##############################################################################
##############################################################################
###
### 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

2024-03-01 22:00:42.620 R[85890:919243425] XType: com.apple.fonts is not accessible.
2024-03-01 22:00:42.622 R[85890:919243425] 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'

Quitting from lines 524-532 [define_ers] (recount-quickstart.Rmd)
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
UCSC library operation failed
--- 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
1/100                   
2/100 [vignetteSetup]   
3/100                   
4/100 [installDer]      
5/100                   
6/100 [citation]        
7/100                   
8/100 [ultraQuick]      
9/100                   
10/100 [er_analysis]     
11/100                   
12/100 [install]         
13/100                   
14/100 [start]           
15/100                   
16/100 [search_abstract] 
17/100                   
18/100 [download]        
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

19/100                   
20/100 [explore_rse]     
21/100                   
22/100 [browse]          
23/100                   
24/100 [sample_info]     
25/100                   
26/100 [scale_counts]    
27/100                   
28/100 [add_sample_info] 
29/100                   
30/100 [de_analysis]     
31/100                   
32/100 [maplot]          
2024-03-01 22:03:51.472 R[77826:919508395] XType: com.apple.fonts is not accessible.
2024-03-01 22:03:51.473 R[77826:919508395] XType: XTFontStaticRegistry is enabled.
33/100                   
34/100 [make_report]     
35/100                   
36/100 [make_report_real]
[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'
37/100                   
38/100 [geneSymbols]     
39/100                   
40/100 [define_ers]      

Quitting from lines 524-532 [define_ers] (recount-quickstart.Rmd)
Error in `FUN()`:
! UCSC library operation failed
Backtrace:
 1. recount::expressed_regions(...)
 2. derfinder::loadCoverage(files = meanFile, chr = chr, chrlen = chrlen)
 4. S4Vectors::lapply(...)
 6. base::lapply(as.list(X), match.fun(FUN), ...)
 7. derfinder (local) FUN(X[[i]], ...)
Execution halted
make: *** [recount-quickstart.html] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted