Unable to upgrade matplotlib 1.5.0 through pip

[yannis1962]

When I try to upgrade matplotlib via pip I get the following:

Phoebe:pip-review-0.3.7 yannis$ pip install --upgrade matplotlib
Collecting matplotlib
  Using cached matplotlib-1.5.0-cp27-none-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already up-to-date: numpy>=1.6 in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: pytz in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: python-dateutil in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: cycler in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: pyparsing!=2.0.0,!=2.0.4,>=1.5.6 in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: six>=1.5 in /usr/local/lib/python2.7/site-packages (from python-dateutil->matplotlib)
Installing collected packages: matplotlib
  Found existing installation: matplotlib 1.4.3
    Uninstalling matplotlib-1.4.3:
      Successfully uninstalled matplotlib-1.4.3
  Rolling back uninstall of matplotlib
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 211, in main
    status = self.run(options, args)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 311, in run
    root=options.root_path,
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 646, in install
    **kwargs
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 803, in install
    self.move_wheel_files(self.source_dir, root=root)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 998, in move_wheel_files
    isolated=self.isolated,
  File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 339, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 317, in clobber
    shutil.copyfile(srcfile, destfile)
  File "/usr/local/Cellar/python/2.7.10_2/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/mpl_toolkits/exceltools.py'

I'm running MacOS X 10.11 and I have matplotlib 1.4.3 installed via homebrew (which does not provide 1.5.0 yet).

[jenshnielsen]

Something is wrong tithe the permissions on your files in /usr/local/lib/python2.7/site-packages that is likely caused by your upgrade to OSX 10.11. You can check the output of brew doctor to see if they are set correctly.

[mdboom]

That seems like good advice. FWIW, I couldn't reproduce the problem on Mac 10.10 and the homebrew Python 2.7.

[jenshnielsen]

Closing since this is not a matplotlib issue

[slhck]

I have the same issue going from 1.5.1 to 1.5.2 – @yannis1962, have you ever resolved it?

As far as I can see, there is no issue with Homebrew and its permissions.

Collecting matplotlib
  Using cached matplotlib-1.5.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already up-to-date: pyparsing!=2.0.0,!=2.0.4,!=2.1.2,>=1.5.6 in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: pytz in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: cycler in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: python-dateutil in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: numpy>=1.6 in /usr/local/lib/python2.7/site-packages (from matplotlib)
Requirement already up-to-date: six in /usr/local/Cellar/matplotlib/1.5.1/libexec/lib/python2.7/site-packages (from cycler->matplotlib)
Installing collected packages: matplotlib
  Found existing installation: matplotlib 1.5.1
    Uninstalling matplotlib-1.5.1:
      Successfully uninstalled matplotlib-1.5.1
  Rolling back uninstall of matplotlib
Exception:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/local/lib/python2.7/site-packages/pip/commands/install.py", line 317, in run
    prefix=options.prefix_path,
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_set.py", line 742, in install
    **kwargs
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 831, in install
    self.move_wheel_files(self.source_dir, root=root, prefix=prefix)
  File "/usr/local/lib/python2.7/site-packages/pip/req/req_install.py", line 1032, in move_wheel_files
    isolated=self.isolated,
  File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 346, in move_wheel_files
    clobber(source, lib_dir, True)
  File "/usr/local/lib/python2.7/site-packages/pip/wheel.py", line 324, in clobber
    shutil.copyfile(srcfile, destfile)
  File "/usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 83, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: '/usr/local/lib/python2.7/site-packages/mpl_toolkits/exceltools.py'

The file exists and is executable:

$ ll /usr/local/lib/python2.7/site-packages/mpl_toolkits/exceltools.py
lrwxr-xr-x  1 werner  staff  90 Mar  8 16:41 /usr/local/lib/python2.7/site-packages/mpl_toolkits/exceltools.py -> ../../../../Cellar/matplotlib/1.5.1/lib/python2.7/site-packages/mpl_toolkits/exceltools.py

[jenshnielsen]

As which user are you trying to install matplotlib?

[slhck]

As werner – that's me. I also did a chown -R $(whoami) /usr/local just to be sure.

[jenshnielsen]

I don't know exactly what it wrong but mpl_toolkits is a name space package that is known to be problematic when installing and uninstalling with different tools. In the medium to long term we should get rid of the namespace package. (which is currently needed because basemap etc installs into mpl_toolkits)

I would suggest uninstalling the homebrew python package before you try installing matplotlib from pip. It's almost never a good idea to install with one package manager on top of the install from another.

[slhck]

I would suggest uninstalling the homebrew python package before you try installing matplotlib from pip. It's almost never a good idea to install with one package manager on top of the install from another.

Thanks for your answer, but I'm not sure what exactly you mean by that.

I only have pip from Homebrew:

which -a pip
/usr/local/bin/pip

And as far as I can tell I've only used this to install packages. What other package manager do you assume I have used? By "uninstalling the homebrew python package", do you mean uninstalling matplotlib or Python from Homebrew entirely?

[jenshnielsen]

Ok I understod that you were using homebrew python to install matplotlib. That was the original issue that @yannis1962 raised

[jenshnielsen]

https://github.com/homebrew/homebrew-python

[slhck]

Gotcha, will ask there instead. Thanks.

[jenshnielsen]

Not nessesarily. If you have not installed matplotlib from homebrew-python you should be able to pip install matplotlib

You can check you homebrew python install of matplotlib by doing

brew info matplotlib

[slhck]

Aaah, now I see. I didn't know Homebrew Python did its own package management.

So brew uninstall matplotlib && pip install -U matplotlib did it.

[jenshnielsen]

Ok great. I think the idea of homebrew-python is to provide a subset of python packages such as matplotlib, numpy and so on which may be harder to install than pure python packages.