[Bioperl-l] problem with bioperl install
Kristina Fontanez
fontanez at fas.harvard.edu
Mon Jun 1 12:41:06 UTC 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
---------------------------------------------------------------
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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