On Tue, 26 Jan 2016 10:54:14 +0100, Andreas Tille wrote: > do you have any idea what change might have caused the failures of the > test suite? > Feel free to commit proposed changes to Debian Med Git if this might > simplify your workflow.
I cloned the git repo (very handy :)) and had a look, but I can't
reproduce the test failure, not even when running them manually under
high load.
Some observations:
> > PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM"
> > "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1,
> > 'blib/lib', 'blib/arch')" t/*.t
> > t/01FreeContact.t ..
> > 1..3
> > ok 1 - use FreeContact;
> > ok 2 - FreeContact->can(...)
> > ok 3 - FreeContact::Predictor->can(...)
> > ok
> > will use 1 OMP threads
> > SSE2 veczweight, wchunk = 32
> > total weight (variation) of alignment = 620.777515304633
> >
> > seq weight loop for 1000 seqs took 0.012224 secs
> > will use 1 OMP threads
> > calculated column aa frequencies, gap cols = 4
> > calculated pair frequency table in 0.192089 secs
> > collected apc_mean[MI] = 0.174031486973761
> > aa freq sum (cell) = 0.999997158936352, pairfreq sum (cell) =
> > 0.999994420985606
> > formed covariance matrix (122/126,4)
> > LU factorization took 9.17976 secs, inverted matrix (incl LUf) in 23.7932
> > secs
> > density of inverse covariance matrix = 1 (cksum 346842.2)
> > went back to gapped (126) wwi matrix
> > collected apc_mean[l1norm] = 117.987054769839
> > collected apc_mean[fro] = 3.35437751555787
> > all done in 24.6311 secs
> > will use 1 OMP threads
> > SSE2 veczweight, wchunk = 32
> > total weight (variation) of alignment = 561.595172234625
> > t/02test.t .........
> > 1..10
> > ok 1 - use FreeContact;
> > ok 2 - An object of class 'FreeContact::Predictor' isa
> > 'FreeContact::Predictor'
> > ok 3
> > ok 4
> > ok 5 - precision test
> > ok 6 - timing results test
> > Failed 4/10 subtests
I noticed that the non-perl-test output comes before t/02test.t while
it comes later (after the "ok 3" of t/02test.t) for me. I thought this
might be a parallelization problem but the test was run with -j1, and
it also passes for me with -jN.
> >
> > Test Summary Report
> > -------------------
> > t/02test.t (Wstat: 11 Tests: 6 Failed: 0)
> > Non-zero wait status: 11
> > Parse errors: Bad plan. You planned 10 tests but ran 6.
What's this 11? A timeout?
Maybe related: the last passing test is "timing results test", the
7th test would be (line 47):
like($@, qr/^Caught FreeContact timeout exception:/);
Sorry for being not able to provide more hints; maybe someone is able
to see what's going on here ...
Since the upstream author is also in Uploaders, I'm adding a CC :)
Cheers,
gregor
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