Hervé Pagès
| Snapshot Date: 2025-08-14 13:45 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/BiocGenerics |
| git_branch: devel |
| git_last_commit: bac3ea0 |
| git_last_commit_date: 2025-07-28 13:19:16 -0400 (Mon, 28 Jul 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-15 12:06 -0400 (Fri, 15 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 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" | 4554 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 185/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BiocGenerics 0.55.1 (landing page) Hervé Pagès
| nebbiolo2 | Linux (Ubuntu 24.04.3 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 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 0.55.1 |
| Command: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocGenerics.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BiocGenerics_0.55.1.tar.gz |
| StartedAt: 2025-08-15 00:55:33 -0400 (Fri, 15 Aug 2025) |
| EndedAt: 2025-08-15 00:56:57 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 83.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: BiocGenerics.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BiocGenerics.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings BiocGenerics_0.55.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/BiocGenerics.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BiocGenerics/DESCRIPTION' ... OK
* this is package 'BiocGenerics' version '0.55.1'
* 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 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 7.35 0.43 7.78
containsOutOfMemoryData 5.01 0.25 5.30
* 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
'F:/biocbuild/bbs-3.22-bioc/meat/BiocGenerics.Rcheck/00check.log'
for details.
BiocGenerics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL BiocGenerics ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library' * installing *source* package 'BiocGenerics' ... ** this is package 'BiocGenerics' version '0.55.1' ** 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 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
RUNIT TEST PROTOCOL -- Fri Aug 15 00:56:42 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
2.39 0.18 2.56
BiocGenerics.Rcheck/BiocGenerics-Ex.timings
| name | user | system | elapsed | |
| BiocGenerics-package | 0 | 0 | 0 | |
| Extremes | 0.01 | 0.00 | 0.02 | |
| IQR | 0 | 0 | 0 | |
| Ontology | 3.86 | 0.33 | 4.19 | |
| annotation | 0.01 | 0.00 | 0.01 | |
| aperm | 0.02 | 0.00 | 0.02 | |
| append | 0 | 0 | 0 | |
| as.data.frame | 0 | 0 | 0 | |
| as.list | 0.05 | 0.00 | 0.05 | |
| as.vector | 0 | 0 | 0 | |
| boxplot | 0.13 | 0.06 | 0.19 | |
| cbind | 0.04 | 0.00 | 0.05 | |
| combine | 0.07 | 0.00 | 0.06 | |
| containsOutOfMemoryData | 5.01 | 0.25 | 5.30 | |
| dbconn | 0.10 | 0.02 | 0.11 | |
| density | 0 | 0 | 0 | |
| dims | 0.06 | 0.02 | 0.07 | |
| do.call | 0 | 0 | 0 | |
| duplicated | 0 | 0 | 0 | |
| eval | 0.01 | 0.00 | 0.02 | |
| evalq | 0 | 0 | 0 | |
| fileName | 7.35 | 0.43 | 7.78 | |
| format | 0.01 | 0.00 | 0.02 | |
| funprog | 0 | 0 | 0 | |
| get | 0.02 | 0.00 | 0.01 | |
| grep | 0 | 0 | 0 | |
| image | 0.05 | 0.00 | 0.05 | |
| is.unsorted | 0 | 0 | 0 | |
| lapply | 0.01 | 0.00 | 0.01 | |
| longForm | 0.19 | 0.03 | 0.22 | |
| mad | 0 | 0 | 0 | |
| mapply | 0 | 0 | 0 | |
| match | 0 | 0 | 0 | |
| mean | 0 | 0 | 0 | |
| normalize | 0.05 | 0.00 | 0.05 | |
| nrow | 0.04 | 0.00 | 0.05 | |
| order | 0.02 | 0.00 | 0.01 | |
| organism_species | 0.19 | 0.07 | 0.25 | |
| paste | 0 | 0 | 0 | |
| paste2 | 0.01 | 0.00 | 0.02 | |
| path | 0.02 | 0.00 | 0.02 | |
| plotMA | 4.59 | 0.28 | 4.93 | |
| plotPCA | 2.57 | 0.09 | 2.75 | |
| rank | 0 | 0 | 0 | |
| relist | 0 | 0 | 0 | |
| rep | 0.02 | 0.00 | 0.01 | |
| residuals | 0.01 | 0.00 | 0.02 | |
| row_colnames | 0.02 | 0.02 | 0.03 | |
| saveRDS | 0 | 0 | 0 | |
| score | 0.12 | 0.01 | 0.16 | |
| setops | 0.07 | 0.00 | 0.06 | |
| sort | 0.01 | 0.00 | 0.02 | |
| start | 0.14 | 0.02 | 0.15 | |
| strand | 0.11 | 0.05 | 0.16 | |
| subset | 0.06 | 0.00 | 0.07 | |
| t | 0.03 | 0.00 | 0.03 | |
| table | 0 | 0 | 0 | |
| tapply | 0 | 0 | 0 | |
| testPackage | 0.5 | 0.0 | 0.5 | |
| toTable | 0.13 | 0.03 | 0.15 | |
| type | 0.46 | 0.08 | 0.55 | |
| unique | 0 | 0 | 0 | |
| unlist | 0 | 0 | 0 | |
| unsplit | 0 | 0 | 0 | |
| updateObject | 0.18 | 0.03 | 0.20 | |
| var | 0.01 | 0.00 | 0.01 | |
| weights | 0 | 0 | 0 | |
| which | 0.25 | 0.06 | 0.32 | |
| which.min | 0.08 | 0.00 | 0.08 | |
| xtabs | 0.04 | 0.02 | 0.06 | |