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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
lconway	macOS 12.7.1 Monterey	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4615
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4562
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4541
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 BgeeCall on taishan

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

Version: 1.25.0

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

StartedAt: 2025-08-28 22:12:32 -0000 (Thu, 28 Aug 2025)

EndedAt: 2025-08-28 22:16:04 -0000 (Thu, 28 Aug 2025)

EllapsedTime: 212.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data BgeeCall
###
##############################################################################
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* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* preparing ‘BgeeCall’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bgeecall-manual.Rmd’ using rmarkdown

Quitting from bgeecall-manual.Rmd:150-154 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `listIntergenicReleases()`:
! File describing intergenic releases could not be downloaded 
from FTP.
---
Backtrace:
     ▆
  1. └─BgeeCall::generate_presence_absence(myUserMetadata = user_BgeeCall)
  2.   ├─BgeeCall:::get_ref_intergenic_ids(myBgeeMetadata, myUserMetadata)
  3.   │ └─BgeeCall:::retrieve_intergenic_path(myBgeeMetadata, myUserMetadata)
  4.   │   ├─base::file.path(...)
  5.   │   └─BgeeCall:::get_species_path(myBgeeMetadata, myUserMetadata)
  6.   │     ├─base::file.path(...)
  7.   │     └─BgeeCall:::get_intergenic_release_path(myBgeeMetadata, myUserMetadata)
  8.   │       ├─base::file.path(...)
  9.   │       └─base::paste0(myBgeeMetadata@intergenic_prefix, myBgeeMetadata@intergenic_release)
 10.   └─methods::new("BgeeMetadata")
 11.     ├─methods::initialize(value, ...)
 12.     └─BgeeCall (local) initialize(value, ...)
 13.       └─BgeeCall:::listIntergenicReleases(removeFile = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'bgeecall-manual.Rmd' failed with diagnostics:
File describing intergenic releases could not be downloaded 
from FTP.
--- failed re-building ‘bgeecall-manual.Rmd’

SUMMARY: processing the following file failed:
  ‘bgeecall-manual.Rmd’

Error: Vignette re-building failed.
Execution halted