Re: [R] Problem with mclapply -- losing output/data

2011-06-23 Thread Uwe Ligges
Janet, 1. you posted to the R-help mailing list rather than to "Elizabeth", 2. if posting to a mailing list, please quote the original thread otherwise we do not know what you are talking about if we removed the prior part of the thread. Uwe Ligges On 23.06.2011 04:22, Janet Young wrote:

Re: [R] Problem with mclapply -- losing output/data

2011-06-22 Thread Janet Young
Hi Elizabeth, I just found your thread after experiencing a similar problem (I was also using some IRanges/GenomicRanges functions). You've probably figured it out by this time - I'm actually curious to know what you found? I think I've tracked it down in my case, where a small minority of the

Re: [R] Problem with mclapply -- losing output/data

2011-03-23 Thread Rainer M Krug
On Wed, Mar 23, 2011 at 10:42 AM, Patrick Connolly wrote: > G'day Elizabeth, > > For what it's worth, this is what I'd do were I in a position > like yours: > > I would put a condition near the end of myfunc. that responded > when there was an indication that NULLs were to be returned into > your

Re: [R] Problem with mclapply -- losing output/data

2011-03-23 Thread Patrick Connolly
G'day Elizabeth, For what it's worth, this is what I'd do were I in a position like yours: I would put a condition near the end of myfunc. that responded when there was an indication that NULLs were to be returned into your main list. I'd make an additional list with those bits which would also

Re: [R] Problem with mclapply -- losing output/data

2011-03-22 Thread Elizabeth Purdom
Hello, I forgot to mention that I am looping over ~70K objects. If I do mclapply on the first 200, its fine (i.e. doesn't give NULL values); if I go up to 2K (or over all of them), then I start to see NULL values. Also the function I call uses commands 'restrict', 'gaps' and 'width' from the

[R] Problem with mclapply -- losing output/data

2011-03-22 Thread Elizabeth Purdom
Hello, I am running large simulations, which unfortunately I can't really replicate here because the code is so extensive. I rely heavily on mclapply, but I realize that I'm losing data somewhere. There are two worrisome symptoms: 1) I am getting 'NULL' as a return value for some (but not all)