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perform_nni uses too much memory #13

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teng-gao opened this issue Feb 9, 2022 · 2 comments
Closed

perform_nni uses too much memory #13

teng-gao opened this issue Feb 9, 2022 · 2 comments

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@teng-gao
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teng-gao commented Feb 9, 2022

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@teng-gao
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teng-gao commented Feb 9, 2022 •
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Culprit:

neighbours = phangorn::nni(tree_init)
> neighbours
16858 phylogenetic trees
> neighbours
4.3 Gb

@evanbiederstedt
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There's some issue with phangorn here: https://github.com/KlausVigo/phangorn/blob/master/R/treeRearrangement.R#L102-L145

Not sure precisely where the issue is; I was assuming it was a C error, but I'm not sure. Might be worth reaching out to the phangorn author Klaus Schliep

@evanbiederstedt evanbiederstedt mentioned this issue Mar 11, 2022
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