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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('PureCN_2.19.0.tar.gz','quit-with-status'=TRUE)"
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── Installing PureCN ───────────────────────────────────────────────────────────
✔ Package installed successfully
── PureCN session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpVBF0uP/file1042cad1f9b5/PureCN
→ BiocVersion: 3.24
→ Package: PureCN
→ PackageVersion: 2.19.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/PureCN.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpVBF0uP/file1042cad1f9b5/PureCN
→ installDir: /tmp/RtmpVBF0uP/file1042ca7a644269
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on PureCN ─────────────────────────────────────────────────
* 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: Microarray,
Classification, 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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (52%).
* 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:
    • PureCN.Rnw
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/Quick.Rmd
* Checking package installation calls in R code...
* Checking for library/require of PureCN...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/bootstrapResults.R (line 43, column 37)
    • ...
    • R/setMappingBiasVcf.R (line 164, column 35)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • calculateMappingBiasVcf.R (line 230, column 29)
    • ...
    • segmentationPSCBS.R (line 234, column 48)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/correctCoverageBias.R (line 74, column 13)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/plotAbs.R (line 147, column 10)
    • R/plotAbs.R (line 663, column 75)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
  • .Defunct() in R/processMultipleSamples.R (line 63, column 5)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
  • suppressWarnings() in R/annotateTargets.R (line 34, column 18)
  • ...
  • suppressWarnings() in R/readSegmentationFile.R (line 63, column 33)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 31
functions greater than 50 lines.
  The longest 5 functions are:
    • runAbsoluteCN() (R/runAbsoluteCN.R): 889 lines
    • ...
    • filterVcfBasic() (R/filterVcf.R): 168 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/centromeres.Rd
    • man/purecn.DNAcopy.bdry.Rd
    • man/purecn.example.output.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/calculateTangentNormal.Rd
    • ...
    • man/PureCN-deprecated.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • calculateMappingBiasGatk4.Rd
ℹ NOTE: Usage of dontrun / donttest tags found in man page examples. 4% of man
pages use at least one of these tags.
  Found in files:
    • calculateMappingBiasGatk4.Rd
    • segmentationGATK4.Rd
ℹ NOTE: Use donttest instead of dontrun.
  Found in files:
    • calculateMappingBiasGatk4.Rd
    • segmentationGATK4.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; 573 lines (5%) are > 80 characters long.
  First few lines:
    • R/adjustLogRatio.R#L33 adjustLogRatio <- function(ratio, purity ...
    • ...
    • vignettes/Quick.Rmd#L778 `--normaldb` | `normalDB` (seria ...
ℹ NOTE: Consider 4 spaces instead of tabs; 14 lines (0%) contain tabs.
  First few lines:
    • vignettes/PureCN.Rnw#L128 @HD VN:1.6 ...
    • ...
    • vignettes/PureCN.Rnw#L1484 \item This tool was originally designed ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 488 lines (4%) are
not.
  First few lines:
    • R/annotateTargets.R#L36 "SYMBOL")[, 2]) ...
    • ...
    • vignettes/Quick.Rmd#L704 callable. ...
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.
✖ ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 4 WARNINGS | ℹ 17 NOTES
ℹ See the PureCN.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.