Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-10-21 12:07 -0400 (Tue, 21 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4642
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 217/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biomformat 1.37.0  (landing page)
Paul J. McMurdie
Snapshot Date: 2025-10-20 13:45 -0400 (Mon, 20 Oct 2025)
git_url: https://git.bioconductor.org/packages/biomformat
git_branch: devel
git_last_commit: 1c2a030
git_last_commit_date: 2025-04-15 10:56:51 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    TIMEOUT  


CHECK results for biomformat on taishan

To the developers/maintainers of the biomformat package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biomformat.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: biomformat
Version: 1.37.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:biomformat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biomformat_1.37.0.tar.gz
StartedAt: 2025-10-21 04:59:34 -0000 (Tue, 21 Oct 2025)
EndedAt: 2025-10-21 05:52:30 -0000 (Tue, 21 Oct 2025)
EllapsedTime: 3175.8 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: biomformat.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:biomformat.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings biomformat_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/biomformat.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 ‘biomformat/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘biomformat’ version ‘1.37.0’
* checking package namespace information ... OK
* checking package dependencies ...

Installation output

biomformat.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘biomformat’ ...
** this is package ‘biomformat’ version ‘1.37.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘rownames’ from package ‘base’ in package ‘biomformat’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘biomformat’
** 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 (biomformat)

Tests output

biomformat.Rcheck/tests/testthat-biomformat.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")
> # As suggested for opt-out option on testing by users, recommended by CRAN
> # http://adv-r.had.co.nz/Testing.html
> # Previously, best practice was to put all test files in inst/tests and ensure that R CMD check ran them by putting the following code in tests/test-all.R:  
> # library(testthat)
> # library(yourpackage)
> # test_package("yourpackage")
> # Now, recommended practice is to put your tests in tests/testthat, and ensure R CMD check runs them by putting the following code in tests/test-all.R:
> # library(testthat)
> # test_check("yourpackage")
> # The advantage of this new structure is that the user has control over whether or not tests are installed using the –install-tests parameter to R CMD install, or INSTALL_opts = c(“–install-tests”) argument to install.packages(). I’m not sure why you wouldn’t want to install the tests, but now you have the flexibility as requested by CRAN maintainers.
> test_check("biomformat")
Loading required package: biomformat
[ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ]

[ FAIL 0 | WARN 4 | SKIP 0 | PASS 136 ]
> 
> proc.time()
   user  system elapsed 
  2.933   0.232   3.206 

Example timings

biomformat.Rcheck/biomformat-Ex.timings

nameusersystemelapsed
biom-class0.0490.0010.050
biom-methods0.0400.0000.041
biom_data-methods0.0540.0040.061
biom_shape-methods0.0040.0000.004
colnames-methods0.0040.0000.004
header-methods0.0040.0000.003
make_biom0.050.000.05
matrix_element_type-methods0.0040.0000.004
ncol-methods0.0040.0000.004
nrow-methods0.0040.0000.004
observation_metadata-methods0.0430.0000.044
read_biom0.0070.0000.007
read_hdf5_biom0.0690.0000.071
rownames-methods0.0040.0000.004
sample_metadata-methods0.0280.0000.028
show-methods0.0040.0000.004
write_biom0.0120.0000.012