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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.advanced
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* checking for file ‘OSCA.advanced/DESCRIPTION’ ... OK
* preparing ‘OSCA.advanced’:
* 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'
--- finished re-building ‘stub.Rmd’

"/home/biocbuild/bbs-3.19-bioc/R/bin/R" -e "work.dir <- rebook::bookCache('OSCA.advanced'); 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 4.4.0 (2024-04-24) -- "Puppy Cup"
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

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('OSCA.advanced'); 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: cell-cycle.Rmd
# 1/62                         
# 2/62 [setup]                 
# 3/62                         
# 4/62 [unnamed-chunk-1]       
# 5/62                         
# 6/62 [unnamed-chunk-2]       
# 7/62                         
# 8/62 [heat-cyclin]           
# 9/62                         
# 10/62 [unnamed-chunk-3]       
# 11/62                         
# 12/62 [unnamed-chunk-4]       
# 13/62                         
# 14/62 [unnamed-chunk-5]       
# 15/62                         
# 16/62 [unnamed-chunk-6]       
# 17/62                         
# 18/62 [heat-cyclin-grun]      
# 19/62                         
# 20/62 [unnamed-chunk-7]       
# 21/62                         
# 22/62 [unnamed-chunk-8]       
# 23/62                         
# 24/62 [unnamed-chunk-9]       
# 25/62                         
# 26/62 [unnamed-chunk-10]      
# 27/62                         
# 28/62 [unnamed-chunk-11]      
# 29/62                         
# 30/62 [dist-lef1]             
# 31/62                         
# 32/62 [unnamed-chunk-12]      
# 33/62                         
# 34/62 [unnamed-chunk-13]      
# 35/62                         
# 36/62 [unnamed-chunk-14]      
# 37/62                         
# 38/62 [phaseplot416b]         
# 39/62                         
# 40/62 [unnamed-chunk-15]      
# 41/62                         
# 42/62 [unnamed-chunk-16]      
# 43/62                         
# 44/62 [cell-cycle-regression] 
# 45/62                         
# 46/62 [cell-cycle-regression2]
# 47/62                         
# 48/62 [cell-cycle-regression3]
# 49/62                         
# 50/62 [leng-nocycle]          
# Error in `h()`:
# ! error in evaluating the argument 'x' in selecting a method for function 'colSums': 'assay(<SingleCellExperiment>, i="character", ...)' invalid subscript 'i'
# 'normalized' not in names(assays(<SingleCellExperiment>))
# Backtrace:
#   1. scuttle::logNormCounts(sce.leng, assay.type = "normalized")
#  12. base::.handleSimpleError(...)
#  13. base (local) h(simpleError(msg, call))
# Warning message:
# call dbDisconnect() when finished working with a connection 
# 
# Quitting from lines 317-343 [leng-nocycle] (cell-cycle.Rmd)
# Execution halted

Error in compileChapter(path) : 
  failed to compile '~/.cache/rebook/OSCA.advanced/1.12.0/cell-cycle.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