Fix BiocStyle & pkgdown interaction #108
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out.format needs to be set for knit_theme$get(thm) to work. However, when building a pkgdown article based on a vignette that uses BiocStyle::pdf_document, the out.format is forced to be html, and hardcoding this knit option clashes with pkgdown. By setting and restoring the output format, things keep working as expected
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pkgdown https://pkgdown.r-lib.org/ is an R package to build static websites from package documentation and vignettes.
pkgdown evaluates the output format of the vignettes, but it does not use it, since it generates html documents.
However, BiocStyle manually sets the out.format to "latex". This makes pkgdown generate an html file that then is passed to pdflatex, giving an error "\begin{document}" not found. The temporary .tex file contains an html version of the vignette.
It seems the only reason BiocStyle sets "out.format" to "latex" is to call
knit_theme$get(thm)$highlight, by setting "out.format" to its former value everything seems to keep working.This change restores
"out.format", so pkgdown is still able to generate the html files. pdf vignettes still work as expected.