[BioC] DiffBind error loading dba.count

Gordon Brown Gordon.Brown at cancer.org.uk
Wed Aug 1 11:52:19 CEST 2012

Hi, Paolo,

6Gb ought to be enough.  I suspect there's something else wrong.
Unfortunately, I don't have a Windows machine available to test on.  Can
you provide any other information about the error?  Does it run for a long
time, then fail, or does it fail quickly?  Is there any other diagnostic
message?  Does Rgui crash completely, or can you run "traceback()" to see
where the error is?

Also, can you provide the output of "sessionInfo()" so I can see what
version you're running?


 - Gord

On 01/08/2012 10:34, "Paolo Kunderfranco" <paolo.kunderfranco at gmail.com>

>Hi Gordon,
>I tried test=dba.count(test,bParallel=F) but still facing the same
>problem, it seems that 6 Gb of RAM are not enough to load
>2 GB of bed file, is it possibile?
>I suggest I should switch to a bigger machine..
>2012/7/31 Gordon Brown <Gordon.Brown at cancer.org.uk>:
>> Hi, Paolo,
>> DiffBind uses quite a lot of memory for the dba.count step, because it
>> the whole data file into memory.  (In hindsight, not the best design
>> choice...)  Try running with parallelization turned off:
>>> test=dba.count(test,bParallel=F)
>> so that it only loads one file at a time, to reduce the memory
>> For the upcoming release, we'll probably fix this, at the cost of
>> slower counting.
>> How much RAM does your machine have?
>> Cheers,
>>  - Gord
>> On 2012/07/30 11:00, "Paolo Kunderfranco" <paolo.kunderfranco at gmail.com>
>> wrote:
>>> Dear All,
>>> I am facing some problems with RGUI loading dba.count with my dataset,
>>>> setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data/ChIP-seq
>>>> Roberto/Analisi_PK/DiffBind/H3K27me3/")
>>>> library("DiffBind")
>>>> test= dba(sampleSheet='database.csv')
>>> ES_H3K27 ES H3K27 1  1 raw
>>> CMN_H3K27 CMN H3K27 1  1 raw
>>> CMA_H3K27 CMA H3K27 1  1 raw
>>>> test=dba.count(test)
>>> AppName: rgui.exe  AppVer: 2.150.58871.0  ModName: diffbind.dll
>>> ModVer:  Offset: 00003be1
>>> Did anyone faced the same problem? which are the memory requirements
>>> to run DiffBind?
>>> Thanks,
>>> Paolo
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