Back to Workflows build report for BioC 3.22

This page was generated on 2025-07-11 16:30 -0400 (Fri, 11 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4782
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4522
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4565
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 18/29HostnameOS / ArchINSTALLBUILD
recountWorkflow 1.33.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2025-07-11 12:45 -0400 (Fri, 11 Jul 2025)
git_url: https://git.bioconductor.org/packages/recountWorkflow
git_branch: devel
git_last_commit: 4f05efe
git_last_commit_date: 2025-04-15 10:28:58 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for recountWorkflow on lconway

To the developers/maintainers of the recountWorkflow 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: recountWorkflow
Version: 1.33.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
StartedAt: 2025-07-11 13:05:01 -0400 (Fri, 11 Jul 2025)
EndedAt: 2025-07-11 13:10:33 -0400 (Fri, 11 Jul 2025)
EllapsedTime: 332.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
###
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* checking for file ‘recountWorkflow/DESCRIPTION’ ... OK
* preparing ‘recountWorkflow’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘recount-workflow.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'

Quitting from recount-workflow.Rmd:254-270 [download gene]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download_retry()`:
! 'download_retry()' failed:
  URL: http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata
  error: cannot open URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
---
Backtrace:
    ▆
 1. └─recount::download_study("SRP045638", type = "rse-gene")
 2.   └─recount::download_retry(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
'download_retry()' failed:
  URL: http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata
  error: cannot open URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_gene.Rdata'
--- failed re-building ‘recount-workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘recount-workflow.Rmd’

Error: Vignette re-building failed.
Execution halted