ljmciver
commented
8 years ago Hi Simon,
If you install the header files and a static library for Python (v2.7.11), it should resolve the error message you are seeing. On Ubuntu the package is named python2.7-dev.
Thanks, Lauren
Following the directions in README.md, executing "brew install biobakery_tool_suite" command results in the following error pertaining to Python.h. "which python" and "python --version" confirm version as 2.7.11, and the command was executed in a vagrant VM:
<...snip...> ==> python -c import setuptools... --no-user-cfg install --prefix=/home/vagrant/ Last 15 lines from /home/vagrant/.cache/Homebrew/Logs/metaphlan2/01.python: File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 169, in build_sources self.build_extension_sources(ext) File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources sources = self.generate_sources(sources, ext) File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 402, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 41, in check_types out = check_types(_a, *_kw) File "numpy/core/setup.py", line 263, in check_types "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
The default install path is ~/.linuxbrew. I have verified the existence of Python.h, and I have tried soft-linking Python.h to ~/.linuxbrew/include. I have also tried to execute "brew install metaphlan2", and also executed "sudo yum install python-devel". None of these measures have resolved the problem.