Is there an easy way to run bash scripts on R Markdown, using Windows 10?

Question

I've been learning R Markdown for the past months. It was fairly easy to get Anaconda Python to run within a R Markdown script, but I haven't yet found a way to get to run chunks of bash code within the same document.

Using

```{bash}
echo hello world
```

I get the error message

/bin/bash: C:\Users\MyName\AppData\Local\Temp\Rtmp0MpNfS\chunk-code-4cbc213a3545.txt: No such file or directory

Might any of you guys know what might be the root of this problem?

Answer 1

I know maybe is to late but I had the same problem and I find the solution.

First, in Windows 8.1 or if you don´t have the Windows Subsystem for Linux (WSL) you can install Cygwin: https://cygwin.com/ > Install Cygwin

• This is the recommendation pointed out in R Markdown: The Definitive Guide (https://bookdown.org/yihui/rmarkdown/) > 2.7 Other language engines > 2.7.2 Shell scripts

Second, add Cygwin to the PATH. Usually Cygwin is installed in C:\cygwin64 and the path to include will be in this case C:\cygwin64\bin

Third, check that everything is correct using base::Sys.which("bash") in R

• If everything is correct it will appear something like this "C:\\cygwin64\\bin\\bash.exe"

Fourth, you can run in a Rmarkdown document, the chunk that you pointed out to double check:

```{bash}
echo hello world
```