H5py errors in Homebrew


I’m trying to install the developers version of cell profiler on my mac, but I’m having issues during the brew running stage. I’ve got the error on two different computers now and both of them relate to h5py:

CPU: 8-core 64-bit dunno MacOS: 10.8.2-x86_64 Xcode: 4.5 MacPorts/Fink: port X11: /usr/X11 => /opt/X11 CC: /usr/bin/clang CXX: /usr/bin/clang++ => /usr/bin/clang LD: /usr/bin/clang CFLAGS: -Os -w -pipe -march=native -Qunused-arguments -arch i386 -arch x86_64 CXXFLAGS: -Os -w -pipe -march=native -Qunused-arguments -arch i386 -arch x86_64 CPPFLAGS: -I/Users/James/homebrew/Cellar/libhdf5-universal/1/include -isystem /Users/James/homebrew/include LDFLAGS: -L/Users/James/homebrew/Cellar/libhdf5-universal/1/lib -L/Users/James/homebrew/lib -arch i386 -arch x86_64 MAKEFLAGS: -j8 Error: Failed executing: /usr/bin/arch -x86_64 /Users/James/homebrew/Cellar/cellprofiler-dev/1/../../cellprofiler-dev-python/1/cpdev/bin/python -c import\ h5py;\ print\ h5py.version.version_tuple (cellprofiler-dev.rb:71)

I’ve tried installing h5py separate to homebrew, but this also hasn’t helped. Please let me know if you’ve had this problem before/know anyway of fixing it!

Thank you,

Ok - an update. Messed around with multiple different versions, and found that wxPython 2.8 only seemed to import with python running in 32bit mode. This in turn was uncompatible with H5PY, so I downloaded wxPython 3.0.0 instead.

So I’ve now installed everything without homebrew - and get tantalisingly close to success. When running cellprofiler.py I see the logo come up, and python jumps in my doc, but it fails to ever open.

raise NotImplementedError("No support for synchronizing futures in Python's startup thread on the OS/X in 64-bit mode.") NotImplementedError: No support for synchronizing futures in Python's startup thread on the OS/X in 64-bit mode. Failed to stop Ilastik

Is the last thing in my terminal window.

In case anyone else goes through the same problems as me.
Realised I needed to have everything able to run on python-32 so downgraded my wxPython again.
Messed around trying to install universal HDF5 binaries, didn’t work.
Tried homebrew again, failed at the H5Py point.

Pip install h5py==2.0.1 didn’t work.

Got homebrew to install HDF5 (brew install HDF5).
Downloaded H5py 2.0.1 source.
Activated cellprofiler virtual env.
navigated to H5py 2.0.1 source:
HDF5_DIR=/Users/NAME/homebrewM/Cellar/libhdf5-universal/1 pythonw setup.py install
Then pythonw32 cellprofiler.py works!

Thanks for reporting, and fixing your own issue! We do say on our Mac Dev install page (github.com/CellProfiler/CellPro … on-for-Mac) that “you should install a universal (32-bit and 64-bit) build of Python 2.7”. And we link to the specific universal wxPython dmg. Are these what you tried initially or do we need to update our installation instructions?


Hi David,

I followed all the steps to the letter - the error occurred during the H5py installation (the original error I posted) within homebrew.
I think part of the issue was that H5py 2.0.1 is no longer hosted (pip install h5py==2.0.1 doesn’t work).
Additionally, I think during the install of H5py the HDF5_DIR needs to be specifically set to the libhdf5-universal folder created by homebrew. Those were the only two changes I had to make.


Thanks for sharing your experience - we appreciate that. I added some pointers in our instructions to this thread.

Just so we can try and clarify the directions, had you tried the “All Homebrew” method here? or the individual dependencies plus a little Homebrew?

We had changed the hdf5 homebrew directory a couple months ago (and in the instructions), and just wanted to be sure you tried that: