Back to Workflows build report for BioC 3.20

This page was generated on 2025-04-03 13:02 -0400 (Thu, 03 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
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 1/30HostnameOS / ArchINSTALLBUILD
annotation 1.30.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2025-04-03 11:10 -0400 (Thu, 03 Apr 2025)
git_url: https://git.bioconductor.org/packages/annotation
git_branch: RELEASE_3_20
git_last_commit: e0c27c9
git_last_commit_date: 2024-10-29 10:01:57 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK  
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  

BUILD results for annotation on merida1

To the developers/maintainers of the annotation 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: annotation
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data annotation
StartedAt: 2025-04-03 11:17:04 -0400 (Thu, 03 Apr 2025)
EndedAt: 2025-04-03 11:24:02 -0400 (Thu, 03 Apr 2025)
EllapsedTime: 418.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data annotation
###
##############################################################################
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* checking for file ‘annotation/DESCRIPTION’ ... OK
* preparing ‘annotation’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Annotating_Genomic_Ranges.Rmd’ using rmarkdown
--- finished re-building ‘Annotating_Genomic_Ranges.Rmd’

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

Quitting from Annotation_Resources.Rmd:773-777 [unnamed-chunk-50]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.chooseEnsemblMirror()`:
! Unable to query any Ensembl site
---
Backtrace:
    ▆
 1. └─biomaRt::useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
 2.   └─biomaRt:::.chooseEnsemblMirror(mirror = mirror, http_config = http_config)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotation_Resources.Rmd' failed with diagnostics:
Unable to query any Ensembl site
--- failed re-building ‘Annotation_Resources.Rmd’

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

Error: Vignette re-building failed.
Execution halted