[Biopython] installation failure on mac OS10.6.7
dilara.ally at gmail.com
Mon Jun 6 18:29:15 EDT 2011
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
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
Searching for biopython
Best match: biopython 1.57
Running biopython-1.57/setup.py -q bdist_egg --dist-dir
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
warning: no previously-included files matching '.cvsignore' found under
warning: no previously-included files matching '.gitignore' found under
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
Thanks for the help.
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.
> 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>
> > Hi Ian,
> > That's a very interesting link - do you have anything specific on what it
> > that numpy (and therefore likely also Biopython) doesn't like?
> > Thank you,
> > Peter
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