Back to Workflows build report for BioC 3.19

This page was generated on 2024-07-09 16:30 -0400 (Tue, 09 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4709
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
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 1.28.2  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-07-09 12:45 -0400 (Tue, 09 Jul 2024)
git_url: https://git.bioconductor.org/packages/recountWorkflow
git_branch: RELEASE_3_19
git_last_commit: e702bde
git_last_commit_date: 2024-05-21 13:53:43 -0400 (Tue, 21 May 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  
palomino7Windows Server 2022 Datacenter / x64  OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK  

BUILD results for recountWorkflow on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
StartedAt: 2024-07-09 13:06:28 -0400 (Tue, 09 Jul 2024)
EndedAt: 2024-07-09 13:20:46 -0400 (Tue, 09 Jul 2024)
EllapsedTime: 858.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
###
##############################################################################
##############################################################################


* 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 929-939 [bump_ann] (recount-workflow.Rmd)
Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
failed to load resource
  name: AH75150
  title: Annotated genes for Gencode v25 on hg38 coordinates
  reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
--- failed re-building ‘recount-workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted