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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('DNAcopy_1.86.0.tar.gz','quit-with-status'=TRUE)"
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── Installing DNAcopy ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DNAcopy session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp0KLg7S/file7717630856f7/DNAcopy
→ BiocVersion: 3.23
→ Package: DNAcopy
→ PackageVersion: 1.86.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/DNAcopy.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmp0KLg7S/file7717630856f7/DNAcopy
→ installDir: /tmp/Rtmp0KLg7S/file7717616ea1b5d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DNAcopy ────────────────────────────────────────────────
* 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...
* 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: aCGH
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 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 'URL', '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:
    • DNAcopy.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • DNAcopy.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/DNAcopy.Rnw
* Checking package installation calls in R code...
* Checking for library/require of DNAcopy...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/DNAcopyMethods.R (line 376, column 18)
    • R/plotSample.R (line 18, column 16)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • changepoints.R (line 106, column 37)
    • ...
    • segmentsummary.R (line 24, column 50)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/changepoints.R (line 17, column 25)
    • ...
    • cat() in R/segment.R (line 61, column 25)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/zoomIntoRegion.R (line 16, column 27)
    • R/zoomIntoRegion.R (line 17, column 27)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 2 times:
    • T in R/zoomIntoRegion.R (line 5, column 71)
    • T in R/zoomIntoRegion.R (line 6, column 67)
* 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:
    • plot.DNAcopy() (R/DNAcopyMethods.R): 222 lines
    • ...
    • plotSample() (R/plotSample.R): 62 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/coriell.Rd
    • ...
    • man/zoomIntoRegion.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • getbdry.Rd
  • glFrequency.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; 47 lines (2%) are > 80 characters long.
  First few lines:
    • R/changepoints.R#L17 if (verbose>=3) cat(".... curren ...
    • ...
    • man/plot.DNAcopy.Rd#L101 plot(segment.smoothed.CNA.object, plot.t ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 738 lines (35%) are
not.
  First few lines:
    • R/changepoints.R#L2 NULL, sbdry, sb ...
    • ...
    • vignettes/DNAcopy.Rnw#L205 nperm} and {\tt alpha} which is not th ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the DNAcopy.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.