Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 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 2271/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
VennDetail 1.25.2 (landing page) Kai Guo
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
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. |
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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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.
VennDetail.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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)
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
VennDetail.Rcheck/VennDetail-Ex.timings
name | user | system | elapsed | |
T2DM | 0.067 | 0.058 | 0.125 | |
Venn-class | 0.000 | 0.000 | 0.001 | |
as.data.frame.Venn | 0.008 | 0.001 | 0.009 | |
cash-.Venn | 0.006 | 0.001 | 0.006 | |
compareVenn | 0.020 | 0.001 | 0.021 | |
detail-Venn-method | 0.004 | 0.000 | 0.005 | |
detail | 0.008 | 0.001 | 0.009 | |
dim.Venn | 0.004 | 0.000 | 0.004 | |
dplot-Venn-method | 0.973 | 0.028 | 1.006 | |
dplot | 0.459 | 0.011 | 0.472 | |
getFeature-Venn-method | 0.247 | 0.005 | 0.253 | |
getFeature | 0.085 | 0.001 | 0.086 | |
getSet-Venn-method | 0.031 | 0.001 | 0.032 | |
getSet | 0.059 | 0.001 | 0.060 | |
head.Venn | 0.004 | 0.000 | 0.004 | |
loadVenn | 0.000 | 0.001 | 0.000 | |
make.subset | 0.001 | 0.000 | 0.002 | |
make_subset | 0.001 | 0.001 | 0.002 | |
merge | 0.013 | 0.001 | 0.014 | |
merge.Venn | 0.162 | 0.003 | 0.165 | |
names.Venn | 0.004 | 0.001 | 0.005 | |
newVenn | 0 | 0 | 0 | |
plot.Venn | 3.774 | 0.054 | 3.855 | |
result-Venn-method | 0.005 | 0.000 | 0.005 | |
result | 0.008 | 0.000 | 0.009 | |
rowjoin-data.frame-data.frame-method | 0.033 | 0.000 | 0.034 | |
rowjoin | 0.052 | 0.003 | 0.055 | |
saveVenn | 0 | 0 | 0 | |
setcolor | 0.001 | 0.000 | 0.001 | |
show | 0.005 | 0.001 | 0.005 | |
sub-.Venn | 0.005 | 0.001 | 0.005 | |
summary | 0.005 | 0.001 | 0.005 | |
summary.Venn | 0.011 | 0.001 | 0.012 | |
tail.Venn | 0.005 | 0.000 | 0.006 | |
upsetPlot-Venn-method | 1.632 | 0.008 | 1.646 | |
upsetPlot | 1.731 | 0.012 | 1.748 | |
upset_plot | 2.221 | 0.012 | 2.243 | |
vennApp | 0 | 0 | 0 | |
vennEnrichment | 0.102 | 0.002 | 0.103 | |
vennStats-Venn-method | 0.349 | 0.015 | 0.367 | |
vennStats | 0.007 | 0.001 | 0.008 | |
venndetail | 0.165 | 0.003 | 0.170 | |
vennpie | 0.255 | 0.003 | 0.261 | |