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R: working around “error in La.svd Lapack routine ‘dgesdd'”

That’s a quite enigmatic and unhelpful error message that apparently can be tracked down to some stuff written in *cough* Fortran (source, look for message 26).

I don’t really have a sure solution, but I did manage to evade that error with, so far, a 100% success rate. I got the error while doing some machine learning (feature selection + classification task, not sure at which step it broke), and I noticed that even though it was in a pretty large loop, it seemed to be 100% reproducible for me (loop always crashing on the same iteration). I realized that I was using set.seed() in order to get more stable results (I’m generating lots of artificial data, and having them vary between various experimental conditions adds unwanted noise), and so I thought, since this seems to usually be a random error, maybe setting another seed would work. And indeed it did: changing the seed from 100 to 99 in my case “solved” the issue.

Long story short: If it occurs randomly and you don’t use a seed, if this is a possibility do try setting a seed (try a few if it doesn’t work the first time). If it occurs deterministically and you do use a seed, try another seed value (same, try a few if needed).
If it occurs deterministically and you don’t use a seed, I’m not sure setting a seed would help. If it occurs randomly and you do use a seed, I really don’t think changing the seed would help. But I guess it costs nothing to try…

Posted in programming, R (R-project).


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