tree::tree object cannot be accessed in editor, only in console (or in knitted output)

Setting up an example

I posted this on Github, where I was sent here because this seems to be an RStudio IDE issue. Let's create some small data for a tree::tree approach:

library(tree); set.seed(1)
summary(x <- data.frame(
   Y=factor(rep(letters[1:2], each=250)),
   X1=c(runif(250, 1, 5), runif(250, 3, 7)),
   X2=c(runif(250, 5, 9), runif(250, 1, 5))))

Running a tree on this is unproblematic:

summary(cart.1 <- tree(Y ~ X1+X2, data=x))

Now the problem


  • I knit the document into an HTML file (like attached), the output is shown;
  • I use each of these lines in the console, I will see the output there; BUT
  • I run the following chunk from the editor with CTRL-SHIFT-ENTER or the play button, no output is provided;

One time, I saw the following error message in the editor pane:

Registered S3 method overwritten by 'cli':
method     from
print.tree tree

But I wasn't able to reliably reproduce that one.

However, each of those lines will produce output when I copy and paste it into the console -- why??

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 21.10 
 LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 LC_ADDRESS=C               LC_TELEPHONE=C            

Package version:
base64enc_0.1.3 bslib_0.3.1     digest_0.6.29   evaluate_0.14  
fastmap_1.1.0   fs_1.5.2        glue_1.6.0      graphics_4.1.2 
grDevices_4.1.2 highr_0.9       htmltools_0.5.2 jquerylib_0.1.4
jsonlite_1.7.2  knitr_1.37      magrittr_2.0.1  methods_4.1.2  
R6_2.5.1        rappdirs_0.3.3  rlang_0.4.12    rmarkdown_2.11 
sass_0.4.0      stats_4.1.2     stringi_1.7.6   stringr_1.4.0  
tinytex_0.36    tools_4.1.2     tree_1.0-41     utils_4.1.2    
xfun_0.29       yaml_2.2.1

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