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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:VennDetail.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings VennDetail_1.25.3.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/VennDetail.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘VennDetail/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VennDetail’ version ‘1.25.3’
* 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 loading without being on the library search path ... 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
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
plot.Venn 4.861  0.164    5.02
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL VennDetail
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘VennDetail’ ...
** this is package ‘VennDetail’ version ‘1.25.3’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (VennDetail)

R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(VennDetail)
> test_check("VennDetail")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 1 ]
> 
> proc.time()
   user  system elapsed 
  1.610   0.106   1.704