[Biopython] Biopython and OSX Mavericks problem.

[Peter Cock]

On Wed, Apr 16, 2014 at 6:40 AM, Lenna Peterson <arklenna at gmail.com> wrote:
> On Tue, Apr 15, 2014 at 6:37 PM, Cannatella, David <
> catfish at austin.utexas.edu> wrote:
>
>> I've had the same problem as Mike Shaffer (8 April) on the discussion list
>> (see my errors below).
>>
>> I had tried the possible solutions mentioned (including the export
>> commands below), including those on the stackoverflow site, but none has
>> worked so far.
>>
>
> Have you tried the ARCHFLAGS option? http://stackoverflow.com/a/22372751
>
> Are you installing with sudo?
>
>>
>> Some posted solutions have included installing other versions of python,
>> etc., but this is not practical for several reasons.
>>
>> Is re-installing an earlier version of XCode a viable option for me?
>>
>
> Apple is not particularly supportive of downgrading, so I imagine this
> could have unforeseen side effects. clang will have this behavior
> indefinitely; the problem is an incompatibility between clang (part of
> XCode) and the python version distributed with the OS. Hopefully there will
> be an OS update soon fixing the python version.

The other option (which is actually the recommended route
according the NumPy/SciPy folk) is to ignore the Apple provides
Python (don't try to remove it!), and install your own direct from
python.org.

They do provide precompiled binaries for the Mac, but I like to
do this myself under $HOME in order to test with the newer
releases like Python 3.3 and 3.4 etc. Try something like:

$ cd ~/Downloads
$ wget http://www.python.org/ftp/python/3.3.3/Python-3.33.tgz
$ tar -zxvf Python-3.3.3.tgz
$ cd Python-3.3.3
$ ./configure --prefix=$HOME
$ make
$ make test
$ make install

Then modify your $HOME/.bash_profile to add $HOME/bin
to your path:

export PATH=$HOME/bin:$PATH

Then install NumPy, and try installing Biopython from source.

Peter