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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('GenomicPlot_1.11.0.tar.gz','quit-with-status'=TRUE)"
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── Installing GenomicPlot ──────────────────────────────────────────────────────
✔ Package installed successfully
── GenomicPlot session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpjEz6RF/filea493143391dd/GenomicPlot
→ BiocVersion: 3.24
→ Package: GenomicPlot
→ PackageVersion: 1.11.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/GenomicPlot.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpjEz6RF/filea493143391dd/GenomicPlot
→ installDir: /tmp/RtmpjEz6RF/filea49311a02226e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on GenomicPlot ────────────────────────────────────────────
* 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 4.4.0 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...
* 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 (44%).
* 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...
ℹ NOTE: Vignette(s) found with missing chunk labels
  Found in files:
    • GenomicPlot_vignettes.rmd
* Checking package installation calls in R code...
* Checking for library/require of GenomicPlot...
* Checking coding practice...
ℹ NOTE: Avoid 1:...; use seq_len() or seq_along()
  Found in files:
    • Plot_peak_annotation.R (line 412, column 44)
    • Plot_peak_annotation.R (line 428, column 44)
ℹ NOTE: Avoid 'cat' and 'print' outside of 'show' methods
  Found in files:
    • print() in R/DrawingFunctions.R (line 442, column 7)
    • ...
    • print() in R/Plot_start_end.R (line 467, column 9)
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/DrawingFunctions.R (line 83, column 18)
ℹ NOTE: Avoid the use of 'paste' in condition signals
  Found in files:
    • R/HandleFeatures.R (line 493, column 48)
    • R/HandleFeatures.R (line 637, column 48)
ℹ NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
  Found in files:
    • R/HandleFeatures.R (line 123, column 18)
    • ...
    • R/HandleFeatures.R (line 144, column 18)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid '<<-' if possible (found 1 times)
  • <<- in R/HandleFeatures.R (line 140, column 21)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 30
functions greater than 50 lines.
  The longest 5 functions are:
    • plot_region() (R/Plot_region.R): 632 lines
    • ...
    • plot_peak_annotation() (R/Plot_peak_annotation.R): 400 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/extdata.Rd
    • ...
    • man/txdb.sql.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/GenomicPlot.Rd
ℹ NOTE: Consider adding runnable examples to man pages that document exported
objects.
  • draw_stacked_plot.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; 66 lines (1%) are > 80 characters long.
  First few lines:
    • R/data.R#L33 #' \href{https://ftp.ebi.ac.uk/pub/ ...
    • ...
    • vignettes/GenomicPlot_vignettes.rmd#L241 ```{r, bed overlap, eval = TRUE,
    fig.sho ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/ReadData.R#L693 GenomeInfoDb::seqlevelsStyle(queryRegio ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 952 lines (10%) are
not.
  First few lines:
    • R/DrawingFunctions.R#L78 collapse = " "), " ...
    • ...
    • vignettes/GenomicPlot_vignettes.rmd#L259 stranded = FALSE, outPrefix =
    NULL ...
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 ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 2 WARNINGS | ℹ 15 NOTES
ℹ See the GenomicPlot.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.