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[ANN] igraph 0.9.0 Released

Alex Gutteridge

11/19/2007 7:23:00 AM

igraph version 0.9.0 has been released!

* <http://igraph.rubyforg...

IGraph is a Ruby extension for interfacing with igraph (http://cneurocvs.rmki.kfki....
), a C library for creating and manipulating graphs with a particular
emphasis on network analysis functions.

IGraph now wraps 99% of igraph functions including functions for
randomly and deterministically generating graphs, many functions for
analysing the structure of graphs, 2D and 3D graph layout functions
and support for reading and writing graphs in various file formats.

This release basically completes the wrapping process. Future releases
will be for bug fixes and behind the scenes code clean-up.

Changes:

# 0.9 2007-11-19

* All igraph functions wrapped
* Documentation updated with examples

* <http://igraph.rubyforg...

Alex Gutteridge

Bioinformatics Center
Kyoto University
6 Answers

unbewusst.sein

11/19/2007 3:09:00 PM

0

Alex Gutteridge <alexg@kuicr.kyoto-u.ac.jp> wrote:

> igraph version 0.9.0 has been released!

does it install successfully on Mac OS X 10.4.11 ???

because with :
----------------------------------------------------------------------
----------------------------------------------------------------------

I got :
RubyMate r6354 running Ruby r1.8.6 (/opt/local/bin/ruby)
>>> essai_1.rb

dyld: NSLinkModule() error
dyld: Symbol not found: _open_memstream
Referenced from:
/opt/local/lib/ruby/gems/1.8/gems/igraph-0.9.0/test/igraph.bundle
Expected in: flat namespace

How did i install it ?

igraph :

$ ./configure --prefix=/opt/local
$ make
$ make check

>>> everything OK

$ sudo make install

and the gem afterwards :

~/work/Ruby/iGraph/igraph-0.4.4%> sudo gem install igraph --
--with-igraph-include=/opt/local/include/igraph
Building native extensions. This could take a while...
Successfully installed igraph-0.9.0
Installing ri documentation for igraph-0.9.0...
Installing RDoc documentation for igraph-0.9.0...


may be i've forgotten something ???
--
Une Bévue

unbewusst.sein

11/19/2007 3:11:00 PM

0

Une Bévue <unbewusst.sein@weltanschauung.com.invalid> wrote:

> because with :

OOPS :
> ----------------------------------------------------------------------

#! /usr/bin/env ruby

require 'igraph'

g = IGraph::GenerateRandom.erdos_renyi_game(IGraph::ERDOS_RENYI_GNP,
1000, 5.0/1000,
false, false)

d = g.diameter(false,true).size-1
puts "Diameter of a random graph with average degree 5: #{d}"

> ----------------------------------------------------------------------


--
Une Bévue

csardi.gabor

11/19/2007 10:00:00 PM

0

Une, maybe Alex has a better answer, but it seems that the Ruby igraph
extension uses the open_memstream function, which is not available in
OSX.
A temporary solution would be to find open_memstream calls in the code
and comment out functions which use it. This way you might lose some
exporting functions, maybe all of them.

Gabor

On Nov 19, 4:10 pm, unbewusst.s...@weltanschauung.com.invalid (Une
Bévue) wrote:
> Une Bévue <unbewusst.s...@weltanschauung.com.invalid> wrote:
> > because with :
>
> OOPS :
>
> > ----------------------------------------------------------------------
>
> #! /usr/bin/env ruby
>
> require 'igraph'
>
> g = IGraph::GenerateRandom.erdos_renyi_game(IGraph::ERDOS_RENYI_GNP,
> 1000, 5.0/1000,
> false, false)
>
> d = g.diameter(false,true).size-1
> puts "Diameter of a random graph with average degree 5: #{d}"
>
> > ----------------------------------------------------------------------
>
> --
> Une Bévue

Alex Gutteridge

11/20/2007 1:01:00 AM

0

Yup, I'd not tested on OSX, but I'll get on it and see if there's a =20
better way to implement the read/write functions.

Until then Gabor's fix should work (though like he says you won't be =20
able to use the read/write methods): get the source from svn, remove =20
ext/cIGraph_file.c, run extconf.rb and make by hand to install.

AlexG

On 20 Nov 2007, at 07:00, csardi.gabor@gmail.com wrote:

> Une, maybe Alex has a better answer, but it seems that the Ruby igraph
> extension uses the open_memstream function, which is not available in
> OSX.
> A temporary solution would be to find open_memstream calls in the code
> and comment out functions which use it. This way you might lose some
> exporting functions, maybe all of them.
>
> Gabor
>
> On Nov 19, 4:10 pm, unbewusst.s...@weltanschauung.com.invalid (Une
> B=E9vue) wrote:
>> Une B=E9vue <unbewusst.s...@weltanschauung.com.invalid> wrote:
>>> because with :
>>
>> OOPS :
>>
>>> =
----------------------------------------------------------------------
>>
>> #! /usr/bin/env ruby
>>
>> require 'igraph'
>>
>> g =3D =
IGraph::GenerateRandom.erdos_renyi_game(IGraph::ERDOS_RENYI_GNP,
>> 1000, 5.0/1000,
>> false, false)
>>
>> d =3D g.diameter(false,true).size-1
>> puts "Diameter of a random graph with average degree 5: #{d}"
>>
>>> =
----------------------------------------------------------------------
>>
>> --
>> Une B=E9vue
>
>

Alex Gutteridge

Bioinformatics Center
Kyoto University

Alex Gutteridge

11/20/2007 4:36:00 AM

0

On 20 Nov 2007, at 00:10, Une B=E9vue wrote:

> Alex Gutteridge <alexg@kuicr.kyoto-u.ac.jp> wrote:
>
>> igraph version 0.9.0 has been released!
>
> does it install successfully on Mac OS X 10.4.11 ???

I've released a new gem (0.9.1) which disables the file read/write =20
methods under OSX. This allows the rest of the library to compile and =20=

function correctly, but obviously isn't an ideal solution. In the =20
longer term I'll look into re-doing those functions so that they don't =20=

use open_memstream and friends.

NB: Under 10.5 running on my PPC Powerbook I had to use:

sudo env ARCHFLAGS=3D'-arch ppc' gem install igraph -t -- --with-igraph-=20=

include=3D/usr/local/include/igraph/

To get it to install (otherwise it tries to build a universal binary =20
that isn't compatible with my PPC igraph install), though under 10.4 I =20=

don't think you'll need that and:

sudo gem install igraph -t -- --with-igraph-include=3D/usr/local/include/=20=

igraph/

Should be enough. Let me know if it still gives you problems and I'll =20=

hit it again.

Alex Gutteridge

Bioinformatics Center
Kyoto University

unbewusst.sein

11/20/2007 8:14:00 AM

0

Alex Gutteridge <alexg@kuicr.kyoto-u.ac.jp> wrote:

> Should be enough. Let me know if it still gives you problems and I'll
> hit it again.

It is enough with :

~%> sudo gem uninstall igraph
Password:
Successfully uninstalled igraph-0.9.0
~%> sudo gem install igraph --
--with-igraph-include=/opt/local/include/igraph
Bulk updating Gem source index for: http://gems.rub...
Building native extensions. This could take a while...
Successfully installed igraph-0.9.1
1 gem installed
Installing ri documentation for igraph-0.9.1...
Installing RDoc documentation for igraph-0.9.1...

i should mention i've upgraded gem system itself to 0.9.5 in the
meantime

thanks to all !
--
Une Bévue