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This page was generated on 2025-10-16 11:38 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 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 181/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocBaseUtils 1.10.0  (landing page)
Marcel Ramos
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/BiocBaseUtils
git_branch: RELEASE_3_21
git_last_commit: af524da
git_last_commit_date: 2025-04-15 12:51:45 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for BiocBaseUtils on merida1

To the developers/maintainers of the BiocBaseUtils package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BiocBaseUtils.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: BiocBaseUtils
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocBaseUtils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocBaseUtils_1.10.0.tar.gz
StartedAt: 2025-10-14 00:35:45 -0400 (Tue, 14 Oct 2025)
EndedAt: 2025-10-14 00:36:36 -0400 (Tue, 14 Oct 2025)
EllapsedTime: 51.2 seconds
RetCode: 0
Status:   OK  
CheckDir: BiocBaseUtils.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocBaseUtils.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocBaseUtils_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/BiocBaseUtils.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 ‘BiocBaseUtils/DESCRIPTION’ ... OK
* this is package ‘BiocBaseUtils’ version ‘1.10.0’
* 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 ‘BiocBaseUtils’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘tinytest.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: OK

Installation output

BiocBaseUtils.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘BiocBaseUtils’ ...
** this is package ‘BiocBaseUtils’ version ‘1.10.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (BiocBaseUtils)

Tests output

BiocBaseUtils.Rcheck/tests/tinytest.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.

> if (requireNamespace("tinytest", quietly = TRUE))
+     tinytest::test_package("BiocBaseUtils")

test_assertions.R.............    1 tests OK 
test_assertions.R.............    2 tests OK 
test_assertions.R.............    3 tests OK 
test_assertions.R.............    4 tests OK 
test_assertions.R.............    5 tests OK 
test_assertions.R.............    6 tests OK 
test_assertions.R.............    7 tests OK 
test_assertions.R.............    8 tests OK 
test_assertions.R.............    9 tests OK 
test_assertions.R.............   10 tests OK 
test_assertions.R.............   11 tests OK 
test_assertions.R.............   12 tests OK 
test_assertions.R.............   13 tests OK 0.1s
 You are using 'tinytest::' to express test expectations.
 The results from these tests are not collected. Found the following occurrences:
 > test_checkInstalled.R#006: tinytest::expect_match 
 Remove the 'tinytest::' prefix to register the test results.FALSE
The following package(s) are required for this function:

  BiocManager::install("abc123xyzjfk")


test_checkInstalled.R.........    1 tests OK 
test_checkInstalled.R.........    1 tests OK 
test_checkInstalled.R.........    2 tests OK 55ms

test_internals.R..............    0 tests    
test_internals.R..............    0 tests    
test_internals.R..............    0 tests    
test_internals.R..............    1 tests OK 
test_internals.R..............    1 tests OK 
test_internals.R..............    2 tests OK 
test_internals.R..............    3 tests OK 27ms

test_lifeCycle.R..............    0 tests    
test_lifeCycle.R..............    1 tests OK 
test_lifeCycle.R..............    2 tests OK 
test_lifeCycle.R..............    3 tests OK 
test_lifeCycle.R..............    3 tests OK 
test_lifeCycle.R..............    4 tests OK 
test_lifeCycle.R..............    5 tests OK 
test_lifeCycle.R..............    6 tests OK 29ms

test_showUtils.R..............    1 tests OK 
test_showUtils.R..............    2 tests OK 
test_showUtils.R..............    3 tests OK 
test_showUtils.R..............    4 tests OK 
test_showUtils.R..............    5 tests OK 
test_showUtils.R..............    6 tests OK 7ms
All ok, 30 results (0.2s)
> 
> proc.time()
   user  system elapsed 
  0.540   0.149   1.082

Example timings

BiocBaseUtils.Rcheck/BiocBaseUtils-Ex.timings

nameusersystemelapsed
Assertions0.0020.0040.006
askUserYesNo0.0000.0010.003
checkInstalled0.0000.0010.001
lifeCycle0.0030.0010.006
selectSome0.0000.0020.004
setSlots0.0210.0030.028