installation issue with a non-standard location of a python build
Hi, I'm having an installation issue building numpy 1.3.0 using python 2.6.2 which has been built in my local area in a non-standard place and was configured with --prefix=/users/wd15/usr/i686/4.0. When I run numpy's config ("python setup.py config") everything seems to be fine. However, when I run "python setup.py build", it gives the following error: $ python --version Python 2.6.2 $ uname -a Linux xxx.xxx.xxx 2.6.18-4-k7 #1 SMP Mon Mar 26 17:57:15 UTC 2007 i686 GNU/Linux $ python setup.py build Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 ... File "numpy/core/setup.py", line 186, in check_types "Cannot compiler 'Python.h'. Perhaps you need to "\ SystemError: Cannot compiler 'Python.h'. Perhaps you need to install python-dev|python-devel. $ Now, as I compiled python from source, "Python.h" is sitting neatly in "/users/wd15/usr/i686/4.0/include/python2.6". The output from build (not included above) even claims that the compile options point there: C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/src -Inumpy/core/include -I/users/wd15/usr/i686/4.0/include/python2.6 -c' so the build seems to be aware of the include location. Any ideas? Cheers -- Daniel Wheeler
On Wed, Jul 29, 2009 at 12:38 AM, Daniel
Wheeler
Hi,
I'm having an installation issue building numpy 1.3.0 using python 2.6.2 which has been built in my local area in a non-standard place and was configured with --prefix=/users/wd15/usr/i686/4.0. When I run numpy's config ("python setup.py config") everything seems to be fine. However, when I run "python setup.py build", it gives the following error:
Can you post the full output of python setup.py build ? cheers, David
On Tue, Jul 28, 2009 at 12:02 PM, David Cournapeau
On Wed, Jul 29, 2009 at 12:38 AM, Daniel Can you post the full output of python setup.py build ?
Here it is: Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /users/wd15/usr/i686/4.0/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /users/wd15/usr/i686/4.0/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib NOT AVAILABLE atlas_blas_info: libraries f77blas,cblas,atlas not found in /users/wd15/usr/i686/4.0/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib/atlas FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c include_dirs = ['/usr/include'] /users/wd15/Documents/python/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) customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy/distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-c' gcc: _configtest.c gcc: error trying to exec 'cc1': execvp: No such file or directory gcc: error trying to exec 'cc1': execvp: No such file or directory failure. removing: _configtest.c _configtest.o Status: 255 Output: FOUND: libraries = ['f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = c define_macros = [('NO_ATLAS_INFO', 2)] include_dirs = ['/usr/include'] lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /users/wd15/usr/i686/4.0/lib libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /users/wd15/usr/i686/4.0/lib libraries lapack_atlas not found in /users/wd15/usr/i686/4.0/lib libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas libraries lapack_atlas not found in /usr/lib/atlas libraries ptf77blas,ptcblas,atlas not found in /usr/lib numpy.distutils.system_info.atlas_threads_info NOT AVAILABLE atlas_info: libraries f77blas,cblas,atlas not found in /users/wd15/usr/i686/4.0/lib libraries lapack_atlas not found in /users/wd15/usr/i686/4.0/lib libraries f77blas,cblas,atlas not found in /usr/local/lib libraries lapack_atlas not found in /usr/local/lib libraries f77blas,cblas,atlas not found in /usr/lib/atlas libraries lapack_atlas not found in /usr/lib/atlas numpy.distutils.system_info.atlas_info FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 include_dirs = ['/usr/include'] customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config compiling '_configtest.c': /* This file is generated from numpy/distutils/system_info.py */ void ATL_buildinfo(void); int main(void) { ATL_buildinfo(); return 0; } C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-c' gcc: _configtest.c gcc: error trying to exec 'cc1': execvp: No such file or directory gcc: error trying to exec 'cc1': execvp: No such file or directory failure. removing: _configtest.c _configtest.o Status: 255 Output: FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['/usr/lib'] language = f77 define_macros = [('NO_ATLAS_INFO', 2)] include_dirs = ['/usr/include'] running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building py_modules sources building library "npymath" sources building extension "numpy.core._sort" sources Generating build/src.linux-i686-2.6/numpy/core/include/numpy/config.h customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler using config C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/src -Inumpy/core/include -I/users/wd15/usr/i686/4.0/include/python2.6 -c' gcc: _configtest.c gcc: error trying to exec 'cc1': execvp: No such file or directory gcc: error trying to exec 'cc1': execvp: No such file or directory failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "setup.py", line 172, in <module> setup_package() File "setup.py", line 165, in setup_package configuration=configuration ) File "/users/wd15/Documents/python/numpy-1.3.0/numpy/distutils/core.py", line 184, in setup return old_setup(**new_attr) File "/users/wd15/usr/i686/4.0/lib/python2.6/distutils/core.py", line 152, in setup dist.run_commands() File "/users/wd15/usr/i686/4.0/lib/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/users/wd15/usr/i686/4.0/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/users/wd15/Documents/python/numpy-1.3.0/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/users/wd15/usr/i686/4.0/lib/python2.6/distutils/command/build.py", line 134, in run self.run_command(cmd_name) File "/users/wd15/usr/i686/4.0/lib/python2.6/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/users/wd15/usr/i686/4.0/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/users/wd15/Documents/python/numpy-1.3.0/numpy/distutils/command/build_src.py", line 130, in run self.build_sources() File "/users/wd15/Documents/python/numpy-1.3.0/numpy/distutils/command/build_src.py", line 147, in build_sources self.build_extension_sources(ext) File "/users/wd15/Documents/python/numpy-1.3.0/numpy/distutils/command/build_src.py", line 250, in build_extension_sources sources = self.generate_sources(sources, ext) File "/users/wd15/Documents/python/numpy-1.3.0/numpy/distutils/command/build_src.py", line 307, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 286, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 30, in check_types out = check_types(*a, **kw) File "numpy/core/setup.py", line 186, in check_types "Cannot compiler 'Python.h'. Perhaps you need to "\ SystemError: Cannot compiler 'Python.h'. Perhaps you need to install python-dev|python-devel. -- Daniel Wheeler
On Wed, Jul 29, 2009 at 2:38 AM, Daniel
Wheeler
-Wall -Wstrict-prototypes -fPIC
compile options: '-c' gcc: _configtest.c gcc: error trying to exec 'cc1': execvp: No such file or directory gcc: error trying to exec 'cc1': execvp: No such file or directory
That's your problem right there: your compiler is broken. What happens if you call gcc by yourself on a trivial C program ? David
Oh dear. I'd changed some environment variables when I switched to
using python 2.6 and was accidentally using a local version of gcc,
which evidently doesn't work correctly. Everything builds fine now.
Thanks and sorry for the wasted time.
On Tue, Jul 28, 2009 at 7:57 PM, David Cournapeau
On Wed, Jul 29, 2009 at 2:38 AM, Daniel Wheeler
wrote: -Wall -Wstrict-prototypes -fPIC
compile options: '-c' gcc: _configtest.c gcc: error trying to exec 'cc1': execvp: No such file or directory gcc: error trying to exec 'cc1': execvp: No such file or directory
That's your problem right there: your compiler is broken. What happens if you call gcc by yourself on a trivial C program ?
David _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
-- Daniel Wheeler
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