Newbie question installing on MacOSX

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Newbie question installing on MacOSX

James-357
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

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Re: Newbie question installing on MacOSX

Adam Witney

Hi James,

You are mixing up your installation methods. Either install with fink, or download the source and install from there, not both.

I would personally recommend installing it from source or better still install from cpan. Take a look here:

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_Build.PL
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#INSTALLING_BIOPERL_THE_EASY_WAY_USING_CPAN

If you really want to use fink then take a look here:

http://www.bioperl.org/wiki/Getting_BioPerl#Mac_OS_X_using_fink

It looks like the command for this is:

fink install bioperl-pm588

but I don't use fink any more so I am not certain of how that works.

adam


On 29 Jul 2010, at 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
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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Re: Newbie question installing on MacOSX

Roy Chaudhuri-3
In reply to this post by James-357
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
> [hidden email]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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Re: Newbie question installing on MacOSX

Roy Chaudhuri-3
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
>>> [hidden email]
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>

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Re: Newbie question installing on MacOSX

James-357
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
>>>> [hidden email]
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
>
>

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