[Pythonmac-SIG] Errors building Cython extensions on 10.9...
Chris Barker
chris.barker at noaa.gov
Tue Feb 11 02:03:36 CET 2014
Hi all,
Have people in general been able to get extensions to build right under
10.9? I"ve got a bunch of C++ code (and Cython-generated C++ wrappers),
that hav been building fine on OS-X up to 10.8, and Windows, and LInux, but
now I've got a user trying to build under 10.9, and they get a bunch of
errors.
They reported trying both clang and gcc, with the same (or similar) results.
Error 1):
In file included from gnome/cy_gnome/cy_mover.cpp:561:
In file included from
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/complex:246:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:1:
error:
'inline' can only appear on functions
inline _LIBCPP_INLINE_VISIBILITY float round(float __x) _NOEXCEP...
that's in the library code! -- weird.
Then there is:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1571:46:
error:
call to 'scalbln' is ambiguous
scalbln(_A1 __x, long __y) _NOEXCEPT {return scalbln((double)__x, __y);}
^~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1565:46:
note:
candidate function
inline _LIBCPP_INLINE_VISIBILITY float scalbln(float __x, long __y...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1566:46:
note:
candidate function
inline _LIBCPP_INLINE_VISIBILITY long double scalbln(long double __x, lo...
Again in the library...
gnome/cy_gnome/cy_mover.cpp:5082:13: error: call to 'isspace' is ambiguous
if (isspace(*ts))
^~~~~~~
/usr/include/ctype.h:267:1: note: candidate function
isspace(int _c)
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype:124:38:
note:
candidate function
inline _LIBCPP_INLINE_VISIBILITY int isspace(int __c) {return __libcpp_i...
Another library issue.
So all this seems to be related to what librares 10.9 is using.
Hint:
On the Cython list, there was this thread:
https://groups.google.com/forum/#!topic/cython-users/XfUMB1vhM3g
in which the user had the same "isspace" problem. In that thread someone
suggested:
"""
The problem seems to stem
from the fact that libc++ requires the std:: namespacing. Compiling and
linking with the GNU libstdc++ can use the isspace function without
namespacing fine. Mavericks changed the default C++ library to libc++
"""
Is there a way to get it to use the old lib, rather than changing our
source and Cython, and ????
I think that Cython has been patched to remove the call to isspace, but who
knows what other issues may crop up....
I don't have a 10.9 system to test on, so this will be a trick to debug,
but any suggestions are welcome.
Thanks,
-Chris
Full Error report:
cc -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common
-fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX
-DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv
-Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -pipe -arch x86_64
-DpyGNOME=1 -I../lib_gnome
-I/Users/kthyng/.virtualenvs/default/lib/python2.7/site-packages/numpy/core/include
-I../third_party_lib/netcdf-4.3/darwin/x86_64/include -I.
-I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7
-c gnome/cy_gnome/cy_mover.cpp -o
build/temp.macosx-10.9-intel-2.7/gnome/cy_gnome/cy_mover.o
clang: warning: argument unused during compilation: '-mno-fused-madd'
In file included from gnome/cy_gnome/cy_mover.cpp:350:
../lib_gnome/ShioTimeValue_c.h:88:18: warning:
'ShioTimeValue_c::ReadTimeValues' hides overloaded virtual function
[-Woverloaded-virtual]
virtual OSErr ReadTimeValues (char *path);
^
../lib_gnome/OSSMTimeValue_c.h:74:18: note: hidden overloaded virtual
function
'OSSMTimeValue_c::ReadTimeValues' declared here
virtual OSErr ReadTimeValues (char *path, shor...
^
In file included from gnome/cy_gnome/cy_mover.cpp:352:
In file included from ../lib_gnome/TimeGridVel_c.h:24:
In file included from ../lib_gnome/Replacements.h:18:
../lib_gnome/CurrentMover_c.h:43:17: warning:
'CurrentMover_c::UpdateUncertainty' hides overloaded virtual function
[-Woverloaded-virtual]
virtual OSErr UpdateUncertainty(const Seconds& elapsed...
^
../lib_gnome/Mover_c.h:58:17: note: hidden overloaded virtual function
'Mover_c::UpdateUncertainty' declared here
virtual OSErr UpdateUncertainty(void);
^
In file included from gnome/cy_gnome/cy_mover.cpp:352:
In file included from ../lib_gnome/TimeGridVel_c.h:24:
In file included from ../lib_gnome/Replacements.h:19:
../lib_gnome/CATSMover_c.h:62:17: warning: 'CATSMover_c::AddUncertainty'
hides
overloaded virtual function [-Woverloaded-virtual]
virtual OSErr AddUncertainty(long setIndex, long leInd...
^
../lib_gnome/Mover_c.h:49:17: note: hidden overloaded virtual function
'Mover_c::AddUncertainty' declared here
virtual OSErr AddUncertainty (long setIndex, long leIn...
^
In file included from gnome/cy_gnome/cy_mover.cpp:352:
In file included from ../lib_gnome/TimeGridVel_c.h:24:
In file included from ../lib_gnome/Replacements.h:20:
../lib_gnome/WindMover_c.h:73:17: warning: 'WindMover_c::UpdateUncertainty'
hides overloaded virtual function [-Woverloaded-virtual]
virtual OSErr UpdateUncertainty(const Seconds& elapsed...
^
../lib_gnome/Mover_c.h:58:17: note: hidden overloaded virtual function
'Mover_c::UpdateUncertainty' declared here
virtual OSErr UpdateUncertainty(void);
^
In file included from gnome/cy_gnome/cy_mover.cpp:360:
../lib_gnome/GridCurrentMover_c.h:49:17: warning:
'GridCurrentMover_c::AddUncertainty' hides overloaded virtual function
[-Woverloaded-virtual]
virtual OSErr AddUncertainty(long setIndex, long leInd...
^
../lib_gnome/Mover_c.h:49:17: note: hidden overloaded virtual function
'Mover_c::AddUncertainty' declared here
virtual OSErr AddUncertainty (long setIndex, long leIn...
^
In file included from gnome/cy_gnome/cy_mover.cpp:365:
In file included from
/Users/kthyng/.virtualenvs/default/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from
/Users/kthyng/.virtualenvs/default/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from
/Users/kthyng/.virtualenvs/default/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:
/Users/kthyng/.virtualenvs/default/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2:
warning:
"Using deprecated NumPy API, disable it by " "#defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by " \
^
In file included from gnome/cy_gnome/cy_mover.cpp:561:
In file included from
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/complex:246:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:1:
error:
'inline' can only appear on functions
inline _LIBCPP_INLINE_VISIBILITY float round(float __x) _NOEXCEP...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:46:
error:
redefinition of 'floor' as different kind of symbol
inline _LIBCPP_INLINE_VISIBILITY float round(float __x) _NOEXCEP...
^
../lib_gnome/TypeDefs.h:197:18: note: expanded from macro 'round'
#define round(n) floor((n) + 0.5)
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:833:1:
note:
previous definition is here
floor(_A1 __x) _NOEXCEPT {return floor((double)__x);}
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:58:
error:
expected ')'
inline _LIBCPP_INLINE_VISIBILITY float round(float __x) _NOEXCEP...
^
../lib_gnome/TypeDefs.h:197:25: note: expanded from macro 'round'
#define round(n) floor((n) + 0.5)
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:46:
note:
to match this '('
inline _LIBCPP_INLINE_VISIBILITY float round(float __x) _NOEXCEP...
^
../lib_gnome/TypeDefs.h:197:24: note: expanded from macro 'round'
#define round(n) floor((n) + 0.5)
^
In file included from gnome/cy_gnome/cy_mover.cpp:561:
In file included from
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/complex:246:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1552:62:
error:
expected ';' after top level declarator
inline _LIBCPP_INLINE_VISIBILITY float round(float __x) _NOEXCEP...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1571:46:
error:
call to 'scalbln' is ambiguous
scalbln(_A1 __x, long __y) _NOEXCEPT {return scalbln((double)__x, __y);}
^~~~~~~
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1565:46:
note:
candidate function
inline _LIBCPP_INLINE_VISIBILITY float scalbln(float __x, long __y...
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cmath:1566:46:
note:
candidate function
inline _LIBCPP_INLINE_VISIBILITY long double scalbln(long double __x, lo...
^
gnome/cy_gnome/cy_mover.cpp:2049:64: warning: implicit conversion loses
integer
precision: 'Py_ssize_t' (aka 'long') to 'int' [-Wshorten-64-to-32]
...= __pyx_v_self->mover->ReallocateUncertainty(__pyx_v_num_LEs,
(&(*__Pyx_...
~~~~~~~~~~~~ ^~~~~~~~~~~~~~~
gnome/cy_gnome/cy_mover.cpp:5082:13: error: call to 'isspace' is ambiguous
if (isspace(*ts))
^~~~~~~
/usr/include/ctype.h:267:1: note: candidate function
isspace(int _c)
^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/c++/v1/cctype:124:38:
note:
candidate function
inline _LIBCPP_INLINE_VISIBILITY int isspace(int __c) {return __libcpp_i...
^
7 warnings and 6 errors generated.
error: command 'cc' failed with exit status 1
--
Christopher Barker, Ph.D.
Oceanographer
Emergency Response Division
NOAA/NOS/OR&R (206) 526-6959 voice
7600 Sand Point Way NE (206) 526-6329 fax
Seattle, WA 98115 (206) 526-6317 main reception
Chris.Barker at noaa.gov
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