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

[Yurii Aulchenko]

What about keeping default as before ("ped"), but introduce a message
when "ped" is used warning that with large datas sets it is strongly
recommended to use "tped" format.

Yurii

On Mon, Jul 2, 2012 at 7:59 PM, L.C. Karssen <lennart at karssen.org> wrote:
> 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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