Multiple platform build/check report for BioC 3.22 - CHECK results for biocthis on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4843
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4631
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4575
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4576
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*

CHECK results for biocthis on taishan

To the developers/maintainers of the biocthis package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biocthis.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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results

Summary

Package: biocthis

Version: 1.19.0

Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biocthis.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biocthis_1.19.0.tar.gz

StartedAt: 2025-09-30 05:14:47 -0000 (Tue, 30 Sep 2025)

EndedAt: 2025-09-30 06:23:50 -0000 (Tue, 30 Sep 2025)

EllapsedTime: 4143.6 seconds

RetCode: None

Status: TIMEOUT

CheckDir: biocthis.Rcheck

Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:biocthis.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biocthis_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/biocthis.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biocthis/DESCRIPTION’ ... OK
* this is package ‘biocthis’ version ‘1.19.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'

Installation output

biocthis.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL biocthis
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘biocthis’ ...
** this is package ‘biocthis’ version ‘1.19.0’
** 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 (biocthis)

Tests output

biocthis.Rcheck/tests/testthat.Rout


R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> library(testthat)
> library(biocthis)
> 
> test_check("biocthis")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  1.248   0.076   4.377

Example timings

biocthis.Rcheck/biocthis-Ex.timings

name	user	system	elapsed
bioc_badges	0.000	0.000	0.001
bioc_style	0.683	0.060	0.747
biocthis_example_pkg	0.091	0.004	0.096
use_bioc_citation	0.324	0.072	0.401
use_bioc_coc	0.286	0.007	0.296
use_bioc_description	0.575	0.004	0.585
use_bioc_feature_request_template	0.193	0.004	0.203
use_bioc_github_action	0	0	0
use_bioc_issue_template	0.146	0.012	0.159
use_bioc_news_md	0.158	0.000	0.161
use_bioc_pkg_templates	0.520	0.012	0.537
use_bioc_pkgdown_css	0.164	0.004	0.170
use_bioc_readme_rmd	0.404	0.028	0.437
use_bioc_support	0.292	0.012	0.306
use_bioc_vignette	1.703	0.082	1.812