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#error "SSE2 instruction set not included" when installing scikit-bio via pip

I want to install the scikit-bio python library via pip using the following command:

sudo pip install scikit-bio

on my system:

uname -a
Linux grassgis 3.2.0-69-generic-pae #103-Ubuntu SMP Tue Sep 2 05:15:53 UTC 2014 i686 i686 i386 GNU/Linux

However, this throws an error:

gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/lib/python2.7/dist-packages/numpy/core/include -I/usr/include/python2.7 -c skbio/alignment/_ssw/_ssw_wrapper.c -o build/temp.linux-i686-2.7/skbio/alignment/_ssw/_ssw_wrapper.o
    In file included from skbio/alignment/_ssw/ssw.h:17:0,
                     from skbio/alignment/_ssw/_ssw_wrapper.c:355:
    /usr/lib/gcc/i686-linux-gnu/4.6/include/emmintrin.h:32:3: error: #error "SSE2 instruction set not enabled"
    /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__multiarray_api.h:1532:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
    /usr/lib/python2.7/dist-packages/numpy/core/include/numpy/__ufunc_api.h:226:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
    error: command 'gcc' failed with exit status 1

I have run already sudo apt-get update

and sudo apt-get upgrade

to get the latest installed software.

My GCC version:

gcc --version
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3

How can I successfully install scikit-bio packages for python?

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1 answer


This issue was previously reported by a user with an i686 machine on the scikit-bio tracker. The error occurs when compiling SSW, an external C program supplied with scikit-bio. SSW author recommended passing it to the -msse2

compiler to fix the problem.

A fix was merged into the scikit-bio development branch to enable this flag for i686 machines.

If you are installing a scikit-bio version, you can specify this flag with CFLAGS

on the command line:

CFLAGS=-msse2 pip install scikit-bio


or

sudo CFLAGS=-msse2 pip install scikit-bio

Alternatively, the scikit-bio file setup.py

can be modified to be included '-msse2'

in the SSW extra_compile_args

.

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