (line 339, column 18)
    • ...
    • spatialCorrelation.R (line 243, column 12)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/computeCoMethylatedPostions.R (line 99, column 3)
    • ...
    • cat() in R/spatialCorrelation.R (line 101, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/computeCoMethylatedPostions.R (line 156, column 15)
    • ...
    • R/Replicates.R (line 579, column 34)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/computeCoMethylatedPostions.R (line 115, column 15)
    • ...
    • R/Replicates.R (line 300, column 15)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 19 times)
  • suppressWarnings() in R/computeCoMethylatedPostions.R (line 103, column 16)
  • ...
  • suppressWarnings() in R/Replicates.R (line 282, column 16)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 52
functions greater than 50 lines.
  The longest 5 functions are:
    • readONTbam() (R/ONTdata.R): 673 lines
    • ...
    • .computeDMRsNoiseFilter() (R/computeDMRs.R): 215 lines
* Checking man page documentation...
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • computeCoMethylatedPositions.Rd
  • ...
  • selectCytosine.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 39% of man
pages use at least one of these tags.
  Found in files:
    • computeCoMethylatedPositions.Rd
    • ...
    • selectCytosine.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • computeCoMethylatedPositions.Rd
    • ...
    • selectCytosine.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; 1235 lines (10%) are > 80 characters long.
  First few lines:
    • R/computeCoMethylatedPostions.R#L3 #' @title Compute pairwise
    co-methylatio ...
    • ...
    • vignettes/DMRcaller.Rmd#L935 When using 10 cores, it can take between ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 4419 lines (36%) are
not.
  First few lines:
    • R/computeCoMethylatedPostions.R#L88 ...
    • ...
    • vignettes/DMRcaller.Rmd#L922 ) ...
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 | ⚠ 0 WARNINGS | ℹ 17 NOTES
ℹ See the DMRcaller.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.