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This page was generated on 2025-08-21 11:38 -0400 (Thu, 21 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 0.54.0  (landing page)
Hervé Pagès
Snapshot Date: 2025-08-18 13:40 -0400 (Mon, 18 Aug 2025)
git_url: https://git.bioconductor.org/packages/BiocGenerics
git_branch: RELEASE_3_21
git_last_commit: 75c4815
git_last_commit_date: 2025-04-15 10:11:46 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for BiocGenerics on nebbiolo1

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: 0.54.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BiocGenerics_0.54.0.tar.gz
StartedAt: 2025-08-20 20:29:33 -0400 (Wed, 20 Aug 2025)
EndedAt: 2025-08-20 20:30:24 -0400 (Wed, 20 Aug 2025)
EllapsedTime: 51.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BiocGenerics.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BiocGenerics_0.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocGenerics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.54.0’
* 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 loading without being on the library search path ... 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 6.227  0.265   6.504
* 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
  ‘/home/biocbuild/bbs-3.21-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.


Installation output

BiocGenerics.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL BiocGenerics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘BiocGenerics’ ...
** this is package ‘BiocGenerics’ version ‘0.54.0’
** 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 (2025-06-13) -- "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.

> 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 -- Wed Aug 20 20:30:18 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 
  1.853   0.107   1.948 

Example timings

BiocGenerics.Rcheck/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package0.0010.0010.002
Extremes0.0060.0020.009
IQR0.0020.0000.002
Ontology3.1460.1493.296
annotation0.0100.0010.012
aperm0.0030.0000.002
append0.0000.0010.002
as.data.frame0.0020.0010.003
as.list0.0190.0060.025
as.vector0.0030.0000.003
boxplot0.1170.0100.128
cbind0.0200.0030.023
combine0.0400.0030.043
containsOutOfMemoryData4.0000.1354.136
dbconn0.0740.0080.084
density0.0070.0000.006
dims0.0300.0000.031
do.call0.0010.0020.002
duplicated0.0050.0000.004
eval0.0010.0010.003
evalq0.0000.0000.001
fileName6.2270.2656.504
format0.0150.0010.015
funprog0.0090.0010.010
get0.0030.0010.004
grep0.0010.0010.003
image0.0460.0010.048
is.unsorted0.0030.0000.003
lapply0.0040.0010.005
longForm0.1640.0060.170
mad0.0020.0010.002
mapply0.0000.0020.002
match0.0140.0030.017
mean0.0120.0020.015
normalize0.0310.0020.033
nrow0.0480.0010.049
order0.0030.0010.004
organism_species0.1930.0080.202
paste0.0020.0010.004
paste20.0060.0010.007
path0.0250.0090.034
plotMA3.6900.2303.921
plotPCA1.9650.0141.980
rank0.0020.0020.004
relist0.0110.0000.011
rep0.0110.0010.012
residuals0.0080.0020.011
row_colnames0.0290.0040.032
saveRDS0.0020.0000.002
score0.0790.0040.082
setops0.0510.0000.051
sort0.0130.0000.012
start0.0860.0060.092
strand0.0830.0060.089
subset0.0400.0030.042
t0.0110.0010.013
table0.0020.0000.003
tapply0.0020.0010.003
testPackage0.2970.0050.304
toTable0.0830.0170.101
type0.3420.0120.355
unique0.0030.0020.005
unlist0.0040.0000.004
unsplit0.0020.0010.002
updateObject0.1670.0070.174
var0.0030.0000.003
weights0.0110.0020.012
which0.1750.0080.183
which.min0.0530.0030.056
xtabs0.0310.0020.033