R bioconductor package `rtracklayer` possible memory leakage
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5.6 years ago
Chirag Parsania ★ 2.0k

Hi, I have been stretching my head to understand possible memory usage in one of my complex R script. What I found is quite surprising. Using a function rtracklayer::readGFF() occupies quite a bit memory (about 400 MB) in the R even without loading the package rtracklayer. See the step by step use case and output.

NOTE: Though question is more about programming and related to R, I find it worth posting to the biostars as rtracklayer is well used in the bioinformatics community.


Amount of memory used in fresh R session. (NOTE: No prior package or objects are loaded)

## fresh R session memory usage 
pryr::mem_used()
39.4 MB

Amount of memory used once rtracklayer::readGFF() function executed.

## read gff using rtracklayer::readGFF(), (NOTE: no file supplied to the  function)

rtracklayer::readGFF()
pryr::mem_used()
416 MB

As we can see, there is 10X larger memory occupied though nothing has been returned from the rtracklayer::readGFF() execution. Can anyone explain why this is ? and how to prevent R occupying additional ~400 MB of memory while using rtracklayer::readGFF() ?

gff R bioconductor memory leakage • 1.3k views
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This post is more suitable to GitHub issues, see:

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i did but it got deleted :(, i think

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What do you mean "got deleted"? The author deleted it?

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Sorry. !! Now it appears there. GitHub behaving weirdly. See the link in above comment.

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They're having data consistency issues, so things will be weird for the next few hours at least.

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