html_notebook error in Rmarkdown

[jonask137]

Hi

I am experiencing that my notebook will suddenly convert code and output to the following, see the picture.

In general nothing has been done to the code chunk, but after a while a the chunk will convert to this.

The solution is to merely run the code again, and then the problem is solved.

Although as this is my notebook, the code is not always as structured as it would be in a report or etc. hence it is not always possible to run the notebook from one end to the other.

Has anyone had similar issues? Any tips to avoid this from happening?

My notebook as the following setup:

---

title: "Classification"
author: "Jonas R. Korsholm"
output:
html_notebook:
toc: true
toc_depth: 4
toc_float: true
number_sections: true
theme: readable
highlight: haddock
code_folding: show
fig_caption: yes

[cderv]

Can you share the version you are using of RStudio and rmarkdown ?

Also, do you have a Rmd document to share where you have this error ?

Either by joining a file or sharing the code here without screenshot and correctly formatted ?

FAQ: How to format your code

Formatting Code: the Basics All code or console output you include in your posts should be formatted properly. Luckily, this is very easy to do! Just use the code formatting button at the top of the post editing box: [image] Select some code Click the </> button! The code formatting button automatically adds special Markdown formatting symbols to whatever you selected. If you check the preview pane to the right of your post, you'll see that the forum software now outputs nicely formatted code . [04] The code formatting button is pretty smart! It can tell the difference between snippets of code that are part of a sentence and blocks of code that stand alone. …

[jonask137]

Thank you for the quick reply!

I have the following RStudio version: Version 1.3.1073, "Giant Goldenrod" (718e6d75, 2020-07-29) for macOS

Where my Rmarkdown package is version 2.5

Here is an example of some code, where the output format yields an error. I have tried to attached the markdown file, although it does not appear to be possible, please let me know if I can do it in another way

library(ISLR)

Smarket <- Smarket
str(Smarket)

this is followed by the following in the preview and .nb.html file

<!-- rnb-source-end -->

<!-- rnb-output-begin 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 -->

[jonask137]

another example:

code chunk:

standardized.X <- scale(Caravan[,-86]) #Creates a standardized table, without the response varaiable

with the following output in the preview and .nb.html file

<!-- rnb-source-end -->

<!-- rnb-chunk-end -->


<!-- rnb-text-begin -->


We see, that the dataframe has 5822 observations and 86 predictors.

The response variable is 'Purchase'


<!-- rnb-text-end -->


<!-- rnb-chunk-begin -->


<!-- rnb-source-begin eyJkYXRhIjoiYGBgclxuYGBgclxudmFyKENhcmF2YW5bLDFdKVxuYGBgXG5gYGAifQ== -->

```r
```r
var(Caravan[,1])

[jonask137]

Hi cderv

I think I have solved the issued.

Apparantly a space had sneaked its way in-between ``` and {r}, hence that yields the error.

Thus I think the problem is solved

[cderv]

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