dealing with RF/RFutils (#95)

[achubaty]

• provide these pkgs via r-universe repo (should be changed to use ropensci's r-universe)

• mv these pkgs to Suggests

• use these pkg conditionally in functions and tests

• fixed other R CMD check problems along the way

[achubaty]

Since RF depends on RFutils, it's not strictly necessary to depends on RFutils.

[achubaty]

@bitbacchus I just pushed an update to this PR that explicitly adds the additional repository to the 2 failing GitHub Actions configs, which should hopefully resolve those failures. (Though note I switched to v2 of the r-setup from v1, without updating the downstream Actions -- i.e., there may be more tweaking of the Actions config needed)

[achubaty]

updated all R actions to v2 -- not sure why it wasn't finding the packages in the r-universe repo, because they are there and working on other test systems :/

[mhesselbarth]

Seems like it's still not finding the packages unfortunately

[achubaty]

:cry: looks like a bug in pak::pkg_install() which is being used in that action.

Trying locally, I get:

> getOption('repos')
                                                           CRAN 
"https://packagemanager.rstudio.com/all/__linux__/focal/latest" 
                                                             PE 
                    "https://predictiveecology.r-universe.dev/" 
> pak::pkg_install('RandomFields')
✓ Updated metadata database: 2.08 MB in 7 files.                          
ℹ source packages are missing from predictiveecology.r-universe.dev        
✓ Updating metadata database ... done                                     
Error: Cannot install packages:                                            
* RandomFields: Can't find package called RandomFields.
Type .Last.error.trace to see where the error occurred

[achubaty]

@mhesselbarth, I finally figured it out. pak choked on the trailing slash in the repo url (https://github.com/r-lib/pak/issues/400).

Removing the slash is worknig for me locally now, and I've pushed 7702bf5963b7ca4fdf3191eee9323f4e7ffccf96 to deal with this.

[bitbacchus]

Hm, the build fails for Linux and macOS. Apparently, the XML package can't be installed on Linux, but I don't see an obvious reason at the moment. At least, libxml2-dev seems to install successfully.

[achubaty]

perhaps a weird blip? my other GitHub Actions workflows that install XML on Linux are working.

[bitbacchus]

The issue seems to be with pak and R 4.2: https://github.com/r-lib/actions/issues/559

Can you try if this helps?

extra-packages: any::rcmdcheck, any::XML

Thanks a lot for your effort!

[achubaty]

@bitbacchus thanks for tracking down the issue in pak. I've pushed the workaround for XML. :crossed_fingers:

[bitbacchus]

macOS still fails:

Why though?

[mhesselbarth]

I tried to install RandomFields locally on my macOS, and needed to manually install gfortran because apparently thats shipped differently with the newest gcc compiler updates which caused issue. Maybe somehow related to that?

(https://github.com/fxcoudert/gfortran-for-macOS)

[achubaty]

The brew setup should automatically be getting the compiler tools needed, so I don't think that's the issue -- on my macOS machine, pak is trying to get the pkg from CRAN (and failing) but isn't trying the r-universe repo for some reason. Also note that the r-universe repo has pre-built binaries.

I'm going to try manual install.

[achubaty]

@mhesselbarth @bitbacchus this is now passing for me :tada:

[bitbacchus]

Awesome, thanks a ton, @achubaty :-)

[achubaty]

Thanks - any idea how soon you plan to get updated package version to CRAN?