##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data BiocBookDemo
###
##############################################################################
##############################################################################


* checking for file ‘BiocBookDemo/DESCRIPTION’ ... OK
* preparing ‘BiocBookDemo’:
* 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’

quarto render ../inst/

[1/6] index.qmd


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

WARNING: Warning: diff of engine output timed out. No source lines will be available.


processing file: index.qmd
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4/9 [docker]      
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6/9 [rstudio]     
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8/9 [session info]
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output file: index.knit.md

WARNING: Warning: diff of engine output timed out. No source lines will be available.

[2/6] pages/preamble.qmd

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


processing file: Chapter-1.qmd
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output file: Chapter-1.knit.md



processing file: Chapter-1.qmd
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output file: Chapter-1.knit.md


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


processing file: Chapter-2.qmd
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running: sh  -c 'find ../ -name "*.qmd"'
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30/31 [unnamed-chunk-15]
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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()).


processing file: Chapter-2.qmd
1/31                   
2/31 [unnamed-chunk-1] 
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24/31 [unnamed-chunk-12]
running: sh  -c 'find ../ -name "*.qmd"'
25/31                   
26/31 [unnamed-chunk-13]
27/31                   
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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
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output file: Chapter-3.knit.md



processing file: Chapter-3.qmd
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output file: Chapter-3.knit.md


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


processing file: biocbook-vs-rebook.qmd
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output file: biocbook-vs-rebook.knit.md



processing file: biocbook-vs-rebook.qmd
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output file: biocbook-vs-rebook.knit.md


pandoc 
  to: latex
  output-file: index.tex
  standalone: true
  toc: true
  number-sections: true
  top-level-division: chapter
  pdf-engine: xelatex
  variables:
    graphics: true
    tables: true
  default-image-extension: pdf
  
metadata
  crossref:
    chapters: true
  documentclass: scrreprt
  papersize: letter
  classoption:
    - DIV=11
    - numbers=noendperiod
  header-includes:
    - '\KOMAoption{captions}{tableheading}'
  block-headings: true
  knitr:
    opts_chunk:
      collapse: true
      comment: '## '
      cache: false
      fig.align: center
      python.reticulate: false
      R.options:
        dplyr.print_min: 6
        dplyr.print_max: 6
        pillar.max_footer_lines: 2
        pillar.min_chars: 15
        stringr.view_n: 6
        pillar.bold: true
        width: 77
  title: Write Quarto books with Bioconductor
  
running xelatex - 1
command xelatex not found, attempting install
finding package for xelatex
> 1 package to install
> installing xelatex (1 of 1)
ERROR: tlmgr returned a non zero status code
TLPDB: not a directory, not loading: /home/biocbuild/texmf
tlmgr: user mode not initialized, please read the documentation!


Error: tlmgr returned a non zero status code
TLPDB: not a directory, not loading: /home/biocbuild/texmf
tlmgr: user mode not initialized, please read the documentation!

    at Object.onComplete (file:///opt/quarto/bin/quarto.js:98918:66)
    at async renderFiles (file:///opt/quarto/bin/quarto.js:86654:16)
    at async renderProject (file:///opt/quarto/bin/quarto.js:86800:25)
    at async Command.fn (file:///opt/quarto/bin/quarto.js:90856:32)
    at async Command.execute (file:///opt/quarto/bin/quarto.js:8437:13)
    at async quarto (file:///opt/quarto/bin/quarto.js:127545:5)
    at async file:///opt/quarto/bin/quarto.js:127563:9
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted