0.8.0rc1 implicitly requires numpy to be pre-installed #3207

jwm · 2016-09-22T20:26:03Z

The get_info import in setup.py (https://github.com/statsmodels/statsmodels/blob/master/setup.py#L335) implicitly requires numpy to be installed before statsmodels.

Otherwise, statsmodels installation fails:

[jwm@hobbes:s002 ~> pip install statsmodels==0.8.0rc1
You are using pip version 7.1.0, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting statsmodels==0.8.0rc1 (from -r requirements.txt (line 1))
  Using cached statsmodels-0.8.0rc1.zip
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 20, in <module>
      File "/private/var/folders/8h/7_y8y9rx32jfrn52rl35l2080000gn/T/pip-build-fbiaSB/statsmodels/setup.py", line 330, in <module>
        from numpy.distutils.misc_util import get_info
    ImportError: No module named numpy.distutils.misc_util

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/8h/7_y8y9rx32jfrn52rl35l2080000gn/T/pip-build-fbiaSB/statsmodels

This is especially problematic for applications that declare dependencies using a requirements.txt, since that file may include numpy, but it won't necessarily be completely installed before statsmodels.

This change was introduced in 0.8.0rc1 (8a1a0b9). scipy seems to have a reasonably elegant way of addressing this. If numpy isn't already present, it declares numpy as a setup dependency.

The text was updated successfully, but these errors were encountered:

josef-pkt · 2016-09-22T21:18:36Z

It looks like this would be solved by #3195
I thought we do something similar to scipy already.

However, I'm not really up to date on how our setup.py and requirements currently work.

bpeterman · 2016-12-15T19:18:26Z

I'm also having an issue with this when declaring dependencies using a requirements.txt

ciarancourtney · 2017-02-13T11:58:58Z

This appears to be fixed in 0.8.0

$ test/bin/pip install statsmodels
Collecting statsmodels
  Using cached statsmodels-0.8.0-cp35-cp35m-manylinux1_x86_64.whl
Collecting scipy (from statsmodels)
  Using cached scipy-0.18.1-cp35-cp35m-manylinux1_x86_64.whl
Collecting pandas (from statsmodels)
  Using cached pandas-0.19.2-cp35-cp35m-manylinux1_x86_64.whl
Collecting patsy (from statsmodels)
  Using cached patsy-0.4.1-py2.py3-none-any.whl
Collecting numpy>=1.7.0 (from pandas->statsmodels)
  Downloading numpy-1.12.0-cp35-cp35m-manylinux1_x86_64.whl (16.8MB)
    100% |████████████████████████████████| 16.8MB 54kB/s 
Collecting python-dateutil>=2 (from pandas->statsmodels)
  Using cached python_dateutil-2.6.0-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas->statsmodels)
  Using cached pytz-2016.10-py2.py3-none-any.whl
Requirement already satisfied: six in ./test/lib/python3.5/site-packages (from patsy->statsmodels)
Installing collected packages: scipy, numpy, python-dateutil, pytz, pandas, patsy, statsmodels
Successfully installed numpy-1.12.0 pandas-0.19.2 patsy-0.4.1 python-dateutil-2.6.0 pytz-2016.10 scipy-0.18.1 statsmodels-0.8.0`

jwm · 2017-02-13T14:47:13Z

Hm, not seeing that work with a fresh virtualenv and statsmodels 0.8.0:

(foo)[jwm@hobbes:s000 ~> virtualenv foo
New python executable in foo/bin/python2.7
Also creating executable in foo/bin/python
Installing setuptools, pip, wheel...done.
(foo)[jwm@hobbes:s000 ~> . foo/bin/activate
(foo)[jwm@hobbes:s000 ~> pip list | grep -i numpy
You are using pip version 7.1.0, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(foo)[jwm@hobbes:s000 ~> pip install statsmodels==0.8.0
You are using pip version 7.1.0, however version 9.0.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting statsmodels==0.8.0
  Using cached statsmodels-0.8.0.tar.gz
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 20, in <module>
      File "/private/var/folders/8h/7_y8y9rx32jfrn52rl35l2080000gn/T/pip-build-RuoYtU/statsmodels/setup.py", line 335, in <module>
        from numpy.distutils.misc_util import get_info
    ImportError: No module named numpy.distutils.misc_util

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/8h/7_y8y9rx32jfrn52rl35l2080000gn/T/pip-build-RuoYtU/statsmodels

ciarancourtney · 2017-02-13T15:00:37Z

Looks like the problem is still prevalent if building from src. There are wheels on pypi for python27 on linux/Mac 64bit, maybe you are 32bit or using windows?

0.8.0rc1 probably failed for me because only windows wheels were available https://pypi.python.org/pypi/statsmodels/0.8.0rc1

markyen · 2017-06-23T06:18:52Z

I encountered this problem when attempting to install the latest version of numpy and statsmodels from the public pypi mirror:

$ virtualenv env
New python executable in env/bin/python2
Also creating executable in env/bin/python
Installing setuptools, pip...done.
$ source env/bin/activate
$ echo "numpy
statsmodels" > requirements.txt
$ pip install -i https://pypi.python.org/simple -r requirements.txt
Downloading/unpacking numpy (from -r requirements.txt (line 1))
Creating supposed download cache at /home/user/.pip/cache
  Storing download in cache at ./.pip/cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F05%2F84%2F0feb999c05f252af50a5fbc463268044feda92cdaad8cb0d0a6073d76057%2Fnumpy-1.13.0.zip
  Running setup.py (path:/tmp/pip-build-SBFo6g/numpy/setup.py) egg_info for package numpy
    Running from numpy source directory.
    /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'python_requires'
      warnings.warn(msg)
    
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
    warning: no previously-included files matching '*.pyd' found anywhere in distribution
Downloading/unpacking statsmodels (from -r requirements.txt (line 2))
  Storing download in cache at ./.pip/cache/https%3A%2F%2Fpypi.python.org%2Fpackages%2F72%2F16%2Fd7e7a70fc8ca3cc0d783a66e902a7adf80a810695c357cd48bb22c82451a%2Fstatsmodels-0.8.0.tar.gz
  Running setup.py (path:/tmp/pip-build-SBFo6g/statsmodels/setup.py) egg_info for package statsmodels
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/tmp/pip-build-SBFo6g/statsmodels/setup.py", line 335, in <module>
        from numpy.distutils.misc_util import get_info
    ImportError: No module named numpy.distutils.misc_util
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/tmp/pip-build-SBFo6g/statsmodels/setup.py", line 335, in <module>

    from numpy.distutils.misc_util import get_info

ImportError: No module named numpy.distutils.misc_util

----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /tmp/pip-build-SBFo6g/statsmodels
Storing debug log for failure in /home/user/.pip/pip.log

Older versions of pip appear to have trouble installing from wheels. The run above was using pip 1.5.6. Running pip install --upgrade pip fixed the issue for me, because it was then able to install from the wheel properly.

For those stuck on older versions of pip, or on platforms without wheels available, are there plans to merge #3195? It looks like that would fix this issue for everyone.

KFoxder · 2017-09-30T18:30:47Z

Is anyone planning on fixing this?

josef-pkt · 2017-09-30T18:37:23Z

I'm waiting for an "all clear to merge" for #3195
I'm not an expert in this area anymore

josiahjohnston · 2018-05-16T19:00:47Z

I'm getting this bug in v0.9.0, running python 2.7.12, pip 10.0.1, Ubuntu 16.04. Downgrading to v0.8.0 addresses it and is my current workaround.

josiah@msmproc2:~/src/statsmodels.bug$ virtualenv venv --no-site-packages
Running virtualenv with interpreter /usr/bin/python2
New python executable in /home/josiah/src/statsmodels.bug/venv/bin/python2
Also creating executable in /home/josiah/src/statsmodels.bug/venv/bin/python
Installing setuptools, pkg_resources, pip, wheel...done.
josiah@msmproc2:~/src/statsmodels.bug$ source venv/bin/activate
(venv) josiah@msmproc2:~/src/statsmodels.bug$ python --version
Python 2.7.12
(venv) josiah@msmproc2:~/src/statsmodels.bug$ pip --version
pip 10.0.1 from /home/josiah/src/statsmodels.bug/venv/local/lib/python2.7/site-packages/pip (python 2.7)
(venv) josiah@msmproc2:~/src/statsmodels.bug$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.4 LTS
Release:	16.04
Codename:	xenial
(venv) josiah@msmproc2:~/src/statsmodels.bug$ pip install statsmodels
Collecting statsmodels
  Downloading https://files.pythonhosted.org/packages/67/68/eb3ec6ab61f97216c257edddb853cc174cd76ea44b365cf4adaedcd44482/statsmodels-0.9.0.tar.gz (12.7MB)
    100% |████████████████████████████████| 12.7MB 1.8MB/s 
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-RA_ly7/statsmodels/setup.py", line 347, in <module>
        from numpy.distutils.misc_util import get_info
    ImportError: No module named numpy.distutils.misc_util
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-RA_ly7/statsmodels/

josef-pkt · 2018-05-16T19:14:40Z

@josiahjohnston The workaround should be to install numpy before installing pypi.
I don't think there were any changes to this compared to 0.8.

josiahjohnston · 2018-05-16T19:47:27Z

That doesn't work for me. My actual use case is including ggplot as a 'install_requires' in my setup.py, and ggplot lists statsmodels as a dependency. This fails:

from setuptools import setup, find_packages
setup(
	name='statsmodels.test',
	install_requires=[
		'ggplot'
	]
)

This fails too (I tried it before my initial post):

from setuptools import setup, find_packages
setup(
	name='statsmodels.test',
	install_requires=[
		'numpy',
		'ggplot'
	]
)

Moving ggplot to after numpy in the list failed to fix this problem because numpy was downloaded but not fully installed (and available) in the virtual environment before your setup.py executes and requests numpy.

This works for me:

from setuptools import setup, find_packages
setup(
	name='statsmodels.test',
	install_requires=[
		'statsmodels!=0.9.0',
		# Or 'statsmodels==0.8.0',
		'ggplot'
	]
)

The standard simple solution is to avoid importing any dependencies in your setup.py, but I'm guessing you had very good reasons for breaking that guideline. If numpy is optional, you could wrap its import in a try: statement (a PR I offered other developers who had a similar problem as you).

I personally don't know of another way to let you import dependencies in setup.py without breaking pip dependency management. Unfortunately, your workaround of manual non-standard installation is a deal breaker in my applications. If you find another solution for this chicken-and-egg situation, I'd be interested to learning it. This is the second package I've encountered with this type of installation error, and I'm expecting to find more in the future.

Best of luck!

josef-pkt · 2018-05-17T02:11:45Z

My problem is that I have no idea how pip works.

We, or better, pip install seems to have two steps:

discovery of dependencies: during collection we don't need numpy and we could just run check_dependency_versions to see what's already installed and populate the "requires" if missing.
for cythonizing for sdist and for compiling we need numpy and scipy, so we can create numpy and scipy compatible C files and binary files.

The second steps are currently in the main setup.py module code and break if numpy is not installed. If we know what triggers cythonizing and compilation, then we could hide the extension definition in a function and avoid calling that part during the discovery/collection part.

But I have no idea how to do that. Based on the comments, #3195 does not handle this correctly yet.
And I have no idea why this works with 0.8 if it doesn't work with 0.9.

josiahjohnston · 2018-05-17T02:20:30Z

Just checked my terminal. Looks like statsmodels-0.8.0 came from a wheel

...
Collecting statsmodels==0.8.0
  Downloading https://files.pythonhosted.org/packages/a2/2a/0bb4e9e0e0f2bedde21602a2ac89164fa40814b1d3d16c1a7918e81977e9/statsmodels-0.8.0-cp27-cp27mu-manylinux1_x86_64.whl (6.2MB)
    100% |████████████████████████████████| 6.2MB 4.0MB/s 
Collecting pandas (from statsmodels==0.8.0)
... # Continues till success

But statsmodels-0.9.0 comes from a tarball which presumably needs to be compiled.

...
Collecting statsmodels (from ggplot->msm-ml==0.1)
  Downloading https://files.pythonhosted.org/packages/67/68/eb3ec6ab61f97216c257edddb853cc174cd76ea44b365cf4adaedcd44482/statsmodels-0.9.0.tar.gz (12.7MB)
    100% |████████████████████████████████| 12.7MB 2.0MB/s 
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-s5nuEi/statsmodels/setup.py", line 347, in <module>
        from numpy.distutils.misc_util import get_info
    ImportError: No module named numpy.distutils.misc_util

Maybe precompiling wheels for the most common platforms can be a workaround?

josef-pkt · 2018-05-17T02:40:59Z

Linux and Apple wheels should be coming over the next days.
Wheels don't have the setup.py importing numpy problem, but we have a separate issue that wheels don't specify requirements, i.e. pandas and patsy still have to be separately specified as requirement which in turn should also add numpy and scipy. #4638

Re-enable xdist Small adjustment for windows testing closes statsmodels#4635 closes statsmodels#4638 closes statsmodels#4651 closes statsmodels#4654 closes statsmodels#3207 closes statsmodels#3195 closes statsmodels#3977

zengqingfu1442 · 2021-08-02T08:59:19Z

Does this issue fixed already? I still have this issue when use pip to install statsmodels==0.10.0 on alpine:3.14.

bash-5.1# python2.7 -m pip install statsmodels==0.10.0
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Collecting statsmodels==0.10.0
  Downloading statsmodels-0.10.0.tar.gz (14.0 MB)
     |████████████████████████████████| 14.0 MB 6.0 MB/s 



    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python2.7 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-Nu3H9h/statsmodels/setup.py'"'"'; __file__='"'"'/tmp/pip-install-Nu3H9h/statsmodels/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-IdPys2
         cwd: /tmp/pip-install-Nu3H9h/statsmodels/
    Complete output (52 lines):
    DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
    DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
      ERROR: Command errored out with exit status 1:
       command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-hU3nWo/scipy/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-hU3nWo/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-ZW4H1H
           cwd: /tmp/pip-wheel-hU3nWo/scipy/
      Complete output (7 lines):
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/tmp/pip-wheel-hU3nWo/scipy/setup.py", line 492, in <module>
          setup_package()
        File "/tmp/pip-wheel-hU3nWo/scipy/setup.py", line 468, in setup_package
          from numpy.distutils.core import setup
      ImportError: No module named numpy.distutils.core
      ----------------------------------------
      ERROR: Failed building wheel for scipy
      ERROR: Command errored out with exit status 1:
       command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-hU3nWo/scipy/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-hU3nWo/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
           cwd: /tmp/pip-wheel-hU3nWo/scipy
      Complete output (9 lines):
    
      `setup.py clean` is not supported, use one of the following instead:
    
        - `git clean -xdf` (cleans all files)
        - `git clean -Xdf` (cleans all versioned files, doesn't touch
                            files that aren't checked into the git repo)
    
      Add `--force` to your command to use it anyway if you must (unsupported).
    
      ----------------------------------------
      ERROR: Failed cleaning build dir for scipy
    ERROR: Failed to build one or more wheels
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-Nu3H9h/statsmodels/setup.py", line 346, in <module>
        data_files=[('', ['LICENSE.txt', 'setup.cfg'])]
      File "/usr/lib/python2.7/site-packages/setuptools/__init__.py", line 161, in setup
        _install_setup_requires(attrs)
      File "/usr/lib/python2.7/site-packages/setuptools/__init__.py", line 156, in _install_setup_requires
        dist.fetch_build_eggs(dist.setup_requires)
      File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 721, in fetch_build_eggs
        replace_conflicting=True,
      File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
        replace_conflicting=replace_conflicting
      File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
        return self.obtain(req, installer)
      File "/usr/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
        return installer(requirement)
      File "/usr/lib/python2.7/site-packages/setuptools/dist.py", line 777, in fetch_build_egg
        return fetch_build_egg(self, req)
      File "/usr/lib/python2.7/site-packages/setuptools/installer.py", line 130, in fetch_build_egg
        raise DistutilsError(str(e))
    distutils.errors.DistutilsError: Command '['/usr/bin/python2.7', '-m', 'pip', '--disable-pip-version-check', 'wheel', '--no-deps', '-w', '/tmp/tmpH31Aqa', '--quiet', 'scipy>=0.18']' returned non-zero exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output

bashtage · 2021-08-02T09:18:22Z

0.8 is complutely unsupported. This has not been an issue for a number of releases, and we always recommend upgrading to the latest release.

zengqingfu1442 · 2021-08-02T10:51:55Z

I directly use pip to install statsmodels==0.10.0 on alpine:3.14 but failed.

bash-5.1# cat /etc/os-release 
NAME="Alpine Linux"
ID=alpine
VERSION_ID=3.14.0
PRETTY_NAME="Alpine Linux v3.14"
HOME_URL="https://alpinelinux.org/"
BUG_REPORT_URL="https://bugs.alpinelinux.org/"

bashtage · 2021-08-02T11:20:53Z

Try statsmodels 0.12.2.

zengqingfu1442 · 2021-08-03T09:56:45Z

But the latest version for python 2.7 is 0.11.0.

bash-5.1# python2.7 -m pip install numpy
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Processing /root/.cache/pip/wheels/fe/49/d9/dbd8037d1f7b1672ebcdba0c75f1b7000d9e888a33af294c35/numpy-1.16.6-cp27-cp27mu-linux_x86_64.whl
Installing collected packages: numpy
Successfully installed numpy-1.16.6
bash-5.1# python2.7 -m pip install statsmodels
DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
Collecting statsmodels
  Using cached statsmodels-0.11.0.tar.gz (15.4 MB)
  Installing build dependencies ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python2.7 /usr/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-A_gmtq/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'cython>=0.29.14' 'numpy==1.14.5; python_version=='"'"'3.5'"'"'' 'numpy==1.14.5; python_version=='"'"'3.6'"'"'' 'numpy==1.14.5; python_version>='"'"'3.7'"'"'' 'numpy==1.17.5; python_version>='"'"'3.8'"'"'' 'scipy>=1.0'
       cwd: None
  Complete output (311 lines):
  DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
  Ignoring numpy: markers 'python_version == "3.5"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.6"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.7"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.8"' don't match your environment
  Collecting setuptools
    Using cached setuptools-44.1.1-py2.py3-none-any.whl (583 kB)
  Collecting wheel
    Using cached wheel-0.36.2-py2.py3-none-any.whl (35 kB)
  Collecting cython>=0.29.14
    Using cached Cython-0.29.24-py2.py3-none-any.whl (979 kB)
  Collecting scipy>=1.0
    Using cached scipy-1.2.3.tar.gz (23.3 MB)
  Building wheels for collected packages: scipy
    Building wheel for scipy (setup.py): started
    Building wheel for scipy (setup.py): finished with status 'error'
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-iHoKxH
         cwd: /tmp/pip-install-qjbcVy/scipy/
    Complete output (127 lines):
    Running from scipy source directory.
    lapack_opt_info:
    lapack_mkl_info:
    customize UnixCCompiler
      libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
      NOT AVAILABLE
  
    openblas_lapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
      NOT AVAILABLE
  
    openblas_clapack_info:
    customize UnixCCompiler
    customize UnixCCompiler
      libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
      NOT AVAILABLE
  
    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    customize UnixCCompiler
      libraries tatlas,tatlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE
  
    atlas_3_10_info:
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    customize UnixCCompiler
      libraries satlas,satlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE
  
    atlas_threads_info:
    Setting PTATLAS=ATLAS
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    customize UnixCCompiler
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE
  
    atlas_info:
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/local/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib
    customize UnixCCompiler
      libraries lapack_atlas not found in /usr/lib/
    customize UnixCCompiler
      libraries f77blas,cblas,atlas not found in /usr/lib/
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE
  
    accelerate_info:
      NOT AVAILABLE
  
    /usr/lib/python2.7/site-packages/numpy/distutils/system_info.py:639: 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.
      self.calc_info()
    lapack_info:
    customize UnixCCompiler
      libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
      NOT AVAILABLE
  
    /usr/lib/python2.7/site-packages/numpy/distutils/system_info.py:639: 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.
      self.calc_info()
    lapack_src_info:
      NOT AVAILABLE
  
    /usr/lib/python2.7/site-packages/numpy/distutils/system_info.py:639: 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.
      self.calc_info()
      NOT AVAILABLE
  
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-qjbcVy/scipy/setup.py", line 492, in <module>
        setup_package()
      File "/tmp/pip-install-qjbcVy/scipy/setup.py", line 488, in setup_package
        setup(**metadata)
      File "/usr/lib/python2.7/site-packages/numpy/distutils/core.py", line 137, in setup
        config = configuration()
      File "/tmp/pip-install-qjbcVy/scipy/setup.py", line 395, in configuration
        raise NotFoundError(msg)
    numpy.distutils.system_info.NotFoundError: No lapack/blas resources found.
    ----------------------------------------
    ERROR: Failed building wheel for scipy
    Running setup.py clean for scipy
    ERROR: Command errored out with exit status 1:
     command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
         cwd: /tmp/pip-install-qjbcVy/scipy
    Complete output (9 lines):
  
    `setup.py clean` is not supported, use one of the following instead:
  
      - `git clean -xdf` (cleans all files)
      - `git clean -Xdf` (cleans all versioned files, doesn't touch
                          files that aren't checked into the git repo)
  
    Add `--force` to your command to use it anyway if you must (unsupported).
  
    ----------------------------------------
    ERROR: Failed cleaning build dir for scipy
  Failed to build scipy
  Installing collected packages: setuptools, wheel, cython, scipy
      Running setup.py install for scipy: started
      Running setup.py install for scipy: finished with status 'error'
      ERROR: Command errored out with exit status 1:
       command: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8DLdMS/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-A_gmtq/overlay --compile --install-headers /tmp/pip-build-env-A_gmtq/overlay/include/python2.7/scipy
           cwd: /tmp/pip-install-qjbcVy/scipy/
      Complete output (136 lines):
  
      Note: if you need reliable uninstall behavior, then install
      with pip instead of using `setup.py install`:
  
        - `pip install .`       (from a git repo or downloaded source
                                 release)
        - `pip install scipy`   (last SciPy release on PyPI)
  
  
      Running from scipy source directory.
      lapack_opt_info:
      lapack_mkl_info:
      customize UnixCCompiler
        libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
  
      openblas_lapack_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
  
      openblas_clapack_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
  
      atlas_3_10_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
        NOT AVAILABLE
  
      atlas_3_10_info:
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_3_10_info'>
        NOT AVAILABLE
  
      atlas_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_threads_info'>
        NOT AVAILABLE
  
      atlas_info:
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_info'>
        NOT AVAILABLE
  
      accelerate_info:
        NOT AVAILABLE
  
      /usr/lib/python2.7/site-packages/numpy/distutils/system_info.py:639: 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.
        self.calc_info()
      lapack_info:
      customize UnixCCompiler
        libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE
  
      /usr/lib/python2.7/site-packages/numpy/distutils/system_info.py:639: 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.
        self.calc_info()
      lapack_src_info:
        NOT AVAILABLE
  
      /usr/lib/python2.7/site-packages/numpy/distutils/system_info.py:639: 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.
        self.calc_info()
        NOT AVAILABLE
  
      Traceback (most recent call last):
        File "<string>", line 1, in <module>
        File "/tmp/pip-install-qjbcVy/scipy/setup.py", line 492, in <module>
          setup_package()
        File "/tmp/pip-install-qjbcVy/scipy/setup.py", line 488, in setup_package
          setup(**metadata)
        File "/usr/lib/python2.7/site-packages/numpy/distutils/core.py", line 137, in setup
          config = configuration()
        File "/tmp/pip-install-qjbcVy/scipy/setup.py", line 395, in configuration
          raise NotFoundError(msg)
      numpy.distutils.system_info.NotFoundError: No lapack/blas resources found.
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /usr/bin/python2.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-qjbcVy/scipy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-8DLdMS/install-record.txt --single-version-externally-managed --prefix /tmp/pip-build-env-A_gmtq/overlay --compile --install-headers /tmp/pip-build-env-A_gmtq/overlay/include/python2.7/scipy Check the logs for full command output.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python2.7 /usr/lib/python2.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-A_gmtq/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'cython>=0.29.14' 'numpy==1.14.5; python_version=='"'"'3.5'"'"'' 'numpy==1.14.5; python_version=='"'"'3.6'"'"'' 'numpy==1.14.5; python_version>='"'"'3.7'"'"'' 'numpy==1.17.5; python_version>='"'"'3.8'"'"'' 'scipy>=1.0' Check the logs for full command output.

bashtage · 2021-08-03T09:59:28Z

There is no support for 2.7 available from statsmodels developers. If you need 2.7 you will need to find an alternative source of support. We strongly recommend that anyone using statsmodels, or numerical python in general, uses 3.8 or newer.

zengqingfu1442 · 2021-08-03T11:24:42Z

@bashtage But I try to use python3.9 -m pip install statsmodels==0.12.2 on alpine:3.14, it still failed.

bashtage · 2021-08-03T12:32:39Z

Don't use alpine? IIRC alpine can't use standard wheels. I suspect you are having problems building NumPy and especially SciPy which are requirements. Can you get NumPy, SciPy, pandas and Cython all installed in your python 3.9? If you, you can install statsmodels from source.

bashtage · 2021-08-03T12:34:59Z

Read this https://pythonspeed.com/articles/alpine-docker-python/ to understand why Alpine is such a pain to use with Python.

josef-pkt added the build label Sep 22, 2016

bashtage mentioned this issue Oct 22, 2017

Release Engineering/Minimizing Friction Around Releases #4058

Closed

8 tasks

cdeline mentioned this issue Mar 30, 2018

Update master for release NREL/rdtools#73

Merged

josef-pkt closed this as completed in 6b0302f Aug 27, 2018

nealmcb mentioned this issue Jan 31, 2019

fail to install requirements CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers#377

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0.8.0rc1 implicitly requires numpy to be pre-installed #3207

0.8.0rc1 implicitly requires numpy to be pre-installed #3207

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edited

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edited

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zengqingfu1442 commented Aug 2, 2021 •

edited

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bashtage commented Aug 3, 2021

0.8.0rc1 implicitly requires numpy to be pre-installed #3207

0.8.0rc1 implicitly requires numpy to be pre-installed #3207

Comments

jwm commented Sep 22, 2016

josef-pkt commented Sep 22, 2016

bpeterman commented Dec 15, 2016

ciarancourtney commented Feb 13, 2017

jwm commented Feb 13, 2017

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KFoxder commented Sep 30, 2017

josef-pkt commented Sep 30, 2017

josiahjohnston commented May 16, 2018

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josiahjohnston commented May 16, 2018 • edited

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josiahjohnston commented May 16, 2018 •

edited

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zengqingfu1442 commented Aug 2, 2021 •

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zengqingfu1442 commented Aug 2, 2021 •

edited