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

[Jonathan Donges]

Hi Tamas,

That was it. It works now. I was able to compile the Python package from your 
updated version and everything works fine now! ;)

Thanks a lot for your help. Maybe a Lion binary dmg package would make things 
easier for people ;)

Cheers,
Jonathan

Am 07.01.2012 um 17:57 schrieb 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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>>>>>>>> 
>>>>>>>> 
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