[Bioperl-l] Fwd: Bioperl Installation

Dave Messina David.Messina at sbc.su.se
Mon Jul 6 20:26:55 UTC 2009

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] -----




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?


---------- 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"

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



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

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.


View your Twitter and Flickr updates from one place – Learn

More information about the Bioperl-l mailing list