[Bioperl-l] Fwd: Bioperl Installation

Chris Fields cjfields at illinois.edu
Mon Jul 6 17:06:56 EDT 2009


Okay, that makes more sense to me (and also makes sense looking at the  
Data::Stag makefile).  None of those additional modules are required  
for bioperl core functionality.

chris

On Jul 6, 2009, at 3:50 PM, Scott Cain wrote:

> Hi Dave,
>
> I think you are confused about the prereqs for Data::Stag: I have it
> installed and working and don't have Tk.  cpantesters.org also thinks
> that IO::String is the only dependency:
>
>  http://deps.cpantesters.org/?module=Data::Stag;perl=latest
>
> Scott
>
>
> On Mon, Jul 6, 2009 at 4:26 PM, Dave  
> Messina<David.Messina at sbc.su.se> wrote:
>> Hi Steven,
>> Forwarding this to the list so that everyone can follow  
>> along...please keep
>> the list on any replies.
>>
>> Don't quit out of the install -- cpan can automatically detect  
>> required
>> dependencies and will try to install them first.
>>
>> Amidst all of the kerfuffle in your previous install there was this  
>> bit:
>>
>> ---- Unsatisfied dependencies detected during
>> [C/CJ/CJFIELDS/BioPerl-1.6.0.tar.gz] -----
>>
>>    Test::Harness
>>
>>    Data::Stag
>>
>>    CPAN
>>
>> Shall I follow them and prepend them to the queue
>>
>> of modules we are processing right now? [yes]
>>
>>
>> So if you go back into cpan, try the Bioperl-1.6 install again, you  
>> should
>> be prompted again about those missing dependencies.
>>
>>
>>
>> A note to the Bioperl core-devs:
>>
>> Data::Stag seems to have a couple of tricky dependencies of its  
>> own, namely
>> GD and Tk, and it looks like they're for a couple of included  
>> scripts which
>> I'm guessing Bioperl doesn't use.
>>
>> Perhaps we should send a request to the Data::Stag author to make  
>> GD and Tk
>> optional instead of required?
>>
>>
>> Dave
>>
>>
>>
>>
>> ---------- Forwarded message ----------
>> From: Steven McGowan <stevey_mac2k2 at hotmail.com>
>> Date: Mon, Jul 6, 2009 at 22:02
>> Subject: RE: [Bioperl-l] Bioperl Installation
>> To: david.messina at sbc.su.se
>>
>>
>>  Hi Dave,
>>
>> I managed to sort it and have had a go at
>> installing: (install C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz), but upon
>> installing have noticed the error:
>>
>> Checking prerequisites...
>>  - ERROR: Data::Stag is not installed
>>
>> so i have then quit out of the install, and entered "install  
>> Data::Stag"
>> in>CPAN
>>
>> but receive the following error messages:
>>
>> External Module XML::LibXSLT, XSLT,
>>  is not installed on this computer.
>>  Data::Stag::XSLTHandler in Data::Stag needs it for XSLT  
>> Transformations
>>
>> External Module XML::Parser::PerlSAX, SAX Handler,
>>  is not installed on this computer.
>>  Data::Stag::XMLParser in Data::Stag needs it for parsing XML
>>
>> External Module GD, Graphical Drawing Toolkit,
>>  is not installed on this computer.
>>  stag-drawtree.pl in Data::Stag needs it for drawing trees
>>
>> External Module Graph::Directed, Generic Graph data stucture and  
>> algorithms,
>>  is not installed on this computer.
>>  Data::Stag::GraphHandler in Data::Stag needs it for transforming  
>> stag
>> trees to graphs
>>
>> External Module Tk, Tk,
>>  is not installed on this computer.
>>  stag-view.pl in Data::Stag needs it for tree viewer
>>
>> ok so for the C/CJ/CJFIELDS/BioPerl-db-1.6.0.tar.gz install, it's  
>> lacking
>> Data::Stag who's install is lacking the list above. How would i go  
>> about
>> installing the above list? is there an easier way or something i'm  
>> doing
>> wrong?
>>
>> Thanks,
>>
>> Stephen
>>
>> ------------------------------
>> From: David.Messina at sbc.su.se
>> Date: Mon, 6 Jul 2009 21:38:09 +0200
>> Subject: Re: [Bioperl-l] Bioperl Installation
>> To: stevey_mac2k2 at hotmail.com
>> CC: Bioperl-l at lists.open-bio.org
>>
>>
>> Hi Stephen,
>> This is on a Mac, correct?
>>
>> You need to install the developer tools first. The key line in your  
>> log is:
>>
>>  Can't test without successful make
>>
>>
>> Admittedly, that's cryptic. What it means is that it needs the  
>> program
>> called make. That program is installed when you install the  
>> developer tools.
>>
>>
>> Go to developer.apple.com and create an account if you don't  
>> already have
>> one.
>>
>>
>> Go to the Mac Dev Center, and click on "Xcode 3".
>>
>>
>> This should be the right link:
>>
>> Xcode 3
>>
>> You'll need to login to get to it, and then you'll get to the  
>> download page
>> for the massive 986 MB Xcode 3.1.3 download.
>>
>> After you run the Xcode installer, you can check in Terminal that  
>> you've got
>> 'make' installed by typing:
>>
>> which make
>>
>> on the command line. It should give you the answer
>> make is /usr/bin/make
>>
>> If it does, then you're good to try again with the bioperl install.
>>
>> Dave
>>
>>
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>
>
>
> -- 
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
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