[Biopython] Installing biopython on OS X 10.10.5
Michael Muratet
muratetm at gmail.com
Mon May 9 18:53:44 UTC 2016
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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