search

Bioconductor / BiocStyle

Issues and pull requests for BiocStyle should go here.
12 stars 19 forks source link

Vignette Ambiguous Wording for Code Width #39

Closed DarioS closed 6 years ago

DarioS commented 6 years ago

In the vignette, it states

The line length of output code chunks is set to the optimal width of typically 80 characters, so it is not neccessary to adjust it manually through options("width").

This implies that it is possible to use a commands such as options(width = 120);BiocStyle::markdown(); but it has no effect.

aoles commented 6 years ago

Hi, thanks for the inquiry. The cited vignette describes the use of BiocStyle with the newer R Markdown v2 engine based on rmarkdown, while BiocStyle::markdown() was originally developed against the older markdown package. In fact, markdown() does not perform any adjustments to options("width"), this functionality was introduced only recently with the new Biocstyle::html_document format function.

Use knitr::opts_knit$set(width=120) to set the knitr R session option("width").

DarioS commented 6 years ago

Oh, I should remove BiocStyle::markdown() then. I used rmarkdown as the vignette engine and specified a HTML document in the vignette header, so there are a mixture of different markdown versions specified in the vignette file.