[Bioperl-l] Bioperl Installation

[Steven McGowan]

I have since initialised the install and receive the message:

Checking prerequisites...
 - ERROR: Data::Stag is not installed
(I think I'm being run by CPAN, so will rely on CPAN to handle prerequisite installation)
   I'll get CPAN to prepend the installation of this
 - ERROR: Test::Harness (2.56) is installed, but we need version>= 2.62
   I'll get CPAN to prepend the installation of this
 - ERROR: CPAN (1.7602) is installed, but we need version>= 1.81
   I'll get CPAN to prepend the installation of this
Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n] 
do i now want to Install [a]ll optional external modules, [n]one, or choose [i]nteractively? [n]
i'm guessing installing all external modules will include Data::Stag?
StephenFrom: David.Messina at sbc.su.se
Date: Mon, 6 Jul 2009 22:26:55 +0200
Subject: Fwd: [Bioperl-l] Bioperl Installation
To: bioperl-l at lists.open-bio.org
CC: stevey_mac2k2 at hotmail.com

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 answermake is /usr/bin/make
If it does, then you're good to try again with the bioperl install.


Dave

View your Twitter and Flickr updates from one place – Learn more!




_________________________________________________________________
Get the best of MSN on your mobile
http://clk.atdmt.com/UKM/go/147991039/direct/01/