From: Milos I. <mi...@pr...> - 2008-08-08 17:50:23
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Hi Francesc, thanks for your reply. I have tried installing pytables first (step 4) and then trying the import, but I get the same error. I don't have too much experience with installing libraries, but it seems to me that Python is finding the correct library, which is tables/utilsExtension.so, but there is some problem with it, namely ImportError: dlopen(tables/utilsExtension.so, 2): Symbol not found: _compress2 Below is what happens if I delete utilsExtension.so from the tables directory, and type the build command again, which compiles the shared library again. If I understand this correctly, the compilation of the utilsExtension.so library is successful, but when I try to import tables from Python, something goes wrong. I am thinking that there may be something wrong with whatever Python uses to load the shared library ( I have also installed a newer version of libtool, but I am not sure if that helps). If anyone has an idea what may be going wrong, please let me know. Thanks again! Milos ---------- begin output -------------- dynamic-oit-vapornet-c-682:pytables-2.0.4 milos$ python setup.py build_ext --inplace --hdf5=/usr/local/hdf5 * Found numpy 1.1.1 package installed. * Found HDF5 headers at ``/usr/local/hdf5/include``, library at ``/usr/local/hdf5/lib``. * Found LZO 2 headers at ``/usr/local/include``, library at ``/usr/local/lib``. * Skipping detection of LZO 1 since LZO 2 has already been found. * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``. running build_ext building 'tables.utilsExtension' extension C compiler: gcc -arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd -fno-common -dynamic -DNDEBUG -g -O3 compile options: '-DNDEBUG=1 -DHAVE_LZO2_LIB=1 -DHAVE_BZ2_LIB=1 -I/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/core/include -I/usr/include -I/usr/local/include -I/usr/local/hdf5/include -I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5 -c' extra options: '-DH5_USE_16_API' gcc -arch i386 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -g -bundle -undefined dynamic_lookup build/temp.macosx-10.3-i386-2.5/src/utilsExtension.o build/temp.macosx-10.3-i386-2.5/src/utils.o build/temp.macosx-10.3-i386-2.5/src/H5ARRAY.o build/temp.macosx-10.3-i386-2.5/src/H5ATTR.o -L/lib64 -L/lib -L/usr/lib64 -L/usr/lib -L/usr/local/lib64 -L/usr/local/lib -L/usr/local/hdf5/lib -lhdf5 -o tables/utilsExtension.so --------- end output ---------------- On Fri, Aug 8, 2008 at 3:46 AM, Francesc Alted <fa...@py...> wrote: > Hi, > > The truth is that I've no clues about your problem. Did you install the > PyTables package in a locally accessible Python repository, right? > > At any rate, I'm CC'ing this to the PyTables list. Perhaps someone with > more experience with MacOSX can shed some light on this. Incidentally, > it is always a good idea to send this sort of reports to the PyTables > list so that the community as a whole, and not only me, can help you. > > Regards, > > A Friday 08 August 2008, escriguéreu: > > Hi Francesc, > > > > I am sending this just to you first, since it is an installation > > issue, so I don't want to bother the whole user group. I just > > installed Mac OS X Leopard and I have been trying to re-build all my > > tools for development in Python. After installing python, gcc, HDF5, > > LZO and numpy, PyTables is next. When I try to build it, I get the > > following output first: > > > > dynamic-oit-vapornet-a-358:pytables-2.0.4 milos$ python setup.py > > build_ext --inplace > > * Found numpy 1.1.1 package installed. > > * Found HDF5 headers at ``/usr/local/hdf5/include``, library at > > ``/usr/local/hdf5/lib``. > > * Found LZO 2 headers at ``/usr/local/include``, library at > > ``/usr/local/lib``. > > * Skipping detection of LZO 1 since LZO 2 has already been found. > > * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``. > > running build_ext > > > > I am assuming that the first few lines indicate that PyTables is > > happy with what I have installed on the system so far. After that, > > the build runs and finishes with no problem (the full output's rather > > long, but I could try reproducing it and sending it if you want). > > After that, I am trying to import tables and test them (suggested > > step 2 of the installation), but the problem I have is the following: > > > > dynamic-oit-vapornet-a-358:pytables-2.0.4 milos$ python > > Python 2.5.2 (r252:60911, Feb 22 2008, 07:57:53) > > [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin > > Type "help", "copyright", "credits" or "license" for more > > information. > > > > >>> import tables > > > > Traceback (most recent call last): > > File "<stdin>", line 1, in <module> > > File "tables/__init__.py", line 56, in <module> > > from tables.utilsExtension import getPyTablesVersion, > > getHDF5Version ImportError: dlopen(tables/utilsExtension.so, 2): > > Symbol not found: _compress2 > > Referenced from: > > /Users/milos/Work/python/pytables-2.0.4/tables/utilsExtension.so > > Expected in: dynamic lookup > > > > I am not sure what this means, but I am guessing that it doesn't have > > to do with the libraries. Do you have an idea what may be going on? > > Thanks, > > > > Milos > > > > -- > Francesc Alted > Freelance developer > Tel +34-964-282-249 > |