[R-sig-ME] error when looping many MCMCglmm runs

Jarrod Hadfield j.hadfield at ed.ac.uk
Sun Nov 30 10:29:32 CET 2014

Hi Manabu,

Can you post your code so we can take a look?



Quoting Manabu Sakamoto <manabu.sakamoto at gmail.com> on Sun, 30 Nov  
2014 08:13:55 +0000:

> Dear list,
> I'm not quite sure if this is the right list for this, but I only get this
> issue when I am running MCMCglmm, so I post it here.
> I am wondering if anyone has come across this issue: I am experiencing some
> errors when running MCMCglmm in nested loops.
> I have three datasets and a set of model formulations for each. So I loop
> through the datasets (i) with nested loops (j) for each model formulation,
> and I store the results in a list for each dataset. I then save the
> workspace, and move onto the second dataset (i+1).
> The first time I noticed something strange was after the workspace is saved
> at the end of the ith iteration, and I read in the data for the i+1th
> dataset. Normally, I'd read in the names of the files using list.files()
> and do some regular expressions to select the right filename to read in,
> but in this case, the vector of filenames somehow became empty. If I do
> this manually, then there's nothing wrong. I thought maybe R was jumping
> ahead of itself so at the end of the ith loop I set it so that R sleeps for
> 1 second, which for some reason resolved this issue.
> Today, I noticed something different. I get an error with MCMCglmm stating
> that the mixed model was singular. I never get this when I run the same
> model on its own or even if inside a loop, if within a single dataset. It
> happened when I looped through different datasets. Is there some known
> issue about too many loops, and maybe something to do with memory use that
> corrupts MCMCglmm runs?
> Would setting R to sleep or removing R objects more frequently help resolve
> this issue?
> I can try these but every loop takes hours so debugging errors that only
> occur over multiple nested loops is painstakingly time consuming.
> Any suggestions or thoughts would be most appreciated.
> Many thanks,
> Manabu
> --
> Manabu Sakamoto, PhD
> manabu.sakamoto at gmail.com
> 	[[alternative HTML version deleted]]
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