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

2024-06-27 17:50:28.162 R[73726:199023848] XType: com.apple.fonts is not accessible.
2024-06-27 17:50:28.163 R[73726:199023848] 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