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Re: [igraph] Problem installing python-igraph on Mac OS X Lion related t
From: |
Tamás Nepusz |
Subject: |
Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK |
Date: |
Sat, 7 Jan 2012 17:57:35 +0100 |
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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> igraph-help mailing list
>>>>>>>>> address@hidden
>>>>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> igraph-help mailing list
>>>>>>>> address@hidden
>>>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> igraph-help mailing list
>>>>>>> address@hidden
>>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> igraph-help mailing list
>>>>>> address@hidden
>>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> igraph-help mailing list
>>>>> address@hidden
>>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> igraph-help mailing list
>>>> address@hidden
>>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
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>
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, (continued)
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/06
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/06
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Tamás Nepusz, 2012/01/06
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Tamás Nepusz, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Tamás Nepusz, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Tamás Nepusz, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK,
Tamás Nepusz <=
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Jonathan Donges, 2012/01/07
- Re: [igraph] Problem installing python-igraph on Mac OS X Lion related to ARPACK, Tamás Nepusz, 2012/01/07