I generated a new GeoPackage with GDAL:
ogr2ogr -f GPKG my.gpkg my.geojson
I can open the GPKG in QGIS and all of the data is there, but when I open a SQLite client and run a spatial query, for instance
select count(*) from my_table m join another_table a where st_intersects(m.geom, a.geom)
I get an error:
no such function: ST_Intersects
Does GeoPackage not support SpatiaLite-style query functions?