Unable to run R script on Ubuntu

[careyshan]

Hey, I installed the Processing R Provider plugin and set up my paths. I then try and run the sample script Min_Max and it tries to install a lot of R packages - however it fails saying it cannot configure properly. It appears that the problem package is 'sf'. Has anyone else had a similar issue and if so, how do you fix it?

Thanks

[gavg712]

Hi @careyshan.

If I understand correctly, you are wanting to use the system R libraries and not the qgis user libraries. For that, you must disable the one that says "Use user library folder instead of system libraries". This will make Processing R provider use the libraries installed through the R console or Rstudio.

[careyshan]

Hey @gavg712,

I tried that but it doesn't seem to make any difference for me.

Cheers

[gavg712]

It is not easy for me to imagine what the issue might be. Could you share more details about the problem?

• QGIS version
• R version
• Ubuntu version
• Error message
• Anything else you think might be helpful?

Cheers

[careyshan]

Fair point. When I try to run it, it gives me this: And it just hangs there forever without an error

QGIS 3.20 R version 3.6.3 Ubuntu 20.04

[gavg712]

Two reasons can trigger the installation of packages in the Processing R provider.

• The option to use the user library instead of the system library is active.
• In the system library the necessary packages are not installed (sf, raster, sp, rgdal, ..., and script libraries included).

In Ubuntu most of the packages are installed from source code. That may explain the excessive time spent when running a rscript from processing (maybe more than half an hour, depending on the computer). Although this will be done only once and they will be installed in the new library configured inside the ~/.local/share/QGIS/QGIS3/profiles/default/processing/rlibs directory by default. So if everything goes well the first time, the following times will be faster running.

The last recommendation is to update R to the latest version (4.1.1) to take advantage of the many improvements it brings. Perhaps also some packages may depend on newer versions of R.

[careyshan]

Ok so I update to the latest R version and let it run. This is the error I get:

[gavg712]

Some packages require system libraries in order to be compiled from source code. For example sf requires libudunits2-dev, libgdal-dev, etc... etc. These must be installed separately from the Ubuntu package manager (apt, aptidude, etc) before installing the packages. Not all packages depend on these libraries and they are not always the same libraries. It is therefore recommended to install from an R or Rstudio session in order to see which dependency each package requires.

For a reference of what I mean you can watch this video (sorry, in spanish) on how to solve dependency issues in Linux: https://youtu.be/8Dx40TlF4fk?t=1212

[gavg712]

If it helps, here is a list of dependencies for some R packages: https://packagemanager.rstudio.com/client/#/repos/1/overview

Make sure you select the correct Linux version (Ubuntu 20.04 in your case).

[careyshan]

Thanks @gavg712 - sf is the problem package and when I follow that youtube clip, I get an error saying fix held broken packages. I'll try figure that out and hopefully that should sort it - thanks for all your help. Cheers

[careyshan]

Hey @gavg712 - your video helped great - I got it working in the end thanks to your help. That's super - cheers

[gavg712]

It is a pleasure. When you are ready you could close the issue.

CC: @nyalldawson

[careyshan]

Thanks for the great work