Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK

[Tamás Nepusz]

Hi,

Whoops. Sorry, it looks like the Python interface is lagging behind a bit. 
Something seems to be wrong with our nightly build server. I'll check it soon 
-- in the meanwhile, I have uploaded the most recent Python interface here:

http://dl.dropbox.com/u/1911856/python-igraph_nightly_0.6-2633-20120107.tar.gz

Please try again with this version and let me know.

Cheers,
T.

On 7 Jan 2012, at 17:29, Jonathan Donges wrote:

> Hi,
> 
> I obtained the archive python-igraph_nightly_0.6-2596-20111130.tar.gz from 
> the latest nightly build from Google Code. I'm trying to compile from this 
> archive. I it surely version 0.6 of the Python interface.
> 
> Cheers,
> Jonathan
> 
> Am 07.01.2012 um 16:28 schrieb Tamás Nepusz:
> 
>> Hi,
>> 
>> It is likely that you are compiling the 0.5.x source code of the Python 
>> interface against the C core of 0.6. You have to update the source code of 
>> the Python interface to the 0.6 branch as well.
>> 
>> -- 
>> T.
>> 
>> On 7 Jan 2012, at 16:27, Jonathan Donges wrote:
>> 
>>> Hi Tamas,
>>> 
>>> I removed these 0.5.x files and made sure that the igraph 0.6 files are 
>>> installed in /usr/local/lib and /usr/local/include/igraph (Yes, I ran "make 
>>> install"). I made sure that these files are graph version 0.6. There are no 
>>> igraph files left in the /opt subdirectories anymore.
>>> 
>>> The compilation of python-igraph proceeds much further now, but I get an 
>>> error here:
>>> 
>>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 
>>> -g -O2 -DNDEBUG -g -O3 -I/opt/local/include/igraph -I../../build/include 
>>> -I../../include -I/usr/local/include -I/usr/include 
>>> -I/usr/local/include/igraph 
>>> -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c 
>>> src/graphobject.c -o build/temp.macosx-10.6-intel-2.7/src/graphobject.o
>>> src/graphobject.c: In function ‘igraphmodule_Graph_Weighted_Adjacency’:
>>> src/graphobject.c:3016: error: too few arguments to function 
>>> ‘igraph_weighted_adjacency’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_layout_kamada_kawai’:
>>> src/graphobject.c:5795: error: too few arguments to function 
>>> ‘igraph_layout_kamada_kawai’
>>> src/graphobject.c:5798: error: too few arguments to function 
>>> ‘igraph_layout_kamada_kawai_3d’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_layout_kamada_kawai_3d’:
>>> src/graphobject.c:5850: error: too few arguments to function 
>>> ‘igraph_layout_kamada_kawai_3d’
>>> src/graphobject.c: In function 
>>> ‘igraphmodule_Graph_layout_fruchterman_reingold’:
>>> src/graphobject.c:6033: error: too few arguments to function 
>>> ‘igraph_layout_fruchterman_reingold’
>>> src/graphobject.c:6036: error: too few arguments to function 
>>> ‘igraph_layout_fruchterman_reingold_3d’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_laplacian’:
>>> src/graphobject.c:6620: warning: passing argument 3 of ‘igraph_laplacian’ 
>>> makes pointer from integer without a cast
>>> src/graphobject.c:6620: warning: passing argument 4 of ‘igraph_laplacian’ 
>>> makes integer from pointer without a cast
>>> src/graphobject.c:6620: error: too few arguments to function 
>>> ‘igraph_laplacian’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_Weighted_Adjacency’:
>>> src/graphobject.c:3016: error: too few arguments to function 
>>> ‘igraph_weighted_adjacency’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_layout_kamada_kawai’:
>>> src/graphobject.c:5795: error: too few arguments to function 
>>> ‘igraph_layout_kamada_kawai’
>>> src/graphobject.c:5798: error: too few arguments to function 
>>> ‘igraph_layout_kamada_kawai_3d’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_layout_kamada_kawai_3d’:
>>> src/graphobject.c:5850: error: too few arguments to function 
>>> ‘igraph_layout_kamada_kawai_3d’
>>> src/graphobject.c: In function 
>>> ‘igraphmodule_Graph_layout_fruchterman_reingold’:
>>> src/graphobject.c:6033: error: too few arguments to function 
>>> ‘igraph_layout_fruchterman_reingold’
>>> src/graphobject.c:6036: error: too few arguments to function 
>>> ‘igraph_layout_fruchterman_reingold_3d’
>>> src/graphobject.c: In function ‘igraphmodule_Graph_laplacian’:
>>> src/graphobject.c:6620: warning: passing argument 3 of ‘igraph_laplacian’ 
>>> makes pointer from integer without a cast
>>> src/graphobject.c:6620: warning: passing argument 4 of ‘igraph_laplacian’ 
>>> makes integer from pointer without a cast
>>> src/graphobject.c:6620: error: too few arguments to function 
>>> ‘igraph_laplacian’
>>> lipo: can't figure out the architecture type of: /var/tmp//ccKfaou7.out
>>> error: command 'gcc-4.2' failed with exit status 1
>>> 
>>> Now this seems to an error related to the compiler or the code, not a 
>>> missing file error anymore.
>>> 
>>> Cheers,
>>> Jonathan
>>> 
>>> Am 07.01.2012 um 15:34 schrieb Tamás Nepusz:
>>> 
>>>> Hi,
>>>> 
>>>> These are the include files of igraph 0.5.x, not igraph 0.6. Have you run 
>>>> "make install" after having compiled igraph 0.6?
>>>> 
>>>> -- 
>>>> T.
>>>> 
>>>> On 7 Jan 2012, at 15:14, Jonathan Donges wrote:
>>>> 
>>>>> Hi,
>>>>> 
>>>>> No, both files are not there. There are the following files in 
>>>>> /opt/local/include/igraph:
>>>>> 
>>>>> -rw-r--r--  1 root  admin    1042  7 Jan 13:11 DensityGrid.h
>>>>> -rw-r--r--  1 root  admin    1085  7 Jan 13:11 DensityGrid_3d.h
>>>>> -rw-r--r--  1 root  admin   22624  7 Jan 13:11 NetDataTypes.h
>>>>> -rw-r--r--  1 root  admin    2468  7 Jan 13:11 NetRoutines.h
>>>>> -rw-r--r--  1 root  admin   13492  7 Jan 13:11 arpack.h
>>>>> -rw-r--r--  1 root  admin    5676  7 Jan 13:11 arpack_internal.h
>>>>> -rw-r--r--  1 root  admin    2111  7 Jan 13:11 array.h
>>>>> -rw-r--r--  1 root  admin    2563  7 Jan 13:11 array.pmt
>>>>> -rw-r--r--  1 root  admin   24822  7 Jan 13:11 attributes.h
>>>>> -rw-r--r--  1 root  admin    1833  7 Jan 13:11 dqueue.h
>>>>> -rw-r--r--  1 root  admin    7413  7 Jan 13:11 dqueue.pmt
>>>>> -rw-r--r--  1 root  admin     563  7 Jan 13:11 drl_Node.h
>>>>> -rw-r--r--  1 root  admin     579  7 Jan 13:11 drl_Node_3d.h
>>>>> -rw-r--r--  1 root  admin    2834  7 Jan 13:11 drl_graph.h
>>>>> -rw-r--r--  1 root  admin    2513  7 Jan 13:11 drl_graph_3d.h
>>>>> -rw-r--r--  1 root  admin    1211  7 Jan 13:11 drl_layout.h
>>>>> -rw-r--r--  1 root  admin    1210  7 Jan 13:11 drl_layout_3d.h
>>>>> -rw-r--r--  1 root  admin     835  7 Jan 13:11 drl_parse.h
>>>>> -rw-r--r--  1 root  admin   21083  7 Jan 13:11 error.h
>>>>> -rw-r--r--  1 root  admin    4688  7 Jan 13:11 f2c.h
>>>>> -rw-r--r--  1 root  admin    1727  7 Jan 13:11 gengraph_box_list.h
>>>>> -rw-r--r--  1 root  admin    3689  7 Jan 13:11 gengraph_definitions.h
>>>>> -rw-r--r--  1 root  admin    1443  7 Jan 13:11 gengraph_degree_sequence.h
>>>>> -rw-r--r--  1 root  admin    6567  7 Jan 13:11 
>>>>> gengraph_graph_molloy_hash.h
>>>>> -rw-r--r--  1 root  admin   10317  7 Jan 13:11 
>>>>> gengraph_graph_molloy_optimized.h
>>>>> -rw-r--r--  1 root  admin    7284  7 Jan 13:11 gengraph_hash.h
>>>>> -rw-r--r--  1 root  admin    1993  7 Jan 13:11 gengraph_header.h
>>>>> -rw-r--r--  1 root  admin    2113  7 Jan 13:11 gengraph_powerlaw.h
>>>>> -rw-r--r--  1 root  admin    9831  7 Jan 13:11 gengraph_qsort.h
>>>>> -rw-r--r--  1 root  admin    6445  7 Jan 13:11 gengraph_random.h
>>>>> -rw-r--r--  1 root  admin    1311  7 Jan 13:11 gengraph_vertex_cover.h
>>>>> -rw-r--r--  1 root  admin    3012  7 Jan 13:11 gml_tree.h
>>>>> -rw-r--r--  1 root  admin    1925  7 Jan 13:11 heap.h
>>>>> -rw-r--r--  1 root  admin    9136  7 Jan 13:11 heap.pmt
>>>>> -rw-r--r--  1 root  admin  115521  7 Jan 13:11 igraph.h
>>>>> -rw-r--r--  1 root  admin    2010  7 Jan 13:11 igraph_math.h
>>>>> -rw-r--r--  1 root  admin    2790  7 Jan 13:11 igraph_pmt.h
>>>>> -rw-r--r--  1 root  admin    1793  7 Jan 13:11 igraph_pmt_off.h
>>>>> -rw-r--r--  1 root  admin    5707  7 Jan 13:11 interrupt.h
>>>>> -rw-r--r--  1 root  admin    7567  7 Jan 13:11 matrix.h
>>>>> -rw-r--r--  1 root  admin   38279  7 Jan 13:11 matrix.pmt
>>>>> -rw-r--r--  1 root  admin    4423  7 Jan 13:11 pottsmodel_2.h
>>>>> -rw-r--r--  1 root  admin    1640  7 Jan 13:11 stack.h
>>>>> -rw-r--r--  1 root  admin    6500  7 Jan 13:11 stack.pmt
>>>>> -rw-r--r--  1 root  admin   26043  7 Jan 13:11 types.h
>>>>> -rw-r--r--  1 root  admin    8862  7 Jan 13:11 vector.h
>>>>> -rw-r--r--  1 root  admin   54712  7 Jan 13:11 vector.pmt
>>>>> -rw-r--r--  1 root  admin    6458  7 Jan 13:11 walktrap_communities.h
>>>>> -rw-r--r--  1 root  admin    3389  7 Jan 13:11 walktrap_graph.h
>>>>> -rw-r--r--  1 root  admin    4285  7 Jan 13:11 walktrap_heap.h
>>>>> 
>>>>> Best,
>>>>> Jonathan
>>>>> 
>>>>> 
>>>>> Am 07.01.2012 um 13:45 schrieb Tamás Nepusz:
>>>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> Do you have igraph_arpack.h, igraph_error.h and similar header files in 
>>>>>> /opt/local/include/igraph?
>>>>>> 
>>>>>> -- 
>>>>>> T.
>>>>>> 
>>>>>> On 7 Jan 2012, at 13:43, Jonathan Donges wrote:
>>>>>> 
>>>>>>> Hi Tamas,
>>>>>>> 
>>>>>>> That helped to reduce a lot of the errors. But still there are some 
>>>>>>> left related to arpack again:
>>>>>>> 
>>>>>>>>> sudo python setup.py install
>>>>>>> 
>>>>>>> Include path: /opt/local/include/igraph
>>>>>>> Library path: /opt/local/lib
>>>>>>> running install
>>>>>>> running bdist_egg
>>>>>>> running egg_info
>>>>>>> writing python_igraph.egg-info/PKG-INFO
>>>>>>> writing top-level names to python_igraph.egg-info/top_level.txt
>>>>>>> writing dependency_links to python_igraph.egg-info/dependency_links.txt
>>>>>>> reading manifest file 'python_igraph.egg-info/SOURCES.txt'
>>>>>>> reading manifest template 'MANIFEST.in'
>>>>>>> writing manifest file 'python_igraph.egg-info/SOURCES.txt'
>>>>>>> installing library code to build/bdist.macosx-10.6-intel/egg
>>>>>>> running install_lib
>>>>>>> running build_py
>>>>>>> running build_ext
>>>>>>> building 'igraph._igraph' extension
>>>>>>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch 
>>>>>>> x86_64 -g -O2 -DNDEBUG -g -O3 -I/opt/local/include/igraph 
>>>>>>> -I../../build/include -I../../include -I/usr/local/include 
>>>>>>> -I/usr/include 
>>>>>>> -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 
>>>>>>> -c src/arpackobject.c -o 
>>>>>>> build/temp.macosx-10.6-intel-2.7/src/arpackobject.o
>>>>>>> In file included from src/arpackobject.c:24:
>>>>>>> src/arpackobject.h:28:27: error: igraph_arpack.h: No such file or 
>>>>>>> directory
>>>>>>> In file included from src/arpackobject.c:26:
>>>>>>> src/error.h:28:26: error: igraph_error.h: No such file or directory
>>>>>>> In file included from src/arpackobject.c:24:
>>>>>>> src/arpackobject.h:28:27: error: igraph_arpack.h: No such file or 
>>>>>>> directory
>>>>>>> In file included from src/arpackobject.c:26:
>>>>>>> src/error.h:28:26: error: igraph_error.h: No such file or directory
>>>>>>> lipo: can't figure out the architecture type of: /var/tmp//cclTdhxd.out
>>>>>>> error: command 'gcc-4.2' failed with exit status 1
>>>>>>> 
>>>>>>> What else can be done?
>>>>>>> 
>>>>>>> Cheers,
>>>>>>> Jonathan
>>>>>>> 
>>>>>>> 
>>>>>>> Am 06.01.2012 um 15:14 schrieb Tamás Nepusz:
>>>>>>> 
>>>>>>>> Hi,
>>>>>>>> 
>>>>>>>> I think I know what the problem is. igraph 0.6 currently puts its 
>>>>>>>> include files in an igraph/ subfolder within the include dir (I guess 
>>>>>>>> /usr/local/include), but setup.cfg still refers to /usr/local/include. 
>>>>>>>> Try using /usr/local/include/igraph instead. The library path can stay 
>>>>>>>> as is.
>>>>>>>> 
>>>>>>>> Cheers,
>>>>>>>> Tamas
>>>>>>>> 
>>>>>>>> On 6 Jan 2012, at 15:06, Jonathan Donges wrote:
>>>>>>>> 
>>>>>>>>> Hi,
>>>>>>>>> 
>>>>>>>>> I removed all older versions of the igraph C libraries and made sure 
>>>>>>>>> that the libs are installed in /usr/local/lib. The headers are 
>>>>>>>>> installed in /usr/local/include. I made sure that these directories 
>>>>>>>>> are referenced both in the setup.cfg and setup.py files as 
>>>>>>>>> recommended:
>>>>>>>>> 
>>>>>>>>> sudo python setup.py install
>>>>>>>>> Using default include and library paths for compilation
>>>>>>>>> If the compilation fails, please edit the LIBIGRAPH_FALLBACK_*
>>>>>>>>> variables in setup.py or include_dirs and library_dirs in 
>>>>>>>>> setup.cfg to point to the correct directories and libraries
>>>>>>>>> where the C core of igraph is installed
>>>>>>>>> ()
>>>>>>>>> Include path: /usr/include /usr/local/include
>>>>>>>>> Library path: /usr/lib /usr/local/lib
>>>>>>>>> 
>>>>>>>>> I still get the same errors as before when trying to install 
>>>>>>>>> python-igraph on Lion:
>>>>>>>>> 
>>>>>>>>> …
>>>>>>>>> building 'igraph._igraph' extension
>>>>>>>>> gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -arch i386 -arch 
>>>>>>>>> x86_64 -g -O2 -DNDEBUG -g -O3 -I/usr/include -I/usr/local/include 
>>>>>>>>> -I../../build/include -I../../include -I/usr/local/include 
>>>>>>>>> -I/usr/include 
>>>>>>>>> -I/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 
>>>>>>>>> -c src/arpackobject.c -o 
>>>>>>>>> build/temp.macosx-10.6-intel-2.7/src/arpackobject.o
>>>>>>>>> In file included from src/arpackobject.c:24:
>>>>>>>>> src/arpackobject.h:28:27: error: igraph_arpack.h: No such file or 
>>>>>>>>> directory
>>>>>>>>> In file included from src/arpackobject.h:29,
>>>>>>>>>         from src/arpackobject.c:24:
>>>>>>>>> src/graphobject.h:28:20: error: igraph.h: No such file or directory
>>>>>>>>> …
>>>>>>>>> 
>>>>>>>>> Do you have an idea what I could do next?
>>>>>>>>> 
>>>>>>>>> Thanks,
>>>>>>>>> Jonathan
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> Am 05.01.2012 um 22:53 schrieb Tamás Nepusz:
>>>>>>>>> 
>>>>>>>>>>> The igraph headers reside in /usr/local/include on my system. 
>>>>>>>>>>> Still, I get the same error. Maybe the version is not correct (I 
>>>>>>>>>>> had an earlier version of graph installed before upgrading to Lion 
>>>>>>>>>>> from Leopard)? How can I check the version of the headers?
>>>>>>>>>> Check out /usr/local/include/igraph_version.h, it should contain the 
>>>>>>>>>> version number. If you don't have this file then the headers are 
>>>>>>>>>> from 0.5.x since this header has been added only in the 0.6 branch.
>>>>>>>>>> 
>>>>>>>>>> Cheers,
>>>>>>>>>> T.
>>>>>>>>>> _______________________________________________
>>>>>>>>>> igraph-help mailing list
>>>>>>>>>> address@hidden
>>>>>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> _______________________________________________
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>>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
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