Why does R notebook display truncated lines in "html_notebook" output?

Question

I have a R notebook named "test.Rmd" with the following content:

---
title: "R Notebook"
output: html_notebook
---
```{sh}
faToTwoBit dmel-all-chromosome-r6.04.fasta dmel-all-chromosome-r6.04.2bit
```

Then rstudio will create "test.nb.html" automatically. However, the code chunks are wrongly displayed in the html:

It only displayed bit, instead of the entire line (faToTwoBit dmel-all-chromosome-r6.04.fasta dmel-all-chromosome-r6.04.2bit). Is there something wrong with my .Rmd?

Using output: html_document in your YAML header should work. — J_F
– J_F, Commented Oct 29, 2017 at 18:33

Kevin Arseneau · Accepted Answer · 2017-10-30 02:42:01Z

2

I'm not familiar with the shell command you are running, however, it seems that the language engine is getting confused with the way to display it.

Given that the form is meant to be faToTwoBit in.fa [in2.fa in3.fa ...] out.2bit, I recommend explicitly stating the engine.

---
title: "R Notebook"
output: html_notebook
---

```{test1, engine="sh"}
faToTwoBit dmel-all-chromosome-r6.04.fasta dmel-all-chromosome-r6.04.2bit
```

You could also lodge an issue on github, where they may be able to provide a more permanent solution.

answered Oct 30, 2017 at 2:42

Kevin Arseneau

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4 Comments

mt1022 Over a year ago

Hi, Kevin. Thanks for the answer. In fact I just want to display the shell commands as a code chunk in final report instead of running the commands. I also filed an issue on github following your suggestion.

Kevin Arseneau Over a year ago

@mt1022, you can add eval=FALSE to your code chunk to display the code but not evaluate it

mt1022 Over a year ago

sure. I have set the options as {test1, engine="sh", eval=FALSE}.

Kevin Arseneau Over a year ago

@mt1022, does that provide you the result you are after?

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