Re: [R] Error: cannot allocate vector of size 3.4 Gb

2009-11-11 Thread Benilton Carvalho
Hi Peng, the major problem about your specific case is that when creating the final object, we need to set dimnames() appropriately. This triggers a copy of the object and that's where you get the error you describe. With the current release, unfortunately, there isn't much to do (unless

Re: [R] Error: cannot allocate vector of size 3.4 Gb

2009-11-07 Thread Peng Yu
On Fri, Nov 6, 2009 at 8:19 PM, Benilton Carvalho bcarv...@jhsph.edu wrote: this is converging to bioc. let me know what your sessionInfo() is and what type of CEL files you're trying to read, additionally provide exactly how you reproduce the problem. Here is my sessionInfo(). pname is

Re: [R] Error: cannot allocate vector of size 3.4 Gb

2009-11-07 Thread Benilton Carvalho
you haven't answered how much resource you have available when you try reading in the data. with the mouse exon chip, the math is the same i mentioned before. having 8 GB, you should be able to read in 70 samples of this chip. if you can't, that's because you don't have enough resources

Re: [R] Error: cannot allocate vector of size 3.4 Gb

2009-11-07 Thread Peng Yu
Most of the 8GB was available, when I run the code, because R was the only computation session running. On Sat, Nov 7, 2009 at 7:51 AM, Benilton Carvalho bcarv...@jhsph.edu wrote: you haven't answered how much resource you have available when you try reading in the data. with the mouse exon

Re: [R] Error: cannot allocate vector of size 3.4 Gb

2009-11-07 Thread Benilton Carvalho
ok, i'll take a look at this and get back to you during the week. b On Nov 7, 2009, at 1:19 PM, Peng Yu wrote: Most of the 8GB was available, when I run the code, because R was the only computation session running. On Sat, Nov 7, 2009 at 7:51 AM, Benilton Carvalho bcarv...@jhsph.edu wrote: