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### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.multisample
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* checking for file ‘OSCA.multisample/DESCRIPTION’ ... OK
* preparing ‘OSCA.multisample’:
* 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.
  Defaulting to 'stub.knit' as the title.
  To specify a title, use 'title' in metadata or --metadata title="...".
--- finished re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.21-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.multisample'); 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 Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"
Copyright (C) 2024 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

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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('OSCA.multisample'); 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: merged-pancreas.Rmd
# 1/48                              
# 2/48 [unref-setup]                
# 3/48                              
# 4/48 [unnamed-chunk-1]            
# 5/48                              
# 6/48 [unnamed-chunk-2]            
# 7/48                              
# 8/48 [unnamed-chunk-3]            
# 9/48                              
# 10/48 [unnamed-chunk-4]            
# 11/48                              
# 12/48 [unnamed-chunk-5]            
# 13/48                              
# 14/48 [tsne-pancreas-rescaled]     
# 15/48                              
# 16/48 [tsne-pancreas-mnn]          
# 17/48                              
# 18/48 [unnamed-chunk-6]            
# 19/48                              
# 20/48 [unnamed-chunk-7]            
# 21/48                              
# 22/48 [unnamed-chunk-8]            
# 23/48                              
# 24/48 [unnamed-chunk-9]            
# 25/48                              
# 26/48 [unnamed-chunk-10]           
# 27/48                              
# 28/48 [unnamed-chunk-11]           
# 29/48                              
# 30/48 [tsne-pancreas-mnn-many]     
# 31/48                              
# 32/48 [unnamed-chunk-12]           
# 33/48                              
# 34/48 [tsne-pancreas-mnn-donor]    
# 35/48                              
# 36/48 [unnamed-chunk-13]           
# 37/48                              
# 38/48 [unnamed-chunk-14]           
# 39/48                              
# 40/48 [tsne-pancreas-mnn-donor-all]
# 41/48                              
# 42/48 [unnamed-chunk-15]           
# 43/48                              
# 44/48 [unnamed-chunk-16]           
# 45/48                              
# 46/48 [unnamed-chunk-17]           
# Error:
# ! pairwiseRand(proposed[nonna], clusters[nonna], mode = "index") >  .... is not TRUE
# Backtrace:
#   1. rmarkdown::render(commandArgs(TRUE))
#   2. knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
#   3. knitr:::process_file(text, output)
#   6. knitr:::process_group(group)
#   7. knitr:::call_block(x)
#      ...
#  14. base::withRestarts(...)
#  15. base (local) withRestartList(expr, restarts)
#  16. base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
#  17. base (local) docall(restart$handler, restartArgs)
#  19. evaluate (local) fun(base::quote(`<smplErrr>`))
# 
# Quitting from lines 253-256 [unnamed-chunk-17] (merged-pancreas.Rmd)
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.multisample/1.15.1/merged-pancreas.Rmd'
Calls: <Anonymous> ... .precompile_book -> .locked_compile_chapter -> compileChapter
Execution halted
make: *** [Makefile:4: compiled] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted