Mailman 3 January 2009 - NumPy-Discussion

Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 3, 2009

Jan. 3, 2009

I cd'd out of numpy and site-packages and re-ran the package tests. both numpy.test() and scipy.test() ran without serious errors. Some DeprecationWarnings and integrals that are probably divergent or slowly convergent... It's looking much more promising. Two gotchas on top of each other - not deleting the previously existing source, and running scripts from within the site-packages directory. Whew! numpy/scipy was looking scarily unstable until discovering my install and pilot errors. Thanks for all of the help ...

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Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 3, 2009

Jan. 3, 2009

Maybe the following will also be useful... Recall that I completely deleted numpy and scipy and reinstalled each from their respective superpacks, then ran: >>> import numpy; numpy.__file__ 'D:\\Programs\\Python25\\lib\\site-packages\\numpy\\__init__.pyc' >>> import scipy; scipy.__file__ 'D:\\Programs\\Python25\\lib\\site-packages\\scipy\\__init__.pyc' $ cd site-packages\numpy; python setup.py config This is the wrong setup.py file to run $ cd site-packages\scipy; python setup.py config non-existing path in 'cluster': 'src\\vq_module.c' non-existing path in 'cluster': 'src\\vq.c' non-existing path in 'cluster': 'src\\hierarchy_wrap.c' non-existing path in 'cluster': 'src\\hierarchy.c' Appending scipy.cluster configuration to scipy Ignoring attempt to set 'name' (from 'scipy' to 'scipy.cluster') Warning: No configuration returned, assuming unavailable. Appending scipy.constants configuration to scipy Ignoring attempt to set 'name' (from 'scipy' to 'scipy.constants') could not resolve pattern in 'fftpack': 'src/dfftpack\\*.f' non-existing path in 'fftpack': 'fftpack.pyf' non-existing path in 'fftpack': 'src/zfft.c' non-existing path in 'fftpack': 'src/drfft.c' non-existing path in 'fftpack': 'src/zrfft.c' non-existing path in 'fftpack': 'src/zfftnd.c' non-existing path in 'fftpack': 'src/zfft_fftpack.c' non-existing path in 'fftpack': 'src/drfft_fftpack.c' non-existing path in 'fftpack': 'src/zfftnd_fftpack.c' non-existing path in 'fftpack': 'convolve.pyf' non-existing path in 'fftpack': 'src/convolve.c' Appending scipy.fftpack configuration to scipy Ignoring attempt to set 'name' (from 'scipy' to 'scipy.fftpack') d:\Programs\Python25\lib\site-packages\numpy\distutils\system_info.py:1340: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) d:\Programs\Python25\lib\site-packages\numpy\distutils\system_info.py:1349: UserWarning: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. warnings.warn(BlasNotFoundError.__doc__) d:\Programs\Python25\lib\site-packages\numpy\distutils\system_info.py:1352: UserWarning: Blas (http://www.netlib.org/blas/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [blas_src]) or by setting the BLAS_SRC environment variable. warnings.warn(BlasSrcNotFoundError.__doc__) Traceback (most recent call last): File "setup.py", line 32, in <module> setup(**configuration(top_path='').todict()) File "setup.py", line 8, in configuration config.add_subpackage('integrate') File "d:\Programs\Python25\lib\site-packages\numpy\distutils\misc_util.py", line 851, in add_subpackage caller_level = 2) File "d:\Programs\Python25\lib\site-packages\numpy\distutils\misc_util.py", line 834, in get_subpackage caller_level = caller_level + 1) File "d:\Programs\Python25\lib\site-packages\numpy\distutils\misc_util.py", line 781, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "D:\Programs\Python25\Lib\site-packages\scipy\integrate\setup.py", line 10, in configuration blas_opt = get_info('blas_opt',notfound_action=2) File "d:\Programs\Python25\lib\site-packages\numpy\distutils\system_info.py", line 267, in get_info return cl().get_info(notfound_action) File "d:\Programs\Python25\lib\site-packages\numpy\distutils\system_info.py", line 416, in get_info raise self.notfounderror,self.notfounderror.__doc__ numpy.distutils.system_info.BlasNotFoundError: Blas (http://www.netlib.org/blas/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [blas]) or by setting the BLAS environment variable. At 10:40 PM 1/3/2009, you wrote: >Make sure that when you import scipy that you get the correct version. > > >>> import scipy > >>> scipy.__file__ >'C:\\Programs\\Python25\\lib\\site-packages\\scipy\\__init__.pyc' > > >From your error messages, I would think python is loading the source >distribution and not the compiled and installed version. It would be >helpful to see your actual error messages from nose, with copy and >paste, at least the first few and last parts of the nose tests. Your >summary error message is not very helpful because it doesn't show your >actual error path and trace backs. > >When I installed the 0.7.0 b1 superpack on WindowsXP, it worked out of >the box. The only thing to do, before installing a new version of >numpy or scipy, is to uninstall or delete any old version in >site-packages, since the directory names of scipy and numpy do not >include version numbers. Installing on top of an old version, can >leave some old files around which sometimes cause errors. > > >Josef >_______________________________________________ >Numpy-discussion mailing list >Numpy-discussion(a)scipy.org >http://projects.scipy.org/mailman/listinfo/numpy-discussion

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Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 3, 2009

Jan. 3, 2009

Josef (sorry about spelling your name wrong in a previous post), Thanks for the continued suggestions. I deleted the site-packages: numpy and scipy, and reinstalled each using the current release superpacks (numpy first, then scipy). then I ran: python -c 'import numpy; numpy.test()' and got: Running unit tests for numpy NumPy version 1.2.1 NumPy is installed in d::\Programs\Python25\lib\site-packages\numpy Python version 2.5.2 (r252:60911, Mar 27 2008, 17:57:18) IMSC v.1310 32 bit (ntel)] nose version 0.10.4 Traceback (most recent call last): File "(string)", line 1, in <module> File "d::\Programs\Python25\lib\site-packages\numpy\testing\nosetester.py", line 264, in test import doctest File"d:\Programs\Python25\lib\doctest.p", line 99, in <module> import unittest, difflib, pd, tempfile File "d:\programs\python25\lib\tempfile.py", line 33, in <module> from random import Random as __Random ImportError: cannot import name Random scipy.test() bombs out with the exact same Traceback, except that it mentions the scipy version (0,7.0.dev5180) and scipy install directory just before it echoes the line with the python version number. So, it's not getting as far as it was with the source mixed in. At 10:40 PM 1/3/2009, you wrote: >Make sure that when you import scipy that you get the correct version. > > >>> import scipy > >>> scipy.__file__ >'C:\\Programs\\Python25\\lib\\site-packages\\scipy\\__init__.pyc' > > >From your error messages, I would think python is loading the source >distribution and not the compiled and installed version. It would be >helpful to see your actual error messages from nose, with copy and >paste, at least the first few and last parts of the nose tests. Your >summary error message is not very helpful because it doesn't show your >actual error path and trace backs. > >When I installed the 0.7.0 b1 superpack on WindowsXP, it worked out of >the box. The only thing to do, before installing a new version of >numpy or scipy, is to uninstall or delete any old version in >site-packages, since the directory names of scipy and numpy do not >include version numbers. Installing on top of an old version, can >leave some old files around which sometimes cause errors. > > >Josef >_______________________________________________ >Numpy-discussion mailing list >Numpy-discussion(a)scipy.org >http://projects.scipy.org/mailman/listinfo/numpy-discussion

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Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 3, 2009

Jan. 3, 2009

Thanks for the suggestion Joseph - the scipy test suite runs, but it produces lots of errors. Some deprecation warnings in numpy\lib\utils.py (line 110) and scipy\linalg\decomp.py (line 1173) Than it complains about a '_bad_path_' (doesn't exist or not writable). Couldn't remove <user>\appdata]local\temp\tmpc192_pcat_test (directory not empty) Then the crap hits the fan... the following crashes are all due to: test_polyint.CheckKrogh test_derivative crashes on line 38 of scipy\interpolate\tests\test_polyint.py test_derivatives crashes on line 26 test_empty crashes in the same file on line 73 test_hermite crashes in the same file on line 57 test_high_derivative crashes in the same file on line 44 test_lagrange crashes in the same file on line 19 test_low_derivatives crashes in the same file line 32 test_scalar on line 22 test_shapes_1d_vectorvalue on line 95 test_shapes_scalarvalue on line 76 test_shapes_scalarvalue_derivative on line 82 test_shapes_vectorvalue on line 89 test_shapes_vectorvalue_derivative on line 101 test_vector on line 63 test_wrapper on line 108 The following crashes are due to test_polyint.CheckPiecewise test_construction on line 186 test_derivative on line 193 test_derivatives on line 196 test_incremental on line 217 test_scalar on line 189 test_shapes_scalarvalue on line 221 test_shapes_scalarvalue_derivative on line 227 test_shapes_vectorvalue on line 235 test_shapes_vectorvalue_1d on line 242 test_shapes_vectorvalue_derivative on line 248 test_vector on line 205 test_wrapper on line 255 The following crashes are due to test_polyint.CheckTaylor test_exponential on line 116 Failure: AttributeError ('module' object has no attribute 'byteordercodes') nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name numpyio) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name fblas) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name flapack) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name fblas) AGAIN nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name flapack) AGAIN nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: NameError (name 'pilutil is not defined) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name cobyla) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name nonlin) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name zeros) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: NameError (name 'pilutil is not defined) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: ImportError (cannot import name linsolve) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: AttributeError ('module' object has no attribute '_cephes') nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: NameError (name 'pilutil is not defined) nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName Failure: AttributeError ('module' object has no attribute 'convolve') nose-0.10.30py2.5.egg\nose\loader.py on line 364 in loadTestsFromName That was with nose-0.10.3-py2.5. I upgrades to the latest nose-0.10.4-py2.5, but it still produced an armload of (what look like the same) errors. Does this symptomology point to anything (configuration error, package out of date, ???) At 10:50 AM 1/3/2009, you wrote: >On Sat, Jan 3, 2009 at 10:13 AM, Mike Landis <mlandis001(a)comcast.net> wrote: > > I do not have cygwin in my windows path, so I guess that's already hidden. > > > > I patched d:\programs\python25\lib\distutils\cygwinccompiler.py, line 424 > > to read > > > > ld_version = StrictVersion(result.group(1).rsplit('.',1)[0]) > > > > but I still got crash and a traceback. > > > > David Cournapeau suggested using the scipy superpack, so i tried > > scipy-0.7.0b1-win32-superpack-python2.5.exe. If there were errors I > > wouldn't know about them, but running > > > > 'python -c 'import scipy; print scipy.__version__ ' > > > > produces a version number (0.7.0.dev5180 ... not exactly the 0.7.0b1 you'd > > expect, but not a stack trace either). > > > > Now all I have to do is find some test cases so I can verify a > little deeper > > than the version number. > > > >If you have nose installed, you can run the scipy test suite with > >import scipy >scipy.test() > >Josef >_______________________________________________ >Numpy-discussion mailing list >Numpy-discussion(a)scipy.org >http://projects.scipy.org/mailman/listinfo/numpy-discussion > >No virus found in this incoming message. >Checked by AVG - http://www.avg.com >Version: 8.0.176 / Virus Database: 270.10.2/1872 - Release Date: >1/2/2009 1:10 PM

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debugging scipy install
by Mike Landis Jan. 3, 2009

Jan. 3, 2009

running "python -c 'import scipy; scipy.test()' " finding one of the earliest errors referencing a bad_path, I found scipy's INSTALL.txt, paragraph 5, under the TROUBLESHOOTING says to "cd scipy/Lib/linalg" so you can run: 'python setup_atlas_version.py build_ext --inplace --force' [ setup_atlas_version.py is actually in scipy/linalg (at least on Windows) ] ... but that shell command bombs out with the following Traceback File "setup_atlas_version.py", line 7 in <module> from numpy.distutils.misc_util_import get_path, default_config_dict ImportError: cannot import name get_path Seems like getting the path could be source of a '_bad_path_' problem. Does anyone know where get_path is defined, and if so, where the file is downloadable from? After taking the superpack install routes with both numpy and scipy, shouldn't these issues have been taken care of already?

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genloadtxt : ready for inclusion
by Pierre GM Jan. 3, 2009

Jan. 3, 2009

All, You'll probably remember that last December, I started rewriting np.loadtxt and ame up with a series of functions that support missing data. I tried to copy/paste the code in numpy.lib.io.py but ran into dependency problems and left it at that. I think that part of the reason is that the code relies on numpy.ma which can't be loaded when numpy.lib gets loaded. As I needed a way to grant access to the code to anybody, I created a small project on launchpad: you can access it to: https://code.launchpad.net/~pierregm/numpy/numpy_addons The loadtxt reimplementation functions can be found in the numpy.io.fromascii module, their unittest in the corresponding test directory. In addition, you'll find several other functions and their unittest to manipulate arrays w/ flexible data-type. They are basically rewritten version of some functions in matplotlib.mlab. Would anybody be willing to try inserting the new functions in numpy ? I was hoping the genfromtxt and consorts would make it to numpy 1.3.x (I'd need the code for the scikits.timeseries package). As usual, I'd need all the feedback you can share. Thanks a lot in advance. P.

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Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 3, 2009

Jan. 3, 2009

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Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 2, 2009

Jan. 2, 2009

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installing numpy with Python2.5 already present
by Mike Landis Jan. 2, 2009

Jan. 2, 2009

This time I included both ATLAS and MKL in the site.cfg file and got a little further... D:\temp\numpy-1.2.1\site.cfg now looks like: [atlas] library_dirs = d:\Docs\ATLAS\build\lib atlas_libs = lapack, f77blas, cblas, atlas [mkl] include_dirs = D:\Programs\Intel\MKL\10.1.0.018\include library_dirs = D:\Programs\Intel\MKL\10.1.0.018\ia32\lib mkl_libs = mkl_ia32, mkl_c_dll, libguide40 lapack_libs = mkl_lapack ----------------------------------------------------------------------------------- FOUND a few more things... though still having problems finding blas_opt_info, blas_mkl_info (even though it finds MKL later???) Install log follows... ----------------------------------------------------------------------------------- Running from numpy source directory. F2PY Version 2_5972 blas_opt_info: blas_mkl_info: libraries mkl_ia32,mkl_c_dll,libguide40 not found in D:\Programs\Intel\MKL\10.1.0.018\ia32\lib NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c No module named msvccompiler in numpy.distutils; trying from distutils FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')] lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl_ia32,mkl_c_dll,libguide40 not found in D:\Programs\Intel\MKL\10.1.0.018\ia32\lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas not found in d:\Docs\ATLAS\build\lib numpy.distutils.system_info.atlas_threads_info Setting PTATLAS=ATLAS d:\temp\numpy-1.2.1\numpy\distutils\system_info.py:955: UserWarning: ********************************************************************* Lapack library (from ATLAS) is probably incomplete: size of d:\Docs\ATLAS\build\lib\liblapack.a is 251k (expected >4000k) Follow the instructions in the KNOWN PROBLEMS section of the file numpy/INSTALL.txt. ********************************************************************* warnings.warn(message) Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c No module named msvccompiler in numpy.distutils; trying from distutils FOUND: libraries = ['lapack', 'f77blas', 'cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')] could not resolve pattern in '': '*.txt' non-existing path in '': 'COMPATIBILITY' running install 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 extension "numpy.core.multiarray" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_numpy_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__multiarray_api.h' to sources. adding 'build\src.win32-2.5\numpy\core\src' to include_dirs. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\src\\scalartypes.inc', 'build\\src.win32-2.5\\numpy\\core\\src\\arraytypes.inc', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_ufunc_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__ufunc_api.h' to sources. adding 'build\src.win32-2.5\numpy\core\src' to include_dirs. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\src\\scalartypes.inc', 'build\\src.win32-2.5\\numpy\\core\\src\\arraytypes.inc', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__ufunc_api.h'] building extension "numpy.core._sort" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_numpy_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__multiarray_api.h' to sources. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__multiarray_api.h'] building extension "numpy.core.scalarmath" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_numpy_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__multiarray_api.h' to sources. executing numpy\core\code_generators\generate_ufunc_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__ufunc_api.h' to sources. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__multiarray_api.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__ufunc_api.h'] building extension "numpy.core._dotblas" sources adding 'numpy\core\blasdot\_dotblas.c' to sources. building extension "numpy.lib._compiled_base" sources building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources ### Warning: python_xerbla.c is disabled ### adding 'numpy\linalg\lapack_litemodule.c' to sources. building extension "numpy.random.mtrand" sources Traceback (most recent call last): File "setup.py", line 96, in <module> setup_package() File "setup.py", line 89, in setup_package configuration=configuration ) File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\core.py", line 184, in setup File "d:\programs\python25\lib\distutils\core.py", line 151, in setup dist.run_commands() File "d:\programs\python25\lib\distutils\dist.py", line 974, in run_commands self.run_command(cmd) File "d:\programs\python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\install.py", line 49, in run File "d:\programs\python25\lib\distutils\command\install.py", line 506, in run self.run_command('build') File "d:\programs\python25\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "d:\programs\python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build.py", line 37, in run File "d:\programs\python25\lib\distutils\command\build.py", line 112, in run self.run_command(cmd_name) File "d:\programs\python25\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "d:\programs\python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 130, in run File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 147, in build_sources File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 250, in build_extension_sources File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 307, in generate_sources File "numpy\random\setup.py", line 11, in generate_libraries if config_cmd.try_run(tc): File "d:\programs\python25\lib\distutils\command\config.py", line 278, in try_run self._check_compiler() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\config.py", line 26, in _check_compiler File "d:\programs\python25\lib\distutils\command\config.py", line 107, in _check_compiler dry_run=self.dry_run, force=1) File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\ccompiler.py", line 366, in new_compiler File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\mingw32ccompiler.py", line 46, in __init__ File "d:\programs\python25\lib\distutils\cygwinccompiler.py", line 84, in __init__ get_versions() File "d:\programs\python25\lib\distutils\cygwinccompiler.py", line 424, in get_versions ld_version = StrictVersion(result.group(1)) File "d:\programs\python25\lib\distutils\version.py", line 40, in __init__ self.parse(vstring) File "d:\programs\python25\lib\distutils\version.py", line 107, in parse raise ValueError, "invalid version number '%s'" % vstring ValueError: invalid version number '2.18.50.20080625'

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Re: [Numpy-discussion] building numpy/scipy
by Mike Landis Jan. 2, 2009

Jan. 2, 2009

Maybe the reason I'm having trouble is that I'm trying to get it working on Windows, when almost everyone else is running on Linux? I have cygwin with f77, g++, make, ... installed, but it's definitely not a Linux machine. I'm working from the windows install documentation page. Maybe there are additional steps that you wouldn't have on Linux. It's not clear whether BLAS and LAPACK and ATLAS are all distinct or if building one gets you one or more of the others, e.g. the ATLAS build produces both blas and lapack directories. Is there a third ATLAS library? When I set up site.cfg in site-packages/numpy and run "python setup.py install" from there, it complains that this isn't the right place to run setup.py, so I put the site.cfg in d:\temp\numpy-1.2.1\ and ran setup.py install there. I now have ATLAS libraries, so my site.cfg looks like this: [atlas] library_dirs = d:\Docs\ATLAS\build\lib atlas_libs = lapack, f77blas, cblas, atlas ----------------------------------------------------- Some good news, some bad, details below. Any suggestions would be appreciated... Thanks, Mike Running from numpy source directory. blas_opt_info: blas_mkl_info: libraries mkl, vml, guide not found in d:\Programs\Python25\lib libraries mkl, vml, guide not found in C:\ libraries mkl, vml, guide not found in d:\Programs\Python25\libs NOT AVAILABLE atlas_blas_threads_info: Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'f77blas', ;cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c No module named msvccompiler in numpy.disutils; trying from disutils FOUND: libraries = ['lapack', 'f77blas', ;cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')] lapack_opt_info: lapack_mkl_info: mkl_info: libraries mkl, vml, guide not found in d:\Programs\Python25\lib libraries mkl, vml, guide not found in C:\ libraries mkl, vml, guide not found in d:\Programs\Python25\libs NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas not found in d:\Docs\ATLAS\build\lib numpy.disutils.system_info.atlas_threads_info Setting PTATLAS=ATLAS d:\temp\numpy-1.2.1\numpy\disutils\system_info.py:955: UserWarning: ******************************************************************************** Lapack library (from ATLAS) is probably incomplete: size of d:\Docs\ATLAS\build\lib\libapack.a is 251k (expected >4000k) Follow the instructions in the KNOWN PROBLEMS section of the file numpy/INSTALL.txt. [ NOTE: There is no such section in this file. ] ******************************************************************************** warnings.warn(message) Setting PTATLAS=ATLAS FOUND: libraries = ['lapack', 'lapack', 'f77blas', ;cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c No module named msvccompiler in numpy.disutils; trying from disutils FOUND: libraries = ['lapack', 'lapack', 'f77blas', ;cblas', 'atlas'] library_dirs = ['d:\\Docs\\ATLAS\\build\\lib'] language = c define_macros = [('ATLAS_INFO', '"\\"?.?.?\\""')] could not resolve pattern in '': '*.txt' non-existing path in '': 'COMPATIBILITY' running install running build running config_cc unifying config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifying config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src building py_modules sources building extension "numpy.core.multiarray" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_numpy_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__multiarray_api.h' to sources. adding 'build\src.win32-2.5\numpy\core\src' to include_dirs. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\src\\scalartypes.inc', 'build\\src.win32-2.5\\numpy\\core\\src\\arraytypes.inc', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__multiarray_api.h'] building extension "numpy.core.umath" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_ufunc_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__ufunc_api.h' to sources. adding 'build\src.win32-2.5\numpy\core\src' to include_dirs. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\src\\scalartypes.inc', 'build\\src.win32-2.5\\numpy\\core\\src\\arraytypes.inc', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__ufunc_api.h'] building extension "numpy.core._sort" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_numpy_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__multiarray_api.h' to sources. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__multiarray_api.h'] building extension "numpy.core.scalarmath" sources adding 'build\src.win32-2.5\numpy\core\include/numpy\config.h' to sources. adding 'build\src.win32-2.5\numpy\core\include/numpy\numpyconfig.h' to sources. executing numpy\core\code_generators\generate_numpy_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__multiarray_api.h' to sources. executing numpy\core\code_generators\generate_ufunc_api.py adding 'build\src.win32-2.5\numpy\core\include/numpy\__ufunc_api.h' to sources. numpy.core - nothing done with h_files = ['build\\src.win32-2.5\\numpy\\core\\include/numpy\\config.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\numpyconfig.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__multiarray_api.h', 'build\\src.win32-2.5\\numpy\\core\\include/numpy\\__ufunc_api.h'] building extension "numpy.core._dotblas" sources adding 'numpy\core\blasdot\_dotblas.c' to sources. building extension "numpy.lib._compiled_base" sources building extension "numpy.numarray._capi" sources building extension "numpy.fft.fftpack_lite" sources building extension "numpy.linalg.lapack_lite" sources ### Warning: python_xerbla.c is disabled ### adding 'numpy\linalg\lapack_litemodule.c' to sources. building extension "numpy.random.mtrand" sources Traceback (most recent call last): File "setup.py", line 96, in <module> setup_package() File "setup.py", line 89, in setup_package configuration=configuration ) File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\core.py", line 184, in setup File "d:\programs\python25\lib\distutils\core.py", line 151, in setup dist.run_commands() File "d:\programs\python25\lib\distutils\dist.py", line 974, in run_commands self.run_command(cmd) File "d:\programs\python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\install.py", line 49, in run File "d:\programs\python25\lib\distutils\command\install.py", line 506, in run self.run_command('build') File "d:\programs\python25\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "d:\programs\python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build.py", line 37, in run File "d:\programs\python25\lib\distutils\command\build.py", line 112, in run self.run_command(cmd_name) File "d:\programs\python25\lib\distutils\cmd.py", line 333, in run_command self.distribution.run_command(command) File "d:\programs\python25\lib\distutils\dist.py", line 994, in run_command cmd_obj.run() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 130, in run File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 147, in build_sources File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 250, in build_extension_sources File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\build_src.py", line 307, in generate_sources File "numpy\random\setup.py", line 11, in generate_libraries if config_cmd.try_run(tc): File "d:\programs\python25\lib\distutils\command\config.py", line 278, in try_run self._check_compiler() File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\command\config.py", line 26, in _check_compiler File "d:\programs\python25\lib\distutils\command\config.py", line 107, in _check_compiler dry_run=self.dry_run, force=1) File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\ccompiler.py", line 366, in new_compiler File "D:\Programs\Python25\Lib\site-packages\numpy-1.2.1\numpy\distutils\mingw32ccompiler.py", line 46, in __init__ File "d:\programs\python25\lib\distutils\cygwinccompiler.py", line 84, in __init__ get_versions() File "d:\programs\python25\lib\distutils\cygwinccompiler.py", line 424, in get_versions ld_version = StrictVersion(result.group(1)) File "d:\programs\python25\lib\distutils\version.py", line 40, in __init__ self.parse(vstring) File "d:\programs\python25\lib\distutils\version.py", line 107, in parse raise ValueError, "invalid version number '%s'" % vstring ValueError: invalid version number '2.18.50.20080625'

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