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### Running command:
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###   /home/rapidbuild/bbs-3.23-bioc-rapid/R/bin/Rscript -e "BiocCheck::BiocCheck('ggtreeExtra_1.22.0.tar.gz','quit-with-status'=TRUE)"
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── Installing ggtreeExtra ──────────────────────────────────────────────────────
✔ Package installed successfully
── ggtreeExtra session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpDQmEvr/file7bdff1e6024f6/ggtreeExtra
→ BiocVersion: 3.23
→ Package: ggtreeExtra
→ PackageVersion: 1.22.0
→ BiocCheckDir: /media/volume/teran2_disk/rapidbuild/bbs-3.23-bioc-rapid/meat/ggtreeExtra.BiocCheck
→ BiocCheckVersion: 1.48.0
→ sourceDir: /tmp/RtmpDQmEvr/file7bdff1e6024f6/ggtreeExtra
→ installDir: /tmp/RtmpDQmEvr/file7bdff14579283
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on ggtreeExtra ────────────────────────────────────────────
* 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...
* 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 that Package field matches directory/tarball name...
* 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 (10%).
* 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:
    • ggtreeExtra.Rmd
* Checking package installation calls in R code...
* Checking for library/require of ggtreeExtra...
! WARNING: Avoid the use of 'library' or 'require' in R code
  Found in files:
    • require() in R/fromnamespace.R (line 27, column 9)
* Checking coding practice...
ℹ NOTE: Avoid using '=' for assignment and use '<-' instead
  Found in files:
    • R/method-ggplot-add.R (line 91, column 24)
    • ...
    • R/method-ggplot-add.R (line 146, column 11)
* Checking parsed R code in R directory, examples, vignettes...
ℹ NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
  • suppressWarnings() in R/utilities-ggplot-add.R (line 29, column 27)
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 3
functions greater than 50 lines.
  The longest 5 functions are:
    • ggplot_add.fruit_plot() (R/method-ggplot-add.R): 125 lines
    • geom_fruit() (R/geom_fruit.R): 98 lines
    • build_axis() (R/utilities_grid_axis.R): 81 lines
* Checking man page documentation...
! WARNING: Empty or missing \format sections found in data man page(s).
  Found in files:
    • man/ggplot2-ggproto.Rd
    • man/PositionJitterdodgex.Rd
    • man/PositionJitterx.Rd
! WARNING: Empty or missing \value sections found in man page(s).
  Found in files:
    • man/position_jitterdodgex.Rd
    • ...
    • man/position_raincloudx.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
  The following pages do not:
    • position_jitterdodgex.Rd
    • ...
    • reexports.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; 190 lines (8%) are > 80 characters long.
  First few lines:
    • R/geom_axis_text.R#L3 ## ##' 'geom_axis_text' was designed to ...
    • ...
    • vignettes/ggtreeExtra.Rmd#L316 Here is the output of sessionInfo() on t
    ...
ℹ NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs.
  First few lines:
    • R/utilities-ggplot-add.R#L32 } ...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 475 lines (19%) are
not.
  First few lines:
    • R/geom_fruit.R#L161 data=NULL, ...
    • ...
    • vignettes/ggtreeExtra.Rmd#L306 scale_fill_manual(values=c("#00AED ...
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 v1.48.0 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 3 WARNINGS | ℹ 9 NOTES
ℹ See the ggtreeExtra.BiocCheck folder and run
  browseVignettes(package = 'BiocCheck')
  for details.