Apt installation fails on Debian Sid

Hi!

I tried installing the graph_tool package as per the instructions on the
download page, but apt-get fails with the following error:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 graph-tool : Depends: libcgal7 but it is not installable

It seems libcgal7 was recently renamed to libcgal8, as this is the only
available package in both testing and Wheezy.
Can I install using libcgal8, or will  have to wait for a version compatible
with this?

Thanks!
Tue

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Installing in a virtual environment

Hi all,
I've tried to install graph-tool inside a virtual environment in
multiple ways now, e.g.

1. pip install graph-tool
2. pip install http://downloads.skewed.de/graph-tool/graph-tool-2.2.15.tar.bz2
3. easy_install graph-tool
4. Running "configure-make-make install" from source

The first three failed basically because there's no setup.py and the
fourth one failed because it couldn't find numpy (which is already
installed in the virtual environment). I could do a system-wide
installation, but that's not what I want. Have you guys successfully
installed graph-tool inside a virtual environment?
Best,
--

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 Hector
_______________________________________________
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Veronoi Diagram and Data locality

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Building on windows (windows 7 64 bit building for win32)

Hello,

 Has anyone had much luck with this?

 I've been trying under cygwin with very little luck. Specifically I'm
running ./configure, and it runs for a reasonable period of time
(after I installed various requirements), but am now getting:

checking for boostlib >= 1.38.0... yes
checking whether the Boost::Python library is available... no
configure: error: No usable boost::python found

 Even though I feel like claiming that there is indeed a viable
boost::python available (that is to say, I claim I've installed it).

 Is there any hope for me here? Is there a better way to get it
running (as a part of a .exe) under windows? I'll continue onward, but
would love some words of encouragement, if anyone has them ...

--

-- 
Noon Silk

Fancy a quantum lunch? http://groups.google.com/group/quantum-lunch?hl=en

"Every morning when I wake up, I experience an exquisite joy — the joy
of being this signature."

graph-tool on Mac OS Lion - running!

Hi!

Wonders seem to happen once in a while. Finally I got graph-tool running on my Lion machine. Here are my steps
which lead to a running graph-tool:

1. deinstall Macports python 2.7 such that it is never in the way (reinstall whatever you need in macports
with python with the python26 branch)
2. install boost 1.47.0 into $HOME/.local; linked against python 2.7 from apple
3. install numpy/scipy from the SuperPack, see scipy.org
4. install cgal 3.9 with gmp and other dependencies coming from macports; install dir is $HOME/.local
5. grab graph-tool from git and configure it with

PYTHON_VERSION=2.7 PYTHON=/usr/bin/python2.7 CXXFLAGS="-I/$HOME/.local/include
-I/opt/local/include" CFLAGS="-I$HOME/.local/include -I/opt/local/include"
LDFLAGS="-L$HOME/.local/lib -L/opt/local/lib" ./configure --prefix=$HOME/.local
--with-boost=$HOME/.local/
--with-numpy=/Library/Python/2.7/site-packages/numpy-2.0.0.dev_3b3735d_20111219-py2.7-macosx-10.7-x86_64.egg/numpy/
--with-scipy=/Library/Python/2.7/site-packages/scipy-0.11.0.dev_c2ff01c_20111219-py2.7-macosx-10.7-x86_64.egg/scipy/
--disable-debug --disable-openmp

Compile it a very long time and then install it. Of course, I use the latest Xcode 4.2.1. I found it really hard
to get graph tool running on Lion.

Cheers,

Sebastian

--

-- 
Sebastian Weber
Group of Cell Communication and Control
Freiburg Institute for Advanced Studies - FRIAS
School of Life Sciences - LIFENET
Albert-Ludwigs-Universität Freiburg
Albertstr. 19
79104 Freiburg
T.: +49-761-203-97237
Fax:+49-761-203-97334

about graph-tool and mac os x lion

Hello,

I see recently many people have had one problem or another to run graph-tool on mac os x.
I've been able to build graph-tool on Lion, with apple gcc 4.2, boost
1.47 and python 2.7.2 (these last two from homebrew).
The problem is that graph_tool doesn't import:

ImportError                               Traceback (most recent call last)
/Users/hammer/TIS/java-hacking/giraph/≤ipython-input-1-100bbe2bc9d9>
in <module>()
----> 1 from graph_tool.all import *

/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/__init__.py
in <module>()
    89 import scipy.stats
    90
---> 91 from dl_import import *
    92 dl_import("import libgraph_tool_core as libcore")
    93 import libgraph_tool_core as libcore   # for pylint

/usr/local/Cellar/python/2.7.2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/dl_import.py
in <module>()
    25     # handle strange python installations, by importing from
the deprecated dl

    26     # module

---> 27     from dl import RTLD_LAZY, RTLD_GLOBAL
    28
    29 __all__ = ["dl_import"]

ImportError: No module named dl

I noticed that DLFCN module is missing on my python install. I tried
to substitute the RTLD_LAZY and RTLD_GLOBAL values (0x1 and 0x8) taken
from the include file dlfcn.h into the setdlopenflags call in that
same dl_import.py, but i get a trap back:

Fatal Python error: Interpreter not initialized (version mismatch?)
Abort trap: 6

Do you have any idea? How did you guys get graph_tool working on mac os?

thanks!
--
    Claudio Martella
    claudio.martella <at> vu.nl

current git version not working...

autogen.sh results in 

configure.ac:331: required file `src/graph/draw/Makefile.in' not found

looking into it shows that there is no draw directory inside graph. Something not checked into git?

Cheers,

--

-- 
Sebastian Weber
Group of Cell Communication and Control
Freiburg Institute for Advanced Studies - FRIAS
School of Life Sciences - LIFENET
Albert-Ludwigs-Universität Freiburg
Albertstr. 19
79104 Freiburg
T.: +49-761-203-97237
Fax:+49-761-203-97334

graph-tool on MacOSX Lion

Hi!

Anyone got graph-tool working on Lion? It was a real mess to set it up under Snow Leopard, and I am running into
some issues again. Hence did someone make it work?

Macports?
Python version?
scipy/numpy version?
boost version?
CGAL?

Which compiler - the apple one? If Macports, what did you compile with which option?

Thanks a lot for any hint here.

Cheers,

--

-- 
Sebastian Weber
Group of Cell Communication and Control
Freiburg Institute for Advanced Studies - FRIAS
School of Life Sciences - LIFENET
Albert-Ludwigs-Universität Freiburg
Albertstr. 19
79104 Freiburg
T.: +49-761-203-97237
Fax:+49-761-203-97334

gml compilation issues

Hi!

I just failed to compile the latest graph-tool svn with gml enabled. The log of the compiler is enclosed. My
system is

Mac OSX Lion,
boost 1.47.0
python 2.7.1 from Apple,
gcc 4.2 compiler

The 2.2.15 version finished flawlessly to compile. BTW, what about the macports graph-tool port? Is it
known to work? What compiler, which boost, and what python version is required? MacOS is a mess in this regard…

Cheers,

--

-- 
Sebastian Weber
Group of Cell Communication and Control
Freiburg Institute for Advanced Studies - FRIAS
School of Life Sciences - LIFENET
Albert-Ludwigs-Universität Freiburg
Albertstr. 19
79104 Freiburg
T.: +49-761-203-97237
Fax:+49-761-203-97334

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graph-tool and boost 1.48 (mac os)

Hi,

I'm trying to build according to the linked homebrew Formula (but i
also tried downloading the source and building straight ahead).

I have llvm gcc 4.2 (mac os x standard) and boost 1.48.

I get the following error pretty straight ahead at compile time (for
graph_betweenness):

/usr/local/include/boost/property_map/property_map.hpp:361: error: no
match for 'operator[]' in '(const
boost::unchecked_vector_property_map<double,
boost::adj_list_edge_property_map<boost::bidirectional_tag, long
unsigned int, long unsigned int&, long unsigned int,
boost::property<boost::edge_index_t, long unsigned int,
boost::no_property>, boost::edge_index_t> >&)((const
boost::unchecked_vector_property_map<double,
boost::adj_list_edge_property_map<boost::bidirectional_tag, long
unsigned int, long unsigned int&, long unsigned int,
boost::property<boost::edge_index_t, long unsigned int,
boost::no_property>, boost::edge_index_t> >*)(& pa))[k]'
./../fast_vector_property_map.hh:170: note: candidates are: typename
std::iterator_traits<typename std::vector<T, std::allocator<_CharT>
>::iterator>::reference boost::unchecked_vector_property_map<T,
IndexMap>::operator[](const typename
boost::property_traits<IndexMap>::key_type&) const [with T = double,
IndexMap = boost::adj_list_edge_property_map<boost::bidirectional_tag,
long unsigned int, long unsigned int&, long unsigned int,
boost::property<boost::edge_index_t, long unsigned int,
boost::no_property>, boost::edge_index_t>]

preceded by a looong series of "instantiated from" etc.

What am I doing wrong?

Thanks

--

-- 
   Claudio Martella
   claudio.martella <at> gmail.com

boost errors building on Mac OSX

Hi all,

I've been trying to build graph-tool on my Mac (10.7.2) for the past few
days. The issues occur with graph-tool-2.2.15 (though I've also had issues
with the lastest code from github). At this point I have reached a bit of a
dead end. Looking at what I posted below, does anyone have any suggestions??
Many thanks!!

Jesse

Here is my configure command:

./configure --enable-openmp --with-boost-python=boost_python_mt
--with-numpy=/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy
--with-scipy=/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/scipy
LDFLAGS=-L/opt/local/lib CXXFLAGS="-I/opt/local/include"

The additional args stem from the fact that I'm using the Enthought python
distribution and macports, both of which put stuff in non-standard places it
seems. The graph-tool build error is related to boost, which I installed
using macports (version 1.47) . So I doubt my problems have to do with
Enthought. 

Now, here's the compiler/make output:

jberwald <at> hyperion:~/src/graph-tool-2.2.15$ make
make  all-recursive
Making all in src
Making all in graph
Making all in centrality
  CXX    graph_betweenness.lo
  CXX    graph_centrality_bind.lo
  CXX    graph_eigentrust.lo
  CXX    graph_eigenvector.lo
  CXX    graph_pagerank.lo
  CXX    graph_trust_transitivity.lo
  CXXLD  libgraph_tool_centrality.la
Making all in clustering
  CXX    graph_clustering.lo
  CXX    graph_extended_clustering.lo
  CXX    graph_motifs.lo
graph_motifs.hh: In member function 'void
graph_tool::get_all_motifs::operator()(Graph&, size_t, boost::any&,
std::vector<long unsigned int, std::allocator&lt;long unsigned int> >&,
Sampler, double, bool, bool, graph_tool::rng_t&) const [with Graph =
boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS,
boost::no_property, boost::property&lt;boost::edge_index_t, long unsigned
int, boost::no_property>, boost::no_property, boost::listS>, Sampler =
graph_tool::sample_all]':
graph_motifs.hh:415: internal compiler error: in lower_stmt, at
gimple-low.c:319
Please submit a full bug report,
with preprocessed source if appropriate.
See <URL:http://developer.apple.com/bugreporter> for instructions.
make[4]: *** [graph_motifs.lo] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Also, I attempted to install from macports originally. But macports tells me
the following:

Error: Cannot install py27-graph-tool for the arch(s) 'i386 x86_64' because
> Error: its dependency py27-scipy does not build for the required
> arch(s) by default
> Error: and does not have a universal variant.
> Error: Unable to execute port: architecture mismatch

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