Back to Workflows build report for BioC 3.24

This page was generated on 2026-05-26 16:30 -0400 (Tue, 26 May 2026).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.4 LTS)x86_644.6.0 RC (2026-04-17 r89917) -- "Because it was There" 4938
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 1/28HostnameOS / ArchINSTALLBUILD
annotation 1.37.0  (landing page)
Bioconductor Package Maintainer
Snapshot Date: 2026-05-26 12:45 -0400 (Tue, 26 May 2026)
git_url: https://git.bioconductor.org/packages/annotation
git_branch: devel
git_last_commit: 77a311d
git_last_commit_date: 2026-04-28 08:40:17 -0400 (Tue, 28 Apr 2026)
nebbiolo2Linux (Ubuntu 24.04.4 LTS) / x86_64  OK    ERROR  

BUILD results for annotation on nebbiolo2

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: 1.37.0
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotation
StartedAt: 2026-05-26 13:04:16 -0400 (Tue, 26 May 2026)
EndedAt: 2026-05-26 13:05:53 -0400 (Tue, 26 May 2026)
EllapsedTime: 96.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data annotation
###
##############################################################################
##############################################################################


* checking for file ‘annotation/DESCRIPTION’ ... OK
* preparing ‘annotation’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘Annotating_Genomic_Ranges.Rmd’ using rmarkdown

Quitting from Annotating_Genomic_Ranges.Rmd:76-78 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.Hub_get1()`:
! no records found for the given index
---
Backtrace:
    ▆
 1. ├─query(hub, c("clinvar.vcf", "GRCh37"))[[1]]
 2. └─query(hub, c("clinvar.vcf", "GRCh37"))[[1]]
 3.   └─AnnotationHub (local) .local(x, i, j = j, ...)
 4.     └─AnnotationHub:::.Hub_get1(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'Annotating_Genomic_Ranges.Rmd' failed with diagnostics:
no records found for the given index
--- failed re-building ‘Annotating_Genomic_Ranges.Rmd’

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

Quitting from Annotation_Resources.Rmd:639-643 [unnamed-chunk-36]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.chooseEnsemblMirror()`:
! Unable to query any Ensembl site
---
Backtrace:
    ▆
 1. └─biomaRt::useEnsembl(biomart = "genes")
 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 files failed:
  ‘Annotating_Genomic_Ranges.Rmd’ ‘Annotation_Resources.Rmd’

Error: Vignette re-building failed.
Execution halted