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###
### Running command:
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###   /home/biocbuild/bbs-3.22-books/R/bin/R CMD build --keep-empty-dirs --no-resave-data SingleRBook
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* checking for file ‘SingleRBook/DESCRIPTION’ ... OK
* preparing ‘SingleRBook’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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/3.22/SingleRBook
HttpExceptionRequest Request {
  host                 = "bioconductor.org"
  port                 = 80
  secure               = False
  requestHeaders       = []
  path                 = "/books/3.22/SingleRBook"
  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’

"/home/biocbuild/bbs-3.22-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('SingleRBook'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> work.dir <- rebook::bookCache('SingleRBook'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)


processing file: index.Rmd
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output file: index.knit.md



processing file: introduction.Rmd
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output file: introduction.knit.md



processing file: bulkref.Rmd
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output file: bulkref.knit.md



processing file: scref.Rmd
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output file: scref.knit.md



processing file: diagnostics.Rmd
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output file: diagnostics.knit.md



processing file: multiple.Rmd
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output file: multiple.knit.md



processing file: ontology.Rmd
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output file: ontology.knit.md



processing file: advanced.Rmd
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output file: advanced.knit.md



processing file: pancreas.Rmd
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output file: pancreas.knit.md



processing file: brain.Rmd
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output file: brain.knit.md



processing file: authors.Rmd
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output file: authors.knit.md



processing file: bibliography.Rmd
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output file: bibliography.knit.md

/usr/bin/pandoc +RTS -K512m -RTS SingleR-book.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output SingleR-book.html --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /home/biocbuild/bbs-3.22-bioc/R/site-library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpSq0a5K/file3950de4b934a9d --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.22-bioc/R/site-library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --mathjax --include-in-header /tmp/RtmpSq0a5K/rmarkdown-str3950de6dfbb2d3.html --filter /usr/bin/pandoc-citeproc 

Output created: docs/index.html
[1] "/home/biocbuild/.cache/rebook/SingleRBook/1.20.0/docs/index.html"
> 
SUMMARY: processing the following file failed:
  ‘stub.Rmd’

Error: Vignette re-building failed.
Execution halted