[Feature-dev] Re: Test error
Gurgen Tumanian
tumanian at gmail.com
Wed Jul 1 22:44:29 PDT 2009
Mike,
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.
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.
here is the result of make check
regression/copy-tools.................ok
regression/unpack-tools...............ok
regression/copy-feature...............ok
regression/unpack-feature.............ok
regression/configure-feature..........ok
regression/build-feature..............ok
regression/trypsin-ser-og-positive....ok 1/2
# Failed test at regression/trypsin-ser-og-positive.t line 6.
# Looks like you failed 1 test of 2.
regression/trypsin-ser-og-positive....dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 2
Failed 1/2 tests, 50.00% okay
regression/trypsin-ser-og-negative....ok 1/2
# Failed test at regression/trypsin-ser-og-negative.t line 6.
# Looks like you failed 1 test of 2.
regression/trypsin-ser-og-negative....dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 2
Failed 1/2 tests, 50.00% okay
regression/trypsin-ser-og-model.......ok 1/2
# Failed test at regression/trypsin-ser-og-model.t line 6.
# Looks like you failed 1 test of 2.
regression/trypsin-ser-og-model.......dubious
Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 2
Failed 1/2 tests, 50.00% okay
regression/build-1bqy-pointfile.......ok
regression/featurize-1bqy.............ok
regression/score-1bqy.................ok
regression/build-1ufo-pointfile.......ok
regression/featurize-1ufo.............ok
regression/score-1ufo.................ok
Failed Test Stat Wstat Total Fail List of Failed
-------------------------------------------------------------------------------
regression/trypsin-ser-og-model.t 1 256 2 1 2
regression/trypsin-ser-og-negative.t 1 256 2 1 2
regression/trypsin-ser-og-positive.t 1 256 2 1 2
Failed 3/15 test scripts. 3/18 subtests failed.
Files=15, Tests=18, 48 wallclock secs (35.84 cusr + 6.72 csys = 42.56 CPU)
Failed 3/15 test programs. 3/18 subtests failed.
make[1]: *** [test] Error 255
make[1]: Leaving directory `/home/tumanian/dev/feature/trunk/tests'
make: *** [test] Error 2
I can send the test.log if needed.
Regards
Gurgen
On Wed, Jul 1, 2009 at 3:56 PM, Mike Wong <mikewong at sfsu.edu> wrote:
> Hi Mauricio,
>
> I found one of the problems. It's a combination of Proteins.h and Atoms.h.
>
> 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.
>
> This is precisely the kind of problem that we can prevent with both a
> coding convention and using strong type-checking.
>
> Best regards,
>
> - m.
>
> __________________________________
> Mike Wong, Staff Research Associate
> Center for Computing for Life Sciences (CCLS)
> San Francisco State University
> 1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132
> (415) 405-2119
> mikewong at sfsu.edu
>
> ------------------------------
> *From:* Mauricio Ardila <willy_se_free at hotmail.com>
> *To:* mike <mikewong at sfsu.edu>
> *Sent:* Wednesday, July 1, 2009 11:43:40 AM
> *Subject:* RE: Test error
>
>
> hi Mike
> 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.
>
> additionally the only thing i found out was that in neighborhood.h
> in lines 24 to 30 a new Point3DList list is created and the it is
> populated with the coordinates of each atom.
>
> however there was a change in which instead of using
>
> retList->push_back(&protein->GetAtom(i)->coord);
>
>
> now
>
> Atom *atom;
> for (int i = 0; i < numAtoms; i++) {
> atom = (*protein)[ i ];
> retList->push_back( &(atom->coord) );
>
> the logic is the same, but the [] operator does seems to create a problem.
>
> so, in conclusion that was all that i found that can cause a problem.
>
> i was not able to fully complete pass the test but i think it is a start.
>
> let me know if you need anything
>
> Mauricio
>
> ------------------------------
> Date: Wed, 24 Jun 2009 21:08:53 -0700
> From: mikewong at sfsu.edu
> Subject: Re: Test error
> To: willy_se_free at hotmail.com
>
> Hi Mauricio,
>
> Thursday at 3pm sounds good. See you at CCLS. We may wander over to the
> library and look at some software testing books.
>
> Thanks,
>
> - m.
>
> __________________________________
> Mike Wong, Staff Research Associate
> Center for Computing for Life Sciences (CCLS)
> San Francisco State University
> 1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132
> (415) 405-2119
> mikewong at sfsu.edu
>
> ------------------------------
> *From:* Mauricio Ardila <willy_se_free at hotmail.com>
> *To:* mike <mikewong at sfsu.edu>
> *Sent:* Wednesday, June 24, 2009 4:26:05 PM
> *Subject:* RE: Test error
>
>
> do you wanna meet tomorrow like at 3?
> Mauricio
>
> ------------------------------
> Date: Tue, 23 Jun 2009 11:21:15 -0700
> From: mikewong at sfsu.edu
> Subject: Re: Test error
> To: willy_se_free at hotmail.com
>
> Hi Mauricio,
>
> Yes, when's a good time for you this week? I'm free Wed-Fri 1-4pm.
>
> Best regards,
>
> - m.
>
> __________________________________
> Mike Wong, Staff Research Associate
> Center for Computing for Life Sciences (CCLS)
> San Francisco State University
> 1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132
> (415) 405-2119
> mikewong at sfsu.edu
>
> ------------------------------
> *From:* Mauricio Ardila <willy_se_free at hotmail.com>
> *To:* mike <mikewong at sfsu.edu>
> *Sent:* Thursday, June 18, 2009 3:10:16 PM
> *Subject:* RE: Test error
>
> Hi mike
> do you wanna meet soon to talk about this new task?
>
> Mauricio
>
> ------------------------------
> Date: Thu, 18 Jun 2009 12:51:31 -0700
> From: mikewong at sfsu.edu
> Subject: Test error
> To: feature-dev at simtk.org
> CC: tumanyan at sfsu.edu; mardila at sfsu.edu
>
>
> Hi all,
>
> 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.
>
> 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.
>
> 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.
>
> Developers can continue to develop, but sometime in the near future we will
> need a temporary code freeze to implement the bug patches.
>
> Best regards,
>
> - m.
>
> __________________________________
> Mike Wong, Staff Research Associate
> Center for Computing for Life Sciences (CCLS)
> San Francisco State University
> 1600 Holloway Avenue, Hensill Hall 301, SF, CA 94132
> (415) 405-2119
> mikewong at sfsu.edu
>
> ------------------------------
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