[Bioperl-l] bioperl installation

Jason Stajich jason at cgt.duhs.duke.edu
Thu Jul 22 11:25:41 EDT 2004

Did you install Inline::C?
>From the README in bioperl-ext directory
  o Installing

 Depending on your choise of extensions, you might need
 Inline::MakeMaker and Inline::C to create the makefile. Use for
 example the cpan program to install Inline::MakeMaker and answer yes
 when prompted to install Inline::C.

This line gives you a hint:
> Can't locate Inline/MakeMaker.pm in @INC (@INC contains:

Did you also install the staden library?
On Thu, 22 Jul 2004, Xiang Deng wrote:

> To whom it may concern,
> I am trying to install bioperl locally under my peronal folder. The  core
> modules were successfully installed. I ran through a simple perl script to
> use bio::perl or bio::seq without complain. but I got problem with
> installing bioperl-ext-1.4.
> When I installed core modules I used this
> >perl Makefile.PL LIB=/my_local_directory/
> My first question is whether or not I have to use the same way to deal
> with ext modules too and I can use the same directory or a separate one.
> Actually I tried both and both failed with error message as follows:
> mendel 207% perl Makefile.PL
> Checking if your kit is complete...
> Looks good
> Writing Makefile for Bio::Ext::Align
> ERROR from evaluation of
> /v0/users/deng0007/my_bioperl/bioperl-ext-1.4/Bio/SeqIO/staden/Makefile.PL:
> Can't locate Inline/MakeMaker.pm in @INC (@INC contains:
> /usr/local/lib/perl5/5.6.1/IP27-irix /usr/local/lib/perl5/5.6.1
> /usr/local/lib/perl5/site_perl/5.6.1/IP27-irix
> /usr/local/lib/perl5/site_perl/5.6.1 /usr/local/lib/perl5/site_perl
> /v0/users/deng0007/my_bioperl/bioperl-ext-1.4 .) at ./Makefile.PL line 1.
> BEGIN failed--compilation aborted at ./Makefile.PL line 1.
> could you please let me know what I did wrong or miss in there? thanks a
> lot,
> Xiang
> Department of Pharmacology and Cancer Biology
> Duke University Medical Center
> Durham, NC 27710
> Phone: 919-4792339

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

More information about the Bioperl-l mailing list