Created
July 16, 2014 12:12
-
-
Save calmrat/71517b08536776399198 to your computer and use it in GitHub Desktop.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| cd /tmp | |
| cat > ./setup.py <<DELIM | |
| #!/usr/bin/env python | |
| # -*- coding: utf-8 -*- | |
| # Author: "Chris Ward" <[email protected]> | |
| from setuptools import setup | |
| default_setup = dict( | |
| name='numpy_install_test', | |
| description='https://github.com/numpy/numpy/issues/2434', | |
| provides=['numpy_install_test'], | |
| install_requires=['pandas'], | |
| requires=['pandas'], | |
| license='GPLv3', | |
| author='Chris Ward', | |
| author_email='[email protected]', | |
| ) | |
| setup(**default_setup) | |
| DELIM | |
| virtualenv --no-site-packages ~/virtenvs/nonumpy | |
| source ~/virtenvs/nonumpy/bin/activate | |
| python setup.py install |
But if i just do 'pip install pandas' manually, everything works. So this might be an issue with Pandas or setuptools... but the failure is only occuring when installing numpy as a dependency (of a dependency) through install_requires director, it seems.
pip install pandas isn't quite the same dependency link, but putting this setup.py in a tmpdir and then doing pip install . works fine, so it's indeed a difference between setuptools and pip.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
output:
running install
running bdist_egg
running egg_info
writing requirements to numpy_install_test.egg-info/requires.txt
writing numpy_install_test.egg-info/PKG-INFO
writing top-level names to numpy_install_test.egg-info/top_level.txt
writing dependency_links to numpy_install_test.egg-info/dependency_links.txt
reading manifest file 'numpy_install_test.egg-info/SOURCES.txt'
writing manifest file 'numpy_install_test.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
warning: install_lib: 'build/lib' does not exist -- no Python modules to install
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying numpy_install_test.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying numpy_install_test.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying numpy_install_test.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying numpy_install_test.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying numpy_install_test.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
zip_safe flag not set; analyzing archive contents...
creating 'dist/numpy_install_test-0.0.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing numpy_install_test-0.0.0-py2.7.egg
Copying numpy_install_test-0.0.0-py2.7.egg to /home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages
Adding numpy-install-test 0.0.0 to easy-install.pth file
Installed /home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/numpy_install_test-0.0.0-py2.7.egg
Processing dependencies for numpy-install-test==0.0.0
Searching for pandas
Reading https://pypi.python.org/simple/pandas/
Best match: pandas 0.14.1
Downloading https://pypi.python.org/packages/source/p/pandas/pandas-0.14.1.zip#md5=f634a6db924351328021fd28105da1d6
Processing pandas-0.14.1.zip
Writing /tmp/easy_install-KSRKPk/pandas-0.14.1/setup.cfg
Running pandas-0.14.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-KSRKPk/pandas-0.14.1/egg-dist-tmp-P2atv6
Searching for numpy>=1.6.1
Reading https://pypi.python.org/simple/numpy/
Best match: numpy 1.8.1
Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.8.1.zip#md5=b8b3a99d6ed0913543abb49911205e95
Processing numpy-1.8.1.zip
Writing /tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/setup.cfg
Running numpy-1.8.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/egg-dist-tmp-mE4r35
Running from numpy source directory.
Warning: distutils distribution has been initialized, it may be too late to add a subpackage commandWarning: distutils distribution has been initialized, it may be too late to add a subpackage fcompilernon-existing path in 'numpy/distutils': 'site.cfg'
Warning: distutils distribution has been initialized, it may be too late to add a subpackage distutilsWarning: distutils distribution has been initialized, it may be too late to add a subpackage testing/bin/sh: svnversion: command not found
Warning: distutils distribution has been initialized, it may be too late to add a subpackage f2pyWarning: distutils distribution has been initialized, it may be too late to add an extension _dummyWarning: distutils distribution has been initialized, it may be too late to add a library npysortWarning: distutils distribution has been initialized, it may be too late to add an extension multiarrayWarning: distutils distribution has been initialized, it may be too late to add an extension umathWarning: distutils distribution has been initialized, it may be too late to add an extension scalarmath/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/system_info.py:1521: 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)
/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/system_info.py:1530: 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)
/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/system_info.py:1533: 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)
Warning: distutils distribution has been initialized, it may be too late to add an extension _dotblasWarning: distutils distribution has been initialized, it may be too late to add an extension umath_testsWarning: distutils distribution has been initialized, it may be too late to add an extension test_rationalWarning: distutils distribution has been initialized, it may be too late to add an extension struct_ufunc_testWarning: distutils distribution has been initialized, it may be too late to add an extension multiarray_testsWarning: distutils distribution has been initialized, it may be too late to add an extension operand_flag_tests/bin/sh: svnversion: command not found
Warning: distutils distribution has been initialized, it may be too late to add a subpackage coreWarning: distutils distribution has been initialized, it may be too late to add an extension _compiled_basenon-existing path in 'numpy/lib': 'benchmarks'
Warning: distutils distribution has been initialized, it may be too late to add a subpackage libWarning: distutils distribution has been initialized, it may be too late to add a subpackage oldnumericWarning: distutils distribution has been initialized, it may be too late to add an extension _capiWarning: distutils distribution has been initialized, it may be too late to add a subpackage numarrayWarning: distutils distribution has been initialized, it may be too late to add an extension fftpack_liteWarning: distutils distribution has been initialized, it may be too late to add a subpackage fft/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/system_info.py:1427: 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)
/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/system_info.py:1438: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.doc)
/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/system_info.py:1441: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.doc)
Warning: distutils distribution has been initialized, it may be too late to add an extension lapack_liteWarning: distutils distribution has been initialized, it may be too late to add an extension _umath_linalgWarning: distutils distribution has been initialized, it may be too late to add a subpackage linalgWarning: distutils distribution has been initialized, it may be too late to add an extension mtrandWarning: distutils distribution has been initialized, it may be too late to add a subpackage randomWarning: distutils distribution has been initialized, it may be too late to add a subpackage maWarning: distutils distribution has been initialized, it may be too late to add a subpackage matrixlibWarning: distutils distribution has been initialized, it may be too late to add a subpackage compatWarning: distutils distribution has been initialized, it may be too late to add a subpackage polynomialWarning: distutils distribution has been initialized, it may be too late to add a subpackage docWarning: distutils distribution has been initialized, it may be too late to add a subpackage numpy_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ [enabled by default]
int exp (void);
^
_configtest.o: In function
main': /tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/_configtest.c:6: undefined reference toexp'collect2: error: ld returned 1 exit status
_configtest.o: In function
main': /tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/_configtest.c:6: undefined reference toexp'collect2: error: ld returned 1 exit status
_configtest.c:1:5: warning: conflicting types for built-in function ‘exp’ [enabled by default]
int exp (void);
^
_configtest.c:1:20: fatal error: Python.h: No such file or directory
#include <Python.h>
^
compilation terminated.
_configtest.c:1:20: fatal error: Python.h: No such file or directory
#include <Python.h>
^
compilation terminated.
Traceback (most recent call last):
File "setup.py", line 18, in
setup(**default_setup)
File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/install.py", line 73, in run
self.do_egg_install()
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/install.py", line 101, in do_egg_install
cmd.run()
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 358, in run
self.easy_install(spec, not self.no_deps)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 574, in easy_install
return self.install_item(None, spec, tmpdir, deps, True)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 625, in install_item
self.process_distribution(spec, dist, deps)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 671, in process_distribution
[requirement], self.local_index, self.easy_install
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/pkg_resources.py", line 563, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/pkg_resources.py", line 801, in best_match
return self.obtain(req, installer) # try and download/install
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/pkg_resources.py", line 813, in obtain
return installer(requirement)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 593, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 623, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 809, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1015, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1000, in run_setup
run_setup(setup_script, args)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/sandbox.py", line 50, in run_setup
lambda: execfile(
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/sandbox.py", line 100, in run
return func()
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/sandbox.py", line 52, in
{'file':setup_script, 'name':'main'}
File "setup.py", line 606, in
File "/usr/lib64/python2.7/distutils/core.py", line 112, in setup
_setup_distribution = dist = klass(attrs)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/dist.py", line 239, in init
self.fetch_build_eggs(attrs.pop('setup_requires'))
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/dist.py", line 263, in fetch_build_eggs
parse_requirements(requires), installer=self.fetch_build_egg
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/pkg_resources.py", line 563, in resolve
dist = best[req.key] = env.best_match(req, self, installer)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/pkg_resources.py", line 801, in best_match
return self.obtain(req, installer) # try and download/install
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/pkg_resources.py", line 813, in obtain
return installer(requirement)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/dist.py", line 313, in fetch_build_egg
return cmd.easy_install(req)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 593, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 623, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 809, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1015, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1000, in run_setup
run_setup(setup_script, args)
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/sandbox.py", line 50, in run_setup
lambda: execfile(
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/sandbox.py", line 100, in run
return func()
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/sandbox.py", line 52, in
{'file':setup_script, 'name':'main'}
File "setup.py", line 239, in
File "setup.py", line 231, in setup_package
File "/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/core.py", line 169, in setup
File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/lib64/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/metrique/virtenvs/nonumpy/lib/python2.7/site-packages/setuptools/command/bdist_egg.py", line 177, in run
self.run_command("egg_info")
File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/command/egg_info.py", line 10, in run
File "/usr/lib64/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/usr/lib64/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/command/build_src.py", line 153, in run
File "/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/command/build_src.py", line 170, in build_sources
File "/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
File "/tmp/easy_install-KSRKPk/pandas-0.14.1/temp/easy_install-HPZBUo/numpy-1.8.1/numpy/distutils/command/build_src.py", line 386, in generate_sources
File "numpy/core/setup.py", line 428, in generate_config_h
File "numpy/core/setup.py", line 42, in check_types
File "numpy/core/setup.py", line 289, in check_types
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.