[Bioperl-l] Fw: problem with bioperl install

Mark A. Jensen maj at fortinbras.us
Fri May 29 17:32:27 EDT 2009


one more time.
----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Kristina Fontanez" <fontanez at fas.harvard.edu>
Sent: Friday, May 29, 2009 5:08 PM
Subject: Re: [Bioperl-l] problem with bioperl install


> 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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