[FIXED] R kernel constantly crashes in Jupyter Notebooks due to graphics

Issue

I'm running R 4.3.2 on a Ubuntu 22.04 remote machine. I use vscode to SHH into it for all coding purposes except for R, as every time I run a Jupyter Notebook and execute code, the R kernel crashes immediately. The log says:

 unable to start device PNG
Calls: <Anonymous> ... evaluate -> dev.new -> do.call -> <Anonymous> -> ok_device
In addition: Warning message:
In ok_device(filename, ...) : unable to open connection to X11 display ''
Execution halted

which naturally led me to this post, so as recommended, I've tried switching

options(bitmapType='cairo')

in my ~/.Rprofile. This doesn't work either, but the logs now says:

13:52:48.798 [warn] StdErr from Kernel Process Error in dev.control(displaylist = "enable") : 
  dev.control() called without an open graphics device
Calls: <Anonymous> ... tryCatch -> tryCatchList -> evaluate -> dev.control
In addition: Warning message:
In ok_device(filename, ...) :
13:52:48.798 [warn] StdErr from Kernel Process type = "cairo" is unavailable. trying "Xlib"
Execution halted

Running R in the terminal seems fine, until I try to talk to the graphics by png():

> png()
Error in .External2(C_X11, paste0("png::", filename), g$width, g$height,  : 
  unable to start device PNG
In addition: Warning message:
In png() : could not open PNG file 'Rplot001.png'

I've also made sure to install

sudo apt install libpng-dev
sudo apt install libcairo2-dev
sudo apt install libjpeg-dev

I think my $LD_LIBRARY_PATHis also set correctly:

/usr/lib/x86_64-linux-gnu/libpng.so:/usr/lib/x86_64-linux-gnu/libcairo.so:/usr/lib/x86_64-linux-gnu/libpng.so:/usr/lib/x86_64-linux-gnu/libcairo.so:

What am I missing? Thanks

EDIT: Result of capabilities():

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
      FALSE       FALSE       FALSE        TRUE       FALSE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE       FALSE        TRUE        TRUE        TRUE 
        NLS       Rprof     profmem       cairo         ICU long.double 
       TRUE        TRUE       FALSE       FALSE        TRUE        TRUE 
    libcurl 
       TRUE 

Solution

For the afterworld, this is how I solved it:

I checked capabilities() as @M.Viking suggested in the comments and saw that PNG, but also cairo and X11 were FALSE, which is odd, as I've manually installed them.

I realized that my R dist probably was compiled without these capabilities, for some odd reason. I thus re-compiled and reinstalled R like this:

#  getting R 4.3.2 from CRAN
wget https://cran.r-project.org/src/base/R-4/R-4.3.2.tar.gz
tar -xzvf R-4.3.2.tar.gz
cd R-4.3.2

# THIS is the crucial config part
./configure --with-x=yes --with-libpng=yes --enable-R-shlib

make
sudo make install

However, the error first persisted as X11 was still set to FALSE so I followed the common advice and switched to cairo by appending:

options(bitmapType='cairo')

to ~/.Rprofile (or wherever your .Rprofile lives)

This did the trick :)

Answered By - Comfort Eagle