Error running: easy_install numpy (Trac #1423) #2021
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trac user rjain wrote on 2010-03-05 Let me know if you need details. rajeeja@gmail.com Rajeev Jain |
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@cournape wrote on 2010-03-06 There is no need to use easy_install, just install from sources with python setup.py install. It seems also that your blas/lapack is built with gfortran: you should make sure to use gfortran when building numpy as well: python setup.py build_ext --fcompiler=gnu95 install |
certik
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Nov 14, 2012
The return from PyArray_DescrFromObject PyArray_SearchSorted needed to be checked for NULL. Also added checks in other spots where PyArray_DescrFromObject was called. Added regression test for same. Made a few small code cleanups along the way. All the checks may not be necessary, but 1) No one should have to waste brain cycles figuring that out. 2) Bugs happen. 3) Things change.
GaelVaroquaux
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to GaelVaroquaux/numpy
that referenced
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Nov 15, 2012
The return from PyArray_DescrFromObject PyArray_SearchSorted needed to be checked for NULL. Also added checks in other spots where PyArray_DescrFromObject was called. Added regression test for same. Made a few small code cleanups along the way. All the checks may not be necessary, but 1) No one should have to waste brain cycles figuring that out. 2) Bugs happen. 3) Things change.
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Original ticket http://projects.scipy.org/numpy/ticket/1423 on 2010-03-05 by trac user rjain, assigned to unknown.
(demoenv)jain@jain-desktop:/sandbox/demoenv$ easy_install numpy
Searching for numpy
Reading http://pypi.python.org/simple/numpy/
Reading http://numpy.scipy.org
Reading http://sourceforge.net/project/showfiles.php?group_id=1369&package_id=175103
Reading http://numeric.scipy.org
Best match: numpy 1.3.0
Downloading http://sourceforge.net/projects/numpy/files/NumPy/1.3.0/numpy-1.3.0.zip/download
Processing download
Running numpy-1.3.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-zpQwWp/numpy-1.3.0/egg-dist-tmp-mmTb5S
Running from numpy source directory.
non-existing path in 'numpy/distutils': 'site.cfg'
/tmp/easy_install-zpQwWp/numpy-1.3.0/numpy/distutils/command/config.py:361: DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of get_output is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
DeprecationWarning)
Found executable /usr/bin/g77
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
compiling '_configtest.c':
/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
ATL_buildinfo();
return 0;
}
/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to
_gfortran_st_write_done' /usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to_gfortran_transfer_integer'/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to
_gfortran_stop_numeric' /usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to_gfortran_st_write'/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to
_gfortran_transfer_character' collect2: ld returned 1 exit status /usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to_gfortran_st_write_done'/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to
_gfortran_transfer_integer' /usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to_gfortran_stop_numeric'/usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to
_gfortran_st_write' /usr/lib/gcc/x86_64-linux-gnu/4.2.4/../../../../lib/libf77blas.so: undefined reference to_gfortran_transfer_character'collect2: ld returned 1 exit status
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
compiling '_configtest.c':
/* This file is generated from numpy/distutils/system_info.py */
void ATL_buildinfo(void);
int main(void) {
ATL_buildinfo();
return 0;
}
ATLAS version 3.6.0 built by root on Thu Jun 3 21:13:07 UTC 2004:
UNAME : Linux ravel 2.6.5 #3 SMP Tue Apr 13 13:41:54 UTC 2004 x86_64 GNU/Linux
INSTFLG :
MMDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/gemm
ARCHDEF : /home/camm/atlas3-3.6.0/CONFIG/ARCHS/HAMMER64SSE2/gcc/misc
F2CDEFS : -DAdd__ -DStringSunStyle
CACHEEDGE: 720896
F77 : /home/camm/usr/bin/g77, version GNU Fortran (GCC) 3.3.3 (Debian 20040422)
F77FLAGS : -fomit-frame-pointer -O -m64
CC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422)
CC FLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64
MCC : /usr/bin/gcc, version gcc (GCC) 3.3.3 (Debian 20040422)
MCCFLAGS : -fomit-frame-pointer -O -mfpmath=387 -m64
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c: In function ‘main’:
_configtest.c:5: error: size of array ‘test_array’ is negative
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c: In function ‘main’:
_configtest.c:5: error: size of array ‘test_array’ is negative
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c: In function ‘main’:
_configtest.c:5: error: size of array ‘test_array’ is negative
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c: In function ‘main’:
_configtest.c:5: error: size of array ‘test_array’ is negative
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c: In function ‘main’:
_configtest.c:7: error: size of array ‘test_array’ is negative
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c: In function ‘main’:
_configtest.c:7: error: size of array ‘test_array’ is negative
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:5: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:4: warning: function declaration isn’t a prototype
_configtest.c:5: warning: function declaration isn’t a prototype
/tmp/easy_install-zpQwWp/numpy-1.3.0/numpy/distutils/command/config.py:39: DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of try_run is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
DeprecationWarning)
_configtest.o: In function
main': /tmp/easy_install-zpQwWp/numpy-1.3.0/_configtest.c:5: undefined reference toexp'collect2: ld returned 1 exit status
_configtest.o: In function
main': /tmp/easy_install-zpQwWp/numpy-1.3.0/_configtest.c:5: undefined reference toexp'collect2: ld returned 1 exit status
_configtest.c:1: warning: conflicting types for built-in function ‘asin’
_configtest.c:2: warning: conflicting types for built-in function ‘cos’
_configtest.c:3: warning: conflicting types for built-in function ‘log’
_configtest.c:4: warning: conflicting types for built-in function ‘fabs’
_configtest.c:5: warning: conflicting types for built-in function ‘tanh’
_configtest.c:6: warning: conflicting types for built-in function ‘atan’
_configtest.c:7: warning: conflicting types for built-in function ‘acos’
_configtest.c:8: warning: conflicting types for built-in function ‘floor’
_configtest.c:9: warning: conflicting types for built-in function ‘fmod’
_configtest.c:10: warning: conflicting types for built-in function ‘sqrt’
_configtest.c:11: warning: conflicting types for built-in function ‘cosh’
_configtest.c:12: warning: conflicting types for built-in function ‘modf’
_configtest.c:13: warning: conflicting types for built-in function ‘sinh’
_configtest.c:14: warning: conflicting types for built-in function ‘frexp’
_configtest.c:15: warning: conflicting types for built-in function ‘exp’
_configtest.c:16: warning: conflicting types for built-in function ‘tan’
_configtest.c:17: warning: conflicting types for built-in function ‘ceil’
_configtest.c:18: warning: conflicting types for built-in function ‘log10’
_configtest.c:19: warning: conflicting types for built-in function ‘sin’
_configtest.c:20: warning: conflicting types for built-in function ‘ldexp’
_configtest.c:1: warning: conflicting types for built-in function ‘expm1’
_configtest.c:2: warning: conflicting types for built-in function ‘log2’
_configtest.c:3: warning: conflicting types for built-in function ‘rint’
_configtest.c:4: warning: conflicting types for built-in function ‘atanh’
_configtest.c:5: warning: conflicting types for built-in function ‘asinh’
_configtest.c:6: warning: conflicting types for built-in function ‘acosh’
_configtest.c:7: warning: conflicting types for built-in function ‘exp2’
_configtest.c:8: warning: conflicting types for built-in function ‘log1p’
_configtest.c:9: warning: conflicting types for built-in function ‘trunc’
_configtest.c:1: warning: conflicting types for built-in function ‘cosf’
_configtest.c:2: warning: conflicting types for built-in function ‘coshf’
_configtest.c:3: warning: conflicting types for built-in function ‘rintf’
_configtest.c:4: warning: conflicting types for built-in function ‘fabsf’
_configtest.c:5: warning: conflicting types for built-in function ‘floorf’
_configtest.c:6: warning: conflicting types for built-in function ‘tanhf’
_configtest.c:7: warning: conflicting types for built-in function ‘log10f’
_configtest.c:8: warning: conflicting types for built-in function ‘logf’
_configtest.c:9: warning: conflicting types for built-in function ‘sinhf’
_configtest.c:10: warning: conflicting types for built-in function ‘acosf’
_configtest.c:11: warning: conflicting types for built-in function ‘sqrtf’
_configtest.c:12: warning: conflicting types for built-in function ‘ldexpf’
_configtest.c:13: warning: conflicting types for built-in function ‘hypotf’
_configtest.c:14: warning: conflicting types for built-in function ‘log2f’
_configtest.c:15: warning: conflicting types for built-in function ‘exp2f’
_configtest.c:16: warning: conflicting types for built-in function ‘atanf’
_configtest.c:17: warning: conflicting types for built-in function ‘fmodf’
_configtest.c:18: warning: conflicting types for built-in function ‘atan2f’
_configtest.c:19: warning: conflicting types for built-in function ‘modff’
_configtest.c:20: warning: conflicting types for built-in function ‘ceilf’
_configtest.c:21: warning: conflicting types for built-in function ‘log1pf’
_configtest.c:22: warning: conflicting types for built-in function ‘asinf’
_configtest.c:23: warning: conflicting types for built-in function ‘acoshf’
_configtest.c:24: warning: conflicting types for built-in function ‘sinf’
_configtest.c:25: warning: conflicting types for built-in function ‘tanf’
_configtest.c:26: warning: conflicting types for built-in function ‘atanhf’
_configtest.c:27: warning: conflicting types for built-in function ‘truncf’
_configtest.c:28: warning: conflicting types for built-in function ‘asinhf’
_configtest.c:29: warning: conflicting types for built-in function ‘frexpf’
_configtest.c:30: warning: conflicting types for built-in function ‘powf’
_configtest.c:31: warning: conflicting types for built-in function ‘expf’
_configtest.c:32: warning: conflicting types for built-in function ‘expm1f’
_configtest.c:1: warning: conflicting types for built-in function ‘tanhl’
_configtest.c:2: warning: conflicting types for built-in function ‘log10l’
_configtest.c:3: warning: conflicting types for built-in function ‘coshl’
_configtest.c:4: warning: conflicting types for built-in function ‘cosl’
_configtest.c:5: warning: conflicting types for built-in function ‘floorl’
_configtest.c:6: warning: conflicting types for built-in function ‘rintl’
_configtest.c:7: warning: conflicting types for built-in function ‘fabsl’
_configtest.c:8: warning: conflicting types for built-in function ‘acosl’
_configtest.c:9: warning: conflicting types for built-in function ‘ldexpl’
_configtest.c:10: warning: conflicting types for built-in function ‘sqrtl’
_configtest.c:11: warning: conflicting types for built-in function ‘logl’
_configtest.c:12: warning: conflicting types for built-in function ‘expm1l’
_configtest.c:13: warning: conflicting types for built-in function ‘hypotl’
_configtest.c:14: warning: conflicting types for built-in function ‘log2l’
_configtest.c:15: warning: conflicting types for built-in function ‘exp2l’
_configtest.c:16: warning: conflicting types for built-in function ‘atanl’
_configtest.c:17: warning: conflicting types for built-in function ‘frexpl’
_configtest.c:18: warning: conflicting types for built-in function ‘atan2l’
_configtest.c:19: warning: conflicting types for built-in function ‘sinhl’
_configtest.c:20: warning: conflicting types for built-in function ‘fmodl’
_configtest.c:21: warning: conflicting types for built-in function ‘log1pl’
_configtest.c:22: warning: conflicting types for built-in function ‘asinl’
_configtest.c:23: warning: conflicting types for built-in function ‘ceill’
_configtest.c:24: warning: conflicting types for built-in function ‘sinl’
_configtest.c:25: warning: conflicting types for built-in function ‘acoshl’
_configtest.c:26: warning: conflicting types for built-in function ‘atanhl’
_configtest.c:27: warning: conflicting types for built-in function ‘tanl’
_configtest.c:28: warning: conflicting types for built-in function ‘truncl’
_configtest.c:29: warning: conflicting types for built-in function ‘powl’
_configtest.c:30: warning: conflicting types for built-in function ‘expl’
_configtest.c:31: warning: conflicting types for built-in function ‘modfl’
_configtest.c:32: warning: conflicting types for built-in function ‘asinhl’
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
_configtest.c:6: warning: function declaration isn’t a prototype
File: build/src.linux-x86_64-2.5/numpy/core/include/numpy/config.h
define SIZEOF_SHORT 2
define SIZEOF_INT 4
define SIZEOF_LONG 8
define SIZEOF_FLOAT 4
define SIZEOF_DOUBLE 8
define SIZEOF_PY_INTPTR_T 8
define SIZEOF_PY_LONG_LONG 8
define MATHLIB m
define HAVE_SIN
define HAVE_COS
define HAVE_TAN
define HAVE_SINH
define HAVE_COSH
define HAVE_TANH
define HAVE_FABS
define HAVE_FLOOR
define HAVE_CEIL
define HAVE_SQRT
define HAVE_LOG10
define HAVE_LOG
define HAVE_EXP
define HAVE_ASIN
define HAVE_ACOS
define HAVE_ATAN
define HAVE_FMOD
define HAVE_MODF
define HAVE_FREXP
define HAVE_LDEXP
define HAVE_EXPM1
define HAVE_LOG1P
define HAVE_ACOSH
define HAVE_ASINH
define HAVE_ATANH
define HAVE_RINT
define HAVE_TRUNC
define HAVE_EXP2
define HAVE_LOG2
define HAVE_SINF
define HAVE_COSF
define HAVE_TANF
define HAVE_SINHF
define HAVE_COSHF
define HAVE_TANHF
define HAVE_FABSF
define HAVE_FLOORF
define HAVE_CEILF
define HAVE_RINTF
define HAVE_TRUNCF
define HAVE_SQRTF
define HAVE_LOG10F
define HAVE_LOGF
define HAVE_LOG1PF
define HAVE_EXPF
define HAVE_EXPM1F
define HAVE_ASINF
define HAVE_ACOSF
define HAVE_ATANF
define HAVE_ASINHF
define HAVE_ACOSHF
define HAVE_ATANHF
define HAVE_HYPOTF
define HAVE_ATAN2F
define HAVE_POWF
define HAVE_FMODF
define HAVE_MODFF
define HAVE_FREXPF
define HAVE_LDEXPF
define HAVE_EXP2F
define HAVE_LOG2F
define HAVE_SINL
define HAVE_COSL
define HAVE_TANL
define HAVE_SINHL
define HAVE_COSHL
define HAVE_TANHL
define HAVE_FABSL
define HAVE_FLOORL
define HAVE_CEILL
define HAVE_RINTL
define HAVE_TRUNCL
define HAVE_SQRTL
define HAVE_LOG10L
define HAVE_LOGL
define HAVE_LOG1PL
define HAVE_EXPL
define HAVE_EXPM1L
define HAVE_ASINL
define HAVE_ACOSL
define HAVE_ATANL
define HAVE_ASINHL
define HAVE_ACOSHL
define HAVE_ATANHL
define HAVE_HYPOTL
define HAVE_ATAN2L
define HAVE_POWL
define HAVE_FMODL
define HAVE_MODFL
define HAVE_FREXPL
define HAVE_LDEXPL
define HAVE_EXP2L
define HAVE_LOG2L
define HAVE_DECL_ISNAN
define HAVE_DECL_ISINF
define HAVE_DECL_SIGNBIT
define HAVE_DECL_ISFINITE
ifndef __cplusplus
/* #undef inline */
endif
EOF
_configtest.c:5: warning: function declaration isn’t a prototype
File: build/src.linux-x86_64-2.5/numpy/core/include/numpy/numpyconfig.h
define NPY_SIZEOF_SHORT 2
define NPY_SIZEOF_INT 4
define NPY_SIZEOF_LONG 8
define NPY_SIZEOF_FLOAT 4
define NPY_SIZEOF_DOUBLE 8
define NPY_SIZEOF_LONGDOUBLE 16
define NPY_SIZEOF_PY_INTPTR_T 8
define NPY_SIZEOF_PY_LONG_LONG 8
define NPY_SIZEOF_LONGLONG 8
define NPY_NO_SMP 0
define NPY_HAVE_DECL_ISNAN
define NPY_HAVE_DECL_ISINF
define NPY_HAVE_DECL_SIGNBIT
define NPY_HAVE_DECL_ISFINITE
define NPY_USE_C99_FORMATS 1
define NPY_INLINE inline
ifndef __STDC_FORMAT_MACROS
define __STDC_FORMAT_MACROS 1
endif
EOF
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
gnu: no Fortran 90 compiler found
zip_safe flag not set; analyzing archive contents...
numpy._import_tools: module references file
numpy._import_tools: module references path
numpy.version: module references file
numpy.core.scons_support: module references file
numpy.core.setup: module references file
numpy.core.generate_numpy_api: module references file
numpy.doc.init: module references file
numpy.ma.core: module MAY be using inspect.trace
numpy.numarray.util: module references file
numpy.distutils.system_info: module references file
numpy.distutils.exec_command: module references file
numpy.distutils.misc_util: module references file
numpy.distutils.fcompiler.compaq: module refer 8000 ences file
numpy.distutils.fcompiler.init: module references file
numpy.distutils.command.build_src: module references file
numpy.distutils.command.scons: module references file
numpy.lib.utils: module references file
numpy.lib.utils: module references path
numpy.lib.utils: module MAY be using inspect.getsource
numpy.lib.utils: module MAY be using inspect.getsourcefile
numpy.testing.numpytest: module references file
numpy.testing.utils: module references file
numpy.testing.noseclasses: module references file
numpy.testing.nosetester: module references file
numpy.f2py.setup: module references file
numpy.f2py.f2py2e: module references file
numpy.f2py.setupscons: module references file
numpy.f2py.diagnose: module references file
Adding numpy 1.3.0 to easy-install.pth file
Installing f2py script to /sandbox/demoenv/bin
Installed /sandbox/demoenv/lib/python2.5/site-packages/numpy-1.3.0-py2.5-linux-x86_64.egg
Processing dependencies for numpy
Finished processing dependencies for numpy
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/usr/lib/python2.5/atexit.py", line 24, in _run_exitfuncs
func(_targs, *_kargs)
File "/tmp/easy_install-zpQwWp/numpy-1.3.0/numpy/distutils/misc_util.py", line 219, in clean_up_temporary_directory
SystemError: Parent module 'numpy.distutils' not loaded
Error in sys.exitfunc:
Traceback (most recent call last):
File "/usr/lib/python2.5/atexit.py", line 24, in _run_exitfuncs
func(_targs, *_kargs)
File "/tmp/easy_install-zpQwWp/numpy-1.3.0/numpy/distutils/misc_util.py", line 219, in clean_up_temporary_directory
SystemError: Parent module 'numpy.distutils' not loaded
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