[Bioperl-l] installing bioperl

[Chris Fields]

Did you run

perl Makefile.PL

make

make install

'perl Makefile.PL'  generates the Makefile.

Something screwy with DB_File, apparently, is also going on.

> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/auto/DB_File/ 
> DB_File.so:

Try updating or reinstalling DB_File.

Chris

On Jul 20, 2006, at 4:47 PM, Matthew A. Saunders wrote:

> Dear Bioperl representative,
>
> I have been trying to install bioperl (in order to ultimately run some
> Ensembl APIs) but I seem to be having some problems with the
> bioperl installation.
>
> I have followed the installation directions and I get to the last  
> steps of
> the "make" process, yet this stage fails with the error message below.
> Can you possibly tell me what is the problem.  I am not sure that I
> understand the command "make", but I think that it requires that  
> there be
> a file named "makefile" in the given folder, when I look in my newly
> formed "bioperl-1.4" folder there is no "makefile" in there.   
> Perhaps that
> is a problem.  If so, how might I rectify the matter?
>
> Thanks!
>
> Matt
>
>
> ************************************************************* . .
> .
>     Enjoy the rest of bioperl, which you can use after going 'make  
> install'
>
> Checking if your kit is complete...
> Looks good
> /usr/bin/perl: symbol lookup error:
> /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/auto/DB_File/ 
> DB_File.so:
> undefined symbol: db_version
> Running make test
>    Make had some problems, maybe interrupted? Won't test
> Running make install
>    Make had some problems, maybe interrupted? Won't install
> ***************************************************************
>
>
>
> -----------------------------------------------------
>                    Matthew  A. Saunders
>            UNCF-MERCK Postdoctoral Research Fellow
>
>               Dept. of Ecology and Evolution
>                   University of Chicago
>                      (773)834-3964
>                  Skype: mattsaunders555
>              http://home.uchicago.edu/~saunders
> -------------------------------------------------------
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign