Multiple platform build/check report for BioC 3.22 - BUILD results for GEOmetadb on taishan

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.2 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4796
palomino8	Windows Server 2022 Datacenter	x64	4.5.1 (2025-06-13 ucrt) -- "Great Square Root"	4536
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4578
kjohnson3	macOS 13.7.1 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4519
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4517
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 GEOmetadb on taishan

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

Version: 1.71.0

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

StartedAt: 2025-08-01 00:01:00 -0000 (Fri, 01 Aug 2025)

EndedAt: 2025-08-01 00:11:08 -0000 (Fri, 01 Aug 2025)

EllapsedTime: 607.2 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 GEOmetadb
###
##############################################################################
##############################################################################


* checking for file ‘GEOmetadb/DESCRIPTION’ ... OK
* preparing ‘GEOmetadb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘GEOmetadb.Rmd’ using rmarkdown
trying URL 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz'
Content type 'application/x-gzip' length 20889492 bytes (19.9 MB)
==========
downloaded 4.0 MB


Quitting from GEOmetadb.Rmd:88-98 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! download from 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz' failed
---
Backtrace:
    ▆
 1. └─GEOmetadb::getSQLiteFile(...)
 2.   └─utils::download.file(url_geo, destfile = localfile, mode = "wb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'GEOmetadb.Rmd' failed with diagnostics:
download from 'https://gbnci.cancer.gov/geo/GEOmetadb_demo.sqlite.gz' failed
--- failed re-building ‘GEOmetadb.Rmd’

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

Error: Vignette re-building failed.
Execution halted