[Numpy-discussion] Compilation problems npy_float64

[Johan]

Hello, I searched the forum, but couldn't find a post related to my
problem. I am installing scipy via pip in cygwin environment

pip install scipy

Note: numpy version 1.10.1 was installed with pip install -U numpy


/usr/bin/gfortran -Wall -g -Wall -g -shared -Wl,-gc-sections -Wl,-s
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/geom2.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/geom.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/global.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/io.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/libqhull.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/mem.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/merge.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/poly2.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/poly.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/qset.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/random.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/rboxlib.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/stat.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/user.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/usermem.o
build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/qhull/src/userprintf.o
build/temp.cygwin-2.2.1-x86_64-
2.7/scipy/spatial/qhull/src/userprintf_rbox.o -L/usr/lib -
L/usr/lib/gcc/x86_64-pc-cygwin/4.9.3 -L/usr/lib/python2.7/config -
L/usr/lib -Lbuild/temp.cygwin-2.2.1-x86_64-2.7 -llapack -lblas -
lpython2.7 -lgfortran -o build/lib.cygwin-2.2.1-x86_64-
2.7/scipy/spatial/qhull.dll
building 'scipy.spatial.ckdtree' extension
compiling C++ sources
C compiler: g++ -fno-strict-aliasing -ggdb -O2 -pipe -Wimplicit-
function-declaration -fdebug-prefix-map=/usr/src/ports/python/python-
2.7.10-1.x86_64/build=/usr/src/debug/python-2.7.10-1 -fdebug-prefix-
map=/usr/src/ports/python/python-2.7.10-1.x86_64/src/Python-
2.7.10=/usr/src/debug/python-2.7.10-1 -DNDEBUG -g -fwrapv -O3 -Wall

creating build/temp.cygwin-2.2.1-x86_64-2.7/scipy/spatial/ckdtree
creating build/temp.cygwin-2.2.1-x86_64-
2.7/scipy/spatial/ckdtree/src
compile options: '-I/usr/include/python2.7 -
I/usr/lib/python2.7/site-packages/numpy/core/include -
Iscipy/spatial/ckdtree/src -I/usr/lib/python2.7/site-
packages/numpy/core/include -I/usr/include/python2.7 -c'
g++: scipy/spatial/ckdtree/src/ckdtree_cpp_exc.cxx
cc1plus: warning: command line option ‘-Wimplicit-function-
declaration’ is valid for C/ObjC but not for C++
g++: scipy/spatial/ckdtree/src/ckdtree_query.cxx
cc1plus: warning: command line option ‘-Wimplicit-function-
declaration’ is valid for C/ObjC but not for C++
In file included from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/arrayobject.h:4,
from
scipy/spatial/ckdtree/src/ckdtree_query.cxx:15:
/usr/lib/python2.7/site-
packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by "
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
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 /usr/include/python2.7/pyport.h:325:0,
from /usr/include/python2.7/Python.h:58,
from
scipy/spatial/ckdtree/src/ckdtree_query.cxx:14:
/usr/include/math.h:263:15: note: previous declaration ‘double
infinity()’
extern double infinity _PARAMS((void));
^
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==’
else if (p==infinity) {
^
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);

^
In file included from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/arrayobject.h:4,
from
scipy/spatial/ckdtree/src/ckdtree_query.cxx:15:
/usr/lib/python2.7/site-
packages/numpy/core/include/numpy/__multiarray_api.h: At global scope:
/usr/lib/python2.7/site-
packages/numpy/core/include/numpy/__multiarray_api.h:1634:1: warning:
‘int _import_array()’ defined but not used [-Wunused-function]
_import_array(void)
^
cc1plus: warning: command line option ‘-Wimplicit-function-
declaration’ is valid for C/ObjC but not for C++
In file included from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/ndarraytypes.h:1781:0,
from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/arrayobject.h:4,
from
scipy/spatial/ckdtree/src/ckdtree_query.cxx:15:
/usr/lib/python2.7/site-
packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning: #warning "Using deprecated NumPy API, disable it by "
"#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
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 /usr/include/python2.7/pyport.h:325:0,
from /usr/include/python2.7/Python.h:58,
from
scipy/spatial/ckdtree/src/ckdtree_query.cxx:14:
/usr/include/math.h:263:15: note: previous declaration ‘double
infinity()’
extern double infinity _PARAMS((void));
^
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==’
else if (p==infinity) {
^
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);

^
In file included from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/ndarrayobject.h:27:0,
from /usr/lib/python2.7/site-
packages/numpy/core/include/numpy/arrayobject.h:4,
from
scipy/spatial/ckdtree/src/ckdtree_query.cxx:15:
/usr/lib/python2.7/site-
packages/numpy/core/include/numpy/__multiarray_api.h: At global scope:
/usr/lib/python2.7/site-
packages/numpy/core/include/numpy/__multiarray_api.h:1634:1: warning:
‘int _import_array()’ defined but not used [-Wunused-function]
_import_array(void)
^
error: Command "g++ -fno-strict-aliasing -ggdb -O2 -pipe -Wimplicit-
function-declaration -fdebug-prefix-map=/usr/src/ports/python/python-
2.7.10-1.x86_64/build=/usr/src/debug/python-2.7.10-1 -fdebug-prefix-
map=/usr/src/ports/python/python-2.7.10-1.x86_64/src/Python-
2.7.10=/usr/src/debug/python-2.7.10-1 -DNDEBUG -g -fwrapv -O3 -Wall -
I/usr/include/python2.7 -I/usr/lib/python2.7/site-
packages/numpy/core/include -Iscipy/spatial/ckdtree/src -
I/usr/lib/python2.7/site-packages/numpy/core/include -
I/usr/include/python2.7 -c scipy/spatial/ckdtree/src/ckdtree_query.cxx -
o build/temp.cygwin-2.2.1-x86_64-
2.7/scipy/spatial/ckdtree/src/ckdtree_query.o" failed with exit status 1

----------------------------------------
Command "/usr/bin/python -c "import setuptools,
tokenize;__file__='/tmp/pip-build-
vAliRx/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)
(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --
record /tmp/pip-gxrCbK-record/install-record.txt --single-version-
externally-managed --compile" failed with error code 1 in /tmp/pip-
build-vAliRx/scipy

[Pauli Virtanen]

Post by Johan
Hello, I searched the forum, but couldn't find a post related to my
problem. I am installing scipy via pip in cygwin environment

[clip]

Post by Johan
/usr/include/math.h:263:15: note: previous declaration ‘double
infinity()’
extern double infinity _PARAMS((void));
^

[clip]

This looks like some Cygwin weirdness --- a variable called
"infinity" is apparently there declared by math.h, and thus
a reserved name.

This was fixed by (but not for this reason)
https://github.com/scipy/scipy/commit/832baa20f0b5
so you may have better luck with the dev version.

[Sturla Molden]

Post by Johan
Hello, I searched the forum, but couldn't find a post related to my
problem. I am installing scipy via pip in cygwin environment

I think I introduced this error when moving a global variable from the
Cython module to a C++ module. The name collision with math.h was silent on
Linux, Mac, and Windows (MinGW and MSVC) -- or not even present --, and
thus went under the radar. But it eventually showed up on SunOS, and now
also on Cygwin. :-(

My apologies.

Anyhow, it should be gone now. Try SciPy master.


Sturla