I'm trying to put scikit-learn and pandas into Sage 7.2 (on El Capitan). I'd successfully done this in Sage 6.6. However, when I enter /Applications/SageMath-7.2.app/Contents/Resources/sage/sage --pip install scikit-learn (same result for pandas), I get the following error message.
creating build/temp.macosx-10.9-x86_64-2.7
creating build/temp.macosx-10.9-x86_64-2.7/sklearn
creating build/temp.macosx-10.9-x86_64-2.7/sklearn/svm
creating build/temp.macosx-10.9-x86_64-2.7/sklearn/svm/src
creating build/temp.macosx-10.9-x86_64-2.7/sklearn/svm/src/libsvm
compile options: '-I/Applications/SageMath-7.2.app/Contents/Resources/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-macosx-10.9-x86_64.egg/numpy/core/include -c'
g++: sklearn/svm/src/libsvm/libsvm_template.cpp
In file included from sklearn/svm/src/libsvm/svm.cpp:53:0,
from sklearn/svm/src/libsvm/libsvm_template.cpp:6:
/Applications/SageMath-7.2.app/Contents/Resources/sage/local/lib/gcc/x86_64-apple-darwin15.4.0/4.9.3/include-fixed/math.h:45:23: fatal error: sys/cdefs.h: No such file or directory
#include <sys/cdefs.h>
^
compilation terminated.
In file included from sklearn/svm/src/libsvm/svm.cpp:53:0,
from sklearn/svm/src/libsvm/libsvm_template.cpp:6:
/Applications/SageMath-7.2.app/Contents/Resources/sage/local/lib/gcc/x86_64-apple-darwin15.4.0/4.9.3/include-fixed/math.h:45:23: fatal error: sys/cdefs.h: No such file or directory
#include <sys/cdefs.h>
^
compilation terminated.
error: Command "g++ -fno-strict-aliasing -I/Applications/SageMath-7.2.app/Contents/Resources/sage/local/var/tmp/sage/build/python2-2.7.10.p1/include -DNDEBUG -g -fwrapv -O3 -Wall -Wno-unused -I/Applications/SageMath-7.2.app/Contents/Resources/sage/local/lib/python2.7/site-packages/numpy-1.11.0-py2.7-macosx-10.9-x86_64.egg/numpy/core/include -c sklearn/svm/src/libsvm/libsvm_template.cpp -o build/temp.macosx-10.9-x86_64-2.7/sklearn/svm/src/libsvm/libsvm_template.o" failed with exit status 1
----------------------------------------
Command failed with error code 1
I've been unable to find any way to proceed. The only problem I can think of is that the install instructions refer to macosx-10.9, but El Capitan is 10.11. So maybe that's the problem?
Your problem is the note No such file or directory. I suggest you install the command line tools, or even Xcode. Did you do things in the following order?
If so, probably this is the problem. I just upgraded my Mac and had to reinstall command line tools twice before it would recognize it. Luckily, this isn't very hard nowadays - open a Terminal and try to use gcc or something and it should prompt you, though your mileage may vary.
Then your command should work fine, it works for me.