[Biopython] Biopython and OSX Mavericks problem.

[Lenna Peterson]

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
> =============
>
>
>
>
>
>
>
>
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