[Bioperl-l] problem with bioperl install

Chris Fields cjfields at illinois.edu
Fri May 29 22:27:16 EDT 2009


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.)

I don't know what to say beyond 'it works for me'.  I'll backlog to  
see if I can work it out, but it appears to be something with 'make'.

>> 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.

Actually, don't do it AT ALL.  Various system tools use the native  
perl build only (hence the various breakages when updating Mac OS X).  
Replace it and you'll likely have a huge headache (and have to  
reinstall).  I believe the perl installation docs for Mac indicate  
something along these lines.

If you really need I suggest either installing the latest perl via  
MacPorts/Fink or compiling and and installing it yourself.

chris




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