Support for .Rmd, .Rpres & .Rnw

[AdamSpannbauer]

Related to #95

To support file extensions outside of .R well some additional logic will be needed. If we choose to mirror the support packrat has then this includes adding support for .Rmd / .Rpres & .Rnw.

I'm not familiar with .Rnw tbh. packrat handles it with their helper packrat:::fileDependencies.Rnw which uses utils::Stangle then runs their R dependency finder on the output.

---

Below is a potential start to a string based dependency finder for .Rmd / .Rpres

rmd_lines = readLines("test.Rmd")

# Find lines that start with ```{r
chunk_start_lines = grep("^```\\{r\\b", rmd_lines)

# Find lines that start with ```
potential_chunk_end_lines = grep("^```", rmd_lines)

# Rm ```{r lines from candidates list of chunk enders
potential_chunk_end_lines = setdiff(potential_chunk_end_lines, chunk_start_lines)

rmd_code_chunks = lapply(chunk_start_lines, function(chunk_start_line) {
  # Find which candidate endline occurs most soon after an r code chunk start line
  all_line_diffs = potential_chunk_end_lines - chunk_start_line
  valid_line_diffs = all_line_diffs[all_line_diffs > 0]
  chunk_end_line_diff = valid_line_diffs[which.min(valid_line_diffs)]
  chunk_end_line = potential_chunk_end_lines[all_line_diffs == chunk_end_line_diff]

  # Subset codechunk lines (drop ``` lines)
  rmd_lines[(chunk_start_line + 1):(chunk_end_line - 1)]
})

rmd_r_code = unlist(rmd_code_chunks)

Contents of "test.Rmd":

---
title: "Untitled"
output: html_document
---

```{r, setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{bash, setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

mgsub::mgsub
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.
library(dplyr)
When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

[bmewing]

How critical is it that we support beyond .R and .Rmd/.Rpres?

[AdamSpannbauer]

Probably not too critical. Maybe just work in support for md/pres and then come back to Rnw if requested? As far as I know, I've never come across a Rnw in the wild.

[bmewing]

Agreed

…

On Tue, May 14, 2019, 9:45 AM Adam Spannbauer ***@***.***> wrote: Probably not too critical. Maybe just work in support for md/pres and then come back to Rnw if requested? As far as I know, I've never come across a Rnw in the wild. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#98?email_source=notifications&email_token=AD4VHGURCCV2G3LPU4Z575LPVK655A5CNFSM4HMZEFJKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODVLQU5Y#issuecomment-492243575>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD4VHGT75P467OM2MQWKCBTPVK655ANCNFSM4HMZEFJA> .

[bmewing]

@AdamSpannbauer this was addressed in #105 right?

[AdamSpannbauer]

@bmewing yep

Per this thread, we abandoned support for .Rnw. Longterm all this parsing would be better done by renv if they publish to CRAN with their parser exported (open issue for this in #58)