[Biopython] installation failure on mac OS10.6.7

[Dilara Ally]

thanks a bunch!

On 6/6/11 4:10 PM, Ian Lancaster wrote:
> 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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>>
>