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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('CGHbase_1.73.0.tar.gz','quit-with-status'=TRUE)"
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── Installing CGHbase ──────────────────────────────────────────────────────────
✔ Package installed successfully
── CGHbase session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmppcWqTF/file64f382235e4ee/CGHbase
→ BiocVersion: 3.24
→ Package: CGHbase
→ PackageVersion: 1.73.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/CGHbase.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmppcWqTF/file64f382235e4ee/CGHbase
→ installDir: /tmp/RtmppcWqTF/file64f38baa061
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CGHbase ────────────────────────────────────────────────
* 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 2.10 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...
No vignettes found.
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppcWqTF/file64f382235e4ee/CGHbase/man/WiltingCalled.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppcWqTF/file64f382235e4ee/CGHbase/man/WiltingNorm.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppcWqTF/file64f382235e4ee/CGHbase/man/WiltingRaw.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppcWqTF/file64f382235e4ee/CGHbase/man/WiltingRegions.Rd'
Warning in FUN(X[[i]], ...) :
  incomplete final line found on '/tmp/RtmppcWqTF/file64f382235e4ee/CGHbase/man/WiltingSeg.Rd'
ℹ NOTE: Consider adding these automatically suggested biocViews: Preprocessing,
TwoChannel
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...
✖ ERROR: Remove Maintainer field. Use Authors@R [cre] designation.
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (67%).
* 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...
✖ ERROR: No 'vignettes' directory.
* Checking package installation calls in R code...
* Checking for library/require of CGHbase...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/tools.R (line 27, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/methods-cghCall.R (line 157, column 35)
    • ...
    • R/methods-cghSeg.R (line 68, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • methods-cghCall.R (line 66, column 16)
    • ...
    • private.R (line 215, column 34)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/private.R (line 220, column 5)
    • print() in R/private.R (line 228, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
  Found 3 times:
    • F in R/methods-cghRegions.R (line 112, column 56)
    • T in R/tools.R (line 2, column 73)
    • T in R/tools.R (line 2, column 91)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • tools.R (line 2, column 22)
    • tools.R (line 3, column 26)
    • tools.R (line 5, column 26)
* 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 6
functions greater than 50 lines.
  The longest 5 functions are:
    • _anonymous_.39() (R/methods-cghCall.R): 133 lines
    • ...
    • _anonymous_.19() (R/methods-cghRegions.R): 58 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/plot.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • avedist.Rd
    • ...
    • summaryPlot.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 24% of man
pages use at least one of these tags.
  Found in files:
    • class.cghCall.Rd
    • ...
    • summaryPlot.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • class.cghCall.Rd
    • ...
    • summaryPlot.Rd
* Checking package NEWS...
ℹ NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 225 lines (11%) are > 80 characters long.
  First few lines:
    • R/allGeneric.R#L3 setGeneric("plot.cghRaw", function(x, ...
    • ...
    • man/WiltingSeg.Rd#L13 Wilting, S.M., Snijders, P.J., Meijer, ...
ℹ NOTE: Consider 4 spaces instead of tabs; 49 lines (2%) contain tabs.
  First few lines:
    • CGHbase/NAMESPACE#L15 plot.cghCall, plot.cghRegions, ...
    • ...
    • man/summaryPlot.Rd#L32 \dontrun{ ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 402 lines (20%) are
not.
  First few lines:
    • R/methods-cghCall.R#L64 ...
    • ...
    • man/WiltingSeg.Rd#L13 Wilting, S.M., Snijders, P.J., Meijer, ...
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 ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | ℹ 15 NOTES
ℹ See the CGHbase.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.