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I'm a bit out of my depth here in terms of identifying faults within individual polygons, but it seems to be the case that (as suggested some specific shapes are tripping this up, by my testing of the first four, geo_codes: W06000016 and E07000138 (1 and 4) are fine, whereas S12000013 (2) is causing problems.

A bit more digging into each individual shape in this shapefile seems to indicate that the struggle here relates to the number of parts within each individual MULTIPOLYGON. So row 2 has whereas Shetland, row 244 has 549 parts row 387, has 521 and both lag in similar ways.

I'm a bit out of my depth here in terms of identifying faults within individual polygons, but it seems to be the case that (as suggested some specific shapes are tripping this up, by my testing of the first four, geo_codes: W06000016 and E07000138 (1 and 4) are fine, whereas S12000013 (2) is causing problems.

  test replications elapsed relative user.self sys.self
1 row1            1   0.134        1     0.121    0.006
1 row2            1 964.725        1   961.112    2.294
1 row3            1   0.358        1     0.333    0.015
1 row4            1   0.136        1     0.124    0.008
1 row5            1   0.578        1     0.557    0.012
1 row6            1   0.245        1     0.237    0.004
1 row7            1   8.603        1      8.55    0.041
1 row8            1   0.776        1     0.757    0.011
1 row9            1   0.471        1      0.45     0.01
1 row10            1   0.174        1     0.167    0.003

  test replications elapsed relative user.self sys.self
1 row1            1   0.134        1     0.121    0.006
1 row2            1 964.725        1   961.112    2.294
1 row3            1   0.358        1     0.333    0.015
1 row4            1   0.136        1     0.124    0.008
1 row5            1   0.578        1     0.557    0.012
1 row6            1   0.245        1     0.237    0.004
1 row7            1   8.603        1      8.55    0.041
1 row8            1   0.776        1     0.757    0.011
1 row9            1   0.471        1      0.45     0.01
1 row10            1   0.174        1     0.167    0.003
1 row11            1  83.648        1     83.26    0.246

Note: I've run replications on 1, 3, 4 and 11 and confirmed that execution time remains relatively stable (e.g. short or long depending) so it does seems to be something in the data here.

  test replications elapsed relative user.self sys.self
1 row1            1   0.134        1     0.121    0.006
1 row2            1 964.725        1   961.112    2.294
[still waiting for computations on row 2 and 3 to complete after 10 minutes, will post when they are done]
1 row4            1   0.136        1     0.124    0.008

I'm a bit out of my depth here in terms of identifying faults within individual polygons, but it seems to be the case that (as suggested some specific shapes are tripping this up, by my testing of the first four, geo_codes: W06000016 and E07000138 (1 and 4) are fine, whereas S12000013 and W06000013 (2 and 3) are causing problems. Happy to try testing if someone can steer me in the right direction.

  test replications elapsed relative user.self sys.self
1 row1            1   0.134        1     0.121    0.006
1 row2            1 964.725        1   961.112    2.294
1 row3            1   0.358        1     0.333    0.015
1 row4            1   0.136        1     0.124    0.008
1 row5            1   0.578        1     0.557    0.012
1 row6            1   0.245        1     0.237    0.004
1 row7            1   8.603        1      8.55    0.041
1 row8            1   0.776        1     0.757    0.011
1 row9            1   0.471        1      0.45     0.01
1 row10            1   0.174        1     0.167    0.003

I'm a bit out of my depth here in terms of identifying faults within individual polygons, but it seems to be the case that (as suggested some specific shapes are tripping this up, by my testing of the first four, geo_codes: W06000016 and E07000138 (1 and 4) are fine, whereas S12000013 (2) is causing problems. 

Happy to try testing if someone can steer me in the right direction.