[Biopython] Installing biopython on OS X 10.10.5

[Michael Muratet]

> On May 9, 2016, at 4:16 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> 
> 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?

I have the latest I could get from the App Store, version 7.2. I’ve thought about the next OS upgrade, but I worry every time I upgrade that it will break my system as it gets older.

> 
>> 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?

Yes, and it installed without a glitch, thus solving the problem. I now have the latest biopython. I should have tried conda first ;-)

For the record, I did try commenting out the code and wound up with a missing header. But, I have a current biopython so I’m not going to worry about it anymore.

Thanks

Mike

> 
>> 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