knitr::kable is not rendered in the output of a chunk in R 3.5.0

[chenyenchung]

After upgrading to R 3.5.0 and RStudio 1.1.453, chunk output with knitr::kable() is no longer rendered but kept as raw markdown.

• This happens in the output below a chunk and preview of R Notebook:

• While the result of knit to html is fine.

The output used to be like this in R 3.4.3:

It looks like this now:

On my machine, the minimal example is to open a new Rmarkdown or R Notebook file in RStudio, and run this chunk:

```{r}
knitr::kable(iris)
```

I also tried {r results='asis'} and installed development version of rmakrdown with devtools::install_github("rstudio/rmarkdown"), but neither of them fixed the issue.

Thank you so much for all the help! If there's any thing else I could test, please let me know. This issue happened on a machine with the session info as below:

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16     digest_0.6.15    withr_2.1.2      rprojroot_1.3-2 
 [5] R6_2.2.2         jsonlite_1.5     backports_1.1.2  magrittr_1.5    
 [9] git2r_0.21.0     evaluate_0.10.1  highr_0.6        httr_1.3.1      
[13] stringi_1.2.2    curl_3.2         rmarkdown_1.9.12 devtools_1.13.5 
[17] tools_3.5.0      stringr_1.3.1    yaml_2.1.19      compiler_3.5.0  
[21] base64enc_0.1-3  memoise_1.1.0    htmltools_0.3.6  knitr_1.20  

[yihui]

Duplicate of #1331 (I think).

[chenyenchung]

Hello,
Sorry for the duplication. I guess I was carried away with the paged thingy and did not notice the similarity. One minor thing is that the display issue I encountered is also in Rmarkdown, slightly different from the description in #1331.
I am sorry for opening an redundant issue. Thank you so much for your patience and timely reply!

[yihui]

No worries. Actually I only suspect it is a duplicate. According to rstudio/rstudio#2748 (comment), the current version of RStudio must have fixed the issue. Could you try that? Thanks!

[chenyenchung]

Currently in RStudio 1.1.453 the kable remains displayed as raw markdown on my machine.

I tested on another machine with current version of RStudio and R 3.4.2, the rendering is fine (session info below):

# Before upgrade
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

loaded via a namespace (and not attached):
[1] compiler_3.4.2  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2 htmltools_0.3.6
[6] tools_3.4.2     yaml_2.1.18     Rcpp_0.12.16    stringi_1.1.7   rmarkdown_1.9  
[11] highr_0.6       knitr_1.20      stringr_1.3.0   digest_0.6.15   evaluate_0.10.1

Installing R 3.5.0 breaks the rendering, so I feel this is somewhat reproducible.

# After upgrade
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

loaded via a namespace (and not attached):
[1] compiler_3.5.0 tools_3.5.0    yaml_2.1.19    highr_0.6      knitr_1.20

[yihui]

@kevinushey @jmcphers I feel this is a issue similar to #1331, and the fix in the IDE might be similar, too. Could you take a look at it when you have a chance? Thanks!

[kevinushey]

This is indeed another manifestation of that same bug (changes in S3 dispatch behavior breaking RStudio). We attempt to assign our override here:

https://github.com/rstudio/rstudio/blob/1951f6427261e37ce165e2a14f68904a235345dd/src/cpp/session/modules/NotebookData.R#L126-L136

but we need to use @jmcphers's new solution in this space as well.

[33Vito]

I am having the same issue with R 3.5.0 and Rstudio 1.1.453 - kable produces either raw HTML or raw markdown.

I found a temporary workaround using the kable_styling function from the kableExtra package. i.e.

• kable(head(mtcars)) produces raw html
• kable_styling(kable(head(mtcars))) produces rendered table in both Rstudio and the associated R notebook.

Hope this would be fixed soon!

[jmcphers]

This is fixed the dailies as well as in RStudio 1.1.455 (not yet released). You can try the latter here:

http://s3.amazonaws.com/rstudio-dailybuilds/RStudio-1.1.455.dmg

[chenyenchung]

Thank you so much for the timely fix. I just downloaded the new version of RStudio, and tables are rendered perfectly now.

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