[Bioperl-l] problem with bioperl install

[Dan Bolser]

2009/6/1 Chris Fields <cjfields at illinois.edu>:

...
> 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
...

local::lib is supposed to take care of this. Is this broken on Mac?
Building stuff as root is generally considered to be bad.



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

I tried to write down a clear 'recipe' for getting things installed
(this was actually on the GMod wiki). I really think the install docs
could be improved. Sometimes less verbose is better.

Dan

> 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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