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

[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.
>>>>>>>> _______________________________________________
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>>>>>>> 
>>>>>>> 
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>>>>>>> 
>>>>>> 
>>>>>> 
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>>>>> 
>>>>> 
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