Problem in HPC+warning: chol(): given matrix is not symmetric about shapr HOT 5 CLOSED

Hard to say. If you put future::plan(sequential), parallelization is disabled so at least the "Error in unserialize(node$con)" should not occur. The chol() warning suggests that some of your columns are (close to) linearly dependent on other columns (you may check this by checking whether some of the eigenvalues of your training data matrix are negative or close to zero.

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Hi Martin,

1- I remove this library "future" and try to run it on HPC with 12 cores and 200Gb memory. It cannot give me an output. Do you suggest we should have HPCs with more than 200GB memory?
I think n_combinations has more effect on my code. I consider it 10000 according to your suggestion.
2- Furthermore, I try to solve problem according issue #226 . Please see my comments in #226 .
3- Also, I have another problem, I don't have NA data, but I see this note when I running code. If it is possible I send my data as private?

Note: Feature classes extracted from the model contains NA.
Assuming feature classes from the data are correct.

Thanks in advance

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200gb RAM is more than enough. There is probably some other issue with your data. You can send them to me on [email protected] and might be able to take a look at it some time next week. I promises, though.

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Dear @martinju,

Hope you are doing well;
Please check your email. I have sent you my email with the attached dataset.

Kind regards,
Az

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I can't reproduce this with the latest version of shapr from github. Everything works as intended. Results and script sent by personal email.
The note is nothing to worry about, it is not an error.

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