[Bioperl-l] problem installing bioperl-ext

[Barry Moore]

Alicia-

You'll need both the perl Inline package and the Staden package 
installed to do a complete install of bioperl-ext.  Do you really want 
Staden (tools typically used by sequeincing centers)?  If not, don't use 
the makefile.pl at the base of bioperl-ext, but rather use the 
makefile.pl at the level you want to install (i.e. if you only want the 
alignment stuff, use the makefile.pl at that level found here 
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-ext/Bio/Ext/Align/?cvsroot=bioperl).

Barry
<http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/?cvsroot=bioperl#dirlist>
Alicia Amadoz wrote:

>Hi all,
>
>I finally managed to install Bioperl in Fedora Core 2 with Perl 5.8.5.
>It runs ok and passes the test of James Tisdall's book. But when I try
>to install (with 'cpan>force install B/BI/BIRNEY/bioperl-ext-1.4.tar.gz)
> I have some error:
>
>  CPAN.pm: Going to build B/BI/BIRNEY/bioperl-ext-1.4.tar.gz
> 
>Checking if your kit is complete...
>Looks good
>Writing Makefile for Bio::Ext::Align
>ERROR from evaluation of
>/root/.cpan/build/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL: Can't
>locate Inline/MakeMaker.pm in @INC (@INC contains:
>/home/amadoz/.cpan/build/bioperl-1.4/Bio/Perl.pm
>/home/amadoz/.cpan/build/bioperl-1.4/blib/lib/Bio/Perl.pm
>/usr/lib/perl5/5.8.5/i686-linux /usr/lib/perl5/5.8.5
>/usr/lib/perl5/site_perl/5.8.5/i686-linux /usr/lib/perl5/site_perl/5.8.5
>/usr/lib/perl5/site_perl/5.8.3 /usr/lib/perl5/site_perl/5.8.2
>/usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
>/usr/lib/perl5/site_perl /root/.cpan/build/bioperl-ext-1.4 .) at
>./Makefile.PL line 1.
>BEGIN failed--compilation aborted at ./Makefile.PL line 1.
>Running make test
>  Make had some problems, maybe interrupted? Won't test
>Running make install
>  Make had some problems, maybe interrupted? Won't install
>
>
>I have been searching on the mailing-list archive but i couldn't find
>anything useful. Thanks for your help.
>
>Regards,
>Alicia
>
>************************************************
>Alicia Amadoz
>Evolutionary Genetics Unit
>Cavanilles Institute for Biodiversity and Evolutionary
>Biology
>University of Valencia
>Apartado Oficial 22085
>E-46071 Valencia SPAIN
>Phone: (+34) 96 354 3687
>FAX: (+34) 96 354 3670
>e-mail: alicia.amadoz at uv.es
>http://www.uv.es/~amadoz
>***********************************************
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>Cavanilles de Biodiversidad y Biología Evolutiva,
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>
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>

-- 
Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT