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This page was generated on 2025-12-04 15:41 -0500 (Thu, 04 Dec 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.2 (2025-10-31) -- "[Not] Part in a Rumble" 4878
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 383/435HostnameOS / ArchINSTALLBUILDCHECK
spatialLIBD 1.22.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2025-12-04 07:30 -0500 (Thu, 04 Dec 2025)
git_url: https://git.bioconductor.org/packages/spatialLIBD
git_branch: RELEASE_3_22
git_last_commit: d06d43c
git_last_commit_date: 2025-10-29 10:02:34 -0500 (Wed, 29 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped

BUILD results for spatialLIBD on nebbiolo2

To the developers/maintainers of the spatialLIBD 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: spatialLIBD
Version: 1.22.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialLIBD
StartedAt: 2025-12-04 11:45:55 -0500 (Thu, 04 Dec 2025)
EndedAt: 2025-12-04 11:50:17 -0500 (Thu, 04 Dec 2025)
EllapsedTime: 262.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spatialLIBD
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* checking for file ‘spatialLIBD/DESCRIPTION’ ... OK
* preparing ‘spatialLIBD’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘TenX_data_download.Rmd’ using rmarkdown
--- finished re-building ‘TenX_data_download.Rmd’

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

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

Quitting from multi_gene_plots.Rmd:81-85 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readRDS()`:
! error reading from connection
---
Backtrace:
    ▆
 1. └─spatialLIBD::fetch_data(type = "spatialDLPFC_Visium_example_subset")
 2.   ├─AnnotationHub::query(eh, pattern = c(tag, hub_title))
 3.   └─AnnotationHub::query(eh, pattern = c(tag, hub_title))
 4.     └─AnnotationHub (local) .local(x, pattern, ...)
 5.       └─AnnotationHub:::.db_index_load(x)
 6.         └─base::readRDS(.db_index_file(x))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'multi_gene_plots.Rmd' failed with diagnostics:
error reading from connection
--- failed re-building ‘multi_gene_plots.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted