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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/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 to build vignettes
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty
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/
[1m[34m
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processing file: index.qmd
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[31moutput file: index.knit.md
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[31mrunning: sh -c 'find ../ -name "*.qmd"'
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[31moutput file: Chapter-2.knit.md
[39m[31mWarning messages:
1: In get_engine(options$engine) :
Unknown language engine 'txt' (must be registered via knit_engines$set()).
[39m[31m2: In get_engine(options$engine) :
Unknown language engine 'txt' (must be registered via knit_engines$set()).
[39m[31m
processing file: Chapter-2.qmd
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[31mrunning: sh -c 'find ../ -name "*.qmd"'
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[31moutput file: Chapter-2.knit.md
[39m[31mWarning messages:
1: In get_engine(options$engine) :
[39m[31m Unknown language engine 'txt' (must be registered via knit_engines$set()).
2: In get_engine(options$engine) :
Unknown language engine 'txt' (must be registered via knit_engines$set()).
[39m[1m[34m
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[31moutput file: Chapter-3.knit.md
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processing file: biocbook-vs-rebook.qmd
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[39m
[1mpandoc [22m
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
[1mmetadata[22m
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
[1m[34m
Rendering PDF[39m[22m
[1m[34mrunning xelatex - 1[39m[22m
[1m[34mcommand xelatex not found, attempting install[39m[22m
[1m[34mfinding package for xelatex[39m[22m
[1m[34m> 1 package to install[39m[22m
[1m[34m> installing xelatex (1 of 1)[39m[22m
[91mERROR: 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!
Stack trace:
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:91548:64)
at eventLoopTick (ext:core/01_core.js:183:11)
at async renderFiles (file:///opt/quarto/bin/quarto.js:77075:16)
at async renderProject (file:///opt/quarto/bin/quarto.js:77394:25)
at async Command.fn (file:///opt/quarto/bin/quarto.js:81959:32)
at async Command.execute (file:///opt/quarto/bin/quarto.js:8104:13)
at async quarto (file:///opt/quarto/bin/quarto.js:115002:5)
at async file:///opt/quarto/bin/quarto.js:115020:9[39m
make: *** [Makefile:4: render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) :
running 'make' failed
Execution halted