[Bioperl-l] problem installing bioperl-ext

Barry Moore barry.moore at genetics.utah.edu
Tue Nov 16 12:10:05 EST 2004


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 

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:
>/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.
>Alicia Amadoz
>Evolutionary Genetics Unit
>Cavanilles Institute for Biodiversity and Evolutionary
>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
>NOTE! For shipments by EXPRESS COURIER use "Instituto
>Cavanilles de Biodiversidad y Biología Evolutiva,
>Polígono de la Coma s/n, 46980 Paterna (Valencia),
>Spain" instead of P.O. Box no. and Post Code/City above.
>Bioperl-l mailing list
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Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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