[Bioperl-l] is the Bio::Ext::Align stuff supposed to work?

Andrew.Mather at dpi.vic.gov.au Andrew.Mather at dpi.vic.gov.au
Wed Jul 27 06:52:46 EDT 2005

Hi George
> I've been playing with Bio::Tools::dpAlign, which involved installing
> Bio::Ext.
> Bio::Ext did a really poor job of installing itself (FreeBSD
> 6-{various}, perl 5.8.[67]).  I managed to mv and cp the various parts
> around to where they were supposed to be.
> I'm not sure if it's me, FreeBSD, or Bio::Ext.  Does it work for other
> folks?  The tests all work fine, they get away with some judicious
> -I../this-that-the-other, but if you copy e.g. the Align test file to
> your home directory and just try to run it, it doesn't work.
> In particular, the .so and .bs files didn't end up where they belong,
> and I ended up with /.../Bio/Ext/Align/Align.pm instead
> /.../Bio/Ext/Align.pm.
> I'm sure I can figure it out and pass some patches back, just wanted
> to understand who else might be seeing the problem.

I've been having a few battles with staden io_lib myself, which have 
caused problems with Bio::Ext.

I have a system with a mix of RHEL3 on IA32 and AMD64 machines.  The 
staden compiled fine on the Intel machines and once I'd copied the usual 
.h files to where they were expected, Ext set up fine.

On the AMD's though, no such luck.  I had to find the 1.9 (or is it 1.1.9 
?..I'm not near the machines now)  version before it would even compile, 
however it doesn't create any .so files at all.

This isn't strictly a bioperl problem I suppose, but it is related.

There were a couple of suggestions raised here, but so far no good.

I've had to go on to other things at the moment, but I'm still trying find 
a solution when I can get back to it.


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