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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('geneplotter_1.90.0.tar.gz','quit-with-status'=TRUE)"
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── Installing geneplotter ──────────────────────────────────────────────────────
✔ Package installed successfully
── geneplotter session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpe4DQRb/file7aa4a68035a72/geneplotter
→ BiocVersion: 3.23
→ Package: geneplotter
→ PackageVersion: 1.90.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/geneplotter.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/Rtmpe4DQRb/file7aa4a68035a72/geneplotter
→ installDir: /tmp/Rtmpe4DQRb/file7aa4a7b4c826f
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on geneplotter ────────────────────────────────────────────
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Pathways, GO
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...
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 (33%).
* 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:
    • visualize.Rnw
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • byChroms.Rmd
ℹ NOTE: 'sessionInfo' not found in vignette(s)
  Missing from file(s):
    • vignettes/byChroms.Rmd
    • vignettes/visualize.Rnw
* Checking package installation calls in R code...
* Checking for library/require of geneplotter...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/amplicon.plot.R (line 6, column 5)
    • require() in R/plotExpression.R (line 3, column 5)
* Checking coding practice...
ℹ NOTE: Avoid sapply(); use vapply()
  Found in files:
    • R/amplicon.plot.R (line 12, column 17)
    • ...
    • R/plotChr.R (line 41, column 17)
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • alongChrom.R (line 102, column 16)
    • ...
    • plotChr.R (line 98, column 14)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/alongChrom.R (line 36, column 13)
    • ...
    • print() in R/amplicon.plot.R (line 62, column 5)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/alongChrom.R (line 458, column 29)
    • ...
    • R/savepng.R (line 21, column 6)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/imageMap.R (line 15, column 12)
    • R/plotChr.R (line 107, column 21)
ℹ NOTE: Avoid system() ; use system2()
  Found in files:
    • system() in R/savepng.R (line 36, column 3)
* Checking parsed R code in R directory, examples, vignettes...
ℹ Found @ in vignettes/byChroms.Rmd
ℹ NOTE: Use accessors; don't access S4 class slots via '@' in
examples/vignettes.
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 8
functions greater than 50 lines.
  The longest 5 functions are:
    • plotChr() (R/plotChr.R): 112 lines
    • ...
    • doACImagePlot() (R/alongChrom.R): 61 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/alongChrom.Rd
    • ...
    • man/plotMA.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; 45 lines (2%) are > 80 characters long.
  First few lines:
    • R/alongChrom.R#L588 scale=c("none","zs ...
    • ...
    • vignettes/visualize.Rnw#L67 We will use the example data in \Robject ...
ℹ NOTE: Consider 4 spaces instead of tabs; 39 lines (1%) contain tabs.
  First few lines:
    • R/plotChr.R#L2 cols=rep("black", length(senseObj[[1]]) ...
    • ...
    • man/plotExpressionGraph.Rd#L80 data(IMCAEntrezLink) ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 866 lines (30%) are
not.
  First few lines:
    • R/alongChrom.R#L2 plotFormat=c("cum ...
    • ...
    • vignettes/visualize.Rnw#L148 alongChrom(eset, "1", chrObj, plotForma ...
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 email is ok.
── BiocCheck v1.48.0 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 3 WARNINGS | ℹ 20 NOTES
ℹ See the geneplotter.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.