Back to Workflows build report for BioC 3.18

This page was generated on 2024-04-16 14:00:10 -0400 (Tue, 16 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 1.26.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-04-16 10:45:01 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/recountWorkflow
git_branch: RELEASE_3_18
git_last_commit: 7291d20
git_last_commit_date: 2023-10-24 08:46:55 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK  
merida1macOS 12.7.1 Monterey / x86_64  OK    ERROR  

BUILD results for recountWorkflow on nebbiolo2


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: 1.26.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
StartedAt: 2024-04-16 11:02:59 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 11:27:45 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 1486.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/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

[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

BIO_do_connect() failed
SSL error: unexpected eof while reading
R: getaddrinfo() error on hostName=duffel.rail.bio: System error
: Too many open files
R: getaddrinfo() error on hostName=duffel.rail.bio: System error
: Too many open files
Warning in file(con, "w") :
  cannot open file 'recount-workflow.knit.md': Too many open files
Error: processing vignette 'recount-workflow.Rmd' failed with diagnostics:
cannot open the connection
Error: tangling vignette 'recount-workflow.Rmd' failed with diagnostics:
cannot open file '/home/biocbuild/bbs-3.18-bioc/R/site-library/lubridate/R/lubridate.rdb': Too many open files
--- failed re-building ‘recount-workflow.Rmd’

Warning in `>.POSIXt`(mt.x, mt.y) :
  restarting interrupted promise evaluation
Error in `>.POSIXt`(mt.x, mt.y) : 
  cannot open file '/home/biocbuild/bbs-3.18-bioc/R/site-library/lubridate/R/lubridate.rdb': Too many open files
Calls: <Anonymous> -> file_test -> >.POSIXt
Execution halted