[adegenet-forum] x <- new("genlight"....) hangs

[David Wragg]

I spent some time trapping this and the problem appeared to be the result of not setting the n.iter and n.start attributes of the find.clusters function.

Cheers

Dave



-----Original Message-----
From: Jombart, Thibaut [mailto:t.jombart at imperial.ac.uk] 
Sent: 23 January 2012 22:15
To: David Wragg; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: x <- new("genlight"....) hangs

Cheers, 

keep me posted if you find where this comes from.

Best

Thibaut.
________________________________________
From: David Wragg [plxdw1 at nottingham.ac.uk]
Sent: 23 January 2012 17:46
To: Jombart, Thibaut; David Wragg; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: x <- new("genlight"....) hangs

Both R and the packages are identical, I'm putting it down to system set-up as I can't think what else it could be.

Cheers

Dave



-----Original Message-----
From: Jombart, Thibaut [mailto:t.jombart at imperial.ac.uk]
Sent: 20 January 2012 12:04
To: David Wragg; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: x <- new("genlight"....) hangs

Hello,

this is weird indeed. I have tested this code on two linux computers (Ubuntu 10.10 64bits alternative release, Ubuntu 11.10 64bits server release), with R 2.14.1 and current stable version of adegenet.

Are you sure both versions of R and adegenet are strictly identical?

Cheers

Thibaut
________________________________________
From: David Wragg [plxdw1 at nottingham.ac.uk]
Sent: 19 January 2012 20:12
To: Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: x <- new("genlight"....) hangs

Thanks

The "problem" appears to be intermittent on Linux (Ubuntu, 64 bit, 8 GB ram, 4 cores) and not at all present on Win 7 (64 bit, 6 GB ram, 2 cores). It's not a memory issue as I've had system performance metrics running and memory usage rarely exceeded 30%. I expect CPU usage is the root of the problem, or Linux equivalent to a swapfile (if there is such a thing?). Incidently, the following line in the Windows script:

x <- new("genlight", dat, multicore=F)

Was changed to the following in Linux when it "hanged":

x <- as.genlight(dat)

I tried changing the multicore attribute to TRUE and it still "hanged". I expect this is just a coincidence. Ironically the script runs quicker on the older Win 7 machine. I'm quite happy to just run the script on Windows, but it would be nice to get to the root of the problem causing the unpredictable execution of the script on the Linux machine. I'm pretty sure it's going to be down to the way Linux has been configured and nothing to do with the R packages. I'll have to check with a Linux guru for their thoughts!

Regards

Dave


________________________________________
From: Jombart, Thibaut [t.jombart at imperial.ac.uk]
Sent: 18 January 2012 16:56
To: David Wragg; adegenet-forum at lists.r-forge.r-project.org
Subject: RE: x <- new("genlight"....) hangs

Hello,

I have re-run the example you mention 10 times without problem. The behaviour of the function is not supposed to be stochastic. One thing might be that in some occasions you run out of RAM and thus the procedure takes ages to run.

Otherwise I would need a reproducible example to figure out if there is something wrong.

All the best

Thibaut
________________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of David Wragg [plxdw1 at nottingham.ac.uk]
Sent: 18 January 2012 16:18
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] x <- new("genlight"....) hangs

I'm having issues with the genlight class. Essentially the problem happens when I try and create new object containing data - this can be fabricated data as in one forum example (http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2011-September/000404.html) or it can be my own data. Sometimes the command works, at other times it simply hangs and nothing happens. I've tried this with multicore set to TRUE and again set to FALSE. The data is in the correct format as it has worked previously.

Can you offer any advice?

Cheers

Dave



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