h5py - Project Hosting on Google Code

Today 2 hours ago issue 83 (Check for compound type before testing field names) reported by andrew.collette - With h5py 1.2.1: /usr/local/lib/python2.6/dist-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/highlevel.pyc in __getitem__(self, args) 964 else: 965 for name in names: --> 966 if not name in basetype.names: 967 raise ValueError("Field %s does not appear in this type." % name) 968 new_dtype = numpy.dtype([(name, basetype.fields[name][0]) for name in names]) TypeError: argument of type 'NoneType' is not iterable With h5py 1.2.1: /usr/local/lib/python2.6/dist-packages/h5py-1.2.1-py2.6-linux-x86_64.egg/h5py/highlevel.pyc in __getitem__(self, args) 964 else: 965 for name in names: --> 966 if not name in basetype.names: 967 raise ValueError("Field %s does not appear in this type." % name) 968 new_dtype = numpy.dtype([(name, basetype.fields[name][0]) for name in names]) TypeError: argument of type 'NoneType' is not iterable 17 hours ago r519 (Reorganize test suite) committed by andrew.collette - Reorganize test suite Reorganize test suite 19 hours ago r518 (Update ignore rules) committed by andrew.collette - Update ignore rules Update ignore rules Yesterday 37 hours ago r517 (Implement region reference conversion, fix typemapping glitc...) committed by andrew.collette - Implement region reference conversion, fix typemapping glitch Implement region reference conversion, fix typemapping glitch 39 hours ago r516 (Re-add caching) committed by andrew.collette - Re-add caching Re-add caching 40 hours ago r515 (Fix locking, properties, normalize .file attribute) committed by andrew.collette - Fix locking, properties, normalize .file attribute Fix locking, properties, normalize .file attribute Last 7 days Jan 06, 2010 issue 82 (ImportError after "import h5py") Status changed by andrew.collette - Status: Invalid Status: Invalid Jan 04, 2010 r514 (Fix overzealous close() method and broken __repr__ methods) committed by andrew.collette - Fix overzealous close() method and broken __repr__ methods Fix overzealous close() method and broken __repr__ methods Jan 04, 2010 r513 (Improve HL memoization) committed by andrew.collette - Improve HL memoization Improve HL memoization Jan 04, 2010 r512 (Fix windows DLL issue) committed by andrew.collette - Fix windows DLL issue Fix windows DLL issue Jan 04, 2010 r511 (Fix windows DLL issue) committed by andrew.collette - Fix windows DLL issue Fix windows DLL issue Jan 04, 2010 r510 (Fix windows DLL issue) committed by andrew.collette - Fix windows DLL issue Fix windows DLL issue Jan 04, 2010 r509 (Fix windows DLL issue) committed by andrew.collette - Fix windows DLL issue Fix windows DLL issue Jan 04, 2010 r508 (Improve setup autodetection) committed by andrew.collette - Improve setup autodetection Improve setup autodetection Jan 04, 2010 r507 (Add setup debug line) committed by andrew.collette - Add setup debug line Add setup debug line Jan 04, 2010 r506 (Cleanup) committed by andrew.collette - Cleanup Cleanup Jan 04, 2010 r505 (Implement new caching/locking system) committed by andrew.collette - Implement new caching/locking system Implement new caching/locking system Jan 04, 2010 r504 (Don't force-close File objects (can orphan other open object...) committed by andrew.collette - Don't force-close File objects (can orphan other open objects) Don't force-close File objects (can orphan other open objects) Jan 04, 2010 r503 (Add H5Fget_intent) committed by andrew.collette - Add H5Fget_intent Add H5Fget_intent Jan 04, 2010 r502 (Change per-file locking system, and allow manual binding of ...) committed by andrew.collette - Change per-file locking system, and allow manual binding of File objects Change per-file locking system, and allow manual binding of File objects Jan 04, 2010 r501 (Implement H5Rget_name (LL and HL)) committed by andrew.collette - Implement H5Rget_name (LL and HL) Implement H5Rget_name (LL and HL) Last 30 days Dec 30, 2009 r500 (update docs) committed by andrew.collette - update docs update docs Dec 21, 2009 issue 82 (ImportError after "import h5py") commented on by andrew.collette - That seems to be the correct package version, but I'm not really a mac person. This page: http://py25-h5py.darwinports.com/ seems to suggest that h5py requires hdf5-18, which may include shared libs. That seems to be the correct package version, but I'm not really a mac person. This page: http://py25-h5py.darwinports.com/ seems to suggest that h5py requires hdf5-18, which may include shared libs. Dec 21, 2009 issue 82 (ImportError after "import h5py") commented on by RussianSpy2 - What's the package name? I've tried "py25-h5py" and got: tin-10699S:~ tin$ sudo port install py25-h5py Error: Port py25-h5py not found tin-10699S:~ tin$ What's the package name? I've tried "py25-h5py" and got: tin-10699S:~ tin$ sudo port install py25-h5py Error: Port py25-h5py not found tin-10699S:~ tin$ Dec 21, 2009 issue 82 (ImportError after "import h5py") commented on by andrew.collette - Please make sure that you have a shared-library build of HDF5 installed. You can also try to install h5py via macports as well. Please make sure that you have a shared-library build of HDF5 installed. You can also try to install h5py via macports as well. Dec 21, 2009 issue 82 (ImportError after "import h5py") reported by RussianSpy2 - OS: OSX 10.4 Package manager used to install hdf5: MacPorts Terminal text: tin-10699S:~ tin$ sudo port install hdf5 ---> Fetching hdf5 ---> Attempting to fetch hdf5-1.6.8.tar.gz from ftp://ftp.hdfgroup.org/HDF5/current16/src/ ---> Attempting to fetch hdf5-1.6.8.tar.gz from http://distfiles.macports.org/hdf5 ---> Verifying checksum(s) for hdf5 ---> Extracting hdf5 ---> Applying patches to hdf5 ---> Configuring hdf5 ---> Building hdf5 ---> Staging hdf5 into destroot ---> Installing hdf5 @1.6.8_0 ---> Activating hdf5 @1.6.8_0 ---> Cleaning hdf5 tin-10699S:~ tin$ sudo easy_install h5py Password: Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. Searching for h5py No matching release version found. Searching for latest development version. No matching release version found. Searching for latest development version. Reading http://pypi.python.org/simple/h5py/ Reading http://h5py.alfven.org Reading http://code.google.com/p/h5py/downloads/list Best match: h5py 1.2.1 Downloading http://h5py.googlecode.com/files/h5py-1.2.1.tar.gz Processing h5py-1.2.1.tar.gz Running h5py-1.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-BSOC4-/h5py-1.2.1/egg-dist-tmp-rxTgWk Warning: Can't determine HDF5 version, assuming 1.6 (use --api= to override) Building for HDF5 1.6 (path not specified) h5py/h5g.c: In function ‘__pyx_pf_4h5py_3h5g_iterate’:h5py/h5g.c: In function ‘__pyx_pf_4h5py_3h5g_iterate’: h5py/h5g.c:1941: warning: passing argument 4 of ‘H5Giterate’ from incompatible pointer type h5py/h5g.c:1941: warning: passing argument 4 of ‘H5Giterate’ from incompatible pointer type h5py/h5s.c: In function ‘__pyx_pf_4h5py_3h5s_7SpaceID_select_elements’: h5py/h5s.c:2777: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type h5py/h5s.c: In function ‘__pyx_pf_4h5py_3h5s_7SpaceID_select_elements’: h5py/h5s.c:2777: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_exists’: h5py/h5a.c:1561: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_iterate’: h5py/h5a.c:2024: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_exists’: h5py/h5a.c:1561: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_iterate’: h5py/h5a.c:2024: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5p.c: In function ‘__pyx_pf_4h5py_3h5p_8PropFAID_get_cache’: h5py/h5p.c:5274: warning: passing argument 3 of ‘H5Pget_cache’ from incompatible pointer type h5py/h5p.c: In function ‘__pyx_pf_4h5py_3h5p_8PropFAID_get_cache’: h5py/h5p.c:5274: warning: passing argument 3 of ‘H5Pget_cache’ from incompatible pointer type zip_safe flag not set; analyzing archive contents... h5py.tests.common: module references __file__ Adding h5py 1.2.1 to easy-install.pth file Installed /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg Processing dependencies for h5py Finished processing dependencies for h5py Saving current state... Successfully saved the current state. tin-10699S:~ tin$ python EPD_Py25 (4.3.0) -- http://www.enthought.com Python 2.5.4 \|EPD_Py25 4.3.0\| (r254:67916, May 17 2009, 20:07:12) [GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import h5py Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg/h5py/__init__.py", line 24, in <module> import h5 ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg/h5py/h5.so, 2): Symbol not found: _H5Pget_filter_by_id Referenced from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg/h5py/h5.so Expected in: dynamic lookup >>> OS: OSX 10.4 Package manager used to install hdf5: MacPorts Terminal text: tin-10699S:~ tin$ sudo port install hdf5 ---> Fetching hdf5 ---> Attempting to fetch hdf5-1.6.8.tar.gz from ftp://ftp.hdfgroup.org/HDF5/current16/src/ ---> Attempting to fetch hdf5-1.6.8.tar.gz from http://distfiles.macports.org/hdf5 ---> Verifying checksum(s) for hdf5 ---> Extracting hdf5 ---> Applying patches to hdf5 ---> Configuring hdf5 ---> Building hdf5 ---> Staging hdf5 into destroot ---> Installing hdf5 @1.6.8_0 ---> Activating hdf5 @1.6.8_0 ---> Cleaning hdf5 tin-10699S:~ tin$ sudo easy_install h5py Password: Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. Searching for h5py No matching release version found. Searching for latest development version. No matching release version found. Searching for latest development version. Reading http://pypi.python.org/simple/h5py/ Reading http://h5py.alfven.org Reading http://code.google.com/p/h5py/downloads/list Best match: h5py 1.2.1 Downloading http://h5py.googlecode.com/files/h5py-1.2.1.tar.gz Processing h5py-1.2.1.tar.gz Running h5py-1.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-BSOC4-/h5py-1.2.1/egg-dist-tmp-rxTgWk Warning: Can't determine HDF5 version, assuming 1.6 (use --api= to override) Building for HDF5 1.6 (path not specified) h5py/h5g.c: In function ‘__pyx_pf_4h5py_3h5g_iterate’:h5py/h5g.c: In function ‘__pyx_pf_4h5py_3h5g_iterate’: h5py/h5g.c:1941: warning: passing argument 4 of ‘H5Giterate’ from incompatible pointer type h5py/h5g.c:1941: warning: passing argument 4 of ‘H5Giterate’ from incompatible pointer type h5py/h5s.c: In function ‘__pyx_pf_4h5py_3h5s_7SpaceID_select_elements’: h5py/h5s.c:2777: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type h5py/h5s.c: In function ‘__pyx_pf_4h5py_3h5s_7SpaceID_select_elements’: h5py/h5s.c:2777: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_exists’: h5py/h5a.c:1561: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_iterate’: h5py/h5a.c:2024: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_exists’: h5py/h5a.c:1561: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5a.c: In function ‘__pyx_pf_4h5py_3h5a_iterate’: h5py/h5a.c:2024: warning: passing argument 3 of ‘H5Aiterate’ from incompatible pointer type h5py/h5p.c: In function ‘__pyx_pf_4h5py_3h5p_8PropFAID_get_cache’: h5py/h5p.c:5274: warning: passing argument 3 of ‘H5Pget_cache’ from incompatible pointer type h5py/h5p.c: In function ‘__pyx_pf_4h5py_3h5p_8PropFAID_get_cache’: h5py/h5p.c:5274: warning: passing argument 3 of ‘H5Pget_cache’ from incompatible pointer type zip_safe flag not set; analyzing archive contents... h5py.tests.common: module references __file__ Adding h5py 1.2.1 to easy-install.pth file Installed /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg Processing dependencies for h5py Finished processing dependencies for h5py Saving current state... Successfully saved the current state. tin-10699S:~ tin$ python EPD_Py25 (4.3.0) -- http://www.enthought.com Python 2.5.4 \|EPD_Py25 4.3.0\| (r254:67916, May 17 2009, 20:07:12) [GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import h5py Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg/h5py/__init__.py", line 24, in <module> import h5 ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg/h5py/h5.so, 2): Symbol not found: _H5Pget_filter_by_id Referenced from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/h5py-1.2.1-py2.5-macosx-10.3-fat.egg/h5py/h5.so Expected in: dynamic lookup >>> Dec 21, 2009 r499 (Fix autodetection on Windows) committed by andrew.collette - Fix autodetection on Windows Fix autodetection on Windows Dec 19, 2009 r498 (Fix typo) committed by andrew.collette - Fix typo Fix typo Dec 19, 2009 r497 (Overhaul setup.py) committed by andrew.collette - Overhaul setup.py Overhaul setup.py Dec 15, 2009 FAQ (Design of h5py and supported features) Wiki page edited by andrew.collette - Revision r496 Edited wiki page through web user interface. Revision r496 Edited wiki page through web user interface. Dec 15, 2009 CommonProblems (Frequently-encountered issues and how to correct them) Wiki page edited by andrew.collette - Revision r495 Add wiki info on NumPy functions Revision r495 Add wiki info on NumPy functions Dec 15, 2009 issue 78 (Slow data copy to numpy arrays) Labels changed by andrew.collette - I agree this is a problem, especially when trying to use datasets in a "numpy-like" context. I consider the behavior of numpy.array(dataset) to be a legitimate performance concern, which I will address in the next release of h5py by adding whatever __array__ methods NumPy wants to avoid iteration over the first axis. However, there are limits to what I can do with this. The following code will always be somewhat slow: x = np.zeros_like(dataset) because (according to the source of zeros_like), if "dataset" doesn't inherit from ndarray, it first converts it to an array (by reading in all the data), takes the dtype and shape, and then throws the data away! I think at least a FAQ entry on the limits of how h5py and NumPy interact would be useful. In particular, the recommended cycle for h5py is: 1. Read in (a subset of) your data into memory (i.e. into a NumPy array) 2. Do some work on it 3. Write it back out to the dataset Because reading and writing are in general expensive, this is likely to produce the best results. In this case your example would read: dataset = h5['path to dataset'] a = dataset[...] # a is an in-memory NumPy array b = a > 1 You can dispense with the load_array function and the extra manual copying step. Labels: Priority-High −Priority-Medium I agree this is a problem, especially when trying to use datasets in a "numpy-like" context. I consider the behavior of numpy.array(dataset) to be a legitimate performance concern, which I will address in the next release of h5py by adding whatever __array__ methods NumPy wants to avoid iteration over the first axis. However, there are limits to what I can do with this. The following code will always be somewhat slow: x = np.zeros_like(dataset) because (according to the source of zeros_like), if "dataset" doesn't inherit from ndarray, it first converts it to an array (by reading in all the data), takes the dtype and shape, and then throws the data away! I think at least a FAQ entry on the limits of how h5py and NumPy interact would be useful. In particular, the recommended cycle for h5py is: 1. Read in (a subset of) your data into memory (i.e. into a NumPy array) 2. Do some work on it 3. Write it back out to the dataset Because reading and writing are in general expensive, this is likely to produce the best results. In this case your example would read: dataset = h5['path to dataset'] a = dataset[...] # a is an in-memory NumPy array b = a > 1 You can dispense with the load_array function and the extra manual copying step. Labels: Priority-High −Priority-Medium Dec 15, 2009 issue 78 (Slow data copy to numpy arrays) commented on by mike.thompsonator - This issue is currently coded as an Enhancement, but the effects are so dire to performance that I wonder if it shouldn't be regarded as a bug? Many thanks to "tormodlandet" for giving the clue on how to work around this. # say I start by doing this h5 = h5py.File('some/path', 'r') ds = h5['the_name_of_a_dataset_conotaining_a_numpy_array'] b = ds > 1 # performance when using 'ds' is disastrously slow. unusable. So now, to try and speed things up, using tormodlandet's approach: def load_array(self, ds): a = numpy.empty(shape=ds.shape, dtype=ds.dtype) a[:] = ds[:] return a and I use this function like this: h5 = h5py.File(some_path, 'r') a = load_array(h5['the_name_of_a_dataset_conotaining_a_numpy_array']) b = a > 1 # performance now good This issue is currently coded as an Enhancement, but the effects are so dire to performance that I wonder if it shouldn't be regarded as a bug? Many thanks to "tormodlandet" for giving the clue on how to work around this. # say I start by doing this h5 = h5py.File('some/path', 'r') ds = h5['the_name_of_a_dataset_conotaining_a_numpy_array'] b = ds > 1 # performance when using 'ds' is disastrously slow. unusable. So now, to try and speed things up, using tormodlandet's approach: def load_array(self, ds): a = numpy.empty(shape=ds.shape, dtype=ds.dtype) a[:] = ds[:] return a and I use this function like this: h5 = h5py.File(some_path, 'r') a = load_array(h5['the_name_of_a_dataset_conotaining_a_numpy_array']) b = a > 1 # performance now good Dec 14, 2009 issue 81 (Can't easy_install h5py on Mac OSX 10.4) Status changed by andrew.collette - ^ This applies to the gcc output in the comments you deleted. The original error is related to EPD... you should ask Enthought for support. I believe you can simply download the h5py tarball and install if enstaller doesn't work. Status: Invalid ^ This applies to the gcc output in the comments you deleted. The original error is related to EPD... you should ask Enthought for support. I believe you can simply download the h5py tarball and install if enstaller doesn't work. Status: Invalid Dec 14, 2009 issue 81 (Can't easy_install h5py on Mac OSX 10.4) commented on by andrew.collette - GCC can't find your installation of HDF5. You can set a couple of environment variables before running easy_install which will tell h5py where to look: http://h5py.alfven.org/docs/guide/build.html#custom-installation GCC can't find your installation of HDF5. You can set a couple of environment variables before running easy_install which will tell h5py where to look: http://h5py.alfven.org/docs/guide/build.html#custom-installation Dec 14, 2009 issue 81 (Can't easy_install h5py on Mac OSX 10.4) commented on by korytina - CORRECTION: The actual easy_install error is the following: .. snip .. h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘’ token h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) lipo: can't figure out the architecture type of: /var/tmp//cclgDoiL.out There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. error: Setup script exited with error: command 'gcc' failed with exit status 1 CORRECTION: The actual easy_install error is the following: .. snip .. h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘’ token h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) lipo: can't figure out the architecture type of: /var/tmp//cclgDoiL.out There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. error: Setup script exited with error: command 'gcc' failed with exit status 1 Dec 14, 2009 issue 81 (Can't easy_install h5py on Mac OSX 10.4) commented on by korytina - CORRECTION: The actual error is the following: mcgregor-1924S:~ mcgregor$ sudo /sw/bin/easy_install h5py Searching for h5py Reading http://pypi.python.org/simple/h5py/ Reading http://h5py.alfven.org Reading http://code.google.com/p/h5py/downloads/list Best match: h5py 1.2.1 Downloading http://h5py.googlecode.com/files/h5py-1.2.1.tar.gz Processing h5py-1.2.1.tar.gz Running h5py-1.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-mAPLaZ/h5py-1.2.1/egg-dist-tmp-NKuAWT Warning: Can't determine HDF5 version, assuming 1.6 (use --api= to override) Building for HDF5 1.6 (path not specified) In file included from h5py/h5.c:140: h5py/compat.h:21:18: error: hdf5.h: No such file or directory In file included from h5py/h5.c:143: h5py/typeconv.h:26: error: parse error before ‘h5py_object_type’ h5py/typeconv.h:26: warning: type defaults to ‘int’ in declaration of ‘h5py_object_type’ h5py/typeconv.h:26: warning: data definition has no type or storage class In file included from h5py/h5.c:144: h5py/typeproxy.h:31: error: parse error before ‘H5PY_dset_rw’ h5py/typeproxy.h:31: error: parse error before ‘dset’ h5py/typeproxy.h:32: warning: type defaults to ‘int’ in declaration of ‘H5PY_dset_rw’ h5py/typeproxy.h:32: warning: function declaration isn’t a prototype h5py/typeproxy.h:32: warning: data definition has no type or storage class h5py/typeproxy.h:34: error: parse error before ‘H5PY_attr_rw’ h5py/typeproxy.h:34: error: parse error before ‘attr’ h5py/typeproxy.h:34: warning: type defaults to ‘int’ in declaration of ‘H5PY_attr_rw’ h5py/typeproxy.h:34: warning: function declaration isn’t a prototype h5py/typeproxy.h:34: warning: data definition has no type or storage class h5py/typeproxy.h:46: error: parse error before ‘h5py_copy’ h5py/typeproxy.h:46: error: parse error before ‘type_id’ h5py/typeproxy.h:47: warning: type defaults to ‘int’ in declaration of ‘h5py_copy’ h5py/typeproxy.h:47: warning: function declaration isn’t a prototype h5py/typeproxy.h:47: warning: data definition has no type or storage class h5py/h5.c:424: error: parse error before ‘H5E_auto_t’ h5py/h5.c:424: warning: no semicolon at end of struct or union h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘’ token h5py/h5.c:524: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: warning: function declaration isn’t a prototype h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: warning: function declaration isn’t a prototype h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: warning: function declaration isn’t a prototype h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: warning: implicit declaration of function ‘H5Iget_type’ h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: warning: implicit declaration of function ‘H5Idec_ref’ h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: warning: implicit declaration of function ‘H5Iinc_ref’ h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: warning: implicit declaration of function ‘H5Gget_objinfo’ h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: warning: implicit declaration of function ‘H5Iget_ref’ h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4098: warning: implicit declaration of function ‘H5get_libversion’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4167: warning: implicit declaration of function ‘H5close’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4203: warning: implicit declaration of function ‘H5open’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: warning: implicit declaration of function ‘H5Fget_obj_count’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4283: warning: implicit declaration of function ‘H5Fget_obj_ids’ h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:4379: warning: return type defaults to ‘int’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c:4413: warning: return type defaults to ‘int’ h5py/h5.c:4413: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c:4447: warning: return type defaults to ‘int’ h5py/h5.c:4447: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) error: Setup script exited with error: command 'gcc' failed with exit status 1 CORRECTION: The actual error is the following: mcgregor-1924S:~ mcgregor$ sudo /sw/bin/easy_install h5py Searching for h5py Reading http://pypi.python.org/simple/h5py/ Reading http://h5py.alfven.org Reading http://code.google.com/p/h5py/downloads/list Best match: h5py 1.2.1 Downloading http://h5py.googlecode.com/files/h5py-1.2.1.tar.gz Processing h5py-1.2.1.tar.gz Running h5py-1.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-mAPLaZ/h5py-1.2.1/egg-dist-tmp-NKuAWT Warning: Can't determine HDF5 version, assuming 1.6 (use --api= to override) Building for HDF5 1.6 (path not specified) In file included from h5py/h5.c:140: h5py/compat.h:21:18: error: hdf5.h: No such file or directory In file included from h5py/h5.c:143: h5py/typeconv.h:26: error: parse error before ‘h5py_object_type’ h5py/typeconv.h:26: warning: type defaults to ‘int’ in declaration of ‘h5py_object_type’ h5py/typeconv.h:26: warning: data definition has no type or storage class In file included from h5py/h5.c:144: h5py/typeproxy.h:31: error: parse error before ‘H5PY_dset_rw’ h5py/typeproxy.h:31: error: parse error before ‘dset’ h5py/typeproxy.h:32: warning: type defaults to ‘int’ in declaration of ‘H5PY_dset_rw’ h5py/typeproxy.h:32: warning: function declaration isn’t a prototype h5py/typeproxy.h:32: warning: data definition has no type or storage class h5py/typeproxy.h:34: error: parse error before ‘H5PY_attr_rw’ h5py/typeproxy.h:34: error: parse error before ‘attr’ h5py/typeproxy.h:34: warning: type defaults to ‘int’ in declaration of ‘H5PY_attr_rw’ h5py/typeproxy.h:34: warning: function declaration isn’t a prototype h5py/typeproxy.h:34: warning: data definition has no type or storage class h5py/typeproxy.h:46: error: parse error before ‘h5py_copy’ h5py/typeproxy.h:46: error: parse error before ‘type_id’ h5py/typeproxy.h:47: warning: type defaults to ‘int’ in declaration of ‘h5py_copy’ h5py/typeproxy.h:47: warning: function declaration isn’t a prototype h5py/typeproxy.h:47: warning: data definition has no type or storage class h5py/h5.c:424: error: parse error before ‘H5E_auto_t’ h5py/h5.c:424: warning: no semicolon at end of struct or union h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘’ token h5py/h5.c:524: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: warning: function declaration isn’t a prototype h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: warning: function declaration isn’t a prototype h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: warning: function declaration isn’t a prototype h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: warning: implicit declaration of function ‘H5Iget_type’ h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: warning: implicit declaration of function ‘H5Idec_ref’ h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: warning: implicit declaration of function ‘H5Iinc_ref’ h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: warning: implicit declaration of function ‘H5Gget_objinfo’ h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: warning: implicit declaration of function ‘H5Iget_ref’ h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4098: warning: implicit declaration of function ‘H5get_libversion’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4167: warning: implicit declaration of function ‘H5close’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4203: warning: implicit declaration of function ‘H5open’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: warning: implicit declaration of function ‘H5Fget_obj_count’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4283: warning: implicit declaration of function ‘H5Fget_obj_ids’ h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:4379: warning: return type defaults to ‘int’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c:4413: warning: return type defaults to ‘int’ h5py/h5.c:4413: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c:4447: warning: return type defaults to ‘int’ h5py/h5.c:4447: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) error: Setup script exited with error: command 'gcc' failed with exit status 1 Dec 14, 2009 issue 81 (Can't easy_install h5py on Mac OSX 10.4) reported by korytina - mcgregor-1924S:~ mcgregor$ sudo easy_install h5py Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. Searching for h5py No matching release version found. Searching for latest development version. Reading http://www.enthought.com/repo/epd/eggs/MacOSX/10.4_x86/ Please enter credentials to access this repository: User Name: mcgregor-1924S:~ mcgregor$ sudo easy_install h5py Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc Retrieved config from: /Library/Frameworks/Python.framework/Versions/4.3.0/lib/python2.5/site-packages/.enstallerrc There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. Searching for h5py No matching release version found. Searching for latest development version. Reading http://www.enthought.com/repo/epd/eggs/MacOSX/10.4_x86/ Please enter credentials to access this repository: User Name: Dec 12, 2009 r494 (General cleanup) committed by andrew.collette - General cleanup General cleanup Dec 12, 2009 r493 (Add soft links, external links, references and region refere...) committed by andrew.collette - Add soft links, external links, references and region references Add soft links, external links, references and region references Older Nov 30, 2009 r492 (Per-file locking) committed by andrew.collette - Per-file locking Per-file locking Nov 30, 2009 r491 (Improve locking granularity) committed by andrew.collette - Improve locking granularity Improve locking granularity Nov 30, 2009 issue 80 (h5py doesn't build on OS X SnowLeopard) Status changed by andrew.collette - Glad it works now! Status: Invalid Glad it works now! Status: Invalid Nov 30, 2009 issue 80 (h5py doesn't build on OS X SnowLeopard) commented on by andyfaff - Sorry to being to quick to report this. I had uninstalled and lost my version of MacPorts, which removed my hdf5 directory. This caused h5py to stop easy_installing. Sorry to being to quick to report this. I had uninstalled and lost my version of MacPorts, which removed my hdf5 directory. This caused h5py to stop easy_installing. Nov 30, 2009 issue 80 (h5py doesn't build on OS X SnowLeopard) reported by andyfaff - Tried to install h5py on SnowLeopard 10.6.2, Python 10.6.2 I tried: easy_install h5py and got the attached problem. Tried to install h5py on SnowLeopard 10.6.2, Python 10.6.2 I tried: easy_install h5py and got the attached problem. Nov 27, 2009 r490 (Fix warnings test for 2.5) committed by andrew.collette - Fix warnings test for 2.5 Fix warnings test for 2.5 Nov 27, 2009 r489 (Deprecate old dict methods and remove CoordsList) committed by andrew.collette - Deprecate old dict methods and remove CoordsList Deprecate old dict methods and remove CoordsList Nov 27, 2009 FAQ (Design of h5py and supported features) Wiki page edited by andrew.collette - Revision r488 Add citation info Revision r488 Add citation info Nov 27, 2009 r487 (Bump version number) committed by andrew.collette - Bump version number Bump version number Nov 24, 2009 r486 (Speed up the common case of non-broadcast selection) committed by andrew.collette - Speed up the common case of non-broadcast selection Speed up the common case of non-broadcast selection

issue 81 (Can't easy_install h5py on Mac OSX 10.4) commented on by korytina - CORRECTION: The actual easy_install error is the following: .. snip .. h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘*’ token h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) lipo: can't figure out the architecture type of: /var/tmp//cclgDoiL.out There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. error: Setup script exited with error: command 'gcc' failed with exit status 1

CORRECTION: The actual easy_install error is the following: .. snip .. h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘*’ token h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) lipo: can't figure out the architecture type of: /var/tmp//cclgDoiL.out There is no difference between the current state and the most recent saved state in the enstaller.cache, so the current state does not need to be saved. error: Setup script exited with error: command 'gcc' failed with exit status 1

issue 81 (Can't easy_install h5py on Mac OSX 10.4) commented on by korytina - CORRECTION: The actual error is the following: mcgregor-1924S:~ mcgregor$ sudo /sw/bin/easy_install h5py Searching for h5py Reading http://pypi.python.org/simple/h5py/ Reading http://h5py.alfven.org Reading http://code.google.com/p/h5py/downloads/list Best match: h5py 1.2.1 Downloading http://h5py.googlecode.com/files/h5py-1.2.1.tar.gz Processing h5py-1.2.1.tar.gz Running h5py-1.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-mAPLaZ/h5py-1.2.1/egg-dist-tmp-NKuAWT Warning: Can't determine HDF5 version, assuming 1.6 (use --api= to override) Building for HDF5 1.6 (path not specified) In file included from h5py/h5.c:140: h5py/compat.h:21:18: error: hdf5.h: No such file or directory In file included from h5py/h5.c:143: h5py/typeconv.h:26: error: parse error before ‘h5py_object_type’ h5py/typeconv.h:26: warning: type defaults to ‘int’ in declaration of ‘h5py_object_type’ h5py/typeconv.h:26: warning: data definition has no type or storage class In file included from h5py/h5.c:144: h5py/typeproxy.h:31: error: parse error before ‘H5PY_dset_rw’ h5py/typeproxy.h:31: error: parse error before ‘dset’ h5py/typeproxy.h:32: warning: type defaults to ‘int’ in declaration of ‘H5PY_dset_rw’ h5py/typeproxy.h:32: warning: function declaration isn’t a prototype h5py/typeproxy.h:32: warning: data definition has no type or storage class h5py/typeproxy.h:34: error: parse error before ‘H5PY_attr_rw’ h5py/typeproxy.h:34: error: parse error before ‘attr’ h5py/typeproxy.h:34: warning: type defaults to ‘int’ in declaration of ‘H5PY_attr_rw’ h5py/typeproxy.h:34: warning: function declaration isn’t a prototype h5py/typeproxy.h:34: warning: data definition has no type or storage class h5py/typeproxy.h:46: error: parse error before ‘h5py_copy’ h5py/typeproxy.h:46: error: parse error before ‘type_id’ h5py/typeproxy.h:47: warning: type defaults to ‘int’ in declaration of ‘h5py_copy’ h5py/typeproxy.h:47: warning: function declaration isn’t a prototype h5py/typeproxy.h:47: warning: data definition has no type or storage class h5py/h5.c:424: error: parse error before ‘H5E_auto_t’ h5py/h5.c:424: warning: no semicolon at end of struct or union h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘*’ token h5py/h5.c:524: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: warning: function declaration isn’t a prototype h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: warning: function declaration isn’t a prototype h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: warning: function declaration isn’t a prototype h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: warning: implicit declaration of function ‘H5Iget_type’ h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: warning: implicit declaration of function ‘H5Idec_ref’ h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: warning: implicit declaration of function ‘H5Iinc_ref’ h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: warning: implicit declaration of function ‘H5Gget_objinfo’ h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: warning: implicit declaration of function ‘H5Iget_ref’ h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4098: warning: implicit declaration of function ‘H5get_libversion’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4167: warning: implicit declaration of function ‘H5close’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4203: warning: implicit declaration of function ‘H5open’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: warning: implicit declaration of function ‘H5Fget_obj_count’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4283: warning: implicit declaration of function ‘H5Fget_obj_ids’ h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:4379: warning: return type defaults to ‘int’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c:4413: warning: return type defaults to ‘int’ h5py/h5.c:4413: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c:4447: warning: return type defaults to ‘int’ h5py/h5.c:4447: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) error: Setup script exited with error: command 'gcc' failed with exit status 1

CORRECTION: The actual error is the following: mcgregor-1924S:~ mcgregor$ sudo /sw/bin/easy_install h5py Searching for h5py Reading http://pypi.python.org/simple/h5py/ Reading http://h5py.alfven.org Reading http://code.google.com/p/h5py/downloads/list Best match: h5py 1.2.1 Downloading http://h5py.googlecode.com/files/h5py-1.2.1.tar.gz Processing h5py-1.2.1.tar.gz Running h5py-1.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-mAPLaZ/h5py-1.2.1/egg-dist-tmp-NKuAWT Warning: Can't determine HDF5 version, assuming 1.6 (use --api= to override) Building for HDF5 1.6 (path not specified) In file included from h5py/h5.c:140: h5py/compat.h:21:18: error: hdf5.h: No such file or directory In file included from h5py/h5.c:143: h5py/typeconv.h:26: error: parse error before ‘h5py_object_type’ h5py/typeconv.h:26: warning: type defaults to ‘int’ in declaration of ‘h5py_object_type’ h5py/typeconv.h:26: warning: data definition has no type or storage class In file included from h5py/h5.c:144: h5py/typeproxy.h:31: error: parse error before ‘H5PY_dset_rw’ h5py/typeproxy.h:31: error: parse error before ‘dset’ h5py/typeproxy.h:32: warning: type defaults to ‘int’ in declaration of ‘H5PY_dset_rw’ h5py/typeproxy.h:32: warning: function declaration isn’t a prototype h5py/typeproxy.h:32: warning: data definition has no type or storage class h5py/typeproxy.h:34: error: parse error before ‘H5PY_attr_rw’ h5py/typeproxy.h:34: error: parse error before ‘attr’ h5py/typeproxy.h:34: warning: type defaults to ‘int’ in declaration of ‘H5PY_attr_rw’ h5py/typeproxy.h:34: warning: function declaration isn’t a prototype h5py/typeproxy.h:34: warning: data definition has no type or storage class h5py/typeproxy.h:46: error: parse error before ‘h5py_copy’ h5py/typeproxy.h:46: error: parse error before ‘type_id’ h5py/typeproxy.h:47: warning: type defaults to ‘int’ in declaration of ‘h5py_copy’ h5py/typeproxy.h:47: warning: function declaration isn’t a prototype h5py/typeproxy.h:47: warning: data definition has no type or storage class h5py/h5.c:424: error: parse error before ‘H5E_auto_t’ h5py/h5.c:424: warning: no semicolon at end of struct or union h5py/h5.c:426: error: parse error before ‘}’ token h5py/h5.c:426: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:426: warning: data definition has no type or storage class h5py/h5.c:486: error: parse error before ‘hid_t’ h5py/h5.c:486: warning: no semicolon at end of struct or union h5py/h5.c:489: error: parse error before ‘}’ token h5py/h5.c:524: error: parse error before ‘*’ token h5py/h5.c:524: warning: type defaults to ‘int’ in declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ declared as function returning a function h5py/h5.c:524: warning: function declaration isn’t a prototype h5py/h5.c:524: error: ‘__pyx_t_4h5py_3h5e_err_cookie’ redeclared as different kind of symbol h5py/h5.c:426: error: previous declaration of ‘__pyx_t_4h5py_3h5e_err_cookie’ was here h5py/h5.c:525: warning: parameter names (without types) in function declaration h5py/h5.c:537: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:537: warning: data definition has no type or storage class h5py/h5.c:538: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: error: parse error before ‘void’ h5py/h5.c:538: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:538: warning: function declaration isn’t a prototype h5py/h5.c:538: warning: data definition has no type or storage class h5py/h5.c:539: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: error: parse error before ‘void’ h5py/h5.c:539: warning: type defaults to ‘int’ in declaration of ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:539: warning: function declaration isn’t a prototype h5py/h5.c:539: warning: data definition has no type or storage class h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_6_valid___get__’: h5py/h5.c:2946: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:2946: error: (Each undeclared identifier is reported only once h5py/h5.c:2946: error: for each function it appears in.) h5py/h5.c:2946: error: parse error before ‘__pyx_t_2’ h5py/h5.c:2976: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:2976: warning: implicit declaration of function ‘H5Iget_type’ h5py/h5.c:2976: error: dereferencing pointer to incomplete type h5py/h5.c:2977: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___cinit__’: h5py/h5.c:3094: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:3094: error: parse error before ‘__pyx_v_id_’ h5py/h5.c:3115: error: ‘__pyx_v_id_’ undeclared (first use in this function) h5py/h5.c:3136: error: dereferencing pointer to incomplete type h5py/h5.c:3145: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___dealloc__’: h5py/h5.c:3163: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:3163: error: parse error before ‘__pyx_t_1’ h5py/h5.c:3175: error: dereferencing pointer to incomplete type h5py/h5.c:3176: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:3176: error: dereferencing pointer to incomplete type h5py/h5.c:3177: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c:3179: error: dereferencing pointer to incomplete type h5py/h5.c:3190: warning: implicit declaration of function ‘H5Idec_ref’ h5py/h5.c:3190: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___copy__’: h5py/h5.c:3258: error: dereferencing pointer to incomplete type h5py/h5.c:3286: error: dereferencing pointer to incomplete type h5py/h5.c:3300: warning: implicit declaration of function ‘H5Iinc_ref’ h5py/h5.c:3300: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c:3312: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___hash__’: h5py/h5.c:3629: error: ‘H5G_stat_t’ undeclared (first use in this function) h5py/h5.c:3629: error: parse error before ‘__pyx_v_stat’ h5py/h5.c:3633: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:3633: error: parse error before ‘__pyx_t_2’ h5py/h5.c:3649: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_t_2’ undeclared (first use in this function) h5py/h5.c:3684: warning: implicit declaration of function ‘H5Gget_objinfo’ h5py/h5.c:3684: error: dereferencing pointer to incomplete type h5py/h5.c:3684: error: ‘__pyx_v_stat’ undeclared (first use in this function) h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3721: error: dereferencing pointer to incomplete type h5py/h5.c:3722: error: dereferencing pointer to incomplete type h5py/h5.c:3853: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID___repr__’: h5py/h5.c:3926: warning: implicit declaration of function ‘H5Iget_ref’ h5py/h5.c:3926: error: dereferencing pointer to incomplete type h5py/h5.c:3954: error: dereferencing pointer to incomplete type h5py/h5.c:3978: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_get_libversion’: h5py/h5.c:4083: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4083: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4098: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4098: warning: implicit declaration of function ‘H5get_libversion’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__close’: h5py/h5.c:4156: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4156: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4167: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4167: warning: implicit declaration of function ‘H5close’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__open’: h5py/h5.c:4192: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4192: error: parse error before ‘__pyx_t_1’ h5py/h5.c:4203: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4203: warning: implicit declaration of function ‘H5open’ h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5__exithack’: h5py/h5.c:4229: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4229: error: ‘__pyx_v_objs’ undeclared (first use in this function) h5py/h5.c:4233: error: ‘H5I_type_t’ undeclared (first use in this function) h5py/h5.c:4233: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4245: warning: implicit declaration of function ‘H5Fget_obj_count’ h5py/h5.c:4245: error: ‘H5F_OBJ_ALL’ undeclared (first use in this function) h5py/h5.c:4265: error: parse error before ‘)’ token h5py/h5.c:4283: warning: implicit declaration of function ‘H5Fget_obj_ids’ h5py/h5.c:4303: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c:4304: error: ‘H5I_BADID’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4379: error: parse error before ‘__pyx_f_4h5py_2h5_get_object_type’ h5py/h5.c:4379: warning: return type defaults to ‘int’ h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_get_object_type’: h5py/h5.c:4380: error: ‘hid_t’ undeclared (first use in this function) h5py/h5.c:4380: error: parse error before ‘__pyx_r’ h5py/h5.c:4391: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4392: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4413: error: parse error before ‘__pyx_f_4h5py_2h5_dset_rw’ h5py/h5.c:4413: error: parse error before ‘__pyx_v_dataset_id’ h5py/h5.c:4413: warning: return type defaults to ‘int’ h5py/h5.c:4413: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_dset_rw’: h5py/h5.c:4414: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4414: error: parse error before ‘__pyx_r’ h5py/h5.c:4425: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dataset_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_mem_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_file_space_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_xfer_plist_id’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_outbuf’ undeclared (first use in this function) h5py/h5.c:4425: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4426: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: At top level: h5py/h5.c:4447: error: parse error before ‘__pyx_f_4h5py_2h5_attr_rw’ h5py/h5.c:4447: error: parse error before ‘__pyx_v_attr_id’ h5py/h5.c:4447: warning: return type defaults to ‘int’ h5py/h5.c:4447: warning: function declaration isn’t a prototype h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_attr_rw’: h5py/h5.c:4448: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4448: error: parse error before ‘__pyx_r’ h5py/h5.c:4459: error: ‘__pyx_t_1’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_attr_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_mem_type_id’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_buf’ undeclared (first use in this function) h5py/h5.c:4459: error: ‘__pyx_v_dir’ undeclared (first use in this function) h5py/h5.c:4460: error: ‘__pyx_r’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_f_4h5py_2h5_init_hdf5’: h5py/h5.c:4486: error: ‘herr_t’ undeclared (first use in this function) h5py/h5.c:4486: error: parse error before ‘__pyx_t_3’ h5py/h5.c:4514: error: ‘__pyx_t_3’ undeclared (first use in this function) h5py/h5.c: In function ‘__pyx_pf_4h5py_2h5_8ObjectID_2id___get__’: h5py/h5.c:4666: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_new_4h5py_2h5_ObjectID’: h5py/h5.c:5160: error: dereferencing pointer to incomplete type h5py/h5.c:5161: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_dealloc_4h5py_2h5_ObjectID’: h5py/h5.c:5179: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c:5180: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_traverse_4h5py_2h5_ObjectID’: h5py/h5.c:5187: error: dereferencing pointer to incomplete type h5py/h5.c:5188: error: dereferencing pointer to incomplete type h5py/h5.c: In function ‘__pyx_tp_clear_4h5py_2h5_ObjectID’: h5py/h5.c:5196: error: dereferencing pointer to incomplete type h5py/h5.c:5197: error: dereferencing pointer to incomplete type h5py/h5.c: At top level: h5py/h5.c:5217: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5328: error: invalid application of ‘sizeof’ to incomplete type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c: In function ‘inith5’: h5py/h5.c:5786: error: invalid use of undefined type ‘struct __pyx_obj_4h5py_2h5_ObjectID’ h5py/h5.c:5796: error: ‘__pyx_f_4h5py_3h5e_disable_errors’ undeclared (first use in this function) error: Setup script exited with error: command 'gcc' failed with exit status 1

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