Hervé Pagès
| Snapshot Date: 2026-05-21 13:40 -0400 (Thu, 21 May 2026) |
| git_url: https://git.bioconductor.org/packages/BiocGenerics |
| git_branch: RELEASE_3_23 |
| git_last_commit: 995c7b3 |
| git_last_commit_date: 2026-05-14 00:50:23 -0400 (Thu, 14 May 2026) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-05-22 11:32 -0400 (Fri, 22 May 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 RC (2026-04-17 r89917) -- "Because it was There" | 4995 |
| 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 197/2418 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocGenerics 0.58.1 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| See other builds for BiocGenerics in R Universe. | ||||||||||||||
|
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. |
| Package: BiocGenerics |
| Version: 0.58.1 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BiocGenerics_0.58.1.tar.gz |
| StartedAt: 2026-05-21 21:56:26 -0400 (Thu, 21 May 2026) |
| EndedAt: 2026-05-21 22:07:13 -0400 (Thu, 21 May 2026) |
| EllapsedTime: 646.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocGenerics.Rcheck |
| Warnings: 1 |
##############################################################################
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### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings BiocGenerics_0.58.1.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/BiocGenerics.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-22 01:56:27 UTC
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.58.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://bioconductor.org/packages/3.23/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.23/bioc/src/contrib/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.23/data/experiment/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.23/data/experiment/src/contrib/PACKAGES'
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 5.713 0.265 5.985
* 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-3.23-bioc/meat/BiocGenerics.Rcheck/00check.log’
for details.
BiocGenerics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL BiocGenerics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘BiocGenerics’ ... ** this is package ‘BiocGenerics’ version ‘0.58.1’ ** 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)
BiocGenerics.Rcheck/tests/run_unitTests.Rout
R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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 -- Thu May 21 22:07:07 2026
***********************************************
Number of test functions: 26
Number of errors: 0
Number of failures: 0
1 Test Suite :
BiocGenerics RUnit Tests - 26 test functions, 0 errors, 0 failures
Number of test functions: 26
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
1.791 0.098 1.876
BiocGenerics.Rcheck/BiocGenerics-Ex.timings
| name | user | system | elapsed | |
| BiocGenerics-package | 0.000 | 0.001 | 0.002 | |
| Extremes | 0.005 | 0.003 | 0.008 | |
| IQR | 0.001 | 0.001 | 0.001 | |
| Ontology | 2.900 | 0.143 | 3.042 | |
| annotation | 0.009 | 0.001 | 0.011 | |
| aperm | 0.002 | 0.000 | 0.002 | |
| append | 0.001 | 0.001 | 0.002 | |
| as.data.frame | 0.002 | 0.001 | 0.003 | |
| as.list | 0.038 | 0.003 | 0.041 | |
| as.vector | 0.002 | 0.000 | 0.002 | |
| boxplot | 0.091 | 0.004 | 0.096 | |
| cbind | 0.019 | 0.002 | 0.020 | |
| combine | 0.035 | 0.004 | 0.039 | |
| containsOutOfMemoryData | 3.517 | 0.138 | 3.667 | |
| dbconn | 0.048 | 0.002 | 0.051 | |
| density | 0.005 | 0.001 | 0.006 | |
| dims | 0.025 | 0.001 | 0.026 | |
| do.call | 0.002 | 0.000 | 0.002 | |
| duplicated | 0.004 | 0.000 | 0.005 | |
| eval | 0.002 | 0.001 | 0.003 | |
| evalq | 0.001 | 0.000 | 0.000 | |
| fileName | 5.713 | 0.265 | 5.985 | |
| format | 0.011 | 0.000 | 0.011 | |
| funprog | 0.007 | 0.000 | 0.008 | |
| get | 0.002 | 0.002 | 0.004 | |
| grep | 0.002 | 0.000 | 0.002 | |
| image | 0.029 | 0.001 | 0.030 | |
| is.unsorted | 0.001 | 0.001 | 0.002 | |
| lapply | 0.004 | 0.000 | 0.004 | |
| longForm | 0.096 | 0.003 | 0.099 | |
| mad | 0.002 | 0.000 | 0.002 | |
| mapply | 0.002 | 0.000 | 0.002 | |
| match | 0.012 | 0.001 | 0.014 | |
| mean | 0.009 | 0.001 | 0.011 | |
| normalize | 0.018 | 0.005 | 0.024 | |
| nrow | 0.807 | 0.000 | 0.806 | |
| order | 0.003 | 0.000 | 0.003 | |
| organism_species | 0.134 | 0.014 | 0.147 | |
| paste | 0.002 | 0.000 | 0.002 | |
| paste2 | 0.003 | 0.003 | 0.005 | |
| path | 0.023 | 0.002 | 0.026 | |
| plotMA | 2.242 | 0.172 | 2.415 | |
| plotPCA | 1.791 | 0.067 | 1.857 | |
| rank | 0.004 | 0.002 | 0.005 | |
| relist | 0.007 | 0.008 | 0.015 | |
| rep | 0.009 | 0.003 | 0.013 | |
| residuals | 0.007 | 0.002 | 0.010 | |
| row_colnames | 0.025 | 0.006 | 0.031 | |
| saveRDS | 0.001 | 0.001 | 0.002 | |
| score | 0.060 | 0.004 | 0.065 | |
| setops | 0.063 | 0.005 | 0.068 | |
| sort | 0.010 | 0.000 | 0.011 | |
| start | 0.061 | 0.004 | 0.065 | |
| strand | 0.060 | 0.001 | 0.062 | |
| subset | 0.030 | 0.002 | 0.032 | |
| t | 0.011 | 0.000 | 0.012 | |
| table | 0.001 | 0.001 | 0.003 | |
| tapply | 0.003 | 0.000 | 0.003 | |
| testPackage | 0.264 | 0.003 | 0.269 | |
| toTable | 0.050 | 0.004 | 0.053 | |
| type | 0.276 | 0.011 | 0.287 | |
| unique | 0.003 | 0.001 | 0.004 | |
| unlist | 0.003 | 0.000 | 0.003 | |
| unsplit | 0.002 | 0.000 | 0.002 | |
| updateObject | 0.131 | 0.006 | 0.137 | |
| var | 0.001 | 0.001 | 0.002 | |
| weights | 0.008 | 0.001 | 0.009 | |
| which | 0.113 | 0.006 | 0.119 | |
| which.min | 0.033 | 0.005 | 0.038 | |
| xtabs | 0.021 | 0.001 | 0.023 | |