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This page was generated on 2025-10-13 11:40 -0400 (Mon, 13 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4586
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 186/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocGenerics 0.54.1  (landing page)
Hervé Pagès
Snapshot Date: 2025-10-09 13:40 -0400 (Thu, 09 Oct 2025)
git_url: https://git.bioconductor.org/packages/BiocGenerics
git_branch: RELEASE_3_21
git_last_commit: 4fc4bea
git_last_commit_date: 2025-07-28 13:19:16 -0400 (Mon, 28 Jul 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for BiocGenerics on kjohnson1

To the developers/maintainers of the BiocGenerics package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocGenerics.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: BiocGenerics
Version: 0.54.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.54.1.tar.gz
StartedAt: 2025-10-10 14:43:55 -0400 (Fri, 10 Oct 2025)
EndedAt: 2025-10-10 14:45:05 -0400 (Fri, 10 Oct 2025)
EllapsedTime: 69.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.54.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocGenerics.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 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.54.1’
* 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 ‘BiocGenerics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘graphics’ ‘stats’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'as.data.frame.Rd':
  ‘[IRanges]{as.data.frame,IntegerRanges-method}’

Missing link(s) in Rd file 'order.Rd':
  ‘[IRanges]{order,IntegerRanges-method}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
fileName                7.622  0.323   8.045
containsOutOfMemoryData 4.861  0.230   5.176
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.


Installation output

BiocGenerics.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘BiocGenerics’ ...
** this is package ‘BiocGenerics’ version ‘0.54.1’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘aperm’ in package ‘BiocGenerics’
Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
Creating a new generic function for ‘Find’ in package ‘BiocGenerics’
Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
Creating a new generic function for ‘get’ in package ‘BiocGenerics’
Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘match’ in package ‘BiocGenerics’
Creating a new generic function for ‘order’ in package ‘BiocGenerics’
Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
Creating a new generic function for ‘saveRDS’ in package ‘BiocGenerics’
Creating a new generic function for ‘table’ in package ‘BiocGenerics’
Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
Creating a new generic function for ‘var’ in package ‘BiocGenerics’
Creating a new generic function for ‘sd’ in package ‘BiocGenerics’
Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
Creating a new generic function for ‘basename’ in package ‘BiocGenerics’
Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’
** help
*** installing help indices
** building package indices
** 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 (BiocGenerics)

Tests output

BiocGenerics.Rcheck/tests/run_unitTests.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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.

> require("BiocGenerics") || stop("unable to load BiocGenerics package")
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

[1] TRUE
> BiocGenerics:::.test()
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname



RUNIT TEST PROTOCOL -- Fri Oct 10 14:44:51 2025 
*********************************************** 
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
BiocGenerics RUnit Tests - 25 test functions, 0 errors, 0 failures
Number of test functions: 25 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  2.284   0.202   2.511 

Example timings

BiocGenerics.Rcheck/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package0.0000.0020.002
Extremes0.0090.0020.010
IQR0.0010.0000.002
Ontology3.8460.2244.127
annotation0.0140.0020.017
aperm0.0020.0000.002
append0.0020.0010.002
as.data.frame0.0020.0010.003
as.list0.0300.0050.035
as.vector0.0040.0010.004
boxplot0.1600.0300.195
cbind0.0300.0030.032
combine0.0440.0040.048
containsOutOfMemoryData4.8610.2305.176
dbconn0.1230.0130.139
density0.0070.0000.007
dims0.0480.0040.054
do.call0.0020.0010.002
duplicated0.0040.0010.005
eval0.0030.0010.004
evalq0.0000.0000.001
fileName7.6220.3238.045
format0.0160.0010.016
funprog0.0080.0020.011
get0.0040.0000.003
grep0.0020.0000.003
image0.2680.0060.279
is.unsorted0.0040.0000.005
lapply0.0050.0010.006
longForm0.1980.0130.216
mad0.0020.0010.003
mapply0.0020.0010.003
match0.0160.0020.018
mean0.0120.0010.013
normalize0.0430.0040.047
nrow0.0540.0030.061
order0.0040.0010.008
organism_species0.2350.0240.266
paste0.0020.0000.003
paste20.0060.0020.008
path0.0310.0020.034
plotMA4.2260.1844.512
plotPCA2.3340.0772.441
rank0.0050.0000.006
relist0.0140.0010.016
rep0.0150.0010.016
residuals0.0090.0000.010
row_colnames0.0310.0030.033
saveRDS0.0020.0000.002
score0.1100.0080.118
setops0.0530.0030.059
sort0.0110.0000.012
start0.0990.0070.108
strand0.1080.0090.117
subset0.0510.0030.056
t0.0170.0010.018
table0.0020.0000.003
tapply0.0020.0000.003
testPackage0.3310.0140.355
toTable0.1010.0070.109
type0.4520.0430.504
unique0.0050.0010.006
unlist0.0030.0000.004
unsplit0.0020.0010.003
updateObject0.1710.0070.182
var0.0030.0010.003
weights0.0090.0010.010
which0.2130.0150.240
which.min0.0660.0040.070
xtabs0.0400.0030.044