Back to Build/check report for BioC 3.21 annotations
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This page was generated on 2025-10-15 07:00 -0400 (Wed, 15 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
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 12/47HostnameOS / ArchINSTALLBUILDCHECK
BioMartGOGeneSets 0.99.11  (landing page)
Zuguang Gu
Snapshot Date: 2025-10-15 05:45 -0400 (Wed, 15 Oct 2025)
git_url: https://git.bioconductor.org/packages/BioMartGOGeneSets
git_branch: RELEASE_3_21
git_last_commit: 25ee53f
git_last_commit_date: 2023-09-23 07:29:45 -0400 (Sat, 23 Sep 2023)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for BioMartGOGeneSets on nebbiolo1

To the developers/maintainers of the BioMartGOGeneSets package:
- 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: BioMartGOGeneSets
Version: 0.99.11
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BioMartGOGeneSets
StartedAt: 2025-10-15 06:01:11 -0400 (Wed, 15 Oct 2025)
EndedAt: 2025-10-15 06:02:52 -0400 (Wed, 15 Oct 2025)
EllapsedTime: 101.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BioMartGOGeneSets
###
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* checking for file ‘BioMartGOGeneSets/DESCRIPTION’ ... OK
* preparing ‘BioMartGOGeneSets’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘biomart.Rmd’ using rmarkdown

Quitting from biomart.Rmd:72-75 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.getAttributes()`:
! biomaRt error: looks like we're connecting to incompatible version of BioMart.
---
Backtrace:
    ▆
 1. └─biomaRt::useDataset(dataset = "hsapiens_gene_ensembl", mart = ensembl)
 2.   └─biomaRt:::.getAttributes(mart, verbose = verbose)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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

--- re-building ‘genesets.Rmd’ using rmarkdown
--- finished re-building ‘genesets.Rmd’

--- re-building ‘supported_organisms.Rmd’ using rmarkdown
--- finished re-building ‘supported_organisms.Rmd’

--- re-building ‘version.Rmd’ using rmarkdown
--- finished re-building ‘version.Rmd’

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

Error: Vignette re-building failed.
Execution halted