Numpy Install RuntimeError: Broken toolchain: cannot link a simple C program

Question

(macbook air)

I spent a while trying to install this. First off, I can't use Homebrew because I installed it but then the 'network connection' dropped and now my computer can't find the 'brew' command, but it says homebrew in installed. So I don't know how to uninstall it without using the brew command.

So I am trying to install numpy from the command line. I have xcode, command line tools, gcc fortran 4.2.3, and downloaded numpy. I am getting a RuntimeError when trying to install it! I've read and tried everything from previous posts.

I have attached my Path to show you all, maybe I messed that up?

 echo $PATH
/Library/Frameworks/Python.framework/Versions/2.6/bin:/Library/Frameworks/Python.framework/Versions/3.4 bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin

Would love your help!!

Traceback (most recent call last):
  File "setup.py", line 251, in <module>
    setup_package()
  File "setup.py", line 243, in setup_package
    setup(**metadata)
  File "/Users/Anisa/Downloads/numpy-1.9.1/numpy/distutils/core.py", line 169, in setup
    return old_setup(**new_attr)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/Users/Anisa/Downloads/numpy-1.9.1/numpy/distutils/command/build.py", line 39, in run
    old_build.run(self)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py", line 134, in run
    self.run_command(cmd_name)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/Users/Anisa/Downloads/numpy-1.9.1/numpy/distutils/command/build_src.py", line 153, in run
    self.build_sources()
  File "/Users/Anisa/Downloads/numpy-1.9.1/numpy/distutils/command/build_src.py", line 164, in build_sources
    self.build_library_sources(*libname_info)
  File "/Users/Anisa/Downloads/numpy-1.9.1/numpy/distutils/command/build_src.py", line 299, in build_library_sources
    sources = self.generate_sources(sources, (lib_name, build_info))
  File "/Users/Anisa/Downloads/numpy-1.9.1/numpy/distutils/command/build_src.py", line 386, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 686, in get_mathlib_info
    raise RuntimeError("Broken toolchain: cannot link a simple C program")
RuntimeError: Broken toolchain: cannot link a simple C program

Solution 1

I ran into this issue twice, and both times I fixed it this way: abandoning pip.

First time was on osx I did brew install numpy. Homebrew will take care of all of the dependencies.

Second time was on centos7 and much like above I just yum install -y numpy.

Solution 2

I'm having this same problem (only I'm using brew install numpy), with:

File "numpy/core/setup.py", line 686, in get_mathlib_info
    raise RuntimeError("Broken toolchain: cannot link a simple C program")
RuntimeError: Broken toolchain: cannot link a simple C program

(Here is a full gist-log of my error.)

This question has some potential solutions: Problems with pip install numpy - RuntimeError: Broken toolchain: cannot link a simple C program.

Though I don't want to resort to sudo, and I want to stick with homebrew (because I'm really aiming for a homebrewed opencv), so I've had no luck so far.

Edit: adding export ARCHFLAGS=-Wno-error=unused-command-line-argument-hard-error-in-future to my .bash_profile (as was suggested in the other question I linked) let brew install numpy almost flawlessly. All that remained after was that I had to brew link --overwrite numpy (because I had a non-brew installation of numpy before). Seems to be working now.

Solution 3

update the pip using python -m pip install --upgrade pip

then install your library pip install your_library

Solution 4

I had a similar issue with Python3 numpy install in Fedora 24

Solution provided here by Ollegn that worked for me was:

sudo dnf install python3-devel
sudo dnf install make automake gcc gcc-c++ gcc-gfortran
sudo dnf install redhat-rpm-config
sudo dnf install subversion
sudo pip3 install -U numpy

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Comments

[AMC]

Does this answer your question? Problems with pip install numpy - RuntimeError: Broken toolchain: cannot link a simple C program

[Trolley_Theif]

I think you're supposed to use something called Virtual Environment to install numpy. I've been using matlab but I'll try virtual environment and let you all know.

[agtoever]

Thanks! I had to combine two solutions to install numpy under homebrew pypy (4.0.1) on OS X (el capitan): 1. don't use pip ot get numpy, but get it from github: pypy -m pip install git+https://bitbucket.org/pypy/[email protected] and using the export mentioned in this answer.