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This page was generated on 2024-07-24 11:41 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1678/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recount 1.31.2  (landing page)
Leonardo Collado-Torres
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/recount
git_branch: devel
git_last_commit: f4d2db9
git_last_commit_date: 2024-05-21 13:22:52 -0400 (Tue, 21 May 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    ERROR    OK  

BUILD results for recount on lconway

To the developers/maintainers of the recount package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recount.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: recount
Version: 1.31.2
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount
StartedAt: 2024-07-23 18:01:58 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 18:13:06 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 667.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount
###
##############################################################################
##############################################################################


* checking for file ‘recount/DESCRIPTION’ ... OK
* preparing ‘recount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘recount-quickstart.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

2024-07-23 18:04:11.151 R[68596:448182902] XType: com.apple.fonts is not accessible.
2024-07-23 18:04:11.151 R[68596:448182902] 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 'SRP009615-results.knit'
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'

Quitting from lines 524-530 [download_bigwigs] (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
'download_retry()' failed:
  URL: http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw
  error: cannot open URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'
--- failed re-building ‘recount-quickstart.Rmd’

"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "library(rmarkdown); render('recount-quickstart.Rmd')"

Attaching package: ‘BiocStyle’

The following objects are masked from ‘package:rmarkdown’:

    html_document, md_document, pdf_document



processing file: recount-quickstart.Rmd
1/102                   
2/102 [vignetteSetup]   
3/102                   
4/102 [installDer]      
5/102                   
6/102 [citation]        
7/102                   
8/102 [ultraQuick]      
9/102                   
10/102 [er_analysis]     
11/102                   
12/102 [install]         
13/102                   
14/102 [start]           
15/102                   
16/102 [search_abstract] 
17/102                   
18/102 [download]        
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Error in `download_retry()`:
! 'download_retry()' failed:
  URL: http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata
  error: cannot open URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Backtrace:
 1. recount::download_study(project_info$project)
 2. recount::download_retry(...)

Quitting from lines 310-318 [download] (recount-quickstart.Rmd)
Execution halted
make: *** [recount-quickstart.html] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted