[Bioperl-l] problem with bioperl install

[Chris Fields]

A autogenerated passthrough Makefile.PL is generated with the  
distribution:

http://cpansearch.perl.org/src/CJFIELDS/BioPerl-1.6.0/Makefile.PL

We may remove that in future releases, but it should work regardless  
(i.e. call Module::Build and Build.PL).  I'm pretty convinced that the  
issue was permissions-based at heart.  Note Kristina ran 'cpan'  
instead of 'sudo cpan' to invoke the shell, so the shell is using  
current user config instead of su for installation.  You need to use  
'sudo' to install anything /Library/Perl on Mac (unless you are  
already 'root', but on recent OS X version logging in as 'root' is  
turned off).

I just noticed nothing is mentioned along these lines in the  
installation docs, so we'll need to update those.

chris

On May 29, 2009, at 4:08 PM, Mark A. Jensen wrote:

> Hi Kristina,
>
> [Don't forget to reply-all, so the list stays in the loop. Many many  
> more helpers
> there.]
>
> Apparently cpan can't make the Makefile, but can download and expand  
> the
> library directories, in your .cpan directory (see edited highlights  
> below).
>
> Let's appeal to the BioPerl brethren/sestren---answers?
>
> MAJ
>
>
> term dump:
>
> dhcp-0019353043-25-35:BioPerl-1.6.0 kristinafontanez$ cpan
> Terminal does not support AddHistory.
>
> cpan shell -- CPAN exploration and modules installation (v1.7602)
> ReadLine support available (try 'install Bundle::CPAN')
>
> cpan> install Test::Harness
> CPAN: Storable loaded ok
> Going to read /Users/kristinafontanez/.cpan/Metadata
> Database was generated on Fri, 29 May 2009 11:27:00 GMT
> Running install for module Test::Harness
> Running make for A/AN/ANDYA/Test-Harness-3.17.tar.gz
> CPAN: Digest::MD5 loaded ok
> CPAN: Compress::Zlib loaded ok
> Checksum for /Users/kristinafontanez/.cpan/sources/authors/id/A/AN/ 
> ANDYA/Test-Harness-3.17.tar.gz ok
> Scanning cache /Users/kristinafontanez/.cpan/build for sizes
> Test-Harness-3.17/
> Test-Harness-3.17/Build.PL
> ...
> Test-Harness-3.17/xt/perls/sample-tests/
> Test-Harness-3.17/xt/perls/sample-tests/perl_version
> Removing previously used /Users/kristinafontanez/.cpan/build/Test- 
> Harness-3.17
>
> CPAN.pm: Going to build A/AN/ANDYA/Test-Harness-3.17.tar.gz
>
> Checking if your kit is complete...
> Looks good
> Writing Makefile for Test::Harness
>   -- NOT OK
> Running make test
> Can't test without successful make
> Running make install
> make had returned bad status, install seems impossible
>
> cpan> install File::HomeDir
> ...[more of same]...
>
>
> ----- Original Message ----- From: "Kristina Fontanez" <fontanez at fas.harvard.edu 
> >
> To: "Mark A. Jensen" <maj at fortinbras.us>
> Sent: Friday, May 29, 2009 3:56 PM
> Subject: Re: [Bioperl-l] problem with bioperl install
>
>
>> Mr. Jensen-
>>
>> Thank you for your help but unfortunately the installation of
>> Test::Harness etc didn't work. I copied my terminal output and
>> attached the file. Any advice on what's still going wrong?
>>
>> Thanks,
>> 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 3:35 PM, Mark A. Jensen wrote:
>>
>> The message says you are first updating your CPAN.pm.
>> That module needs modules you don't have, so
>>
>> use cpan to install the dependencies you don't have, viz.
>>>   Test::Harness
>>>   File::HomeDir
>>
>> $ cpan
>>> install Test::Harness
>> etc.
>> Then install CPAN.pm again (or run the Bioperl install again).
>>
>> Lather, rinse, repeat the install of Bioperl until it completes
>> without errors.
>>
>> ----- Original Message ----- From: "Kristina Fontanez" <fontanez at fas.harvard.edu
>> >
>> To: <bioperl-l at bioperl.org>
>> Sent: Friday, May 29, 2009 3:07 PM
>> Subject: [Bioperl-l] problem with bioperl install
>>
>>
>>> Hello-
>>>
>>> I am trying to install bioperl and I ran into some problems. See
>>> list  below.
>>>
>>>
>>> CPAN.pm: Going to build A/AN/ANDK/CPAN-1.94.tar.gz
>>>
>>> Checking if your kit is complete...
>>> Looks good
>>> Warning: prerequisite File::HomeDir 0.69 not found.
>>> Warning: prerequisite Test::Harness 2.62 not found. We have 2.56.
>>> Writing Makefile for CPAN
>>> ---- Unsatisfied dependencies detected during [A/AN/ANDK/
>>> CPAN-1.94.tar.gz] -----
>>>   Test::Harness
>>>   File::HomeDir
>>>
>>>
>>> How can I fix this?
>>>
>>>
>>> Thanks,
>>> 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
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>
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