When compliting the latest sources from the web-site I get:
Error installing package scipy-0.9.p1
What should I do (apart from getting the binaries)?
Revision history [back]
 | 1 | initial version |
Error compiling 5.0: scipy-0.9.p1
| | 2 | No.2 Revision |
Error compiling 5.0: scipy-0.9.p1
When compliting the latest sources from the web-site I get:
Error installing package scipy-0.9.p1
What should I do (apart from getting the binaries)?
Here's the last ~100 lines of the build:
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/ckdtree.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/ckdtree.c:158:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__:
scipy/spatial/ckdtree.c:2033:14: warning: variable __pyx_bshape_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2032:14: warning: variable __pyx_bstride_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2030:14: warning: variable __pyx_bshape_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2029:14: warning: variable __pyx_bshape_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2028:14: warning: variable __pyx_bstride_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2027:14: warning: variable __pyx_bstride_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2025:14: warning: variable __pyx_bshape_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2024:14: warning: variable __pyx_bstride_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2022:14: warning: variable __pyx_bshape_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2021:14: warning: variable __pyx_bstride_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__:
scipy/spatial/ckdtree.c:3413:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query:
scipy/spatial/ckdtree.c:4461:14: warning: variable __pyx_bshape_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4460:14: warning: variable __pyx_bshape_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4459:14: warning: variable __pyx_bstride_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4458:14: warning: variable __pyx_bstride_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: At top level:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:236:1: warning: _import_umath defined but not used [-Wunused-function]
scipy/spatial/ckdtree.c:2012:13: warning: __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree___init__ defined but not used [-Wunused-variable]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/ckdtree.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/ckdtree.so
building 'scipy.spatial._distance_wrap' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-2.7/scipy/spatial/src
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/src/distance_wrap.c
In file included from /home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/Python.h:8:0,
from scipy/spatial/src/distance_wrap.c:39:
/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/pyconfig.h:1155:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
/usr/include/features.h:215:0: note: this is the location of the previous definition
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/src/distance_wrap.c:40:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/src/distance_wrap.c: In function pdist_weighted_minkowski_wrap:
scipy/spatial/src/distance_wrap.c:866:7: warning: assignment discards const qualifier from pointer target type [enabled by default]
gcc: scipy/spatial/src/distance.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from scipy/spatial/src/distance.c:37:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/src/distance_wrap.o build/temp.linux-x86_64-2.7/scipy/spatial/src/distance.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/_distance_wrap.so
building 'scipy.special._cephes' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/special/_cephesmodule.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
error: Command "gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c scipy/special/_cephesmodule.c -o build/temp.linux-x86_64-2.7/scipy/special/_cephesmodule.o" failed with exit status 1
Error building scipy.
real 8m36.650s
user 7m51.421s
sys 0m22.869s
************************************************************************
Error installing package scipy-0.9.p1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/logs/scipy-0.9.p1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1' && '/home/boris/its/soft/sft/sage-5.0-x86_64/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[1]: *** [installed/scipy-0.9.p1] Error 1
make[1]: Leaving directory `/home/boris/its/soft/sft/sage-5.0-x86_64/spkg'
real 202m39.727s
user 169m59.525s
sys 11m1.101s
Error building Sage.
I'm on Kubuntu 12.04, I have build several previous version of Sage on my machine. Actually the cited part of the log point to the locally installed numpy:
/home/boris/.local/lib/python2.7/site-packages/numpy
This is strange: why would Sage use my locally installed numpy, when he has its own? Also this might be the source of the issue - since I'm using latest NumPy/SciPy - and if Sage looks at them he might go mad.
| | 3 | No.3 Revision |
Error compiling 5.0: scipy-0.9.p1
When compliting the latest sources from the web-site I get:
Error installing package scipy-0.9.p1
What should I do (apart from getting the binaries)?
Here's the last ~100 lines of the build:
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/ckdtree.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/ckdtree.c:158:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__:
scipy/spatial/ckdtree.c:2033:14: warning: variable __pyx_bshape_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2032:14: warning: variable __pyx_bstride_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2030:14: warning: variable __pyx_bshape_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2029:14: warning: variable __pyx_bshape_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2028:14: warning: variable __pyx_bstride_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2027:14: warning: variable __pyx_bstride_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2025:14: warning: variable __pyx_bshape_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2024:14: warning: variable __pyx_bstride_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2022:14: warning: variable __pyx_bshape_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2021:14: warning: variable __pyx_bstride_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__:
scipy/spatial/ckdtree.c:3413:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query:
scipy/spatial/ckdtree.c:4461:14: warning: variable __pyx_bshape_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4460:14: warning: variable __pyx_bshape_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4459:14: warning: variable __pyx_bstride_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4458:14: warning: variable __pyx_bstride_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: At top level:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:236:1: warning: _import_umath defined but not used [-Wunused-function]
scipy/spatial/ckdtree.c:2012:13: warning: __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree___init__ defined but not used [-Wunused-variable]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/ckdtree.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/ckdtree.so
building 'scipy.spatial._distance_wrap' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-2.7/scipy/spatial/src
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/src/distance_wrap.c
In file included from /home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/Python.h:8:0,
from scipy/spatial/src/distance_wrap.c:39:
/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/pyconfig.h:1155:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
/usr/include/features.h:215:0: note: this is the location of the previous definition
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/src/distance_wrap.c:40:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/src/distance_wrap.c: In function pdist_weighted_minkowski_wrap:
scipy/spatial/src/distance_wrap.c:866:7: warning: assignment discards const qualifier from pointer target type [enabled by default]
gcc: scipy/spatial/src/distance.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from scipy/spatial/src/distance.c:37:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/src/distance_wrap.o build/temp.linux-x86_64-2.7/scipy/spatial/src/distance.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/_distance_wrap.so
building 'scipy.special._cephes' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/special/_cephesmodule.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
error: Command "gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c scipy/special/_cephesmodule.c -o build/temp.linux-x86_64-2.7/scipy/special/_cephesmodule.o" failed with exit status 1
Error building scipy.
real 8m36.650s
user 7m51.421s
sys 0m22.869s
************************************************************************
Error installing package scipy-0.9.p1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/logs/scipy-0.9.p1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1' && '/home/boris/its/soft/sft/sage-5.0-x86_64/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[1]: *** [installed/scipy-0.9.p1] Error 1
make[1]: Leaving directory `/home/boris/its/soft/sft/sage-5.0-x86_64/spkg'
real 202m39.727s
user 169m59.525s
sys 11m1.101s
Error building Sage.
I'm on Kubuntu 12.04, I have build several previous version of Sage on my machine. Actually the cited part of the log point to the locally installed numpy:
/home/boris/.local/lib/python2.7/site-packages/numpy
This is strange: why would Sage use my locally installed numpy, when he has its own? Also this might be the source of the issue - since I'm using latest NumPy/SciPy - and if Sage looks at them he might go mad.
Edit:
I made a clean user at my notebook, and have succedded in compiling sage there. Then I've chown -R the compiled sources, and moved them to my primary account. But sage wouldn't start:
./sage
----------------------------------------------------------------------
| Sage Version 5.0, Release Date: 2012-05-14 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/boris/its/soft/sft/sage-5.0-x86_64/local/bin/sage-ipython", line 18, in <module>
import IPython
File "/usr/lib/python2.7/dist-packages/IPython/__init__.py", line 46, in <module>
from .frontend.terminal.embed import embed
File "/usr/lib/python2.7/dist-packages/IPython/frontend/terminal/embed.py", line 37, in <module>
from IPython.frontend.terminal.ipapp import load_default_config
File "/usr/lib/python2.7/dist-packages/IPython/frontend/terminal/ipapp.py", line 38, in <module>
from IPython.core.completer import IPCompleter
File "/usr/lib/python2.7/dist-packages/IPython/core/completer.py", line 84, in <module>
from IPython.utils import generics
File "/usr/lib/python2.7/dist-packages/IPython/utils/generics.py", line 19, in <module>
from IPython.external.simplegeneric import generic
File "/usr/lib/python2.7/dist-packages/IPython/external/simplegeneric/__init__.py", line 4, in <module>
from _simplegeneric import *
ImportError: No module named _simplegeneric
So it starts my system-wide ipython, instead of its own. ???
I tried
./sage -sh
./sage
but no effect. I also renamed previous .sage and .ipython folders - no effect.
| | 4 | retagged |
Error compiling 5.0: scipy-0.9.p1
When compliting the latest sources from the web-site I get:
Error installing package scipy-0.9.p1
What should I do (apart from getting the binaries)?
Here's the last ~100 lines of the build:
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/ckdtree.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/ckdtree.c:158:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___init__:
scipy/spatial/ckdtree.c:2033:14: warning: variable __pyx_bshape_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2032:14: warning: variable __pyx_bstride_0_inner_mins set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2030:14: warning: variable __pyx_bshape_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2029:14: warning: variable __pyx_bshape_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2028:14: warning: variable __pyx_bstride_1_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2027:14: warning: variable __pyx_bstride_0_inner_data set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2025:14: warning: variable __pyx_bshape_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2024:14: warning: variable __pyx_bstride_0_inner_maxes set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2022:14: warning: variable __pyx_bshape_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:2021:14: warning: variable __pyx_bstride_0_inner_indices set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree___dealloc__:
scipy/spatial/ckdtree.c:3413:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
scipy/spatial/ckdtree.c: In function __pyx_pf_5scipy_7spatial_7ckdtree_7cKDTree_query:
scipy/spatial/ckdtree.c:4461:14: warning: variable __pyx_bshape_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4460:14: warning: variable __pyx_bshape_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4459:14: warning: variable __pyx_bstride_1_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c:4458:14: warning: variable __pyx_bstride_0_xx set but not used [-Wunused-but-set-variable]
scipy/spatial/ckdtree.c: At top level:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:236:1: warning: _import_umath defined but not used [-Wunused-function]
scipy/spatial/ckdtree.c:2012:13: warning: __pyx_doc_5scipy_7spatial_7ckdtree_7cKDTree___init__ defined but not used [-Wunused-variable]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/ckdtree.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/ckdtree.so
building 'scipy.spatial._distance_wrap' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
creating build/temp.linux-x86_64-2.7/scipy/spatial/src
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/spatial/src/distance_wrap.c
In file included from /home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/Python.h:8:0,
from scipy/spatial/src/distance_wrap.c:39:
/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7/pyconfig.h:1155:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
/usr/include/features.h:215:0: note: this is the location of the previous definition
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/spatial/src/distance_wrap.c:40:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/spatial/src/distance_wrap.c: In function pdist_weighted_minkowski_wrap:
scipy/spatial/src/distance_wrap.c:866:7: warning: assignment discards const qualifier from pointer target type [enabled by default]
gcc: scipy/spatial/src/distance.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from scipy/spatial/src/distance.c:37:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1666:1: warning: _import_array defined but not used [-Wunused-function]
gcc -pthread -shared -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -shared build/temp.linux-x86_64-2.7/scipy/spatial/src/distance_wrap.o build/temp.linux-x86_64-2.7/scipy/spatial/src/distance.o -L/home/boris/its/soft/sft/sage-5.0-x86_64/local/lib -Lbuild/temp.linux-x86_64-2.7 -lpython2.7 -o build/lib.linux-x86_64-2.7/scipy/spatial/_distance_wrap.so
building 'scipy.special._cephes' extension
compiling C sources
C compiler: gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
compile options: '-I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c'
gcc: scipy/special/_cephesmodule.c
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
In file included from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1973:0,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
from scipy/special/_cephesmodule.c:12:
/home/boris/.local/lib/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
scipy/special/_cephesmodule.c: In function scipy_special_raise_warning:
scipy/special/_cephesmodule.c:1055:5: error: expected =, ,, ;, asm or __attribute__ before char
scipy/special/_cephesmodule.c:1062:5: error: __save__ undeclared (first use in this function)
scipy/special/_cephesmodule.c:1062:5: note: each undeclared identifier is reported only once for each function it appears in
scipy/special/_cephesmodule.c:1063:5: error: expected ; before PyErr_WarnEx
scipy/special/_cephesmodule.c:1065:1: error: expected ; before } token
scipy/special/_cephesmodule.c:1076:18: error: invalid storage class for function errprint_func
scipy/special/_cephesmodule.c:1091:3: error: initializer element is not constant
scipy/special/_cephesmodule.c:1091:3: error: (near initialization for methods[0].ml_meth)
scipy/special/_cephesmodule.c:1177:1: error: expected declaration or statement at end of input
error: Command "gcc -fno-strict-aliasing -fwrapv -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/.local/lib/python2.7/site-packages/numpy/core/include -I/home/boris/its/soft/sft/sage-5.0-x86_64/local/include/python2.7 -c scipy/special/_cephesmodule.c -o build/temp.linux-x86_64-2.7/scipy/special/_cephesmodule.o" failed with exit status 1
Error building scipy.
real 8m36.650s
user 7m51.421s
sys 0m22.869s
************************************************************************
Error installing package scipy-0.9.p1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/logs/scipy-0.9.p1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/home/boris/its/soft/sft/sage-5.0-x86_64/spkg/build/scipy-0.9.p1' && '/home/boris/its/soft/sft/sage-5.0-x86_64/sage' -sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[1]: *** [installed/scipy-0.9.p1] Error 1
make[1]: Leaving directory `/home/boris/its/soft/sft/sage-5.0-x86_64/spkg'
real 202m39.727s
user 169m59.525s
sys 11m1.101s
Error building Sage.
I'm on Kubuntu 12.04, I have build several previous version of Sage on my machine. Actually the cited part of the log point to the locally installed numpy:
/home/boris/.local/lib/python2.7/site-packages/numpy
This is strange: why would Sage use my locally installed numpy, when he has its own? Also this might be the source of the issue - since I'm using latest NumPy/SciPy - and if Sage looks at them he might go mad.
Edit:
I made a clean user at my notebook, and have succedded in compiling sage there. Then I've chown -R the compiled sources, and moved them to my primary account. But sage wouldn't start:
./sage
----------------------------------------------------------------------
| Sage Version 5.0, Release Date: 2012-05-14 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
Traceback (most recent call last):
File "/home/boris/its/soft/sft/sage-5.0-x86_64/local/bin/sage-ipython", line 18, in <module>
import IPython
File "/usr/lib/python2.7/dist-packages/IPython/__init__.py", line 46, in <module>
from .frontend.terminal.embed import embed
File "/usr/lib/python2.7/dist-packages/IPython/frontend/terminal/embed.py", line 37, in <module>
from IPython.frontend.terminal.ipapp import load_default_config
File "/usr/lib/python2.7/dist-packages/IPython/frontend/terminal/ipapp.py", line 38, in <module>
from IPython.core.completer import IPCompleter
File "/usr/lib/python2.7/dist-packages/IPython/core/completer.py", line 84, in <module>
from IPython.utils import generics
File "/usr/lib/python2.7/dist-packages/IPython/utils/generics.py", line 19, in <module>
from IPython.external.simplegeneric import generic
File "/usr/lib/python2.7/dist-packages/IPython/external/simplegeneric/__init__.py", line 4, in <module>
from _simplegeneric import *
ImportError: No module named _simplegeneric
So it starts my system-wide ipython, instead of its own. ???
I tried
./sage -sh
./sage
but no effect. I also renamed previous .sage and .ipython folders - no effect.
