[GenABEL-dev] export.plink() uses too much memory in GenABEL v1.7-0 (beta)

[L.C. Karssen]

Dear List,

Sorry for digging deep into the past, but this issue of export.plink()
still hasn't been resolved. After a recent question by e-mail I opened a
bug report and started a forum thread on the subject:
-
https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=2055&group_id=505
- http://forum.genabel.org/viewtopic.php?f=6&t=652

Since solving the issue costs more time than I can presently afford, I
suggest to make export.plink(..., transpose=TRUE) the default (instead
of transpose=FALSE).
Moving to a new default will need to be communicated very clearly, but I
think shipping a function that is broken by default is even worse.

What are your opinions?


Best,

Lennart.

On 12/07/2011 05:36 PM, L.C. Karssen wrote:
> Dear Yurii,
> 
> We just tried svn revision 827 and had the same problem. We killed the
> program at 51% memory usage (32GB). So, unfortunately I think the
> problem is not solved yet.
> 
> 
> Lennart
> 
> 
> 
> On 07-12-11 11:36, Yury Aulchenko wrote:
>> Ok, should be fixed in r823 just committed.
>>
>> Let me know if the problem persist
>>
>> On Dec 7, 2011, at 11:13 AM, Yury Aulchenko wrote:
>>
>>> I think this is something I introduced in rev. 810-814 (a new without
>>> delete). Now (hopefully) fixed, will commit changes in next hour.
>>> -------------------------------------------------------
>>> Yurii Aulchenko, PhD, Dr. Habil.
>>> Independent researcher and consultant
>>> yurii [dot] aulchenko [at] gmail [dot] com
>>>
>>> On Dec 7, 2011, at 11:03 AM, L.C. Karssen wrote:
>>>
>>>> Dear list,
>>>>
>>>> We just tried to convert a GenABEL object to plink format using
>>>> export.plink() from GenABEL v 1.7-0 (still under development,
>>>> package built from SVN yesterday), and it nearly brought the machine
>>>> to a halt because it used all available memory (RAM + swap).
>>>>
>>>> Our GenABEL object contained almost 3700 individuals and about 700k
>>>> SNPS.
>>>>
>>>> Have others experienced this as well? I haven't looked at Yurii's
>>>> latest implementation of the function in C++ yet. Hopefully I will
>>>> be able to find some time later today. Does anyone here know how we
>>>> could limit memory usage in C++?
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Lennart.
>>
>>
> 



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