[Biopython] Installing biopython on OS X 10.10.5

[Shyam Saladi]

If you're using Anaconda Python, why not

conda install biopython



On Mon, May 9, 2016 at 11:53 AM, Michael Muratet <muratetm at gmail.com> wrote:

> Greetings
>
> I have a MacBook Pro 17” Early 2009 running 10.10.5. I’m using anaconda:
>
> 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
>
> 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).
>     """
>     # see
> http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011240.html
>     if sys.platform != "darwin":
>         return
>     # see also Bio/_py3k/__init__.py (which we can't use in setup.py)
>     if sys.version_info[0] >= 3:
>         from subprocess import getoutput
>     else:
>         from commands import getoutput
>     cc = getoutput("cc -v")
>     if "gcc" in cc or "clang" not in cc:
>         return
>     for flag in ["CFLAGS", "CPPFLAGS"]:
>         if flag not in os.environ:
>             os.environ[flag] = "-Qunused-arguments"
>         elif "-Qunused-arguments" not in os.environ[flag]:
>             os.environ[flag] += " -Qunused-arguments”
>
> My platform is “darwin” but my version comes back as 2. Furthermore, cc
> contains “clang” and so the " -Qunused-arguments” flag is getting set.
>
> 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.
>
> Cheers
>
> Mike
> _______________________________________________
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> http://mailman.open-bio.org/mailman/listinfo/biopython
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