Back to Workflows build report for BioC 3.17

This page was generated on 2023-10-13 14:00:09 -0400 (Fri, 13 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1.24.0  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2023-10-13 07:45:02 -0400 (Fri, 13 Oct 2023)
git_url: https://git.bioconductor.org/packages/recountWorkflow
git_branch: RELEASE_3_17
git_last_commit: af268e2
git_last_commit_date: 2023-04-25 09:45:42 -0400 (Tue, 25 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    ERROR  
palomino3Windows Server 2022 Datacenter / x64  OK    OK  
merida1macOS 12.6.4 Monterey / x86_64  OK    ERROR  

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: 1.24.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data recountWorkflow
StartedAt: 2023-10-13 08:02:55 -0400 (Fri, 13 Oct 2023)
EndedAt: 2023-10-13 08:27:26 -0400 (Fri, 13 Oct 2023)
EllapsedTime: 1471.0 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.17-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

connection timeout to recount-opendata.s3.amazonaws.com
R: Error (Connection reset by peer) reading http header on https://recount-opendata.s3.amazonaws.com/recount2/SRP045638/bw/SRR2071363.bw;byterange=153001984-: Connection reset by peer
connection timeout to recount-opendata.s3.amazonaws.com
R: Error (Connection reset by peer) reading http header on https://recount-opendata.s3.amazonaws.com/recount2/SRP045638/bw/SRR1554557.bw;byterange=0-: Connection reset by peer
BIO_do_connect() failed
SSL error: (null)
R: Error (Connection reset by peer) reading http header on https://recount-opendata.s3.amazonaws.com/recount2/SRP045638/bw/SRR1554537.bw;byterange=154648576-: Connection reset by peer
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-3.17-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-3.17-bioc/R/site-library/lubridate/R/lubridate.rdb': Too many open files
Calls: <Anonymous> -> file_test -> >.POSIXt
Execution halted