[Biopython] installation failure on mac OS10.6.7

[Ian Lancaster]

First of all, make sure everything is in place. Type which gcc-4.2; it should be in /usr/bin. Which easy_install and which python should points to /Library/Frameworks/Python.framework/Versions/2.7/bin if you used the python.org installer. 

You shouldn't have to use sudo to install python packages, unless you are still pointed at the system version of python. I suspect this is the case based on the permissions error. Add the correct python to your path by adding to the end of ~/.bash_profile

	PATH="/Library/Frameworks/Python.framework/Versions/2.7/bin:${PATH}"
	export PATH"

When you run python the shell prompt should display the GCC version in the beginning. You can explicitly set the compiler for distutils before running easy_install with the command export CC=gcc-4.2. Then easy_install biopython.

Also, if you are going to be managing more python packages (why not) pip is much better at this than easy_install, and actually supports uninstallation. Easy_install pip, then pip install biopython or whatever. Not necessary, but useful. www.pip-installer.org

Ian

On Jun 6, 2011, at 6:29 PM, Dilara Ally wrote:

> Hi Ian, 
> 
> I've installed python2.7 and because of an earlier email  I removed Xcode4.0 and installed  Xcode3.0 +10.4 sdk then upgraded to Xcode4.0.  I also changed the version of numpy and tested to see if I could import it.  There was no problem importing numpy.
> 
> I tried to install biopython by directing entering the directory biopython-1.57 and typing the command python setup.py install but got this message:
> 
> creating build/lib.macosx-10.6-intel-2.7
> error: could not create 'build/lib.macosx-10.6-intel-2.7': Permission denied
> 
> Then when I tried the easy install using this command:  
> sudo easy_install -f http://biopython.org/DIST/ biopython
> I got the following error:  Is it still having trouble with the gcc 4.2 compiler
> 
> Searching for biopython
> Reading http://biopython.org/DIST/
> Best match: biopython 1.57
> Downloading http://biopython.org/DIST/biopython-1.57.zip
> Processing biopython-1.57.zip
> Running biopython-1.57/setup.py -q bdist_egg --dist-dir /tmp/easy_install-8RE8Sh/biopython-1.57/egg-dist-tmp-YMF_hu
> warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
> warning: no previously-included files found matching 'Tests/Graphics/*.eps'
> warning: no previously-included files found matching 'Tests/Graphics/*.svg'
> warning: no previously-included files found matching 'Tests/Graphics/*.png'
> warning: no previously-included files matching '*' found under directory 'Tests/UnitTests'
> warning: no previously-included files matching '.cvsignore' found under directory '*'
> warning: no previously-included files matching '.gitignore' found under directory '*'
> warning: no previously-included files matching '*.pyc' found under directory '*'
> unable to execute gcc-4.2: No such file or directory
> error: Setup script exited with error: command 'gcc-4.2' failed with exit status 1
> 
> 
> I'm stumped.
> 
> Thanks for the help.
> 
> Dilara
> 
> 
> 
> On Mon, Jun 6, 2011 at 12:14 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> After gcc 4.0 the Wno-long-double option was removed, among others, which was apparently used in building python. However, I don't think the problem is with gcc per se, but the version of python.
> 
> For instance, installing numpy with Apple's python2.6 and 2.5 failed on my machine with the gcc 4.2 compiler. Then I installed python2.7 from the official package at python.org; numpy and Biopython installed and tested fine (I used pip). This might be a better solution for Snow Leopard users, particularly those who have only installed Xcode 4.
> 
> Ian
> 
> On Jun 6, 2011, at 12:59 PM, Peter Cock wrote:
> 
> > On Mon, Jun 6, 2011 at 5:56 PM, Ian Lancaster <ilancaster at gmail.com> wrote:
> >
> > Hi Ian,
> >
> > That's a very interesting link - do you have anything specific on what it is
> > that numpy (and therefore likely also Biopython) doesn't like?
> >
> > Thank you,
> >
> > Peter
> 
> 
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