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


* checking for file ‘BiocBookDemo/DESCRIPTION’ ... OK
* preparing ‘BiocBookDemo’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[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 'stub.knit'
Could not fetch http://bioconductor.org/books/3.23/BiocBookDemo
HttpExceptionRequest Request {
  host                 = "bioconductor.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/books/3.23/BiocBookDemo"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ResponseTimeout
Error: processing vignette 'stub.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘stub.Rmd’

quarto render ../inst/

[1/6] index.qmd


processing file: index.qmd
1/9               
2/9 [intro]       
3/9               
4/9 [docker]      
5/9               
6/9 [rstudio]     
7/9               
8/9 [session info]
9/9               
output file: index.knit.md


[2/6] pages/preamble.qmd

[3/6] pages/Chapter-1.qmd


processing file: Chapter-1.qmd
1/7                  
2/7 [unnamed-chunk-1]
3/7                  
4/7 [unnamed-chunk-2]
5/7                  
6/7 [unnamed-chunk-3]
7/7                  
output file: Chapter-1.knit.md


[4/6] pages/Chapter-2.qmd


processing file: Chapter-2.qmd
1/31                   
2/31 [unnamed-chunk-1] 
3/31                   
4/31 [unnamed-chunk-2] 
5/31                   
6/31 [unnamed-chunk-3] 
7/31                   
8/31 [unnamed-chunk-4] 
9/31                   
10/31 [unnamed-chunk-5] 
11/31                   
12/31 [unnamed-chunk-6] 
13/31                   
14/31 [unnamed-chunk-7] 
15/31                   
16/31 [unnamed-chunk-8] 
17/31                   
18/31 [unnamed-chunk-9] 
19/31                   
20/31 [unnamed-chunk-10]
21/31                   
22/31 [unnamed-chunk-11]
23/31                   
24/31 [unnamed-chunk-12]
running: sh  -c 'find ../ -name "*.qmd"'
25/31                   
26/31 [unnamed-chunk-13]
27/31                   
28/31 [unnamed-chunk-14]
29/31                   
30/31 [unnamed-chunk-15]
31/31                   
output file: Chapter-2.knit.md

Warning messages:
1: In get_engine(options$engine) :
  Unknown language engine 'txt' (must be registered via knit_engines$set()).
2: In get_engine(options$engine) :
  Unknown language engine 'txt' (must be registered via knit_engines$set()).

[5/6] pages/Chapter-3.qmd


processing file: Chapter-3.qmd
1/15                  
2/15 [unnamed-chunk-1]
3/15                  
4/15 [unnamed-chunk-2]
5/15                  
6/15 [unnamed-chunk-3]
7/15                  
8/15 [unnamed-chunk-4]
9/15                  
10/15 [unnamed-chunk-5]
11/15                  
12/15 [unnamed-chunk-6]
13/15                  
14/15 [unnamed-chunk-7]
15/15                  
output file: Chapter-3.knit.md


[6/6] pages/biocbook-vs-rebook.qmd


processing file: biocbook-vs-rebook.qmd
1/7                  
2/7 [unnamed-chunk-1]
3/7                  
4/7 [unnamed-chunk-2]
5/7                  
6/7 [unnamed-chunk-3]
7/7                  
output file: biocbook-vs-rebook.knit.md


Output created: docs/index.html

mkdir -p ../inst/doc && mv ../inst/docs ../inst/doc/book
SUMMARY: processing the following file failed:
  ‘stub.Rmd’

Error: Vignette re-building failed.
Execution halted