[Bioperl-l] A few burps with 1.0a install on redhat 7.2

Jason Stajich jason@cgt.mc.duke.edu
Wed, 13 Mar 2002 10:56:26 -0500 (EST)

Thanks for taking it for a test drive - do you have any scripts that use
bioperl that hopefully still work without too much noise?

The subject() to hit() transition is the most likely to cause noise will
add a note about any hicups transitioning from 0.7 to 1.0 in the README.

On Wed, 13 Mar 2002, Keith Allen wrote:

> Hey Guys,
> I just snagged the 1.0 alpha release and it only failed
> 11/3037 tests, most of which were the result of things
> that I didn't have installed yet (for some reason I'm having
> a hard time building XML::Writer -- it actually dumps core
> during make test).  The only thing that might be of
> interest is that it fails to find Bio/UnivAln.pm, and hence
> aborts the tests in t/UnivAln.t.
Yeah - I've had the same trouble with XML::Writer on RH7.2 - need to bug
the author about this - you can just do a make install anyways and it will
run fine for what I've seen.  I will add a note about XML::Writer in the

> I can't seem to find UnivAln either, and I can't remember
> if this has been deprecated, and so the test should be
> dropped from the install package?
crap - I did remove UnivAlign but I must have forgotten to remove the
mental not to test on complete bioperl virgin system before release.

> Also, Mark Wilkinson mentioned a script called
> load_seq_database.pl, but I can't find that in the 1.0a
> release either.  Anyone know where it is? (maybe I
> need to look in an 0.7 build?).

I think Mark rm-ed it because the biosql schema changed.  Hmmm. will check
on that.

> Thanks.  You guys rock most fully.
> -Keith Allen
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Jason Stajich
Duke University