[Bioperl-l] problem with bioperl install

Kristina Fontanez fontanez at fas.harvard.edu
Mon Jun 1 08:41:06 EDT 2009

Hey everyone-

Thanks for all the advice. I reinstalled Xcode tools, installed Fink  
and downloaded bioperl successfully. It's now working smoothly.

Thanks again,
Kristina Fontanez
PhD candidate
Department of Organismic and Evolutionary Biology
Cavanaugh lab
Harvard University
16 Divinity Ave.
Cambridge, MA 02138

tel: 617-495-1138
fax: 617-496-6933
email: fontanez at fas.harvard.edu

On May 29, 2009, at 10:40 PM, Chris Fields wrote:


You aren't running as superuser:

 > term dump: > > dhcp-0019353043-25-35:BioPerl-1.6.0 kristinafontanez 
$ cpan

You'll need to run cpan using 'sudo cpan' if installing modules  
anywhere requiring superuser permissions.


On May 29, 2009, at 5:10 PM, Sendu Bala wrote:

> Kristina Fontanez wrote:
>> Hello everyone-
>> Sendu - I took your advice but doing Install Bundle::CPAN did not  
>> take care of the dependencies. It still failed. See attached txt  
>> file with my terminal output. Does anyone have any idea how this  
>> might be?
> From reading the output it seems like perhaps you don't have 'make'  
> or there is something wrong when using it. If you're on a mac you  
> may need to install the dev tools. Someone else want to jump in here  
> with advice?
> Also, check your CPAN configuration to ensure it is trying to use  
> the correct make commands. ('o conf' etc.)
>> If I wanted to wipe all perl from my computer and simply start  
>> over, how might this be accomplished?
> Don't do that. At least not until you know you have a working make  
> setup.
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