R help - Aug 2014 - Rmixmod Memory Leak

Hello,

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 :

library(Rmixmod)
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
Australia

Read

?maintainer

and

the Posting Guide mentioned below.
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Sent from my phone. Please excuse my brevity.

On July 31, 2014 6:00:21 PM PDT, Dario Strbenac <dstr7320 at
uni.sydney.edu.au> wrote:
>Hello,
>
>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 :
>
>library(Rmixmod)
>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
>Australia
>
>______________________________________________
>R-help at r-project.org mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

Hi Dario,
The maintainer of that package is:

Benjamin Auder

and I have copied him on this message. Usually it is best to include 
the maintainer in this sort of situation.

Jim

On Fri, 1 Aug 2014 01:00:21 AM Dario Strbenac wrote:
> Hello,
> 
> 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 :
> 
> library(Rmixmod)
> 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
> Australia
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible 
code.