Looks like a lot of this the rtree module in sqlite3, which seems to
think telling you to go back and rebuild something with different
non-default options is a reasonable approach :-(
sqlite3 with rtree support is a requirement for GeoPackage and Spatialite.
I had not previously grasped that rtree was required, and configure
seems not to test for it.
No rtree isn't tested by GDAL's configure. Looking at sqlite3 own
configure, I see rtree is supposed to be built-in by default
./configure --help | grep rtree
--enable-rtree include rtree support [default=yes]
--
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My software is free, but my time generally not.
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