Multiple platform build/check report for BioC 3.20 - BUILD results for cellbaseR on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4426
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*

BUILD results for cellbaseR on taishan

To the developers/maintainers of the cellbaseR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellbaseR.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: cellbaseR

Version: 1.30.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data cellbaseR

StartedAt: 2025-03-31 22:11:28 -0000 (Mon, 31 Mar 2025)

EndedAt: 2025-03-31 22:12:04 -0000 (Mon, 31 Mar 2025)

EllapsedTime: 36.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data cellbaseR
###
##############################################################################
##############################################################################


* checking for file ‘cellbaseR/DESCRIPTION’ ... OK
* preparing ‘cellbaseR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘cellbaseR.Rmd’ using rmarkdown

Quitting from cellbaseR.Rmd:56-67 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `curl::curl_fetch_memory()`:
! Timeout was reached [ws.zettagenomics.com]: Operation timed out after 10000 milliseconds with 97906 bytes received
---
Backtrace:
     ▆
  1. ├─cellbaseR::getGene(object = cb, ids = genes, resource = "info")
  2. ├─cellbaseR::getGene(object = cb, ids = genes, resource = "info")
  3. │ └─cellbaseR:::fetchCellbase(...)
  4. │   └─cellbaseR:::callREST2(grls = grls)
  5. │     └─httr::GET(...)
  6. │       └─httr:::request_perform(req, hu$handle$handle)
  7. │         ├─httr:::request_fetch(req$output, req$url, handle)
  8. │         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
  9. │           └─curl::curl_fetch_memory(url, handle = handle)
 10. └─curl:::raise_libcurl_error(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'cellbaseR.Rmd' failed with diagnostics:
Timeout was reached [ws.zettagenomics.com]: Operation timed out after 10000 milliseconds with 97906 bytes received
--- failed re-building ‘cellbaseR.Rmd’

SUMMARY: processing the following file failed:
  ‘cellbaseR.Rmd’

Error: Vignette re-building failed.
Execution halted