[GenABEL-dev] export.plink bug: should we change the default?

Wed Apr 3 13:26:15 CEST 2013

On 04/03/2013 01:23 PM, Yurii Aulchenko wrote:
> In theory I agree :)
> 
> In practice submitting to CRAN takes from 4 hours to a full day, so I
> personally would not like to submit unless strictly necessary.

True. It looks simple, but something always pops up.

> 
> As for this particular fix - I expect some more code changes still this
> week, so if we decide to publish on CRAN I would wait till next week.

Good. Let's wait until these changes you mention are in. One or two more
weeks won't make much of a difference, I'd say. Having more changes in
also makes for a nicer Changelog ;-).

Lennart.

> 
> best wishes,
> YA
> 
> On Wed, Apr 3, 2013 at 1:20 PM, L.C. Karssen <lennart at karssen.org> wrote:
> 
>> Hi Yurii, Maria,
>>
>> Indeed, this is more a workaround than a fix. I think we communicated
>> this simple workaround in the past, but I agree with Maria we should
>> either announce it more widely, or, probably better push a new GenABEL
>> release to CRAN (for those people who don't read the announcements :-)).
>>
>> Yurii, what do you think? One the one hand it is not urgent (we've been
>> living with this bug for a while) on the other hand, the present
>> situation is a dangerous one... Are there any developments in GenABEL
>> SVN that are not ready for publishing yet?
>>
>>
>> Best,
>>
>> Lennart.
>>
>> On 04/03/2013 12:19 PM, Yurii Aulchenko wrote:
>>> Hi Maria,
>>>
>>> if my understanding is correct, the fix is now only in the devel-version
>> on
>>> SVN - so you would need to export and build package if you really want it
>>> (see
>> http://genabel.r-forge.r-project.org/tutHowToInstallDevelVersion.html).
>>>
>>> But the 'fix' is very simple (and is not actually fixing anything - just
>>> trying to avoid confusion!): the default option now is set to
>>> 'transpose=TRUE'. So you can simply set this up manually when calling
>>> 'export.plink' :)
>>>
>>> Yurii
>>>
>>>
>>> On Wed, Apr 3, 2013 at 11:58 AM, Maria G <mgmaria at yandex.ru> wrote:
>>>
>>>> Dear Lennart,
>>>>
>>>> that's really helpful, thank you!
>>>>
>>>> Does it mean I have to update the version of GenABEL to get read of the
>>>> bug? Which version is fine?
>>>>
>>>>
>>>> best
>>>> Mariya
>>>>
>>>> 02.04.2013, 20:30, "L.C. Karssen" <lennart at karssen.org>:
>>>>> Dear list,
>>>>>
>>>>> As I didn't get any comments to dissuade me, I've just committed a
>>>>> change that sets the default behaviour of export.plink() in GenABEL to
>>>>> export .tped/.tfam files. This works around bug #2055.
>>>>>
>>>>> Best,
>>>>>
>>>>> Lennart.
>>>>>
>>>>> On 28/03/13 14:34, L.C. Karssen wrote:
>>>>>
>>>>>>  Dear list,
>>>>>>
>>>>>>  We recently got bitten by bug #2055 (ref [1]) in GenABEL's
>>>>>>  export.plink() again. Data was exported to .ped format and everything
>>>>>>  seemed to have gone well, however, we later found out that the
>> exported
>>>>>>  genotypes were wrong. Exporting to .tped (export.plink(...,
>>>>>>  transpose=TRUE)) worked fine.
>>>>>>
>>>>>>  I think we should change the default for the transpose option to TRUE
>>>>>>  and add a warning in case someone sets it to FALSE. I'm of course
>>>>>>  willing to write the necessary code.
>>>>>>  At least this will safeguard the users from this problem until the
>>>>>>  actual bug is fixed.
>>>>>>
>>>>>>  What are you're thoughts on this?
>>>>>>
>>>>>>  Best,
>>>>>>
>>>>>>  Lennart.
>>>>>>
>>>>>>  [1]
>>>>>>
>>>>
>> https://r-forge.r-project.org/tracker/index.php?func=detail&aid=2055&group_id=505&atid=2058
>>>>>>  --
>>>>>>  -----------------------------------------------------------------
>>>>>>  L.C. Karssen
>>>>>>  Utrecht
>>>>>>  The Netherlands
>>>>>>
>>>>>>  lennart at karssen.org
>>>>>>  http://blog.karssen.org
>>>>>>
>>>>>>  Stuur mij aub geen Word of Powerpoint bestanden!
>>>>>>  Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>>>  ------------------------------------------------------------------
>>>>>>
>>>>>>  _______________________________________________
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>>>>>>
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>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>
>>>>> --
>>>>> -----------------------------------------------------------------
>>>>> L.C. Karssen
>>>>> Utrecht
>>>>> The Netherlands
>>>>>
>>>>> lennart at karssen.org
>>>>> http://blog.karssen.org
>>>>>
>>>>> Stuur mij aub geen Word of Powerpoint bestanden!
>>>>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>>>>> ------------------------------------------------------------------
>>>>>
>>>>> ,
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>> --
>> -----------------------------------------------------------------
>> L.C. Karssen
>> Utrecht
>> The Netherlands
>>
>> lennart at karssen.org
>> http://blog.karssen.org
>>
>> Stuur mij aub geen Word of Powerpoint bestanden!
>> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> ------------------------------------------------------------------
>>
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> 
> 
> 

-- 
-----------------------------------------------------------------
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org

Stuur mij aub geen Word of Powerpoint bestanden!
Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
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