[Biopython] Biopython and OSX Mavericks problem.

[Zhigang Wu]

If you cannot get pip working, I recommend you trying
Macport<http://www.macports.org/install.php>,
which often involves  less hassle.
In case you have not used port before, follow the instruction here:
http://www.macports.org/install.php to install port first then you can
install biopython by typing `sudo port install 'py27-biopython' ` (I assume
your OSX running python2.7)


Zhigang



On Tue, Apr 15, 2014 at 10:40 PM, 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.
>
>
> > Or is it likely that there might be a fix in BioPython in the next month?
> >
> > Thanks in advance,
> > Dave
> >
> > =========
> > export CPPFLAGS=-Qunused-arguments
> > export CFLAGS=-Qunused-arguments
> >
> > ===============
> > ...
> > building 'Bio.cpairwise2' extension
> > cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g
> > -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd
> > -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes
> > -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes
> > -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe
> >
> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
> > -c Bio/cpairwise2module.c -o
> > build/temp.macosx-10.9-intel-2.7/Bio/cpairwise2module.o
> > clang: error: unknown argument: '-mno-fused-madd'
> > [-Wunused-command-line-argument-hard-error-in-future]
> > clang: note: this will be a hard error (cannot be downgraded to a
> warning)
> > in the future
> > error: command 'cc' failed with exit status 1
> > =============
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > Biopython mailing list  -  Biopython at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biopython
> >
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