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

[Fields, Christopher J]

On Mar 12, 2014, at 4:59 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Wed, Mar 12, 2014 at 9:48 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>> 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
> 
> This looks relevant, especially this reply from Paul Kehrer which
> suggests this is entirely Apple's fault for shipping a Python and
> clang compiler which don't get along with the default settings:
> 
> http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-psycopg2-installation-failure
> 
> The suggested workaround seems to do the trick,
> 
> $ export CFLAGS=-Qunused-arguments
> $ export CPPFLAGS=-Qunused-arguments
> 
> Perhaps we can add this hack to our setup.py on Mac OS X...
> it seems harmless under gcc (e.g. my locally compiled version
> of Python 3.3 used gcc rather than clang)?
> 
> Or it could be done via the buildbot setup, or on this buildslave
> directly (e.g. the ~/.bash_profile).
> 
> What are folks' thoughts on this? We want it to remain easy
> to install Biopython from source under Mac OS X.
> 
> Peter

That’s scary.  I planned on updating to the latest Xcode myself today, nice to be forewarned.  I’ve been seeing clang complaints with various tools already, so I wouldn’t be surprised if this problem is more wide-spread than python.

chris