[Biopython-dev] Problem on Mac OS X since update Xcode 5.1

[Peter Cock]

Hi all,

I installed the Xcode 5.1 update last night on my work Mac, and
this seems to have broken the builds on Python 2.6 and 2.7
(run via builtbot).

http://testing.open-bio.org/biopython/builders/OS%20X%20-%20Python%202.6/builds/174/steps/compile/logs/stdio
...
running build_ext
building 'Bio.cpairwise2' extension
creating build/temp.macosx-10.9-intel-2.6
creating build/temp.macosx-10.9-intel-2.6/Bio
cc -fno-strict-aliasing -fno-common -dynamic -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/2.6/include/python2.6
-c Bio/cpairwise2module.c -o
build/temp.macosx-10.9-intel-2.6/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

http://testing.open-bio.org/biopython/builders/OS%20X%20-%20Python%202.7/builds/170/steps/compile/logs/stdio
...
running build_ext
building 'Bio.cpairwise2' extension
creating build/temp.macosx-10.9-intel-2.7
creating build/temp.macosx-10.9-intel-2.7/Bio
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

This looks like a problem where distutils is using a gcc argument
which cc (clang) used to ignore but not treats as an error. There
will probably be similar reports on other Python projects as well...

Peter