[Biopython] Unable to install Biopython on Mac OS X

Ravi Tavakley rtavakley at yahoo.com
Fri Jan 15 01:33:19 UTC 2016


I am installing Biopython on MacOSX.  “gcc” fails to find “stdio.h” file. I am running MacOSX version 10.11.2 (ElCapitan).I tried "pip install biopython” and then tried installing from source. gcc fails in both cases. I get the following error message:
gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk -Qunused-arguments -Qunused-arguments -I/Applications/Canopy.app/appdata/canopy-1.5.2.2785.macosx-x86_64/Canopy.app/Contents/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.6-x86_64-2.7/Bio/cpairwise2module.oclang: warning: no such sysroot directory: '/Developer/SDKs/MacOSX10.6.sdk'In file included from Bio/cpairwise2module.c:12:/Applications/Canopy.app/appdata/canopy-1.5.2.2785.macosx-x86_64/Canopy.app/Contents/include/python2.7/Python.h:33:10: fatal error:       'stdio.h' file not found#include <stdio.h>         ^1 error generated.error: command 'gcc' failed with exit status 1
Similar failure occurs with pip install.
Any help will be appreciated. I have python 2.7 with Canopy installed on the system.
Ravi Tavakley
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