Fix BiocStyle & pkgdown interaction#108
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It's been a year without any feedback on this issue. Is there anything I can do to get this merged or discussed? Thanks |
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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…onductor#108) BiocStyle::pdf_document() sets the global knitr option 'out.format' to "latex" to look up the syntax highlighting theme but did not restore its previous value, corrupting state for documents rendered later in the same session (e.g. pkgdown building multiple articles in-process).
…onductor#108) BiocStyle::pdf_document() sets the global knitr option 'out.format' to "latex" to look up the syntax highlighting theme but did not restore its previous value, corrupting state for documents rendered later in the same session (e.g. pkgdown building multiple articles in-process).
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Good news, I can't. Two years ago I had to install this branch in my AlpsNMR GitHub workflow https://github.com/sipss/AlpsNMR or otherwise pkgdown failed. I have been dragging this patch for two years on my package. I recently hit #116 and I combined both patches. Now I just tried using the patch in #116 and dropping this one and the build succeeded. I guess something got fixed elsewhere (possibly pkgdown or some dependency). Anyway, since I can't reproduce the error, I will close this PR. Apologies for all the noise. |
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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.