Thank you, Vladimir! - nice fix! <div><br></div><div>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...</div>
<div><br></div><div>Below please find description of testing of the patch and some minor changes I introduced. I have updated the code on SVN (<a href="http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000575.html">http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000575.html</a>) and closed the bug. </div>
<div><br></div><div>best wishes,</div><div>Yurii<br><div><div><div><div><div><br></div><div>I have added a unit test for this bug in r. 1185, see <a href="http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000574.html">http://lists.r-forge.r-project.org/pipermail/genabel-commits/2013-April/000574.html</a>)</div>
<div><br></div><div>Then I ran unit tests without applying the patch yet by </div><div><br></div><div>cd pkg/GenABEL/inst/unitTests</div><div>make</div><div><br></div><div>which gave me - as expected - </div><div><br></div>
<div><div><div>GenABEL unit testing - 20 test functions, 1 error, 2 failures</div><div>FAILURE in test.export.merlin.bug2525: Error in checkIdentical(xN, xO) : FALSE </div><div>FAILURE in test.exports: Error in checkIdentical(xN, xO) : FALSE </div>
<div>ERROR in test.impute2databel: Error in .Call("iterator",</div></div><div><br></div><div>(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)</div>
<div><br></div><div>Next (from ../../../) I have applied the patch by </div><div><br></div><div>patch -p0 -i ~/Downloads/patch_2525</div><div><br></div><div>and run unit tests again by</div><div><br></div><div><div>cd pkg/GenABEL/inst/unitTests</div>
<div>make</div><div><br></div></div><div>which gave me </div><div><br></div><div><div>GenABEL unit testing - 20 test functions, 1 error, 0 failures</div><div>ERROR in test.impute2databel: Error in .Call("iterator",</div>
</div><div><br></div><div>which I thought was good - basically the test FAILURES were eliminated.</div><div><br></div><div>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 </div>
<div><br></div><div><div>GenABEL unit testing - 20 test functions, 1 error, 0 failures</div><div>ERROR in test.impute2databel: Error in .Call("iterator", </div></div><div><br></div><div>So, I conclude that the bug is fixed!</div>
<div><br></div><div><br></div><div><div class="gmail_quote">On Wed, Apr 3, 2013 at 4:54 PM, Vladimir Naumov <span dir="ltr"><<a href="mailto:looongdog@gmail.com" target="_blank">looongdog@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<a href="http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058" target="_blank">http://r-forge.r-project.org/tracker/index.php?func=detail&aid=2525&group_id=505&atid=2058</a>
</div>
<div><div><br></div><div><font face="Times">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) </font></div><span><font color="#888888"><div>
<br></div><div>-- </div><div>Vladimir Naumov</div><div>0079156727733</div><div>Skype: snow_wow</div><div><br></div></font></span></div>
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