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Thanks for reporting this. That does seem like an issue. I can try to commit a fix, but as you noticed, the DBI code in RDF::Trine is a bit of a mess, and not well maintained.
Development on RDF::Trine has mostly ended at this point, with most new work going on in the Attean project (which despite what seems like an accidental copy-commit, does not have a DBI storage engine). If you have any interest/ability to submit changes to this (or Attean) to improve the mysql code, I'd be more than happy to merge them.
When a SQLite store is initialized, indexes are never created. If you see at next code fragment:
perlrdf/RDF-Trine/lib/RDF/Trine/Store/DBI/SQLite.pm
Lines 125 to 135 in 2db05bf
$self->SUPER::init(); is called before, creating the needed tables. So, check in line 134 should be the opposite, something like:
BTW, in the case of mysql store, init method has some messed code.
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