I have a similar issue to this question PyTables does not seem to acknowledge hdf5 though it is evidently installed. Here is a slightly abbreviated error message from pip.
(And I'm going to ramble a bit more just because I get the annoying "this is mostly code" warning.)
pip install --upgrade h5py
Requirement already up-to-date: h5py in /Library/Python/2.7/site-packages
Cleaning up...
$ pip install --upgrade tables
Downloading/unpacking tables
Downloading tables-3.1.1.tar.gz (6.7MB): 6.7MB downloaded
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
* Using Python 2.7.5 (default, Mar 9 2014, 22:15:05)
* Found numpy 1.9.0 package installed.
* Found numexpr 2.4 package installed.
* Found Cython 0.21 package installed.
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
Complete output from command python setup.py egg_info:
/var/folders/0w/y_9w4kq53pqfgrc72bb7cml40000gn/T/H5closekvR8zE.c:1:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int]
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
* Using Python 2.7.5 (default, Mar 9 2014, 22:15:05)
* Found numpy 1.9.0 package installed.
* Found numexpr 2.4 package installed.
* Found Cython 0.21 package installed.
ld: library not found for -lhdf5
clang: error: linker command failed with exit code 1 (use -v to see invocation)
.. ERROR:: Could not find a local HDF5 installation.
You may need to explicitly state where your local HDF5 headers and
library can be found by setting the ``HDF5_DIR`` environment
variable or by using the ``--hdf5`` command-line option.
