[Biopython] Biopython and OSX Mavericks problem.

Cannatella, David catfish at austin.utexas.edu
Tue Apr 15 22:37:37 UTC 2014


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.

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?
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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