[GenABEL-dev] patch for bug #2525

[Yurii Aulchenko]

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> 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
>
>
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>



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