truncating string with embedded nuls in Notebook

RStudio IDE
1

I am taking my first tentative steps with R-Notebooks and whatever I do, I get dozens of warnings:

In readChar(file, size, TRUE) : truncating string with embedded nuls

Initially I thought it was coming from source-ing a script, but now it seems to happen with almost any code block. I am not using readChar explicitly anywhere.

I also wondered if there was an incompatibility in the encoding of script files, but haven't been able to find a suitable setting to stop it (currently ISO8859-1), but frankly I am just guessing blindly.

Any idea what causes this and how I can stop them?

I am using R version 4.0.0 (2020-04-24) -- "Arbor Day"

2 Likes
2

It is possible that this only happens when Chunk Output Inline is set.
Too early to say for sure, but it has never shown these warnings when sending to the console.

I am curious if anyone else has experience of this.

3

Just wanna chime in and say that I've experienced the same issue after updating to R version 4.0.0. Using any other version of R solves the issue.

I get the error message you mention every time I try and use the kable() function to create an HTML table from a code chunk. The warnings disappear if i change the chunk option so that only the output is shown (echo = FALSE). In addition, the errors causes my R session to freeze, possibly due to high CPU usage.

Note that I cannot reproduce the problem outside my notebook but I'll try and see if I can make a reprex tomorrow.

I am guessing that this issue might be due to an incompatibility between the new R version and the knitr package?

4

A reproducible example would be helpful.

5

Indeed it would, but for me it is every notebook with inline output.

This example did it for me

Notebooks

but I doubt it would for many others.

It is probably more to do with RStudio configuration.
I am guessing that regional settings in Windows plays a role, but really I have no idea.

1 Like
6

Just checked the results for the template notebook and I can reproduce the problem there. If I create the notebook, hit the preview button and then run the code chunk I get 26 instances of the error message:

In readChar(file, size, TRUE) : truncating string with embedded nuls

So I can only reproduce the problem after previewing the notebook by running the code chunk. Note that the errors appear when I knit to PDF or any other format.

System Information:

RStudio Edition: Desktop
RStudio Version: 1.2.5042
OS Version: Windows 10 x64 (build 18363)
R Version: 4.0.0
1 Like
7

Is there a way of at least suppressing the message that there are warnings in the viewer output?

Then I could just ignore it.

When I have chunk_output_type set to inline, it shows in the viewer

There were 50 or more warnings (use warnings() to see the first 50)

The chunk options include echo=FALSE, message=FALSE, warning=FALSE, error=FALSE, but it still messes up the output. If it isn't one of those, what is it?

8

I started having the same issue just after updating to R 4.0.0.
No idea why, and it's a bit annoying.

9

I can recreate this too. For me it seems to require at least two chunks, one of which produces some output like a figure. Run all chunks then preview, and then running the first chunk produces this repeated set of warnings inline or in console that is variable in length each time.

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


```{r}
a <- 1
```
```{r}
plot(cars)
```

platform x86_64-apple-darwin17.0
arch x86_64
os darwin17.0
system x86_64, darwin17.0
status
major 4
minor 0.0
year 2020
month 04
day 24
svn rev 78286
language R
version.string R version 4.0.0 (2020-04-24)
nickname Arbor Day

Rstudio Version 1.2.5042

OS X v 10.15.4

10

Do you also experience Rstudio crashing/freexing in larger notebooks or Rmarkdown documents? I have problems with this but can't recreate the problem in a simple example.

11

Thanks! I've now reproduced this and have filed a bug report here:

It looks like the issue reproduces whenever one attempts to save an R Notebook which contains inline image outputs.

5 Likes
12

Should this be fixed with the latest version of RStudio, 1.3.959? I can still reproduce this error.

13

It looks like it has been fixed in v1.3.1019-1 Preview. See the Release Note.

1 Like
14

Seems similar to an issue when using kableExtra::kable_styling()

that is not resolved with RStudio version: 1.3.1019, which contains this fix.

15

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