Depends checking

[mcnelsonphd]

I was getting consistent install failures on my Mac using sudo python setup.py install, with the following error always coming up:

Processing dependencies for poretools==0.5.1
Searching for h5py>=2.0.0
Reading http://pypi.python.org/simple/h5py/
Reading http://code.google.com/p/h5py/downloads/list
Reading http://h5py.alfven.org
Reading http://www.h5py.org
Best match: h5py 2.4.0
Downloading https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz#md5=80c9a94ae31f84885cc2ebe1323d6758
Processing h5py-2.4.0.tar.gz
Running h5py-2.4.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-ljfYlb/h5py-2.4.0/egg-dist-tmp-aWgyQ0
warning: no previously-included files found matching 'h5py/defs.pyx'
warning: no previously-included files found matching 'h5py/defs.pxd'
warning: no previously-included files found matching 'h5py/config.pxi'
Autodetected HDF5 1.8.14
********************************************************************************
                       Summary of the h5py configuration

    Path to HDF5: None
    HDF5 Version: '1.8.14'
    MPI Enabled: False
    Rebuild Required: False

********************************************************************************
Executing api\_gen rebuild of refs
clang: error: no such file or directory: '/tmp/easy_install-ljfYlb/h5py-2.4.0/h5py/defs.c'

That appears to be due to a failure to install/compile h5py, but I already have that include in my python site packages. To get around the error I deleted the h5py requirement from the requirements.txt and the install then went correctly. I haven't had any issues using poretools by doing that, so I figured I would let you know in case any other users encounter a similar issue.

Cheers, Mike

[roblogan6]

I tried to remove the requirement. However, I was denied the ability to do that because I don't own the requires.txt file and can't write to it.
How were you able to remove the h5py requirement? When I try to run poretools, I get this error: Traceback (most recent call last): File "/usr/local/bin/poretools", line 5, in from pkg_resources import load_entry_point File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2793, in working_set.require(requires) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 673, in require needed = self.resolve(parse_requirements(requirements)) File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 576, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: h5py>=2.0.0

But I have h5py >2.0 installed. Sigh.

[nickloman]

I assume you are installing via pip? Instead try cloning the repository directly and then editing the requirements.txt file.