I'd been converting some shapefiles to GeoPackage with QGIS 2.18.5 on Windows. Now I check my project on Linux (Ubuntu 14.04 with QGIS 2.18.5), and the gpkg files are treated as attribute-only layers.
To test, I made a new project and added some sample vector data from http://www.geopackage.org/#sampledata (the Esri Sample Data, GeoPackage 1.0 and 1.1), with the same result. No geometry is recognized (and the
gpkg_* metadata tables are instead also displayed in the wizard):
Any clues what is wrong? I couldn't find any similar reports, or extra requirements for QGIS on Linux.