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, Oct 29 '17 at 18:33

score 2 · Accepted Answer · answered Oct 30 '17 at 02:42

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 '17 at 02:42

Kevin Arseneau

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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. – mt1022 Oct 31 '17 at 11:42
@mt1022, you can add `eval=FALSE` to your code chunk to display the code but not evaluate it – Kevin Arseneau Oct 31 '17 at 12:03
sure. I have set the options as `{test1, engine="sh", eval=FALSE}`. – mt1022 Oct 31 '17 at 12:16
@mt1022, does that provide you the result you are after? – Kevin Arseneau Oct 31 '17 at 12:18

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

1 Answers1