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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('methylPipe_1.47.0.tar.gz','quit-with-status'=TRUE)"
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── Installing methylPipe ───────────────────────────────────────────────────────
✔ Package installed successfully
── methylPipe session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpa9nHxD/filed696d1bf5743/methylPipe
→ BiocVersion: 3.24
→ Package: methylPipe
→ PackageVersion: 1.47.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/methylPipe.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpa9nHxD/filed696d1bf5743/methylPipe
→ installDir: /tmp/Rtmpa9nHxD/filed696d713865f4
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on methylPipe ─────────────────────────────────────────────
* 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 3.5.0 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: Alignment,
QualityControl, DataImport
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...
ℹ NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (58%).
* 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:
    • methylPipe.rnw
* Checking package installation calls in R code...
* Checking for library/require of methylPipe...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • library() in R/BSdata-methods.R (line 150, column 22)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/Allfunctions.R (line 108, column 20)
    • ...
    • R/BSdata-methods.R (line 85, column 12)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • AllClasses.R (line 48, column 14)
    • ...
    • BSdataSet-methods.R (line 533, column 21)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/Allfunctions.R (line 326, column 36)
    • ...
    • R/GElist-methods.R (line 14, column 15)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/BSdataSet-methods.R (line 265, column 63)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/Allfunctions.R (line 84, column 23)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 10 times:
    • T in R/Allfunctions.R (line 677, column 64)
    • ...
    • T in R/BSdataSet-methods.R (line 325, column 79)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • Allfunctions.R (line 353, column 23)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/Allfunctions.R (line 82, column 27)
    • ...
    • system() in R/Allfunctions.R (line 281, column 9)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
  • suppressWarnings() in R/Allfunctions.R (line 397, column 13)
  • suppressWarnings() in R/Allfunctions.R (line 673, column 9)
  • suppressWarnings() in R/Allfunctions.R (line 738, column 5)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.53() (R/BSdataSet-methods.R): 338 lines
    • ...
    • profileDNAmetBin() (R/Allfunctions.R): 123 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plotMeth.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • BSprepare.Rd
    • ...
    • tabixdata2GR.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; 352 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L61 prototype = prototype(Summarize ...
    • ...
    • vignettes/methylPipe.rnw#L270 hyper.DMRs.conso <- consolidateDMRs(DmrG
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 8 lines (0%) contain tabs.
  First few lines:
    • R/Allfunctions.R#L989 txdb <- transcriptDB ...
    • ...
    • man/methylPipe-package.Rd#L35 \item GElist-class : This class is a set
    ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 679 lines (21%) are
not.
  First few lines:
    • R/AllClasses.R#L2 slots = c(file = 'character', ...
    • ...
    • vignettes/methylPipe.rnw#L263 dmrSize=6, dmrBp=800) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 5 WARNINGS | ℹ 18 NOTES
ℹ See the methylPipe.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.