[Bioperl-l] Newbie question installing on MacOSX

James Platt james-platt at hotmail.co.uk
Thu Jul 29 12:11:48 EDT 2010


when I'm in the directory it exits silently. When I'm not...

James$ perl -MBio::Seq -e ''
Can't locate Bio/Seq.pm in @INC (@INC contains: /sw/lib/perl5/darwin- 
thread-multi-2level /sw/lib/perl5 /sw/lib/perl5/darwin /Library/Perl/ 
Updates/5.8.8 /System/Library/Perl/5.8.8/darwin-thread-multi-2level / 
System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread- 
multi-2level /Library/Perl/5.8.8 /Library/Perl /Network/Library/Perl/ 
5.8.8/darwin-thread-multi-2level /Network/Library/Perl/5.8.8 /Network/ 
Library/Perl /System/Library/Perl/Extras/5.8.8/darwin-thread- 
multi-2level /System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 / 
Library/Perl/5.8.1 .).
BEGIN failed--compilation aborted.

I guess I need to try install it again.

J

On 29 Jul 2010, at 16:36, Roy Chaudhuri wrote:

> Please copy replies to the mailing list, that way others can respond.
>
> Try the command:
> perl -MBio::Seq -e ''
>
> If Bioperl is not installed you will get an error message starting  
> "Can't locate Bio/Seq in @INC". If the command just exits silently  
> then BioPerl is installed correctly.
>
> Roy.
>
> On 29/07/2010 16:29, James Platt wrote:
>> Hi,
>>
>> I tried that, sorry I wasn't clear in the first post.
>>
>> James$ fink install bioperl-pm588
>> Information about 2521 packages read in 0 seconds.
>> Failed: no package found for specification 'bioperl-pm588'!
>>
>> I think I may have installed it through fink commander. how do i  
>> check
>> in unix that it is in fact installed?
>>
>> Thanks,
>>
>> James
>>
>> On 29 Jul 2010, at 16:23, Roy Chaudhuri wrote:
>>
>>> Hi James,
>>>
>>> I don't know anything about Macs, but looking here:
>>> http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink
>>>
>>> shouldn't the command be "fink install bioperl-pm588"?
>>>
>>> Roy.
>>>
>>> On 29/07/2010 15:18, James wrote:
>>>> Sorry for the newbie question.
>>>>
>>>> I am having trouble installing Bioperl.
>>>>
>>>> I'm on MacOSX 10.5.8.
>>>>
>>>> I downloaded and installed fink:
>>>>
>>>> $ fink --version
>>>> Package manager version: 0.27.13
>>>> Distribution version: 0.9.0 i386
>>>>
>>>> I then downloaded Bioperl-1.6.1, I'm trying to install it from
>>>> source,
>>>> as explained (http://www.bioperl.org/wiki/Getting_BioPerl). I have
>>>> Xcode installed etc.
>>>>
>>>> '# fink install bioperl-pmXXX'
>>>>
>>>> I try this:
>>>>
>>>> BioPerl-1.6.1 James$ fink install BioPerl-pm
>>>>
>>>> Information about 2521 packages read in 1 seconds.
>>>> Failed: no package found for specification 'BioPerl-pm'!
>>>>
>>>>
>>>> The version of perl I'm running is 5.8.8, I have tried 'fink  
>>>> install
>>>> BioPerl588' but this doesn't work either.
>>>>
>>>> Thanks very much,
>>>>
>>>> James
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>
>



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