[Bioperl-l] problem with bioperl install

[Kristina Fontanez]

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
---------------------------------------------------------------
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:

Kristina,

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.

chris

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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