The NLS topographic database has been saved into several geopackage files in Puhti at /appl/data/geo/mml/maastotietokanta/20XX/gpkg. The larger layers are in their own gpkg files and the smaller layers have been bundled into a single file. The larger layers are quite large and reading them takes some time. If the whole layers are not however needed it is possible to use SF package in R to only read the desired parts of the files. The examples on how to read only certain rows can be found in the read_gpkg.R script.
In Puhti use the r-env-singularity module for R.
Similar examples for reading the geopackage with Python using Geopandas can be found here.