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

[Peter Cock]

On Sun, Mar 16, 2014 at 9:15 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> On Sun, Mar 16, 2014 at 8:53 PM, Lenna Peterson <arklenna at gmail.com> wrote:
>> On Wed, Mar 12, 2014 at 5:59 AM, Peter Cock <p.j.a.cock at googlemail.com>
>> wrote:
>>>
>>> ...
>>>
>>> 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
>>>
>>
>> I encountered the same problem (clean install of Mavericks, vanilla Python,
>> latest XCode from App Store).
>>
>> One answer [1] suggests this is not a guaranteed solution but offers a
>> different flag (which I did not test).
>>
>> I chose to edit system python files [2] which is definitely not the best
>> option for most users.
>>
>> [1]: http://stackoverflow.com/a/22315129
>> [2]:  http://stackoverflow.com/a/22322068
>>
>>> 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)?
>>
>> Do you mean editing environment variables with `os.environ`? I don't know
>> enough about the details of how packages are built to know what will work
>> with both compiling from source, easy_install, pip, etc.
>
> Yes, I was thinking about editing the environment variables in
> setup.py via the os module. I agree there are potential risks
> with 3rd party installers, but adding -Qunused-arguments to
> any existing CFLAGS (within the scope of the Biopython install)
> is hopefully low risk...
>
>>> Or it could be done via the buildbot setup, or on this buildslave
>>> directly (e.g. the ~/.bash_profile).
>>
>> It's a dilemma, because asking users to edit their .bashrc or .bash_profile
>> before installation is annoying and easy to overlook, but modifying them in
>> setup.py feels hacky (i.e. how long will this solution work?). Crossing my
>> fingers and hoping Apple fixes this in an update...
>>
>
> Fingers crossed Apple pushes another update in the next few
> weeks to resolve this...
>
> Peter

I just retested with XCode 5.1.1 (released last week and updated
via the App Store), and the problem persists.

$ cc -v
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

$ which python-config
/Library/Frameworks/Python.framework/Versions/Current/bin/python-config

$ python-config --cflags
-I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
-I/Library/Frameworks/Python.framework/Versions/2.5/include/python2.5
-arch ppc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk
-fno-strict-aliasing -Wno-long-double -no-cpp-precomp -mno-fused-madd
-fno-common -dynamic -DNDEBUG -g -O3

i.e. Apple's current Python still says to use C compliler options which
Apple's current clang compiler rejects :(

The good news is the environment variable trick still works.

It appears Apple are not going to fix this, so perhaps we do need
to add a hack to our setup.py file?

Peter