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This page was generated on 2025-08-21 11:39 -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 merida1

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: /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_0.54.0.tar.gz
StartedAt: 2025-08-19 01:22:05 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 01:24:12 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 127.2 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_0.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocGenerics.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* 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 ‘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 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                12.114  0.541  13.257
containsOutOfMemoryData  8.097  0.376   9.305
plotMA                   7.488  0.591   9.808
Ontology                 6.916  0.403   8.101
plotPCA                  4.400  0.110   5.060
* 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-x86_64/Resources/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 RC (2025-06-05 r88288) -- "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.

> 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 -- Tue Aug 19 01:23:52 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 
  4.290   0.320   4.772 

Example timings

BiocGenerics.Rcheck/BiocGenerics-Ex.timings

nameusersystemelapsed
BiocGenerics-package0.0010.0080.024
Extremes0.0170.0080.075
IQR0.0030.0010.007
Ontology6.9160.4038.101
annotation0.0220.0040.029
aperm0.0040.0010.005
append0.0040.0020.006
as.data.frame0.0060.0020.008
as.list0.0500.0100.065
as.vector0.0060.0020.012
boxplot0.2580.0280.330
cbind0.0470.0070.063
combine0.0950.0100.128
containsOutOfMemoryData8.0970.3769.305
dbconn0.1600.0200.181
density0.0120.0010.014
dims0.0680.0070.079
do.call0.0040.0010.006
duplicated0.0100.0030.012
eval0.0060.0010.008
evalq0.0000.0000.001
fileName12.114 0.54113.257
format0.0250.0020.035
funprog0.0180.0060.029
get0.0080.0020.012
grep0.0050.0020.009
image0.0760.0080.107
is.unsorted0.0050.0020.008
lapply0.0090.0030.015
longForm0.2710.0290.374
mad0.0040.0020.007
mapply0.0030.0010.005
match0.0310.0050.044
mean0.0240.0030.032
normalize0.0580.0080.100
nrow0.0840.0080.106
order0.0070.0030.011
organism_species0.3730.0500.539
paste0.0050.0020.008
paste20.0120.0030.018
path0.0650.0110.099
plotMA7.4880.5919.808
plotPCA4.400.115.06
rank0.0070.0010.009
relist0.0210.0020.023
rep0.0230.0020.025
residuals0.0180.0010.019
row_colnames0.0580.0080.067
saveRDS0.0040.0010.004
score0.1480.0140.165
setops0.0870.0080.095
sort0.0220.0020.024
start0.1550.0160.174
strand0.1620.0160.181
subset0.0760.0060.083
t0.0250.0020.028
table0.0050.0020.007
tapply0.0060.0020.007
testPackage0.6820.0180.707
toTable0.1430.0130.157
type0.7140.0540.782
unique0.0070.0020.009
unlist0.0060.0010.008
unsplit0.0040.0020.005
updateObject0.3310.0140.351
var0.0050.0010.007
weights0.0190.0020.020
which0.2950.0260.323
which.min0.0930.0090.104
xtabs0.0590.0070.087