<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt">Hi Gurgen,<br><br>Right. What you saw was an earlier form of the regression test suite where all the tests passed. Then I extended the test coverage and corrected the test data.<br><br>Notice now that the trypsin-ser-og-positive and negative have 2 parts and that part 1/2 passes, but part 2/2 fails; part 2 has new test data.<br><br>With the extended test coverage, the system began to fail. At this point I tasked Mauricio and myself to find the bug and eliminate it.<br><br>The patch has not yet been applied and committed to Subversion; I expect that to happen sometime today, hopefully.<br><br>Once the patch is put in place and works, then I'll also commit the retroactive test system.<br><br>Best regards,<br><br>- m.<br><div> </div>__________________________________<br>Mike Wong, Staff Research
Associate<br>Center for Computing for Life Sciences (CCLS)<br>San Francisco State University<br>1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132<br>(415) 405-2119<br>mikewong@sfsu.edu<div><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Gurgen Tumanian <tumanian@gmail.com><br><b><span style="font-weight: bold;">To:</span></b> Mike Wong <mikewong@sfsu.edu><br><b><span style="font-weight: bold;">Cc:</span></b> Mauricio Ardila <willy_se_free@hotmail.com>; FEATURE development team <feature-dev@simtk.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, July 1, 2009 10:44:29 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [Feature-dev] Re: Test error<br></font><br>
Mike,<br><br>There is something that I have noticed, and I have to share, to clarify, if that's a result of your fixes or it is just that testing framework is not stable.<br><br>I was running the tests as in rev 536. The model was faulty indeed, with zeros all the way, but the tests did fail, in contrary to what we saw when running tests on your PC.<br>
<br>here is the result of make check<br><br>regression/copy-tools.................ok <br>regression/unpack-tools...............ok <br>regression/copy-feature...............ok <br>
regression/unpack-feature.............ok <br>regression/configure-feature..........ok <br>regression/build-feature..............ok <br>
regression/trypsin-ser-og-positive....ok 1/2 <br># Failed test at regression/trypsin-ser-og-positive.t line 6.<br># Looks like you failed 1 test of 2.<br>regression/trypsin-ser-og-positive....dubious <br>
Test returned status 1 (wstat 256, 0x100)<br>DIED. FAILED test 2<br> Failed 1/2 tests, 50.00% okay<br>regression/trypsin-ser-og-negative....ok 1/2 <br># Failed test at regression/trypsin-ser-og-negative.t line 6.<br>
# Looks like you failed 1 test of 2.<br>regression/trypsin-ser-og-negative....dubious <br> Test returned status 1 (wstat 256, 0x100)<br>DIED. FAILED test 2<br> Failed 1/2 tests, 50.00% okay<br>
regression/trypsin-ser-og-model.......ok 1/2 <br># Failed test at regression/trypsin-ser-og-model.t line 6.<br># Looks like you failed 1 test of 2.<br>regression/trypsin-ser-og-model.......dubious <br>
Test returned status 1 (wstat 256, 0x100)<br>DIED. FAILED test 2<br> Failed 1/2 tests, 50.00% okay<br>regression/build-1bqy-pointfile.......ok <br>regression/featurize-1bqy.............ok <br>
regression/score-1bqy.................ok <br>regression/build-1ufo-pointfile.......ok <br>regression/featurize-1ufo.............ok <br>
regression/score-1ufo.................ok <br>Failed Test Stat Wstat Total Fail List of Failed<br>-------------------------------------------------------------------------------<br>
regression/trypsin-ser-og-model.t 1 256 2 1 2<br>regression/trypsin-ser-og-negative.t 1 256 2 1 2<br>regression/trypsin-ser-og-positive.t 1 256 2 1 2<br>Failed 3/15 test scripts. 3/18 subtests failed.<br>
Files=15, Tests=18, 48 wallclock secs (35.84 cusr + 6.72 csys = 42.56 CPU)<br>Failed 3/15 test programs. 3/18 subtests failed.<br>make[1]: *** [test] Error 255<br>make[1]: Leaving directory `/home/tumanian/dev/feature/trunk/tests'<br>
make: *** [test] Error 2<br><br>I can send the test.log if needed. <br><br>Regards<br>Gurgen<br><br><div class="gmail_quote">On Wed, Jul 1, 2009 at 3:56 PM, Mike Wong <span dir="ltr"><<a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Hi Mauricio,<br>
<br>I found one of the problems. It's a combination of Proteins.h and Atoms.h.<br><br>The class Proteins is a subclass of Atoms. Atoms has an Objects instance called 'atoms'. Protein also has an Objects instance called 'atoms'. Therefore the instances of atoms are overloaded, and local scope takes precedence.<br>
<br>This is precisely the kind of problem that we can prevent with both a coding convention and using strong type-checking.<div class="im"><br><br>Best regards,<br><br>- m.<br><br>__________________________________<br>Mike Wong, Staff Research Associate<br>
Center for Computing for Life Sciences (CCLS)<br>San Francisco State University<br>1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132<br>(415) 405-2119<br><a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><div>
<br></div></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mauricio Ardila <<a rel="nofollow" ymailto="mailto:willy_se_free@hotmail.com" target="_blank" href="mailto:willy_se_free@hotmail.com">willy_se_free@hotmail.com</a>><br>
<b><span style="font-weight: bold;">To:</span></b> mike <<a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a>><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, July 1, 2009 11:43:40 AM<br>
<b><span style="font-weight: bold;">Subject:</span></b> RE: Test error<br></font><br>
<div><br></div>hi Mike<div><br></div><div>yesterday i found out that the change the schedule of my flight to 5:30 so i will not be able to make the meeting of today.</div><div><br></div><div>additionally the only thing i found out was that in neighborhood.h</div>
<div>in lines 24 to 30 a new Point3DList list is created and the it is populated with the coordinates of each atom.<br></div><div><br></div><div>however there was a change in which instead of using </div><div><br></div>
<div>retList->push_back(&protein->GetAtom(i)->coord);<br></div><div><br></div><div><br></div><div>now </div><div><br></div><div><div>Atom *atom;</div><div> for (int i = 0; i < numAtoms; i++) {</div>
<div><span style="white-space: pre;"> </span>atom = (*protein)[ i ];</div><div> retList->push_back( &(atom->coord)
);</div><div><br></div><div>the logic is the same, but the [] operator does seems to create a problem.</div><div><br></div><div>so, in conclusion that was all that i found that can cause a problem.</div><div><br></div><div>
i was not able to fully complete pass the test but i think it is a start.</div><div><br></div><div>let me know if you need anything</div><div><br></div><div>Mauricio</div></div><div><br><hr>Date: Wed, 24 Jun 2009 21:08:53 -0700<br>
From: <a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><br>Subject: Re: Test error<br>To: <a rel="nofollow" ymailto="mailto:willy_se_free@hotmail.com" target="_blank" href="mailto:willy_se_free@hotmail.com">willy_se_free@hotmail.com</a><br><br>
<div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Hi Mauricio,<br><br>Thursday at 3pm sounds good. See you at CCLS. We may wander over to the library and look at some software testing books.<br><br>Thanks,<div class="im">
<br><br>- m.<br><div> </div>__________________________________<br>Mike Wong, Staff Research Associate<br>Center for Computing for Life Sciences (CCLS)<br>San Francisco State University<br>1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132<br>
(415) 405-2119<br><a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><div><br></div></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">
<font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mauricio Ardila <<a rel="nofollow" ymailto="mailto:willy_se_free@hotmail.com" target="_blank" href="mailto:willy_se_free@hotmail.com">willy_se_free@hotmail.com</a>><br><b><span style="font-weight: bold;">To:</span></b> mike
<<a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a>><br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, June 24, 2009 4:26:05 PM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: Test error<br>
</font><br>
<div><br></div>do you wanna meet tomorrow like at 3?<div><br></div><div>Mauricio<br><br><hr>Date: Tue, 23 Jun 2009 11:21:15 -0700<br>From: <a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><br>Subject: Re: Test error<br>
To: <a rel="nofollow" ymailto="mailto:willy_se_free@hotmail.com" target="_blank" href="mailto:willy_se_free@hotmail.com">willy_se_free@hotmail.com</a><br><br>
<div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;">Hi Mauricio,<br><br>Yes, when's a good time for you this week? I'm free Wed-Fri 1-4pm.<div class="im"><br><br>Best regards,<br><br>- m.<br><div>
</div>__________________________________<br>Mike Wong, Staff Research Associate<br>Center for Computing for Life Sciences (CCLS)<br>San Francisco State University<br>1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132<br>
(415) 405-2119<br><a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><div><br></div></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">
<font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mauricio Ardila <<a rel="nofollow" ymailto="mailto:willy_se_free@hotmail.com" target="_blank" href="mailto:willy_se_free@hotmail.com">willy_se_free@hotmail.com</a>><br><b><span style="font-weight: bold;">To:</span></b> mike <<a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a>><br>
<b><span style="font-weight: bold;">Sent:</span></b> Thursday, June 18, 2009 3:10:16
PM<br><b><span style="font-weight: bold;">Subject:</span></b> RE: Test error<br></font><br>
Hi mike<div><br></div><div>do you wanna meet soon to talk about this new task?</div><div><br></div><div>Mauricio<br><br><hr>Date: Thu, 18 Jun 2009 12:51:31 -0700<br>From: <a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><br>
Subject: Test error<br>To: <a rel="nofollow" ymailto="mailto:feature-dev@simtk.org" target="_blank" href="mailto:feature-dev@simtk.org">feature-dev@simtk.org</a><br>CC: <a rel="nofollow" ymailto="mailto:tumanyan@sfsu.edu" target="_blank" href="mailto:tumanyan@sfsu.edu">tumanyan@sfsu.edu</a>; <a rel="nofollow" ymailto="mailto:mardila@sfsu.edu" target="_blank" href="mailto:mardila@sfsu.edu">mardila@sfsu.edu</a><div>
<div></div><div class="h5"><br><br>
<div style="font-family: arial,helvetica,sans-serif; font-size: 10pt; color: rgb(0, 0, 0);">Hi all,<br><br>I've recently discovered that a hole in our test coverage has been glossing over a particularly bad problem; we may be generating faulty models.<br>
<br>Therefore, I'm tasking myself and Mauricio to become Grade-A Test Engineers. Anyone who's interested in this unglamorous, but unbelievably important, process, please contact me. This is especially important for those who are thinking of a career in industry.<br>
<br>Software Quality Assurance texts spend huge amounts of time explaining how to design tests so that they don't fail. There's very little discussion on tests that have poor coverage, or simply faulty tests, and what to do when you find yourself in those situations. This is where practice diverges from theory, and one of the areas where experience matters most. There is
significant hands-on learning that will happen here, something that can potentially help you nail an interview and land a job or a performance review and score a promotion.<br><br>Developers can continue to develop, but sometime in the near future we will need a temporary code freeze to implement the bug patches.<br>
<br>Best regards,<br><br>- m.<br><div> </div>__________________________________<br>Mike Wong, Staff Research Associate<br>Center for Computing for Life Sciences (CCLS)<br>San Francisco State University<br>1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132<br>
(415) 405-2119<br><a rel="nofollow" ymailto="mailto:mikewong@sfsu.edu" target="_blank" href="mailto:mikewong@sfsu.edu">mikewong@sfsu.edu</a><div><br></div></div></div></div></div><br><hr> <a rel="nofollow" target="_blank" href="http://clk.atdmt.com/MRT/go/119462413/direct/01/">Stay up to date on your PC, the Web, and your mobile phone with Windows Live</a></div>
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