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Error compiling 5.0: scipy-0.9.p1

asked 2012-05-19 03:33:40 -0500

bk322 gravatar image

updated 2015-01-13 13:48:28 -0500

FrédéricC gravatar image

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 ...
(more)
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Comments

2

Can you post some more information from the log about how it failed?

Mike Hansen gravatar imageMike Hansen ( 2012-05-19 07:08:15 -0500 )edit

Also, do you have any numpy-related environment variables set up?

Volker Braun gravatar imageVolker Braun ( 2012-05-21 04:29:38 -0500 )edit

None. I install the lastest sources manually, and I don not set up any environment variables (the path I'm installing is standard - so there's no need to adjust the PYTHONPATH)

bk322 gravatar imagebk322 ( 2012-05-23 02:18:12 -0500 )edit

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answered 2012-05-28 21:23:34 -0500

bk322 gravatar image

Oh, I solved it.

I have latest numpy, scipy, matplotlib installed at

~/.local/lib/python2.7/site-packages

and it makes sage crazy - both during compilation and during the usage.

So renaming that lib directory to lib~ allows one to use sage. Here's a bash function which toggles reanming of lib:

bk-tgls-lcl-lib () { if [ -e ~/.local/lib ]; then mv ~/.local/lib ~/.local/lib~ && echo '!!! Now it is lib~'; else mv ~/.local/lib~ ~/.local/lib && echo '!!! Now it is lib'; fi; }
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Asked: 2012-05-19 03:33:40 -0500

Seen: 823 times

Last updated: May 28 '12