27  Validate R From Spack

This notebook validates the R installation after the Spack layer is installed.

Do not install R packages here.

from rse_workbench.helpers import spython_exec, show_spython

show_spython(
    spython_exec(
        command=r'''
set -euo pipefail
source /work/env/activate.sh

which R
which Rscript
R --version
Rscript -e 'cat("R.home=", R.home(), "\n", sep=""); print(.libPaths()); print(capabilities()[c("cairo", "png", "jpeg", "tiff")])'
''',
        image=project_contract.singularity_image,
        options=["--no-home"],
        bind_project=project_contract.project_dir,
    ),
    tail=160,
)

Expected result:

• R starts
• Rscript starts
• cairo, png, jpeg, and tiff capabilities are TRUE

Stop here if R capabilities are wrong.