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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VennDetail.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VennDetail_1.25.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/VennDetail.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VennDetail/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VennDetail’ version ‘1.25.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘VennDetail’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... WARNING
Rd files with duplicated name 'merge.Venn':
  ‘merge.Rd’ ‘merge.Venn.Rd’
Rd files with duplicated name 'summary.Venn':
  ‘summary.Rd’ ‘summary.Venn.Rd’
Rd files with duplicated alias 'detail,Venn-method':
  ‘detail-Venn-method.Rd’ ‘detail.Rd’
Rd files with duplicated alias 'getSet,Venn-method':
  ‘getSet-Venn-method.Rd’ ‘getSet.Rd’
Rd files with duplicated alias 'merge.Venn':
  ‘merge.Rd’ ‘merge.Venn.Rd’
Rd files with duplicated alias 'result,Venn-method':
  ‘result-Venn-method.Rd’ ‘result.Rd’
Rd files with duplicated alias 'rowjoin,data.frame,data.frame-method':
  ‘rowjoin-data.frame-data.frame-method.Rd’ ‘rowjoin.Rd’
Rd files with duplicated alias 'show,Venn-method':
  ‘show-Venn-method.Rd’ ‘show.Rd’
Rd files with duplicated alias 'summary.Venn':
  ‘summary.Rd’ ‘summary.Venn.Rd’
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in Rd file 'dplot-Venn-method.Rd':
  ‘color’ ‘theme’ ‘title’ ‘xlabel’ ‘ylabel’

Objects in \usage without \alias in Rd file 'dplot.Rd':
  ‘\S4method{dplot}{Venn}’

Objects in \usage without \alias in Rd file 'getFeature.Rd':
  ‘\S4method{getFeature}{Venn}’

Undocumented arguments in Rd file 'plot.Venn.Rd'
  ‘fill’ ‘alpha’ ‘labels’ ‘counts’ ‘showNumbers’ ‘numberSize’
  ‘numberColor’ ‘labelSize’ ‘labelColor’ ‘borderCol’ ‘fillCol’
  ‘fixedCoords’ ‘xlim’ ‘ylim’ ‘show_percentages’ ‘show_unique_only’
  ‘scaled’ ‘subset’ ‘top’ ‘min’ ‘color’ ‘revcolor’ ‘any’ ‘show.number’
  ‘show.x’ ‘sep’ ‘log’ ‘base’ ‘percentage’ ‘nintersects’ ‘min_size’
  ‘sets_bar_color’ ‘main_bar_color’ ‘point_size’ ‘line_size’
  ‘show_numbers’ ‘sort_intersections_by’ ‘sort_sets_by’
  ‘sort_sets_decreasing’ ‘custom_sets_order’
  ‘sort_intersections_decreasing’ ‘custom_intersections_order’
  ‘intersection_color’ ‘highlight_intersections’ ‘highlight_color’
  ‘empty_point_size’ ‘bar_width’ ‘text_angle’ ‘text_size’
  ‘set_label_size’ ‘intersection_label_size’ ‘point_outline_color’
  ‘point_stroke’ ‘set_size_show_values’ ‘intersection_size_show_values’
  ‘show_empty_intersections’ ‘show_set_labels’ ‘plot_margin’
  ‘height_ratio’ ‘width_ratio’ ‘bar_offset’ ‘set_text_size’
  ‘intersection_title’ ‘set_size_title’ ‘matrix_point_shape’
  ‘number_color_threshold’ ‘number_colors’ ‘theme_params’ ‘return_data’
  ‘order’ ‘textsize’ ‘theme’ ‘xlabel’ ‘ylabel’

Documented arguments not in \usage in Rd file 'rowjoin-data.frame-data.frame-method.Rd':
  ‘by’

Documented arguments not in \usage in Rd file 'setcolor.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'vennpie-Venn-method.Rd':
  ‘title’ ‘interactive’ ‘...’

Objects in \usage without \alias in Rd file 'vennpie.Rd':
  ‘\S4method{vennpie}{Venn}’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/VennDetail.Rcheck/00check.log’
for details.