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Working in QGIS 2.18.14 standalone on Windows, is there a way to create a Spatial Index for Geopackage (gpkg) layers?

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I don't believe that it is possible through the QGIS UI at the moment. Read the GDAL GeoPackage vector manual http://www.gdal.org/drv_geopackage.html and use ogrinfo.

ogrinfo -SQL "CreateSpatialIndex('table_name', 'geom_column_name')" geopackage.gpkg
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It's possible in QGIS3. You can click "Create Spatial index" from the Layer Properties Dialog:

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