CODEWITHSUNDEEP
rrstudioknitrr-markdown
Shantanu
Shantanu

Reputation: 331

knitr::kable does not pretty print after running an R chunk

I noticed this weird behavior of kable - the pretty printing goes away after running a chunk.

> knitr::kable(head(iris, 3))


| Sepal.Length| Sepal.Width| Petal.Length| Petal.Width|Species |
|------------:|-----------:|------------:|-----------:|:-------|
|          5.1|         3.5|          1.4|         0.2|setosa  |
|          4.9|         3.0|          1.4|         0.2|setosa  |
|          4.7|         3.2|          1.3|         0.2|setosa  |

Now do File > New File > R Notebook. This creates a demo notebook, with a single chunk containing plot(cars). Execute that chunk within the notebook

> plot(cars)

Then print the table again. This time the output looks different. Why?

> knitr::kable(head(iris, 3))
[1] "| Sepal.Length| Sepal.Width| Petal.Length| Petal.Width|Species |"
[2] "|------------:|-----------:|------------:|-----------:|:-------|"
[3] "|          5.1|         3.5|          1.4|         0.2|setosa  |"
[4] "|          4.9|         3.0|          1.4|         0.2|setosa  |"
[5] "|          4.7|         3.2|          1.3|         0.2|setosa  |"
attr(,"format")
[1] "markdown"
attr(,"class")
[1] "knit_asis"
attr(,"knit_cacheable")
[1] NA



> packageVersion("knitr")
[1] ‘1.17’


> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

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] tools_3.3.3 highr_0.6   knitr_1.17 


> RStudio.Version()
$citation

To cite RStudio in publications use:

  RStudio Team (2016). RStudio: Integrated Development for R. RStudio,
  Inc., Boston, MA URL http://www.rstudio.com/.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {RStudio: Integrated Development Environment for R},
    author = {{RStudio Team}},
    organization = {RStudio, Inc.},
    address = {Boston, MA},
    year = {2016},
    url = {http://www.rstudio.com/},
  }


$mode
[1] "desktop"

$version
[1] ‘1.0.153’

Upvotes: 1

Views: 1405

Answers (1)

user2554330
user2554330

Reputation: 44808

When you run that chunk, the tools:rstudio environment on the search list is changed to add a function called print.knitr_kable which is different from the internal one in the knitr package.

Here's what I see before:

> ls("tools:rstudio")
[1] "debugSource"              "knit_with_parameters"    
[3] "registerShinyDebugHook"   "RStudio.Version"         
[5] "rstudioDiagnosticsReport" "RStudioGD"               
[7] "source.with.encoding"

and here's what I see after:

> ls("tools:rstudio")
[1] "debugSource"                 "dplyr_tibble_print_original"
[3] "knit_with_parameters"        "print.knitr_kable"          
[5] "registerShinyDebugHook"      "RStudio.Version"            
[7] "rstudioDiagnosticsReport"    "RStudioGD"                  
[9] "source.with.encoding"

For whatever reason, the tools:rstudio function is executed instead of the original one. I can get the original behaviour back by running detach("tools:rstudio"), but that messes up Rstudio in several ways, so I don't recommend it. A less extreme way is to say

e <- as.environment("tools:rstudio")
e$print.knitr_kable <- knitr:::print.knitr_kable

but that doesn't last: RStudio apparently fixes it whenever you run a chunk in the notebook. You could also do an explicit call every time you want to print, e.g.

knitr:::print.knitr_kable(knitr::kable(head(iris, 3)))

Probably the best solution is for knitr to change so it does what RStudio wants when run in an RStudio notebook and the pretty printing otherwise, or for RStudio to change to run the knitr function when it's not in a notebook, but I imagine this isn't a huge priority: if you're running a notebook, why would you care what you see in the console?

Upvotes: 1

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