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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 2271/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VennDetail 1.25.2  (landing page)
Kai Guo
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/VennDetail
git_branch: devel
git_last_commit: b77b760
git_last_commit_date: 2025-07-22 00:39:05 -0400 (Tue, 22 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for VennDetail on lconway

To the developers/maintainers of the VennDetail package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VennDetail.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: VennDetail
Version: 1.25.2
Command: /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
StartedAt: 2025-08-09 00:50:01 -0400 (Sat, 09 Aug 2025)
EndedAt: 2025-08-09 00:51:16 -0400 (Sat, 09 Aug 2025)
EllapsedTime: 74.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VennDetail.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /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 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* 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.


Installation output

VennDetail.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL VennDetail
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘VennDetail’ ...
** this is package ‘VennDetail’ version ‘1.25.2’
** 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)

Tests output

VennDetail.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  1.741   0.217   1.972 

Example timings

VennDetail.Rcheck/VennDetail-Ex.timings

nameusersystemelapsed
T2DM0.0670.0580.125
Venn-class0.0000.0000.001
as.data.frame.Venn0.0080.0010.009
cash-.Venn0.0060.0010.006
compareVenn0.0200.0010.021
detail-Venn-method0.0040.0000.005
detail0.0080.0010.009
dim.Venn0.0040.0000.004
dplot-Venn-method0.9730.0281.006
dplot0.4590.0110.472
getFeature-Venn-method0.2470.0050.253
getFeature0.0850.0010.086
getSet-Venn-method0.0310.0010.032
getSet0.0590.0010.060
head.Venn0.0040.0000.004
loadVenn0.0000.0010.000
make.subset0.0010.0000.002
make_subset0.0010.0010.002
merge0.0130.0010.014
merge.Venn0.1620.0030.165
names.Venn0.0040.0010.005
newVenn000
plot.Venn3.7740.0543.855
result-Venn-method0.0050.0000.005
result0.0080.0000.009
rowjoin-data.frame-data.frame-method0.0330.0000.034
rowjoin0.0520.0030.055
saveVenn000
setcolor0.0010.0000.001
show0.0050.0010.005
sub-.Venn0.0050.0010.005
summary0.0050.0010.005
summary.Venn0.0110.0010.012
tail.Venn0.0050.0000.006
upsetPlot-Venn-method1.6320.0081.646
upsetPlot1.7310.0121.748
upset_plot2.2210.0122.243
vennApp000
vennEnrichment0.1020.0020.103
vennStats-Venn-method0.3490.0150.367
vennStats0.0070.0010.008
venndetail0.1650.0030.170
vennpie0.2550.0030.261