Installing Python, virtualenv, NumPy, SciPy, matplotlib and IPython on Lion or Mountain Lion

August 12, 2011 in Data,Technology

Please note that the current version of this guide is available here. This page is no longer updated.

I decided to clear the cobwebs out of my  MacBook Pro (update 8/20/11: new MacBook Air in hand!) and start fresh with Lion, Python and all the other tools I regularly use (virtualenv, NumPy, SciPy, matplotlib and IPython). It was a lengthy process and I was unable to find a comprehensive walkthrough online, so I had to figure it out through trial and error (mostly error). I was surprised at the lack of available information; with such a major release I expected more complete documentation. So, once again quoting Tom Lehrer, I have a modest example here.

The important things we'll accomplish in this guide are (click any section to jump directly there):

  1. A clean install of Mac OS 10.7 Lion
  2. Installing Homebrew
  3. Installing Python
  4. Installing virtualenv
  5. Installing NumPy, SciPy and matplotlib
  6. Installing IPython and the qtconsole

As you may recall, this has been a somewhat more-than-trivial process for Lion's early adopters, as enough was changed behind the scenes to mess up some of the current versions of these tools. I'll detail how to get around those issues by getting cutting-edge distributions. Note that today's cutting-edge works on my machine; tomorrow's may introduce new bugs. When stable Lion-compatible versions of these programs are available, I strongly encourage you to use those instead.

If you would rather skip my commentary, you should be able to simply execute every line of code in sequence.

As always, remember that some of these lines will take you off the beaten path and could cause serious irrevocable damage to your computer! In particular, typing sudo gives you root access and therefore the ability to erase everything with a single keystroke. Please do not execute any code without understanding exactly what it does. In the worst case, I suppose you could always jump back to square one by wiping your hard drive and running a Lion clean install, but use caution nonetheless. YMMV.

Lion Clean Install

To begin, there has been some concern that users can't perform a clean install of Mac OS X 10.7 (Lion) without quite a bit of hacking around with physical media. I'm happy to report that isn't true -- as long as you performed a standard Lion install first. The OSX installer (App Store link) automatically creates a "Recovery HD" partition on your hard drive, just in case something goes wrong. The partition contains just two things: Disk Utility  and the ability to run the Lion installer. To access this recovery mode, hold Command-R while your computer is starting up. Use Disk Utility to erase your hard drive, then run the installer to re-download and load Lion. When you're done, you'll have a clean install of Lion. Download your favorite browser and you're good to go. I have to say, discovering this feature was a pleasant surprise -- hats off to Apple for thinking ahead on this one.

Next, install Xcode 4 -- its bundled compilers have to be available for the next step to work. Here's a link to it in the App Store; it's a free (but large) download. Note that like Lion, the download does not actually install the application. Instead, it puts an "Install Xcode" icon in your applications folder, which you must run to complete the installation. I don't understand this behavior of installing the installer, but it is what it is.


Homebrew

Next up, one of my new favorite tools -- Homebrew. The homepage says it pretty well: "Homebrew is the easiest and most flexible way to install the UNIX tools Apple didn't include with OS X." If you've messed around with MacPorts (or tried to do this sort of stuff  -- gasp -- by yourself), you'll be shocked by the drop-dead simplicity of this tool. Even installing it is a no-brainer; just fire up Terminal and execute the following line:

ruby <(curl -fsSkL raw.github.com/mxcl/homebrew/go)

That's it -- now you have Homebrew. Try running brew update and brew doctor at the command line to make sure it's working properly.

You'll need to add the Homebrew directory to your system path, in order to make sure that Homebrew-installed software is given higher priority than any other version. To do so, open your .bash_profile in your user directory (that's the ~ directory or, more verbosely, /Users/[your_user_name]) and add the following line (if you don't have a .bash_profile, create one with your favorite text editor -- you may need to do this in order to see it, as it will be a hidden file):

export PATH=/usr/local/bin:$PATH

If you haven't already, restart Terminal so it picks up the new path. Homebrew is generally very good about alerting you to any action you need to take after it finishes running, including path modifications. Make sure to pay attention to its output.

Python

Now on to the main event: Python. As of this writing, 2.7.3 is the most recent version. If that's no longer true as you read this, be sure to change any version-specific references! The following instruction will install Python, first installing any prerequisites. Mountain Lion users may have to install XQuartz; simply follow the instructions if prompted to do so. The --framework option tells it to build as a Framework, which has some downstream niceties, and --universal builds a universal (32/64 bit) version:

brew install python --framework --universal

This will install a version of disutils, but you must update your path in order to run it properly. Add the following to your .bash_profile (you may combine it with the previous .bash_profile edit, if you choose):

export PATH=/usr/local/share/python:$PATH

Once again, make sure you reload Terminal to update your path variable. Finally, you need to change Lion's symlink to point at your new Python install. Run the following three lines in sequence:

cd /System/Library/Frameworks/Python.framework/Versions
sudo rm Current
ln -s /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/Current

You will be prompted for your password after executing the sudo command.

To verify that your installation went as planned, type which python at the command line. You should see /usr/local/bin/python in response. Furthermore, if you type python, you should see Python 2.7.3 launch (type quit() to return to Terminal).

You should now have pip available on your system. If you discover that you don't have pip, simply execute:

easy_install pip

Note that depending on your permissions settings, you may have to prepend sudo to the front of many of these lines. Always remember that sudo gives you root access!! Therefore, in the interest of caution, I'm not going to include the sudo command here, but if your installs are failing because of permissions, you may have to add it.

virtualenv

Virtualenv is a tool that allows you to create isolated Python environments, each with its own set of packages and dependencies. This is useful for testing or managing package requirements (for example, if you build an application that is dependent on a certain version of a third-party package but another application requires a more recent version, you may break the first application by upgrading). This is not a required step, and all the commands below should work whether or not you are using virtualenv, so I'm listing it here for convenience only. The only difference will be that directories (such as that returned by which pip) will point to the virtualenv rather than /usr/local.

First, install virtualenv and virtualenvwrapper (a tool which makes working with virtualenv somewhat easier):

pip install virtualenv
pip install virtualenvwrapper

Next, source the virtualenvwrapper script:

source /usr/local/share/python/virtualenvwrapper.sh

This will create a hidden virtualenv directory at ~/.virtualenv. Now you can make your first virtual environment:

mkvirtualenv test1

Your new virtualenv test1 comes with a complete install of Python 2.7.3 and its own version of Pip. It is activated by default, so running any pip command will only impact this environment. Note that if you deactivate the virtualenv, you will lose access to any packages installed in it. You can switch between virtualenvs with the workon command.

In order to delete your test virtualenv, run rmvirtualenv test1. Also, to specify a different version of Python, just use mkvirtualenv -p python3.2 test1 (replacing python3.2 with the shell name of your preferred version).

NumPy

If pip installed properly (executing which pip should return /usr/local/share/python/pip), then you can install NumPy simply with:

pip install numpy

Check your work by executing:

python

followed by:

import numpy
print numpy.__version__
print numpy.__file__
quit()

The version should be 1.6.2 (as of July 2012), and the file should be somewhere in /usr/local/Cellar/....

SciPy

SciPy requires a Fortran compiler, which Lion lacks. To acquire one, use Homebrew:

brew install gfortran

Under Lion, install the stable version of SciPy (0.10) by running:

pip install scipy

Mountain Lion users will need to install the development version of SciPy (0.11) by executing the following line:

pip install -e git+https://github.com/scipy/scipy#egg=scipy-dev

As with NumPy, make sure you have everything working by running:

python

and then:

import scipy
print scipy.__version__
print scipy.__file__
quit()


matplotlib

On Lion, install matplotlib like any other package -- if you like, you can check your work once it finishes.

pip install matplotlib

Mountain Lion users will have to use the development version as of this writing:

pip install git+https://github.com/matplotlib/matplotlib.git#egg=matplotlib-dev

IPython

Installing IPython itself is a fairly straightforward pip command:

pip install ipython

Getting the new qtconsole to run takes a little more work -- but it's well worth it. The qtconsole is like running IPython on steroids -- my favorite feature is that matplotlib output can be displayed inline.

To begin, you'll need Nokia's qt library, which is available here. Make sure you download the library, not the SDK.

Once that's done, begin installing the prerequisites:

brew install pyqt

Note that after installing pyqt, brew will prompt you to add the following to your pythonpath in .bash_profile:

export PYTHONPATH=/usr/local/lib/python:$PYTHONPATH

Continue installing:

brew install zmq
pip install pyzmq
pip install pygments

And that's it -- you should now be able to launch the qtconsole by executing ipython qtconsole. If you want to see the matplotlib output inline (and why wouldn't you?), then execute:

ipython qtconsole --pylab=inline

Fin.

Phew! I hope this works for everyone out there. Until the next software upgrade, anyway.

Updated 9/1/11 to include virtualenv.

{ 147 comments… read them below or add one }

Sharon August 30, 2012 at 5:59 pm

Thanks for the detailed tutorial!
Everything went as written, except for when running “which python” I got usr/bin/python instead of usr/local/bin/python. I had to run “brew link python” to get it to work.
I had just upgraded from Leopard to Mountain Lion (through Snow Leopard), and had previous versions of python installed.

Reply

Dave September 6, 2012 at 7:58 am

Unfortunately I’m still getting “/usr/bin/python” when I’m doing “which python”. More precisely I do:
cd /System/Library/Frameworks/Python.framework/Versions
sudo rm Current
sudo ln -s /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/Current

dave@shadowfax$ which python
/usr/bin/python

Comments:
1. I need to use sudo for linking as otherwise I get an error.
2. The latest version of python appears to be 2.7.3 at the moment.
3. If I run python I get an older version (2.7.1).
4. I’m still on Lion.

Any idea?

Reply

Dave September 6, 2012 at 8:20 am

OK, I have just found out, sorry.
My problem was that /usr/bin was coming before /usr/local/bin in my $PATH.
http://stackoverflow.com/questions/5157678/python-homebrew-by-default

Reply

Volker September 10, 2012 at 4:03 am

Thanks for this useful guide. I tried using an academic license of Enthought Python distribution before, but ran into some trouble with incompatible 32bit and 64bit libraries when installing additional python packages. Building everything from scratch using your guide solved all my troubles and avoids the licensing issues with Enthought as well.

Reply

Dave September 10, 2012 at 7:45 am

At the point of installing scipy, I get the error:

numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini']

Unfortunately the installation of numpy had been fine, getting the same version of this tutorial:

>>> import numpy
>>> print numpy.__version__
1.6.2
>>> print numpy.__file__
/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/__init__.pyc

So, there must be something wrong with the numpy package? Any idea?

Reply

J September 10, 2012 at 10:19 pm

Dave, I was finally able to reproduce your problem. It seems to be an issue with NumPy and pip, and I can’t explain why it doesn’t always happen.

To get around it, you’ll need to install NumPy yourself. The instructions are available here. Basically you’ll git clone the NumPy repository into a temporary folder, then step into that folder and build/install the package. While you’re at it, you may want to install SciPy manually as well, with almost the exact same steps.

Reply

Dave September 11, 2012 at 5:12 am

Thank you J, the tip of using git clone was the winning one!
Have a good day!

Reply

dayigu September 15, 2012 at 11:11 am

I also get this error. I fixed it by a trick.

Get numpy souce of the same version, just build it:
python setup.py build –fcompiler=gnu95

you can find the missing file “npymath.ini” in build/src.macosx-10.8-intel-2.7/numpy/core/lib/npy-pkg-config/, copy the directory npy-pkg-config to /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/lib/

a lib file libnpymath.a is also needed, which can be found in build/temp.macosx-10.8-intel-2.7, copy it to /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/lib/ too.

good luck!

Reply

Alessandro Filisetti September 28, 2012 at 9:34 am

Dear all,

I tried all the procedures and tricks you mentioned but I have still problems in installing Scipy… here the last lines coming out from the compiling procedure:

swig: scipy/sparse/linalg/dsolve/umfpack/umfpack.i
swig -python -I/usr/local/include -I/usr/local/include -I/usr/local/include -o build/src.macosx-10.7-intel-2.7/scipy/sparse/linalg/dsolve/umfpack/_umfpack_wrap.c -outdir build/src.macosx-10.7-intel-2.7/scipy/sparse/linalg/dsolve/umfpack scipy/sparse/linalg/dsolve/umfpack/umfpack.i
unable to execute swig: No such file or directory
error: command ‘swig’ failed with exit status 1

before that I tried with pip install scipy without succeed.

gcc –version 4.2.1

Thank you in advance,

Ale

Reply

Alessandro Filisetti September 28, 2012 at 10:52 am

Dear all,

I solved installing SWIG https://github.com/titanous/homebrew-gnuradio/issues/2.
I still have problems in the scipy.test()… several “ImportError: numpy.core.multiarray failed to import” but anyway it seems to work..
Thank you very much again for these very clear guide and your suggestions…

ale

Reply

Natalie October 12, 2012 at 2:18 am

I ran into the same problem as Dave. However, as I was going through the SciPy install – I got the error that “‘swig’ failed with exit status 1.” After a bit of searching, I found that SciPy requires swig, but you need to specifically download it. Simple fix with “brew install swig,” then build-and-install — but it had me worried for a while that this fix wasn’t quite what I needed. Everything is good to go now! Thanks for your walk-through!

Reply

Grace October 6, 2012 at 6:00 am

I am with mountain now, and I can’t install scipy and matplotlib on my macboook pro.

short error message for matplotlib:
InstallationError: Command /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python -c “import setuptools;__file__=’/var/folders/z6/tmxvx5rn21lblvzlkhdltqpm0000gn/T/pip-_YArQ_-build/setup.py’;exec(compile(open(__file__).read().replace(‘\r\n’, ‘\n’), __file__, ‘exec’))” install –record /var/folders/z6/tmxvx5rn21lblvzlkhdltqpm0000gn/T/pip-i3muKd-record/install-record.txt –single-version-externally-managed failed with error code 1 in /var/folders/z6/tmxvx5rn21lblvzlkhdltqpm0000gn/T/pip-_YArQ_-build

short error message of scipy:

numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/usr/local/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini']

—————————————-
Command python setup.py egg_info failed with error code 1 in /Users/hubuki/src/scipy
Storing complete log in /Users/hubuki/.pip/pip.log

Reply

Amit October 8, 2012 at 12:02 pm

I am on Mountain Lion. I tried installing python etc as described but cannot get past the following point:

ln -s /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/Current
gives the following output:
ln: ./Current: File exists

which python gives:
/usr/bin/python

brew doctor gives:
Warning: Your Homebrew is outdated
You haven’t updated for at least 24 hours, this is a long time in brewland!
Warning: You have unlinked kegs in your Cellar
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these: python

How should I proceed?

Reply

Jon October 11, 2012 at 10:39 am

brew link python
brew update # will get rid of the first Homebrew warning, though its not essential
Double check your path, make sure that /usr/local/bin is before /usr/bin

Reply

Rashid October 16, 2012 at 4:57 pm

1. I’m new to this – running mountain lion

after installing numpy it’s stored in /usr/local/lib/python2.7/site-packages/numpy/__init__.pyc as opposed to
I followed all the steps, double checked paths to make sure they’re correct. I had the same problems with scipy as above, but before continuing I wanted to be sure having numpy there won’t cause probs.

Reply

Rashid October 16, 2012 at 5:10 pm

**as oppsed to in /usr/local/Cellar…

Reply

Wena October 24, 2012 at 3:43 am

I ran into the same problem, my os x version is mountain lion 10.8.2… can this be the cause of the problem?

Reply

Wena October 24, 2012 at 7:40 am

I have solved this problem! The installation of virtualenv is the cause in my case. Follow the instruction about install virtualenv in the hyperlink below, then ‘pip install numpy’ will do the right thing~
http://dubroy.com/blog/so-you-want-to-install-a-python-package/

Reply

ih February 7, 2013 at 8:41 pm

I’m having trouble with the first step at the link:
“Use virtualenv to create a base Python environment for your user account:
python virtualenv.py ~/venv/base”

I saved the virtualenv.py file in my python folder /usr/local/Cellar/python folder, but when I type “python virtualenv.py ~/venv/base” into the command line I receive this error:

/usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python: can’t open file ‘virtualenv.py’: [Errno 2] No such file or directory

Any ideas? Thanks in advance.

Reply

ROBERTO October 19, 2012 at 11:32 am

Hi there,

I’m installing on a macbook pro 13” with LION 10.7.5. I get this error on scipy installation:

numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/usr/local/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini']
—————————————-
Command python setup.py egg_info failed with error code 1 in /var/folders/v1/rhksf40d4y1343qqv_x134p80000gq/T/pip-build/scipy

ONE MORE THING: Ipython installation seemed successful but I’m not able to execute ipython console.

Thanks

Roberto

Reply

Brent October 23, 2012 at 1:04 pm

Same here.

“ipython qtconsole –pylab=inline” fails.

No PySide to import. And “pip install pyside” fails: Failed to locate the Python library /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/libpython2.7.so.1

Reply

Josh November 4, 2012 at 1:22 am

Thanks for this, saved me hours of pain! However, for me Homebrew has trouble finding Numpy from a pip install (if not using a virtualenv). The only solution seems to be to do a

>python setup.py install

for both Numpy and Scipy. After this, all good.

Reply

David James November 8, 2012 at 7:33 pm

Tiny typo: disutils -> distutils

Reply

Pete Windle November 14, 2012 at 10:24 am

Kk, so I appear to have hit every branch on the way down here…

First off don’t forget to update recipes with brew update if you had brew already…

The “npymath.ini” nonsense goes away if you install numpy without using pip from the tarball, as previously trailed.

There is a pyside dependency for ipython at runtime it appears, also need a couple of other bits:

brew install freetype
brew install pyside

Finally I had to link from /usr/local/share/python the ipython and associated scripts to my bin, mainly because i wasn’t interested in running a virtual env.

Reply

Alex Bowe November 18, 2012 at 11:55 pm

Just letting you know that I had to install libpng and libfreetype before matplotlib would install:

brew install freetype
brew install libpng

Reply

Joss Gray November 27, 2012 at 6:04 am

Im getting;

Cannot import PySide >= 1.0.3 or PyQt4 >= 4.7

Even though I have both installed.

Reply

Marc November 29, 2012 at 4:58 pm

Hi,
Great tutorial. Thanks so much. Is there really a need to install the Qt library from Nokia, as brew installs a qt library too as it is a dependency for pyqt etc.?

Thanks!
Marc

Reply

Lorenzaccio December 17, 2012 at 9:39 am

Hi,

Brew easier than Macports ? I tried. I completely failed (running Lion 10.7.4, Xcode 4.4.1)…

>ruby -e “$(curl -fsSkL raw.github.com/mxcl/homebrew/go)”
Illegal variable name.

Never used ruby before, so I don’t know how to fix this.
Then I tried this way (I moved to /usr/local first) :

>mkdir homebrew && curl -L https://github.com/mxcl/homebrew/tarball/master | tar xz –strip 1 -C homebrew

but :
mkdir: homebrew: Permission denied

so I had to sudo every step of it and hand-link to /usr/local/bin

Then I tested brew, as explained but if failed:

>brew update
/System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/pathname.rb:444:in `readlink’: Permission denied – /usr/local/bin/brew (Errno::EACCES)
from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/pathname.rb:444:in `realpath_rec’
from /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/pathname.rb:474:in `realpath’
from /usr/local/bin/brew:14

So I have to conclude I really have no brains or that the claim that it is much better than Macports is preposterous or both… Too bad.
If someone can lend me a brain or some explanation, I would be glad…

Thanks,
Lorenzaccio

Reply

quetzales December 21, 2012 at 8:21 am

I’m on Mountain Lion and after installing numpy I got:

>>> import numpy
>>> print numpy.__version__
1.6.2
>>> print numpy.__file__
/usr/local/lib/python2.7/site-packages/numpy/__init__.pyc

instead of /usr/local/Cellar… can you help? thanks!

Reply

Smiling_C December 22, 2012 at 11:58 pm

same here. There are some comments above having the same issue. I followed the suggestions of “install numpy, and scipy from github” and I am able to install all packages and tested successfully, even though they still in /usr/local/lib/python2.7/site-packages/ instead of /usr/local/Cellar…

Reply

quetzales December 23, 2012 at 9:38 am

yeah I saw the above comments and tried and it seemed the imported numpy did point to /usr/local/Cellar..only when I was in that virtualevn.

so I gave up and tried the ScipySuperpack(http://fonnesbeck.github.com/ScipySuperpack/). after installed I got:

>>> print numpy.__version__
1.8.0.dev-3abd869
>>> print numpy.__file__
/Library/Python/2.7/site-packages/numpy-1.8.0.dev_3abd869_20121222-py2.7-macosx-10.8-intel.egg/numpy/__init__.pyc

Reply

will January 6, 2013 at 3:17 pm

This guide is very useful. Did you try running numpy and scipy’s tests on Mountain Lion after installing them? I get several (over 70) scipy failures and I don’t know how important they are.

Reply

elihu January 7, 2013 at 10:30 pm

Just wanted to post props for this (arrived here from SO). I fought my PC for a day and half before giving up and getting out my iMac for this, and though matplotlib is still the toughest part, I was able to get both numpy and scipy from the regular pip script (no special download required).

Maybe update post to reflect that?

Reply

numpish January 13, 2013 at 10:09 am

scipy installation fails for me on mountain lion, with the following message:
ld: library not found for -lg2c

thanks nonetheless for this info, I am surprised there is less on this on the web.

Reply

Deividas MII January 22, 2013 at 1:28 pm

This article is just amazing. Thank you J!

Though I needed couple days to accomplish every single step.

I stumbled upon problem regarding numpy installation. I’ve solved it (kind of) by using homebrew tap:

bash-$ brew tap samueljohn/python
bash-$ brew install gfortran #(execute this if your system doesn’t have gfortran)
bash-$ pip install nose # for testing purposes (more here: http://www.scipy.org/Installing_SciPy/Mac_OS_X)
bash-$ brew install numpy
bash-$ brew install scipy

After testing both numpy and scipy there were some failures but no errors. Good enough.
It was great experience, maybe too tiresome but still very exciting.

Also, Uri Nieto ( http://bit.ly/XwSiZU ) recommends to delete default python version which comes with clean Mountain Lion install. One may try it if one is having problems regarding incorrect numpy installation location.

Good luck!

Reply

Chris March 17, 2013 at 2:53 pm

Thanks for this guide. I ran into a few road blocks even with theses instructions.

In case it helps others:

Installing X-Code did not automatically install the Command Line Tools. I had to open X-Code > File > Preference > Downloads > Install Command Line Tools in order to have a compiler available for build and make commands in the terminal.

Without doing that I could not install NumPy or SciPy.

Also, As of 3/17/2013 you can just run pip install scipy too.

Matplotlib would not install either because packages freetype, png would not build. I search the web for hours to find a solution, which turned out to be very simple: http://stackoverflow.com/questions/12363557/matplotlib-install-failure-on-mac-osx-10-8-mountain-lion

run these commands to install those packages:
brew install freetype
brew install libpng

then I installed the development version of matplotlib successfully.

everything else worked fine. thanks again.

Reply

Mike March 20, 2013 at 7:34 am
Mike March 24, 2013 at 1:35 am

Don’t use this. It doesn’t work, despite what I read elsewhere.

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Ryan March 23, 2013 at 11:08 pm

I had to do
pip install cython
before I could get scipy to compile and install.

Reply

Thomas Edwards April 20, 2013 at 6:09 am

I get this error at the end when I try to install scipy:

gfortran: error: libgfortran.spec: No such file or directory

gfortran: error: libgfortran.spec: No such file or directory

error: Command “/usr/local/bin/gfortran -Wall -Wall -undefined dynamic_lookup -bundle build/temp.macosx-10.7-intel-2.7/build/src.macosx-10.7-intel-2.7/scipy/fftpack/_fftpackmodule.o build/temp.macosx-10.7-intel-2.7/scipy/fftpack/src/zfft.o build/temp.macosx-10.7-intel-2.7/scipy/fftpack/src/drfft.o build/temp.macosx-10.7-intel-2.7/scipy/fftpack/src/zrfft.o build/temp.macosx-10.7-intel-2.7/scipy/fftpack/src/zfftnd.o build/temp.macosx-10.7-intel-2.7/build/src.macosx-10.7-intel-2.7/scipy/fftpack/src/dct.o build/temp.macosx-10.7-intel-2.7/build/src.macosx-10.7-intel-2.7/scipy/fftpack/src/dst.o build/temp.macosx-10.7-intel-2.7/build/src.macosx-10.7-intel-2.7/fortranobject.o -L/usr/local/lib/gcc/x86_64-apple-darwin11.0.0/4.6.1 -Lbuild/temp.macosx-10.7-intel-2.7 -ldfftpack -lfftpack -lgfortran -o build/lib.macosx-10.7-intel-2.7/scipy/fftpack/_fftpack.so” failed with exit status 1

How do I fix this problem? I’m using Mac OSX 10.7.5

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J April 20, 2013 at 7:22 am

Hi Thomas, did you remember to install the Fortran compiler: brew install gfortran

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Thomas Edwards April 20, 2013 at 8:26 am

Ah, it turns out gfortran WASN’T installed properly.
I executed ‘brew install gfortran’ again and it turned out I needed to ‘brew link –overwrite’ some stuff.

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Thomas Edwards April 20, 2013 at 8:26 am

Thanks!

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Kaushik December 9, 2014 at 10:16 pm

Hi
I am having a problem with the following command on my Mac Lion

python setup.py install
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ld: library not found for -lgomp
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command ‘/usr/bin/clang++’ failed with exit status 1

Previously it used to throw an error with openblas linker errors. Which I sorted by putting openblas into the directories to look for inside setup.py. However the gomp error is really thrown me off. I am clueless at the moment :(

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