[BioC] memory exhausted for readAligned

[Patrick Aboyoun]

Lana,
The definitive guide on R installation can be found in the "R 
Installation and Administration" manual.

http://cran.fhcrc.org/doc/manuals/R-admin.pdf

In particular, you can consult chapter 2 "Installing R under 
Unix-alikes". The basic idea is to grab the R-devel tarball from

ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz

and follow the installation instructions mentioned above. Even if Unix 
is somewhat foreign to you, it is pretty straightforward to create a 
typical installation of R. If you hit any snags, let me know.


Patrick


Lana Schaffer wrote:
> Patrick,
> I have a 64-bit Unix machine but not a 64-bit Windows machine.
> I can't find the R version code for either at the moment.
> lana 
>
> -----Original Message-----
> From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org] 
> Sent: Thursday, February 12, 2009 4:32 PM
> To: Lana Schaffer
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] memory exhausted for readAligned
>
> Lana,
> Given that there is typically a trade-off between memory and speed and
> the ubiquity of 64-bit machines, most of the Bioconductor sequencing
> software was designed with 64-bit architectures in mind in order to
> minimize computation time. Once you move to a 64-bit machine for this
> work, I'm pretty sure this issue will go away.
>
>
> Patrick
>
>
> Lana Schaffer wrote:
>   
>> Patrick,
>> Yes, I am on a 32-bit machine.
>> length=35bp
>> 298,610kb  50% PF and 12% Align
>>  R version 2.9.0 Under development (unstable) (2009-02-12 r47905)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>     
>
>   
>> Thanks,
>> Lana
>>
>> -----Original Message-----
>> From: Patrick Aboyoun [mailto:paboyoun at fhcrc.org]
>> Sent: Thursday, February 12, 2009 4:20 PM
>> To: Lana Schaffer
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] memory exhausted for readAligned
>>
>> Lana,
>> Could you provide your session information for you R session as well 
>> as the number of alignments you are trying to read in? My first guess 
>> is that you are running on a 32-bit architecture, but without more 
>> information we on the list can't help you very much.
>>
>>
>> Patrick
>>
>>
>>
>> Lana Schaffer wrote:
>>   
>>     
>>> Hi,
>>> I am trying to read the alignment in a lane of Solexa data and ran 
>>> out
>>>     
>>>       
>>   
>>     
>>> of memory.
>>> I have 3.2G memory on my desktop computer.
>>> Is there a setting I can use to have enough memory for the 
>>> readAligned
>>>     
>>>       
>>   
>>     
>>> command?
>>> How much memory do i need?
>>>
>>> Lana Schaffer
>>> Biostatistics/Informatics
>>> The Scripps Research Institute
>>> DNA Array Core Facility
>>> La Jolla, CA 92037
>>> (858) 784-2263
>>> (858) 784-2994
>>> schaffer at scripps.edu
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>>   
>>>     
>>>       
>>   
>>     
>
>