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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GeneBreak_1.43.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GeneBreak ────────────────────────────────────────────────────────
✔ Package installed successfully
── GeneBreak session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpCeOQRw/filea2e2d5122975c/GeneBreak
→ BiocVersion: 3.24
→ Package: GeneBreak
→ PackageVersion: 1.43.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GeneBreak.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpCeOQRw/filea2e2d5122975c/GeneBreak
→ installDir: /tmp/RtmpCeOQRw/filea2e2d3105bd5e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GeneBreak ──────────────────────────────────────────────
* 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 3.2 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,
Coverage, Preprocessing, QualityControl
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...
ℹ NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (57%).
* 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:
    • GeneBreak.Rnw
! WARNING: Package listed as VignetteEngine or VignetteBuilder but not
currently Suggested.
  Add the following to Suggests in DESCRIPTION:
    • utils
✖ ERROR: Vignette(s) found with duplicate chunk labels
  Found in files:
    • GeneBreak.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GeneBreak.Rnw
* Checking package installation calls in R code...
* Checking for library/require of GeneBreak...
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/GeneBreakMethods.R (line 119, column 47)
    • ...
    • R/GeneBreakMethods.R (line 710, column 28)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • GeneBreakMethods.R (line 71, column 41)
    • ...
    • GeneBreakMethods.R (line 710, column 36)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • cat() in R/GeneBreakAccessors.R (line 85, column 9)
    • ...
    • cat() in R/private.R (line 18, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/GeneBreakAccessors.R (line 5, column 20)
    • ...
    • R/GeneBreakMethods.R (line 869, column 32)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/GeneBreakMethods.R (line 387, column 38)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
  Found in files:
    • GeneBreakAccessors.R (line 30, column 28)
    • ...
    • private.R (line 6, column 61)
* 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:
    • _anonymous_.240() (R/GeneBreakMethods.R): 165 lines
    • ...
    • _anonymous_.428() (R/GeneBreakMethods.R): 58 lines
* Checking man page documentation...
* 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; 301 lines (11%) are > 80 characters long.
  First few lines:
    • R/AllClasses.R#L7 #' @slot featureAnnotation A dataframe w ...
    • ...
    • vignettes/GeneBreak.Rnw#L279 This section describes the steps taken t ...
ℹ NOTE: Consider 4 spaces instead of tabs; 58 lines (2%) contain tabs.
  First few lines:
    • R/GeneBreakMethods.R#L35 ## slots are the same for CGHcall a ...
    • ...
    • R/GeneBreakMethods.R#L775 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 103 lines (4%) are
not.
  First few lines:
    • R/GeneBreakMethods.R#L205 ifelse( any( is.na(x) ), NA, p ...
    • ...
    • vignettes/GeneBreak.Rnw#L332 return( biomart_genes ) ...
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 ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | ℹ 16 NOTES
ℹ See the GeneBreak.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.