This file is indexed.

/usr/lib/mysql-testsuite/r/subselect_gis.result is in mysql-testsuite-5.6 5.6.16-1~exp1.

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The actual contents of the file can be viewed below.

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drop table if exists t1;
create table t1(City VARCHAR(30),Location geometry);
insert into t1 values("Paris",GeomFromText('POINT(2.33 48.87)'));
select City from t1 where (select
intersects(GeomFromText(AsText(Location)),GeomFromText('Polygon((2 50, 2.5
50, 2.5 47, 2 47, 2 50))'))=0);
City
drop table t1;