compileChapter: Compile a Rmarkdown file

In MarioniLab/simpleSingleCell: A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor

Description

Compile a Rmarkdown file - typically a chapter of a book - so that extractCached calls work correctly in other chapters.

Usage

compileChapter(path, cache = TRUE)

Arguments

path	String containing a path to an Rmarkdown file.
cache	Logical scalar indicating whether the compilation should be cached.

Details

Compilation is performed in an isolated session using r from the callr package. This ensures that settings from one chapter do not affect the next chapter.

If an error is encountered during compilation of any Rmarkdown file, the standard output of render leading up to the error is printed out before the function exists.

Value

All files are (re)compiled to generate the corresponding *_cache directories. NULL is invisibly returned.

Author(s)

Aaron Lun

See Also

extractCached, which calls this function.

Examples

tmp <- tempfile(fileext=".Rmd")
write(file=tmp, "```{r, echo=FALSE, results='asis'}
rebook::chapterPreamble()
```

```{r}
rodan <- 1
```")

compileChapter(tmp)

file.exists(sub(".Rmd$", ".html", tmp)) # output HTML exists.
file.exists(sub(".Rmd$", "_cache", tmp)) # output cache exists.
exists("rodan") # FALSE

MarioniLab/simpleSingleCell documentation built on Aug. 27, 2020, 5:04 a.m.