Workflows build report for BioC 3.19 - BUILD results for recountWorkflow on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4495
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4509
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4408
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*

BUILD results for recountWorkflow on palomino7

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: 1.28.2

Command: chmod a+r recountWorkflow -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data recountWorkflow

StartedAt: 2024-06-28 13:06:58 -0400 (Fri, 28 Jun 2024)

EndedAt: 2024-06-28 13:21:57 -0400 (Fri, 28 Jun 2024)

EllapsedTime: 899.9 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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###
### Running command:
###
###   chmod a+r recountWorkflow -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe 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

[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 912-924 [gencode_txdb] (recount-workflow.Rmd)
Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
Corrupt Cache: index file
  See AnnotationHub's TroubleshootingTheHubs vignette section on corrupt cache
  cache: F:\biocbuild\AnnotationHub_cache
  filename: annotationhub.index.rds
--- failed re-building 'recount-workflow.Rmd'

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

Error: Vignette re-building failed.
Execution halted