Re: [Pytables-users] pytables: could not find the HDF5 runtime
Thanks Anthony. I will check it out. Cheers, Jennifer -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
[Pytables-users] pytables: could not find the HDF5 runtime
Hi, I'm trying to install pytables and its proving difficult (using MAC OS 10.6.4). I have installed in /usr/local/hdf5 and set the environment variable $HDF5_DIR to /usr/local/hdf5. When I run setup, I get a warning about not being able to find the HDF5 runtime. ndmmac149:tables-2.4.0 jflegg$ sudo python setup.py install --hdf5=/usr/local/hdf5 * Found numpy 1.6.1 package installed. * Found numexpr 2.0.1 package installed. * Found Cython 0.17.2 package installed. * Found HDF5 headers at ``/usr/local/hdf5/include``, library at ``/usr/local/hdf5/lib``. .. WARNING:: Could not find the HDF5 runtime. The HDF5 shared library was *not* found in the default library paths. In case of runtime problems, please remember to install it. ld: library not found for -llzo2 collect2: ld returned 1 exit status ld: library not found for -llzo2 collect2: ld returned 1 exit status * Could not find LZO 2 headers and library; disabling support for it. ld: library not found for -llzo collect2: ld returned 1 exit status ld: library not found for -llzo collect2: ld returned 1 exit status * Could not find LZO 1 headers and library; disabling support for it. * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``. running install running build running build_py creating build creating build/lib.macosx-10.5-i386-2.7 creating build/lib.macosx-10.5-i386-2.7/tables copying tables/__init__.py - build/lib.macosx-10.5-i386-2.7/tables copying tables/array.py - build/lib.macosx-10.5-i386-2.7/tables When I import pytables in python, I get the following error message In [1]: import tables - ImportError Traceback (most recent call last) /Users/jflegg/ipython-input-1-389ecae14f10 in module() 1 import tables /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site- packages/tables/__init__.py in module() 28 29 # Necessary imports to get versions stored on the Pyrex extension --- 30 from tables.utilsExtension import getPyTablesVersion, getHDF5Version 31 32 ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/7.3 /lib/python2.7/site-packages/tables/utilsExtension.so, 2): Symbol not found: _H5E_CALLBACK_g Referenced from: /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site- packages/tables/utilsExtension.so Expected in: flat namespace in /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site- packages/tables/utilsExtension.so Any help would be greatly appreciated. Jennifer -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] pytables: could not find the HDF5 runtime
Try leaving the pytables source dir and then running then running IPython. On Mon, Dec 10, 2012 at 9:20 AM, Jennifer Flegg jennifer.fl...@wwarn.orgwrote: Hi, I'm trying to install pytables and its proving difficult (using MAC OS 10.6.4). I have installed in /usr/local/hdf5 and set the environment variable $HDF5_DIR to /usr/local/hdf5. When I run setup, I get a warning about not being able to find the HDF5 runtime. ndmmac149:tables-2.4.0 jflegg$ sudo python setup.py install --hdf5=/usr/local/hdf5 * Found numpy 1.6.1 package installed. * Found numexpr 2.0.1 package installed. * Found Cython 0.17.2 package installed. * Found HDF5 headers at ``/usr/local/hdf5/include``, library at ``/usr/local/hdf5/lib``. .. WARNING:: Could not find the HDF5 runtime. The HDF5 shared library was *not* found in the default library paths. In case of runtime problems, please remember to install it. ld: library not found for -llzo2 collect2: ld returned 1 exit status ld: library not found for -llzo2 collect2: ld returned 1 exit status * Could not find LZO 2 headers and library; disabling support for it. ld: library not found for -llzo collect2: ld returned 1 exit status ld: library not found for -llzo collect2: ld returned 1 exit status * Could not find LZO 1 headers and library; disabling support for it. * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``. running install running build running build_py creating build creating build/lib.macosx-10.5-i386-2.7 creating build/lib.macosx-10.5-i386-2.7/tables copying tables/__init__.py - build/lib.macosx-10.5-i386-2.7/tables copying tables/array.py - build/lib.macosx-10.5-i386-2.7/tables When I import pytables in python, I get the following error message In [1]: import tables - ImportError Traceback (most recent call last) /Users/jflegg/ipython-input-1-389ecae14f10 in module() 1 import tables /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site- packages/tables/__init__.py in module() 28 29 # Necessary imports to get versions stored on the Pyrex extension --- 30 from tables.utilsExtension import getPyTablesVersion, getHDF5Version 31 32 ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/7.3 /lib/python2.7/site-packages/tables/utilsExtension.so, 2): Symbol not found: _H5E_CALLBACK_g Referenced from: /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site- packages/tables/utilsExtension.so Expected in: flat namespace in /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site- packages/tables/utilsExtension.so Any help would be greatly appreciated. Jennifer -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] pytables: could not find the HDF5 runtime
Hi Anthony, Thanks for your reply. I installed HDF5 also from source. The reason I'm building hdf5 and pytables myself is that they don't seem to be available through EPD any more (at least in the free version: http://www.enthought.com/products/epdlibraries.php) They used to both come bundled in EPD, but not anymore, which is a pain. Many thanks, Jennifer -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] pytables: could not find the HDF5 runtime
Hi Jennifer, Yeah, that is right, they are not in EPD Free. However, they are in Anaconda CE (http://continuum.io/downloads.html). Note the CE rather than the full version. Be Well Anthony On Mon, Dec 10, 2012 at 4:07 PM, Jennifer Flegg jennifer.fl...@wwarn.orgwrote: Hi Anthony, Thanks for your reply. I installed HDF5 also from source. The reason I'm building hdf5 and pytables myself is that they don't seem to be available through EPD any more (at least in the free version: http://www.enthought.com/products/epdlibraries.php) They used to both come bundled in EPD, but not anymore, which is a pain. Many thanks, Jennifer -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
