[Biopython] Installing biopython on OS X 10.10.5

[Peter Cock]

Hello Michael,

On Mon, May 9, 2016 at 7:53 PM, Michael Muratet <muratetm at gmail.com> wrote:
> Greetings
>
> I have a MacBook Pro 17” Early 2009 running 10.10.5. I’m using anaconda:
>

So not the latest El Capitan OS X 10.11, which probably also means
you don't have the latest XCode?

> Python 2.7.9 |Anaconda 2.1.0 (x86_64)| (default, Dec 15 2014, 10:37:34)
> [GCC 4.2.1 (Apple Inc. build 5577)] on darwin

Did you install Biopython into Anaconda using the conda install tool?

> I have the command line tools for XCode 7.2, but I can select “Updates”  with the App Store app and they will reinstall every time. Weird.
>
> I’ve installed and/or upgraded earlier biopythons on this machine several times without a problem, but I have run afoul of a known problem that I can’t fix.
>
> Here’s the tail end of the build output from pip:
>
> building 'Bio.cpairwise2' extension
>
> creating build/temp.macosx-10.5-x86_64-2.7
>
> creating build/temp.macosx-10.5-x86_64-2.7/Bio
>
> gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Qunused-arguments -Qunused-arguments -I/Users/mmuratet/anaconda/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.5-x86_64-2.7/Bio/cpairwise2module.o
>
> gcc: error: unrecognized command line option '-Qunused-arguments'
>
> gcc: error: unrecognized command line option '-Qunused-arguments'
>
> error: command 'gcc' failed with exit status 1
>
> I get the same error with easy_install.
>
> I looked inside setup.py and found:
>
>     We can avoid the clang compilation error with -Qunused-arguments which is
>     (currently) harmless if gcc is being used instead (e.g. compiling Biopython
>     against a locally compiled Python rather than the Apple provided Python).
>
> ...
>
> I am tempted to just comment out the code to get rid of the flag,
> but I thought someone might be able to suggest a better solution.
>

It seems on your system, adding '-Qunused-arguments' breaks things.
I agree, just try commenting out this part of setup.py on your Mac.

Since you're not running the latest Mac OS X, its probably not going
to be easy for us to debug this - so I hope that works :)

Peter