Rmarkdown does not reproduce bash code properly

Question

I'm using Rmarkdown to show some bash code:

---
title: "Untitled"
author: "JPD"
date: "20 December 2016"
output: html_document
---

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

```{r gp.setup, engine= 'bash', eval=FALSE}

##Change names to remove dots
g.rename raster=gp_ortho.1,gp_ortho_1,gp_ortho.2,gp_ortho_2,\
gp_ortho.3,gp_ortho_3

##Group bands together
i.group --verbose group=gp_combo input=gp_ortho_1@gp1,gp_ortho_2@gp1,\
gp_ortho_3@gp1
```

However, when knitted to html, the g.rename line(s) mostly disappear. For comparison, the i.group command beneath is displayed correctly:

What is it about the g.rename line of code that is doing this? Is it the .?

Answer 1

bash treats dots/periods (.) as a command to execute what follows, so instead of printing the literal characters it's looking for files called 1, 2, and 3.

I don't have GRASS set up to work without starting a session, but my guess is if you do it your script correctly interprets the g.rename command and looks for the raster files you specify.

I assume GRASS isn't set up in your Rmarkdown file so it's just printing the g.rename... characters then treating the . as a file to execute so isn't printing what follows. To get it to print correctly, use something other than . in your file names, set up your Rmarkdown session to understand g.rename as a command, or escape the characters with \:

```{r gp-setup, engine="bash", eval=FALSE}
# Change names to remove dots

g.rename raster=gp_ortho\.1,gp_ortho_1,gp_ortho\.2,gp_ortho_2, \
gp_ortho\.3,gp_ortho_3

## Group bands together
i.group --verbose group=gp_combo input=gp_ortho_1@gp1,gp_ortho_2@gp1, \
gp_ortho_3@gp1
```