[Bioperl-l] problem with bioperl install

Mark A. Jensen maj at fortinbras.us
Fri May 29 17:08:16 EDT 2009


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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