[GenABEL-dev] patch for bug #2525

[Yurii Aulchenko]

Pity. Thanks for the hint!

----------------------
Yurii Aulchenko
(sent from mobile device)

On 14 May 2013, at 19:13, "L.C. Karssen" <lennart at karssen.org> wrote:

> Dear Yurii,
>
> I just tested export.plink() in the development version of GenABEL (SVN
> r1214) to see if it still leaks memory, so bug 2055 isn't fixed by
> Vladimir's fix, unfortunately.
>
> FYI, to check this I ran:
> library(GenABEL)
> data(srdta)
> export.plink(data=srdta, filebasename="plink", transpose=FALSE)
>
> If you repeat the last statements a couple of times you'll see R's
> memory use increase and only decrease when you exit R.
>
> No idea about a unittest for this... Valgrind should be able to track
> it. I'll have to read up on using Valgrind with C code in R...
>
>
> Best,
>
> Lennart.
>
> On 04-04-13 13:44, Yurii Aulchenko wrote:
>> Thank you, Vladimir! - nice fix!
>>
>> Lennart, I wonder if this fix somehow also address the export.plink bug
>> #2055 discussed earlier. I also wonder what kind of unit test one can
>> introduce for such 'memory leak' problem...
>>
>> Below please find description of testing of the patch and some minor
>> changes I introduced. I have updated the code on SVN
>> (http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000575.html)
>> and closed the bug.
>>
>> best wishes,
>> Yurii
>>
>> I have added a unit test for this bug in r. 1185,
>> see http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000574.html)
>>
>> Then I ran unit tests without applying the patch yet by
>>
>> cd pkg/GenABEL/inst/unitTests
>> make
>>
>> which gave me - as expected -
>>
>> GenABEL unit testing - 20 test functions, 1 error, 2 failures
>> FAILURE in test.export.merlin.bug2525: Error in checkIdentical(xN, xO) :
>> FALSE
>> FAILURE in test.exports: Error in checkIdentical(xN, xO) : FALSE
>> ERROR in test.impute2databel: Error in .Call("iterator",
>>
>> (you can also check report.html for details; the FAILURE's are related
>> to the bug 2525, and the ERROR is related to other bug, so our aim is to
>> eliminate these FAILURES)
>>
>> Next (from ../../../) I have applied the patch by
>>
>> patch -p0 -i ~/Downloads/patch_2525
>>
>> and run unit tests again by
>>
>> cd pkg/GenABEL/inst/unitTests
>> make
>>
>> which gave me
>>
>> GenABEL unit testing - 20 test functions, 1 error, 0 failures
>> ERROR in test.impute2databel: Error in .Call("iterator",
>>
>> which I thought was good - basically the test FAILURES were eliminated.
>>
>> Now, the patch as submitted prints out much debugging (?) related staff
>> to STDOUT, so next I commented out Rprintf's and ran the tests agin,
>> getting
>>
>> GenABEL unit testing - 20 test functions, 1 error, 0 failures
>> ERROR in test.impute2databel: Error in .Call("iterator",
>>
>> So, I conclude that the bug is fixed!
>>
>>
>> On Wed, Apr 3, 2013 at 4:54 PM, Vladimir Naumov <looongdog at gmail.com
>> <mailto:looongdog at gmail.com>> wrote:
>>
>>    http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058
>>
>>
>>    It was problem with cycle that didn't renew sex values - so they
>>    were periodically written into output file with period of 100 (by
>>    default)
>>
>>    --
>>    Vladimir Naumov
>>    0079156727733
>>    Skype: snow_wow
>>
>>
>>    _______________________________________________
>>    genabel-devel mailing list
>>    genabel-devel at lists.r-forge.r-project.org
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>>    https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>>
>>
>> --
>> -----------------------------------------------------
>> Yurii S. Aulchenko
>>
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>>
>>
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>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
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