[Bioperl-l] Bio::Ext::Align?

Kevin Brown Kevin.M.Brown at asu.edu
Thu Nov 8 17:30:24 EST 2007


OK, found the issue.  For whatever reason the Align.pm file is inside
the Align folder and so the package name and path don't match up once it
is installed.  This would cause it to have a name of
"Bio::Ext::Align::Align" instead of "Bio::Ext::Align".  Not sure why
this wasn't caught when I did "perl Makefile.pl && make && make test &&
make install" 

> -----Original Message-----
> From: Joel Martin [mailto:j_martin at lbl.gov] 
> Sent: Wednesday, November 07, 2007 5:37 PM
> To: Kevin Brown
> Subject: Re: [Bioperl-l] Bio::Ext::Align?
> 
> Hello,
>     Might be a side effect of fixing the other bioperl-ext package, 
> what steps exactly did this entail:
> 
> > I installed bioperl-ext from CVS, 
> 
> ?
> 
> you can probably bypass it at the moment by doing this after 
> unpacking the
> bioperl-ext package 
> 
> cd Bio/Ext/Align
> perl Makefile.PL
> make
> make test
> make install
> 
> and
> 
> cd Bio/Ext/HMM
> perl Makefile.PL
> make 
> make test
> make install
> 
> Joel
> 
> but can't figure out what else is
> > missing to utilize Bio::Tools::pSW.  The error I get from 
> the example
> > script in the wiki is:
> > 
> > The C-compiled engine for Smith Waterman alignments 
> (Bio::Ext::Align)
> > has not been installed.
> >  Please read the install the bioperl-ext package
> > 
> > BEGIN failed--compilation aborted at
> > /usr/lib/perl5/site_perl/5.8.5/Bio/Tools/pSW.pm line 128.
> > Compilation failed in require at ./align_test.pl line 3.
> > BEGIN failed--compilation aborted at ./align_test.pl line 3.
> > 
> > In /usr/lib/perl5/site_perl/5.8.5/Bio/Ext there is a folder called
> > Align, but no Align.pm file.
> > 
> > I followed the directions in the wiki to install 1.5.2_102 
> (think I had
> > _100 installed previously).  Any thoughts on what I'm missing?
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 



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