Back to Workflows build report for BioC 3.19

This page was generated on 2024-03-01 14:00:11 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
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 19/30HostnameOS / ArchINSTALLBUILD
recountWorkflow 1.27.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-03-01 07:45:01 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/recountWorkflow
git_branch: devel
git_last_commit: 69c3264
git_last_commit_date: 2023-10-24 08:46:55 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for recountWorkflow on merida1


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: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
StartedAt: 2024-03-01 11:12:43 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 11:30:28 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 1065.4 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 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'
Content type 'binary/octet-stream' length 12604886 bytes (12.0 MB)
==================================================
downloaded 12.0 MB

trying URL 'https://github.com/leekgroup/recount-website/blob/master/predictions/PredictedPhenotypes_v0.0.06.rda?raw=true'
Content type 'application/octet-stream' length 548129 bytes (535 KB)
==================================================
downloaded 535 KB

2024-03-01 11:14:36.346 R[97260:869261725] XType: com.apple.fonts is not accessible.
2024-03-01 11:14:36.347 R[97260:869261725] XType: XTFontStaticRegistry is enabled.
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'gene_report.knit'
trying URL 'http://duffel.rail.bio/recount/v2/SRP045638/rse_exon.Rdata'
Content type 'binary/octet-stream' length 110177449 bytes (105.1 MB)
==================================================
downloaded 105.1 MB


Quitting from lines 733-747 [identify regions] (recount-workflow.Rmd)
Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
UCSC library operation failed
--- failed re-building ‘recount-workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted