[Biopython] Supported MacOS

[Sara D'Angelo]

Hi Peter!
Thanks for the super quick reply.
First I installed GCC-10.7-v2 from here:

	
		
		
	
	
		
			
				
					
						https://github.com/downloads/kennethreitz/osx-gcc-installer/GCC-10.7-
v2.pkg

					
				
			
		
	
Then I tried


sudo easy_install biopython, that¹s when I received the error message.
I have python 2.7.6.

I tried to download the source code and run python setup.py build. This is
the message I get:
MAC60F81DAB731A:biopython-1.65 sdangelo$ python setup.py build
running build
running build_py
running build_ext
building 'Bio.cpairwise2' extension
cc -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common
-fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall
-Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall
-Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -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-10.10-x86_64-2.7/Bio/cpairwise2module.o
<built-in>:0: error: Unknown value Œ10.10¹ of -mmacosx-version-min
<built-in>:0: error: Unknown value Œ10.10¹ of -mmacosx-version-min
Bio/cpairwise2module.c: In function ŒIndexList__verify_free_index¹:
Bio/cpairwise2module.c:89: warning: implicit conversion shortens 64-bit
value into a 32-bit value
Bio/cpairwise2module.c: In function Œcpairwise2__make_score_matrix_fast¹:
Bio/cpairwise2module.c:313: warning: implicit conversion shortens 64-bit
value into a 32-bit value
Bio/cpairwise2module.c:314: warning: implicit conversion shortens 64-bit
value into a 32-bit value
xcrun: error: active developer path ("/Developer") does not exist, use
`xcode-select --switch path/to/Xcode.app` to specify the Xcode that you
wish to use for command line developer tools (or see `man xcode-select`)
error: command 'cc' failed with exit status 1



I am downloading Xcode 6.1 now and see if that will solve the problem. Do
you have any other suggestions?

Sara 


On 2/7/15, 12:15 PM, "Peter Cock" <p.j.a.cock at googlemail.com> wrote:

>Hi Sara,
>
>What command did you run? That's missing from the top of the quoted text.
>
>Which version of Mac OS X do you have? Have you installed Xcode
>including the command line tools? Which version of Python are you
>using?
>
>For installing Biopython on a Mac I would simply download and unzip
>the source code, then run:
>
>python setup.py build
>python setup.py test
>python setup.py install
>
>(The last step may need sudo depending on which Python you are using)
>
>Peter
>
>On Sat, Feb 7, 2015 at 6:38 PM, Sara D'Angelo <SDAngelo at salud.unm.edu>
>wrote:
>> When I tried installing biopython 1.65 on my Mac (OS 10.10.1) using easy
>> install, I get the following error:
>>
>> Searching for biopython
>>
>> Reading https://pypi.python.org/simple/biopython/
>>
>> Reading http://biopython.org/DIST/
>>
>> Reading http://www.biopython.org/
>>
>> Best match: biopython 1.65
>>
>> Downloading
>> 
>>https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz
>>#md5=274a00e5629a135e84a8a7dfc0389935
>>
>> Processing biopython-1.65.tar.gz
>>
>> Writing /tmp/easy_install-MW6Uzg/biopython-1.65/setup.cfg
>>
>> Running biopython-1.65/setup.py -q bdist_egg --dist-dir
>> /tmp/easy_install-MW6Uzg/biopython-1.65/egg-dist-tmp-RPxPO5
>>
>> warning: no previously-included files matching '.cvsignore' found under
>> directory '*'
>>
>> warning: no previously-included files matching '*.pyc' found under
>>directory
>> '*'
>>
>> <built-in>:0: error: Unknown value Œ10.10¹ of -mmacosx-version-min
>>
>>
>>
>>
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