[Bioperl-l] Installing bioperl-ext-1.4

bcur001 at ec.auckland.ac.nz bcur001 at ec.auckland.ac.nz
Sun Dec 12 23:13:05 EST 2004

I am wanting to run code to do smith-waterman alignment. From what I can see, I
need the EMBOSS suite, which appears to come as part of bioperl-ext-1.4.

I have installed bioperl-1.4 fine. when I attempt to install bioperl-ext-1.4
however, I encounter problems. I've worked my way through a few initial errors,
finding and installing the staden library and the Inline pm (both of which
appear to ahve installed fine), I have, however, finally been stumped. Upon
attempting to run `perl Makefile.PL` from the bioperl-ext-1.4/ directory, I get
the following:

Writing Makefile for Bio::Ext::Align
Found Staden io_lib "libread" in /usr/local/lib ...
Automatically using the Read.h found in /usr/local/include/io_lib ...
Writing Makefile for Bio::SeqIO::staden::read
Writing Makefile for Bio
One or more DATA sections were not processed by Inline.

And there it ends. I can't find any similar problems on the mailing list
archives, so I'm wondering if anyone has any suggestions as to where I could be
looking to find out what the problem is. Someway I could elicit some more
informative errors messages would be nice.

If it's of any use, I'm working on a fairly standard Mandrake 10.0 installation.


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