[BioC] justGCRMA memory problem

[Jianping Jin]

I was reading HG-U133_Plus_2 chips. The total 86 chips I tried to upload.

Thanks!

Jianping

--On Thursday, February 09, 2006 11:06 AM -0500 "James W. MacDonald" 
<jmacdon at med.umich.edu> wrote:

> Jianping Jin wrote:
>> Hi Jim, thanks for your quick reply!
>>
>> I tried --max-mem-size=17000M and run just R 2.2.0 without any other
>> programs running at the time. The message I got listed as the following:
>>
>>> data <- justGCRMA(filenames=files)
>>
>> Computing affinities.Computing affinities.Done.
>> Done.
>> Adjusting for optical effect..Error: cannot allocate vector of size
>> 424868 Kb
>>
>>> memory.size(max=TRUE)
>>
>> [1] 1194139648
>>
>>> memory.limit()
>>
>> [1] 1782579200
>>
>> Any ideas about it?
>
> Odd. How many chips and what type are they? Maybe I can try to replicate
> that here.
>
> Jim
>
>
>>
>> Thanks again!
>>
>> Jianping
>>
>> --On Thursday, February 09, 2006 10:21 AM -0500 "James W. MacDonald"
>> <jmacdon at med.umich.edu> wrote:
>>
>>> Hi Jianping,
>>>
>>> Jianping Jin wrote:
>>>
>>>> Dear list:
>>>>
>>>> My PC has 2 GB of RAM. I set the max memory size for R equal to 2000M.
>>>> But  R stopped running when memory size reached 1 GM. Current version I
>>>> use is  R.2.2.0. I do not run into the problem with R 2.1.0. Does
>>>> anyone have the  same problem with new version of R?
>>>
>>>
>>> I haven't noticed any differences in memory usage. However, there are
>>> certain aspects of Windows' memory usage that can cause problems. First,
>>> if a large block of memory has already been allocated (even if it is
>>> subsequently freed up), you may not be able to use it. Can you replicate
>>> the above problem if no other programs are running on your computer with
>>> a fresh instance of R?
>>>
>>> Also, memory.size() will simply give you the amount of RAM that R is
>>> currently using. More informative would be memory.size(max = TRUE).
>>>
>>> Additionally, there is a note in the R-FAQ for Windows that setting the
>>> memory size > 1.7Gb may be detrimental. I have never seen this problem
>>> myself, but you might try setting --max.memory.size = 1700M and try
>>> again.
>>>
>>> HTH,
>>>
>>> Jim
>>>
>>>
>>>
>>> --
>>> James W. MacDonald
>>> Affymetrix and cDNA Microarray Core
>>> University of Michigan Cancer Center
>>> 1500 E. Medical Center Drive
>>> 7410 CCGC
>>> Ann Arbor MI 48109
>>> 734-647-5623
>>
>>
>>
>>
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>> x Jianping Jin Ph.D.            x
>> x Bioinformatics scientist      x
>> x Center for bioinformatics     x
>> x 3133 Bioinformatics Building  x
>> x CB# 7104                      x
>> x University of North Carolina  x
>> x Chapel Hill, NC 27599         x
>> x Tel: (919)843-6105            x
>> x Fax: (919)843-3103            x
>> x E-mail: jjin at email.unc.edu    x
>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
>
> --
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623



xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
x Jianping Jin Ph.D.            x
x Bioinformatics scientist      x
x Center for bioinformatics     x
x 3133 Bioinformatics Building  x
x CB# 7104                      x
x University of North Carolina  x
x Chapel Hill, NC 27599         x
x Tel: (919)843-6105            x
x Fax: (919)843-3103            x
x E-mail: jjin at email.unc.edu    x
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx