well,regarding the scipy problem see
https://mail.scipy.org/pipermail/numpy-discussion/2015-November/074181.html
You might try the developemt version of scipy to see if it helps.

On Wednesday, 13 January 2016 17:32:17 UTC, robert.ma...@web.de wrote:
>
> Hello,
> I've been using the Sage appliance in Virtualbox on Windows 7 for some 
> time now. And I like it very much. Thank you for this wonderful package of 
> software and its interface.
>
> Because I need to access more RAM for calculating 3D parametric plots I 
> want to install it under Cygwin64 and followed the procedures on 
> http://trac.sagemath.org/wiki/Cygwin64Port.
>
> Compilation went fine but rpy2-2.7.5 and scipy-0.16.1 threw installation 
> errors. I tried to rebase and changed the spkg-install for both packages as 
> it is suggested for python in the link above (comment out lines for 
> patches), but the installation errors remain.
>
> My System is Windows 7, 64 bit, 24 GB RAM. I attach the log file for 
> scipy-0.16.1. The error lines from the file are:
>
> In file included from scipy/spatial/ckdtree/src/ckdtree_query.cxx:31:0:
> scipy/spatial/ckdtree/src/ckdtree_cpp_methods.h:12:20: error: 'npy_float64 
> infinity' redeclared as different kind of symbol
>  extern npy_float64 infinity;
>
> In file included from scipy/spatial/ckdtree/src/ckdtree_query.cxx:31:0:
> scipy/spatial/ckdtree/src/ckdtree_cpp_methods.h: In function 'npy_float64 
> _distance_p(const npy_float64*, const npy_float64*, npy_float64, npy_intp, 
> npy_float64)':
> scipy/spatial/ckdtree/src/ckdtree_cpp_methods.h:139:17: error: invalid 
> operands of types 'const npy_float64 {aka const double}' and 'double()' to 
> binary 'operator=='
>
> scipy/spatial/ckdtree/src/ckdtree_query.cxx: In function 'PyObject* 
> query_knn(const ckdtree*, npy_float64*, npy_intp*, const npy_float64*, 
> npy_intp, npy_intp, npy_float64, npy_float64, npy_float64)':
> scipy/spatial/ckdtree/src/ckdtree_query.cxx:431:111: error: cannot convert 
> 'double (*)()' to 'npy_float64 {aka double}' for argument '9' to 'void 
> __query_single_point(const ckdtree*, npy_float64*, npy_intp*, const 
> npy_float64*, npy_intp, npy_float64, npy_float64, npy_float64, npy_float64)'
>                  __query_single_point(self, dd_row, ii_row, xx_row, k, 
> eps, p, distance_upper_bound, ::infinity);
>
> error: Command "g++ -I/usr/include/ncurses -fno-strict-aliasing -g -O2 
> -DNDEBUG -g -fwrapv -O3 -Wall -I/home/robert/sage/local/include/python2.7 
> -I/home/robert/sage/local/lib/python2.7/site-packages/numpy/core/include 
> -Iscipy/spatial/ckdtree/src 
> -I/home/robert/sage/local/lib/python2.7/site-packages/numpy/core/include 
> -I/home/robert/sage/local/include/python2.7 -c 
> scipy/spatial/ckdtree/src/ckdtree_query.cxx -o 
> build/temp.cygwin-2.3.1-x86_64-2.7/scipy/spatial/ckdtree/src/ckdtree_query.o" 
> failed with exit status 1
> Error building scipy.
>
> Any suggestions how to proceed?
>
> Thanks a lot in advance
> Robert
>

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