Multiple platform build/check report for BioC 3.21 - BUILD results for BUSpaRse on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4606
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4547
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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 BUSpaRse on nebbiolo1

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

raw results

Summary

Package: BUSpaRse

Version: 1.22.1

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BUSpaRse

StartedAt: 2025-08-31 16:29:55 -0400 (Sun, 31 Aug 2025)

EndedAt: 2025-08-31 16:34:42 -0400 (Sun, 31 Aug 2025)

EllapsedTime: 287.3 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BUSpaRse
###
##############################################################################
##############################################################################


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

Quitting from sparse-matrix.Rmd:42-46 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'sparse-matrix.Rmd' failed with diagnostics:
HTTP 500 Internal Server Error.
--- failed re-building ‘sparse-matrix.Rmd’

--- re-building ‘tr2g.Rmd’ using rmarkdown

Quitting from tr2g.Rmd:64-69 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getAttributes()`:
! biomaRt error: looks like we're connecting to incompatible version of BioMart.
---
Backtrace:
    ▆
 1. └─BUSpaRse::tr2g_ensembl(...)
 2.   └─BUSpaRse:::my_useMart(ensembl_version, mart_use, ds_name, host_use)
 3.     └─biomaRt::useMart(biomart = mart_use, dataset = ds_name, host = host_use)
 4.       └─biomaRt:::.useMart(...)
 5.         └─biomaRt::useDataset(mart = mart, dataset = dataset, verbose = verbose)
 6.           └─biomaRt:::.getAttributes(mart, verbose = verbose)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'tr2g.Rmd' failed with diagnostics:
biomaRt error: looks like we're connecting to incompatible version of BioMart.
--- failed re-building ‘tr2g.Rmd’

SUMMARY: processing the following files failed:
  ‘sparse-matrix.Rmd’ ‘tr2g.Rmd’

Error: Vignette re-building failed.
Execution halted