[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 10:42:55 EST 2007


------- Comment #7 from cjfields at uiuc.edu  2007-01-12 10:42 -------
(In reply to comment #5)
> (In reply to comment #4)
> > I got a segmentation error too : 
> > 
> > [root at stb006-01 Desktop]# perl -MDBI -e 'unless (eval
> > > {DBI->connect("dbi:mysql:test",undef,undef,{RaiseError=>0,PrintError=>0})})
> > > {
> > > print "Could not connect to test database\n"; } print "ok\n";'
> > Erreur de segmentation
> Ok, there's something wrong wither with your perl module DBI::mysql
> installation or with your actual mySQL installation.
> I don't know what the problem might be or how to fix it, but clearly we don't
> want the Bioperl installation falling over because of it. So I'm leaving this
> bug open until this issue is resolved. Can anyone help?

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?  

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).

> In the mean time, to allow installation to proceed you'll have to hack around
> the problem by altering the Build.PL file: delete the 5 lines starting with the
> line containing 'BioDBSeqFeature_mysql => {' and ending with the corresponding
> '},'.
> Sorry for the inconvenience caused.

You can always force install as well, though it's not always advisable w/o
looking at the reasons why tests are failing. 

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