[R] Rmixmod Memory Leak

Jeff Newmiller jdnewmil at dcn.davis.CA.us
Fri Aug 1 08:55:39 CEST 2014




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On July 31, 2014 6:00:21 PM PDT, Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:
>I would like to provide a helpful bug report to the maintainer of
>Rmixmod, but I'm not skilled in memory profiling.
>The following example illustrates the problem :
>genes <- matrix(rnorm(5000*50, 9, 2), nrow = 5000, ncol = 50)
>selected <- sample(5000, 25)
>columns <- split(1:50, rep(1:10, each = 5))
>lapply(1:100, function(index) # 100 resamples with replacement
>  lapply(1:5, function(fold) # 5-fold cross validation
>  {
>apply(genes[selected, columns[[fold]]], 1, function(aGene)
>mixmodCluster(aGene, nbCluster = 1:3))
>    return(NULL)
>  })
>Even though no data was assigned to any variables, even if I do gc()
>after the loop, 5 GB of RAM is used. This makes the software unusable
>in a loop, because the server freezes when it runs out of RAM.
>May someone who is an expert help me ?
>Dario Strbenac
>PhD Student
>University of Sydney
>Camperdown NSW 2050
>R-help at r-project.org mailing list
>PLEASE do read the posting guide
>and provide commented, minimal, self-contained, reproducible code.

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