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July 25, 2012
 

python mountain lion scipy error

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Written by: arunenigma
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Installing Octave under Mountain Lion. Solution to “illegal byte sequence” error.

 

Quick jot for memory on how to install octave + scientific python for Mountain Lion, since it’s pretty new for now .. These steps are kind of a mess since I’m not really documenting them in sequence.

 

 

1. Install Xcode 4.5 + command line tools

2. Install homebrew
$ /usr/bin/ruby -e “$(/usr/bin/curl -fsSL https://raw.github.com/mxcl/homebrew/master/Library/Contributions/install_homebrew.rb)”

3. Test to make sure everything’s okay
$ brew doctor
$ brew update

4. Get Mountain Lion and Homebrew to Be Happy

Visit http://xquartz.macosforge.org/trac/wiki and download and install 2.7.2+.

$ sudo xcode-select -switch /Applications/Xcode.app/Contents/Developer

$ ln -s /opt/X11 /usr/X11

5. Install python using homebrew (will take a long time)
$ brew install python
(not necessary since OSX already has its own python)

6. Make sure python is at /usr/local/bin/python
$ which python

7. Install pip for python
$ easy_install pip

8. Install gfortran using homebrew
$ brew install gfortran

If this gives the error message:

Currently the gfortran compiler provided by this brew is only supports
the following versions of XCode
– XCode 3.1.4 on OS X 10.5.x
– XCode 3.2.2/3.2.3 — 4.0 on OS X 10.6.x
– XCode 4.1 or newer on OS X 10.7.x
etc.

then
$ brew edit gfortran

replace
if MacOS.xcode_version >= ‘4.2’ and MACOS_VERSION > 10.7
ohai “Installing gfortran 4.2.4 for XCode 4.2 (build 5666)”
with
if MacOS.xcode_version >= ‘4.2’ and MACOS_VERSION >= 10.7
ohai “Installing gfortran 4.2.4 for XCode 4.2 (build 5666) or higher

(not necessary once the gfortran recipe is updated by homebrew)

9. Install scipy and numpy using pip
$ sudo pip install scipy
(scipy will fail with the following error)


/System/Library/Frameworks/vecLib.framework/Headers/vecLib.h:22:4: error: #error “<vecLib/vecLib.h> is deprecated. Please #include <Accelerate/Accelerate.h> and link to Accelerate.framework.”

see the ticket here: http://projects.scipy.org/scipy/ticket/1710

get prebuilt binary from here instead: http://sourceforge.net/projects/scipy/files/
the prebuilt binary cannot be installed either …

monitor the ticket to see if any solutions posted .. no scipy for now ..

$ sudo pip install numpy

10. Install pkg-config using homebrew
$ brew install pkg-config

11. Install gcc using homebrew (not necessary?)
$ brew install gcc –use-llvm

12. Install matplotlib

From http://practicalcomputing.org/node/69:
$ sudo mkdir -p /usr/local/include
$ sudo ln -s /usr/X11/include/freetype2/freetype /usr/local/include/freetype
$ sudo ln -s /usr/X11/include/ft2build.h /usr/local/include/ft2build.h
$ sudo ln -s /usr/X11/include/png.h /usr/local/include/png.h
$ sudo ln -s /usr/X11/include/pngconf.h /usr/local/include/pngconf.h
$ sudo ln -s /usr/X11/include/pnglibconf.h /usr/local/include/pnglibconf.h
$ sudo mkdir -p /usr/local/lib
$ sudo ln -s /usr/X11/lib/libfreetype.dylib /usr/local/lib/libfreetype.dylib
$ sudo ln -s /usr/X11/lib/libpng.dylib /usr/local/lib/libpng.dylib

If you get the error:
unable to execute clang++: No such file or directory
then do

$ sudo ln -s /usr/bin/clang /usr/bin/clang++

Finally
$ sudo pip install matplotlib-1.1.1.tar.gz

13. Install octave (will take a long time)
$ brew install fltk 

If fltk cannot be installed with the following error
Error: Failed executing: make install (fltk.rb:24)
Then just install octave without fltk first (it’s not crucial) .. until it’s fixed

$ brew install –with-magick-plus-plus GraphicsMagick

$ brew install octave –without-fltk
$ brew install gnuplot 

If you get this error while compiling Octave:

sed: RE error: illegal byte sequence

Error: Failed executing: make all (octave.rb:84)

Then unset the LANG environmental variable first

$ unset LANG



14. MacTeX, TeXShop and LyX
Finally, something that can be easily installed ..
http://pages.uoregon.edu/koch/texshop/obtaining.html

Useful references:

 



About the Author

arunenigma
Computer Science Graduate Student @ Case Western Reserve University, Cleveland, USA



 
 

 
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