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

[Jonathan Donges]

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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>>>>>> 
>>>>> 
>>>>> 
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