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

[Peter Cock]

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