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Yes, it was a mistake to store the results in json files and not in the database.
There was no good reason for database storage when first writing this module, I never expected people to have soo many problems. But it turns out that certain shops occasionally do have so many problems.
It' on the roadmap to rewrite this storage, but it has been for a while and I didn't find the time or energy for it yet. So don't expect this to be fixed soon, sorry about that!
If you want a quick fix, I would recommend you try to fix as many problems as possible and then to retry it again.
I've just released version 1.4.0 of this module, which comes with an option to disable checking problems for invisible products. Reasons for this have been discussed in #31
I think that enabling this option could maybe fix your issue in case you have a lot of invisible products in your shop.
I'm not considering this issue fixed though, we still need to rewrite the storage to use the database instead of json files.
Hitting the memory limit when trying to open product_url key report
The file size of the json file is 96mb and the memory limit is 1gb.
Anybody who can clarify why it was decided to store these reports in the filesystem instead of the database?
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