[Bioperl-guts-l] [Bug 2184] segmentation error during BioPerl 1.5.2 installation

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Jan 12 10:58:40 EST 2007


------- Comment #8 from bix at sendu.me.uk  2007-01-12 10:58 -------
(In reply to comment #7)
> (In reply to comment #5)
> Could we run an eval in the relevant tests (which I'm guessing is the
> BioDBSeqFeature stuff) or in the Build.PL, using code simlar to your one-liner
> to make sure DBD::mysql and DBI are working, then skip if they aren't?  

Well yes, that is the whole purpose of these tests. First it checks to see if
the modules load, and only if they load does it then check to see if the test
database is connectable. We need some kind of connectivity test without any
possibility of seg faulting. The question is, what test is suitable?

> As a note, I'm not sure how Lincoln set up detecting the presence of MySQL but
> it doesn't detect MySQL on Windows tests (it bypassed them).

This was quite deliberate but I suspect a hack around an unconfirmed and
uninvestigated problem. If the test can and should pass under Windows, by all
means the 'excludes_os      => ['mswin'],' line should be removed from Build.PL

> > In the mean time, to allow installation to proceed you'll have to hack 
> You can always force install as well

force install only works when tests are failing. In this case, Build.PL is seg
faulting; only Build.PL knows what to install and how, so there is nothing to

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