[Biopython] installation failure on mac OS10.6.7

[Dilara Ally]

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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