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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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Issue 445 map taxonomy #533

Open Insaynoah opened 2 months ago

Insaynoah commented 2 months ago

I optimized the mapTaxonomy function as indicated in #445 by mapping over unique taxa and then mapping back to the original data. Even though the time difference by optimizing doesn't seem staggering, it still improved a little bit.

Insaynoah commented 2 months ago

I implemented the requested changes and ran the biocCheck which didn't seem to have any issue with the new lines. The taxa have to be mapped back to the originial data. Hence the reason it didn't considerably decrease the computation time.

Insaynoah commented 2 months ago

However, I noticed that the issue was closed just after I made the PR. Was this already fixed ?

antagomir commented 2 months ago

Perhaps my mistake - I reopened it.

TuomasBorman commented 2 months ago

I implemented the requested changes and ran the biocCheck which didn't seem to have any issue with the new lines. The taxa have to be mapped back to the originial data. Hence the reason it didn't considerably decrease the computation time.

OK, cool! Hmmm, I ran the BiocCheck and it seems that these new lines are incorrectly indented (should be multiplication of 4 spaces). The indentation in old lines were correct, so I think you should revert the changes related to lines that are not really fixing the problem mentioned in the issue. Sorry about extra work

https://contributions.bioconductor.org/r-code.html?q=indentation#indentation

E: BiocCheck generates file mia.BiocCheck/00BiocCheck.log that has more detailed info than what is printed on console

TuomasBorman commented 1 month ago

The indentation is still off. If there is juts couple lines that you are planning to change, you can create new PR and link this with that

antagomir commented 1 week ago

@Insaynoah what's the status of this PR? Can we get it fixed.