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Pip3: Cython error while installing spicy

This is my requirements.txt file below:
emoji==1.2.0
langdetect==1.0.8
Pillow==9.0.0
PyMySQL==0.10.1
pyOpenSSL==19.1.0
pytz==2020.1
redis==3.5.3
regex==2021.8.3
requests==2.24.0
selenium==3.141.0
nltk==3.6.6
cython==0.29.26
numpy==1.21.1
setuptools==59.6.0
scipy==1.5.4
geograpy3==0.2.2
geotext~=0.4.0
DateTime~=4.3
uuid~=1.30
Jinja2~=2.11.2
boto3==1.17.3
Traceback
Collecting selenium==3.141.0 (from -r requirements.txt (line 10))
Using cached https://files.pythonhosted.org/packages/80/d6/4294f0b4bce4de0abf13e17190289f9d0613b0a44e5dd6a7f5ca98459853/selenium-3.141.0-py2.py3-none-any.whl
Collecting nltk==3.6.6 (from -r requirements.txt (line 11))
Using cached https://files.pythonhosted.org/packages/90/35/8848a41a983a923aa2496fbe4ee4df796c6b32b2a59f04c2b2047aafd3c3/nltk-3.6.6-py3-none-any.whl
Collecting cython==0.29.26 (from -r requirements.txt (line 12))
Using cached https://files.pythonhosted.org/packages/15/29/2abb8975ded365d55b9e14129cabdfb977255911c80d8709028eca5829cd/Cython-0.29.26-py2.py3-none-any.whl
Collecting numpy==1.21.1 (from -r requirements.txt (line 13))
Using cached https://files.pythonhosted.org/packages/0b/a7/e724c8df240687b5fd62d8c71f1a6709d455c4c09432c7412e3e64f4cbe5/numpy-1.21.1.zip
Collecting setuptools==59.6.0 (from -r requirements.txt (line 14))
Using cached https://files.pythonhosted.org/packages/b0/3a/88b210db68e56854d0bcf4b38e165e03be377e13907746f825790f3df5bf/setuptools-59.6.0-py3-none-any.whl
Collecting scipy==1.5.4 (from -r requirements.txt (line 15))
Using cached https://files.pythonhosted.org/packages/aa/d5/dd06fe0e274e579e1dff21aa021219c039df40e39709fabe559faed072a5/scipy-1.5.4.tar.gz
Complete output from command python setup.py egg_info:
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_philox.pyx
Traceback (most recent call last):
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/tools/cythonize.py", line 53, in process_pyx
import Cython
ModuleNotFoundError: No module named 'Cython'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/tools/cythonize.py", line 234, in <module>
main()
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/tools/cythonize.py", line 230, in main
find_process_files(root_dir)
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/tools/cythonize.py", line 221, in find_process_files
process(root_dir, fromfile, tofile, function, hash_db)
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/tools/cythonize.py", line 187, in process
processor_function(fromfile, tofile)
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/tools/cythonize.py", line 60, in process_pyx
raise OSError(msg) from e
OSError: Cython needs to be installed in Python as a module
Running from numpy source directory.
Traceback (most recent call last):
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/setup.py", line 461, in <module>
"generating Cython sources and expanding templates".format(
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/setup.py", line 443, in setup_package
bad_commands[command] = "`setup.py %s` is not supported" % command
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/setup.py", line 248, in generate_cython
f.write(text)
RuntimeError: Running cythonize failed!
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-tqtljvxv/scipy/setup.py", line 583, in <module>
setup_package()
File "/tmp/pip-build-tqtljvxv/scipy/setup.py", line 579, in setup_package
setup(**metadata)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/__init__.py", line 128, in setup
_install_setup_requires(attrs)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/__init__.py", line 123, in _install_setup_requires
dist.fetch_build_eggs(dist.setup_requires)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/dist.py", line 510, in fetch_build_eggs
resolved_dists = pkg_resources.working_set.resolve(
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 772, in resolve
dist = best[req.key] = env.best_match(
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1057, in best_match
return self.obtain(req, installer)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1069, in obtain
return installer(requirement)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/dist.py", line 580, in fetch_build_egg
return cmd.easy_install(req)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 698, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 724, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 909, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 1177, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/command/easy_install.py", line 1163, in run_setup
run_setup(setup_script, args)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 253, in run_setup
raise
File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
self.gen.throw(type, value, traceback)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/usr/lib/python3.8/contextlib.py", line 131, in __exit__
self.gen.throw(type, value, traceback)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 166, in save_modules
saved_exc.resume()
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 141, in resume
six.reraise(type, exc, self._tb)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/_vendor/six.py", line 685, in reraise
raise value.with_traceback(tb)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 154, in save_modules
yield saved
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 195, in setup_context
yield
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 250, in run_setup
_execfile(setup_script, ns)
File "/home/odroid/Documents/data-crawling-env/lib/python3.8/site-packages/setuptools/sandbox.py", line 45, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/setup.py", line 461, in <module>
"generating Cython sources and expanding templates".format(
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/setup.py", line 443, in setup_package
bad_commands[command] = "`setup.py %s` is not supported" % command
File "/tmp/easy_install-5cn5y70d/numpy-1.22.3/setup.py", line 248, in generate_cython
f.write(text)
RuntimeError: Running cythonize failed!
Cythonizing sources
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-tqtljvxv/scipy/
It looks like related to Cython in spicy package? Does anyone got this error.
Thank you guy for helping me.

I fixed this problem.
The reason is my pip3 version was too old (v.9).
So I updated it to the newest version, it work like charm.
sudo python3 -m pip install -U pip

pip install pyublas fails with `NameError: name 'sys_platform' is not defined`

Under Ubuntu 16.04 and Python 2.7.12 sudo -H pip install pyublas fails with the following stacktrace:
Collecting pyublas
Using cached PyUblas-2013.1.tar.gz
Complete output from command python setup.py egg_info:
Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.35.tar.gz
Extracting in /tmp/tmpnYhYMx
Now working in /tmp/tmpnYhYMx/distribute-0.6.35
Building a Distribute egg in /tmp/pip-build-vvsChR/pyublas
Traceback (most recent call last):
File "setup.py", line 248, in <module>
scripts = scripts,
File "/usr/lib/python2.7/distutils/core.py", line 111, in setup
_setup_distribution = dist = klass(attrs)
File "/tmp/tmpnYhYMx/distribute-0.6.35/setuptools/dist.py", line 225, in __init__
_Distribution.__init__(self,attrs)
File "/usr/lib/python2.7/distutils/dist.py", line 287, in __init__
self.finalize_options()
File "/tmp/tmpnYhYMx/distribute-0.6.35/setuptools/dist.py", line 257, in finalize_options
ep.require(installer=self.fetch_build_egg)
File "/tmp/tmpnYhYMx/distribute-0.6.35/pkg_resources.py", line 2027, in require
working_set.resolve(self.dist.requires(self.extras),env,installer))
File "/tmp/tmpnYhYMx/distribute-0.6.35/pkg_resources.py", line 2237, in requires
dm = self._dep_map
File "/tmp/tmpnYhYMx/distribute-0.6.35/pkg_resources.py", line 2466, in _dep_map
self.__dep_map = self._compute_dependencies()
File "/tmp/tmpnYhYMx/distribute-0.6.35/pkg_resources.py", line 2499, in _compute_dependencies
common = frozenset(reqs_for_extra(None))
File "/tmp/tmpnYhYMx/distribute-0.6.35/pkg_resources.py", line 2496, in reqs_for_extra
if req.marker_fn(override={'extra':extra}):
File "/tmp/tmpnYhYMx/distribute-0.6.35/_markerlib/markers.py", line 109, in marker_fn
return eval(compiled_marker, environment)
File "<environment marker>", line 1, in <module>
NameError: name 'sys_platform' is not defined
/tmp/pip-build-vvsChR/pyublas/distribute-0.6.35-py2.7.egg
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-vvsChR/pyublas/setup.py", line 143, in <module>
main()
File "/tmp/pip-build-vvsChR/pyublas/setup.py", line 29, in main
from aksetup_helper import hack_distutils, get_config, setup, \
File "aksetup_helper.py", line 3, in <module>
distribute_setup.use_setuptools()
File "distribute_setup.py", line 152, in use_setuptools
return _do_download(version, download_base, to_dir, download_delay)
File "distribute_setup.py", line 132, in _do_download
_build_egg(egg, tarball, to_dir)
File "distribute_setup.py", line 123, in _build_egg
raise IOError('Could not build the egg.')
IOError: Could not build the egg.
Following various related SO answers, I have confirmed that distribute is not installed, setuptools is up to date (setuptools (36.0.1)).
I have also tried manually running setup per this answer to no avail.

Error importing termcolor in python 2.5

I'm using python 2.5 on a lenny-5 64 bit version. I have installed termcolor before and have used it too. Suddenly I can't use it now. I got this error for import termcolor:
>>> import termcolor
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "termcolor.py", line 124
print((colored(text, color, on_color, attrs)), **kwargs)
^
SyntaxError: invalid syntax
I don't know if I violated any constraint or dependency by installing some other module. I don't even know what happened to this lib. Any idea?
I tried to re-install this package using pip and I got this:
# pip uninstall termcolor
Cannot uninstall requirement termcolor, not installed
Storing complete log in /root/.pip/pip.log
I tried to install it using pip and I got this:
# pip install termcolor
Downloading/unpacking termcolor
Exception:
Traceback (most recent call last):
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/basecommand.py", line 139, in main
status = self.run(options, args)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/commands/install.py", line 266, in run
requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/req.py", line 1026, in prepare_files
url = finder.find_requirement(req_to_install, upgrade=self.upgrade)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/index.py", line 125, in find_requirement
page = self._get_page(main_index_url, req)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/index.py", line 353, in _get_page
return HTMLPage.get_page(link, req, cache=self.cache)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/index.py", line 471, in get_page
resp = urlopen(url)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/download.py", line 143, in __call__
response = self.get_opener(scheme=scheme).open(url)
File "/usr/lib/python2.5/site-packages/pip-1.3-py2.5.egg/pip/download.py", line 201, in get_opener
raise NoSSLError()
NoSSLError:
###################################################################
## You don't have an importable ssl module. You are most ##
## likely using Python 2.5, which did not include ssl ##
## support by default. In this state, we can not provide ##
## ssl certified downloads from PyPI. ##
## ##
## You can do one of 2 things: ##
## 1) Install this: https://pypi.python.org/pypi/ssl/ ##
## (It provides ssl support for older Pythons ) ##
## 2) Use the --insecure option to allow this insecurity ##
## ##
## For more details, go to the "SSL Certificate Verification" ##
## section located here: ##
## http://www.pip-installer.org/en/latest/logic.html ##
## ##
###################################################################
Storing complete log in /root/.pip/pip.log
I tried easy_install to install it again; this is the output:
# easy_install termcolor
Searching for termcolor
Reading http://pypi.python.org/simple/termcolor/
Best match: termcolor 1.1.0
Downloading https://pypi.python.org/packages/source/t/termcolor/termcolor-1.1.0.tar.gz#md5=043e89644f8909d462fbbfa511c768df
Processing termcolor-1.1.0.tar.gz
Running termcolor-1.1.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-YzwLtr/termcolor-1.1.0/egg-dist-tmp-GfHcKR
Traceback (most recent call last):
File "/usr/bin/easy_install", line 8, in <module>
load_entry_point('setuptools==0.6c11', 'console_scripts', 'easy_install')()
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 1712, in main
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 1700, in with_ei_usage
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 1716, in <lambda>
File "/usr/lib/python2.5/distutils/core.py", line 151, in setup
dist.run_commands()
File "/usr/lib/python2.5/distutils/dist.py", line 974, in run_commands
self.run_command(cmd)
File "/usr/lib/python2.5/distutils/dist.py", line 994, in run_command
cmd_obj.run()
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 211, in run
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 446, in easy_install
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 476, in install_item
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 655, in install_eggs
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 930, in build_and_install
File "build/bdist.linux-i686/egg/setuptools/command/easy_install.py", line 919, in run_setup
File "build/bdist.linux-i686/egg/setuptools/sandbox.py", line 62, in run_setup
File "build/bdist.linux-i686/egg/setuptools/sandbox.py", line 105, in run
File "build/bdist.linux-i686/egg/setuptools/sandbox.py", line 64, in <lambda>
File "setup.py", line 35, in <module>
from termcolor import VERSION
File "/tmp/easy_install-YzwLtr/termcolor-1.1.0/termcolor.py", line 124
print((colored(text, color, on_color, attrs)), **kwargs)
^
SyntaxError: invalid syntax

compiling statsmodels example in ubuntu 12.04

I am new to python, and after reading the running some examples, I wanted to try statsmodels.
I copied the following example from statsmodels website,
#!/usr/bin/env python3
import numpy as np
import statsmodels.api as sm
spector_data = sm.datasets.spector.load()
spector_data.exog = sm.add_constant(spector_data.exog, prepend=False)
#Fit and summarize OLS model
mod = sm.OLS(spector_data.endog, spector_data.exog)
res = mod.fit()
print (res.summary())
and I get the following error:
Running unit tests for scipy
Traceback (most recent call last):
File "./statsmodels.py", line 3, in <module>
import statsmodels.api as sm
File "/home/ra/python/statsmodels.py", line 3, in <module>
scipy.test()
File "/usr/lib/python3/dist-packages/numpy/testing/nosetester.py", line 318, in test
self._show_system_info()
File "/usr/lib/python3/dist-packages/numpy/testing/nosetester.py", line 187, in _show_system_info
nose = import_nose()
File "/usr/lib/python3/dist-packages/numpy/testing/nosetester.py", line 69, in import_nose
raise ImportError(msg)
ImportError: Need nose >= 0.10.0 for tests - see http://somethingaboutorange.com/mrl/projects/nose
so, I ran the below command for statsmodels, and it gave me the following message upon running the install:
sudo easy_install3 -U statsmodels
Searching for statsmodels
Reading http://pypi.python.org/simple/statsmodels/
Reading http://statsmodels.sourceforge.net/
Reading https://github.com/statsmodels/statsmodels/downloads
Best match: statsmodels 0.5.0
Downloading https://pypi.python.org/packages/source/s/statsmodels/statsmodels-0.5.0.zip#md5=4ed78e8c6ababdcae0400fc0fe6f31a7
Processing statsmodels-0.5.0.zip
Running statsmodels-0.5.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-hnrc4z/statsmodels-0.5.0/egg-dist-tmp-2_kign
Traceback (most recent call last):
File "setup.py", line 116, in check_dependency_versions
ImportError: No module named pandas.version
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/easy_install3", line 9, in <module>
load_entry_point('distribute==0.6.24dev-r0', 'console_scripts', 'easy_install')()
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1931, in main
with_ei_usage(lambda:
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1912, in with_ei_usage
return f()
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1935, in <lambda>
distclass=DistributionWithoutHelpCommands, **kw
File "/usr/lib/python3.2/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.2/distutils/dist.py", line 917, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.2/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 368, in run
self.easy_install(spec, not self.no_deps)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 608, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 638, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 828, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1105, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1094, in run_setup
run_setup(setup_script, args)
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 31, in run_setup
lambda: exec(compile(open(
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 73, in run
return func()
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 34, in <lambda>
{'__file__':setup_script, '__name__':'__main__'})
File "setup.py", line 463, in <module>
File "setup.py", line 118, in check_dependency_versions
ImportError: statsmodels requires pandas
So, I ran the below to make sure I had the latest pandas (I had run the sudo apt-get install python-pandas before, but since statsmodels did not find that, I did the below:
sudo easy_install3 -U pandas
Searching for pandas
Reading http://pypi.python.org/simple/pandas/
Best match: pandas 0.14.0
Downloading https://pypi.python.org/packages/source/p/pandas/pandas-0.14.0.zip#md5=9afe57bd470a2ddaf67bdfb5fc9c0eee
Processing pandas-0.14.0.zip
Running pandas-0.14.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-deg0nw/pandas-0.14.0/egg-dist-tmp-19hrp_
warning: no files found matching 'README.rst'
no previously-included directories found matching 'doc/build'
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '.git*' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no previously-included files matching '*.png' found anywhere in distribution
pandas/index.c:4:20: fatal error: Python.h: No such file or directory
compilation terminated.
error: Setup script exited with error: command 'gcc' failed with exit status 1
Where's my error this time.
btw, this is the version of pandas I see from my python prompt:
>>> import pandas
/usr/local/lib/python2.7/dist-packages/pandas/io/excel.py:626: UserWarning: Installed openpyxl is not supported at this time. Use >=1.6.1 and <2.0.0.
.format(openpyxl_compat.start_ver, openpyxl_compat.stop_ver))
>>> pandas.__version__
'0.14.0'
I don't understand why I get that message when I import.
Also, I wanted to post the results of which, in case that might be of any use:
ra#ra-VGN-FZ:~$ which python
/usr/bin/python
ra#ra-VGN-FZ:~$ which easy_install
/usr/bin/easy_install
ra#ra-VGN-FZ:~$ which pip3
/usr/local/bin/pip3
To solve openpyxl problem, I did the following:
pip uninstall openpyxl
Cannot uninstall requirement openpyxl, not installed
Storing debug log for failure in /tmp/tmpci3yro
ra#ra-VGN-FZ19:~$ pip install openpyxl==1.8.6
Downloading/unpacking openpyxl==1.8.6
Downloading openpyxl-1.8.6-py2.py3-none-any.whl (190kB): 190kB downloaded
Installing collected packages: openpyxl
Cleaning up...
Exception:
Traceback (most recent call last):
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/basecommand.py", line 122, in main
status = self.run(options, args)
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/commands/install.py", line 283, in run
requirement_set.install(install_options, global_options, root=options.root_path)
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/req.py", line 1435, in install
requirement.install(install_options, global_options, *args, **kwargs)
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/req.py", line 671, in install
self.move_wheel_files(self.source_dir, root=root)
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/req.py", line 901, in move_wheel_files
pycompile=self.pycompile,
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/wheel.py", line 215, in move_wheel_files
clobber(source, lib_dir, True)
File "/usr/local/lib/python3.2/dist-packages/pip-1.5.6-py3.2.egg/pip/wheel.py", line 205, in clobber
os.makedirs(destdir)
File "/usr/lib/python3.2/os.py", line 152, in makedirs
mkdir(name, mode)
OSError: [Errno 13] Permission denied: '/usr/local/lib/python3.2/dist-packages/openpyxl-1.8.6.dist-info'
Storing debug log for failure in /tmp/tmp15h3o4
This is the error with python3:
sudo easy_install3 -U statsmodels
Searching for statsmodels
Reading http://pypi.python.org/simple/statsmodels/
Reading http://statsmodels.sourceforge.net/
Reading https://github.com/statsmodels/statsmodels/downloads
Best match: statsmodels 0.5.0
Downloading https://pypi.python.org/packages/source/s/statsmodels/statsmodels-0.5.0.zip#md5=4ed78e8c6ababdcae0400fc0fe6f31a7
Processing statsmodels-0.5.0.zip
Running statsmodels-0.5.0/setup.py -q bdist_egg --dist-dir /tmp/easy_install-oudla7/statsmodels-0.5.0/egg-dist-tmp-o6dh5a
Traceback (most recent call last):
File "setup.py", line 120, in check_dependency_versions
ImportError: No module named patsy
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/easy_install3", line 9, in <module>
load_entry_point('distribute==0.6.24dev-r0', 'console_scripts', 'easy_install')()
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1931, in main
with_ei_usage(lambda:
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1912, in with_ei_usage
return f()
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1935, in <lambda>
distclass=DistributionWithoutHelpCommands, **kw
File "/usr/lib/python3.2/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.2/distutils/dist.py", line 917, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.2/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 368, in run
self.easy_install(spec, not self.no_deps)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 608, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 638, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 828, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1105, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1094, in run_setup
run_setup(setup_script, args)
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 31, in run_setup
lambda: exec(compile(open(
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 73, in run
return func()
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 34, in <lambda>
{'__file__':setup_script, '__name__':'__main__'})
File "setup.py", line 463, in <module>
File "setup.py", line 122, in check_dependency_versions
ImportError: statsmodels requires patsy. http://patsy.readthedocs.org
ra#ra-VGN-FZ19:~$ sudo easy_install3 -U patsy
Searching for patsy
Reading http://pypi.python.org/simple/patsy/
Best match: patsy 0.2.1
Downloading https://pypi.python.org/packages/source/p/patsy/patsy-0.2.1.zip#md5=d51fa2fcb60018d75073f375c87ddccf
Processing patsy-0.2.1.zip
Running patsy-0.2.1/setup.py -q bdist_egg --dist-dir /tmp/easy_install-l1wpxc/patsy-0.2.1/egg-dist-tmp-2qgd7e
no previously-included directories found matching 'doc/_build'
zip_safe flag not set; analyzing archive contents...
Adding patsy 0.2.1 to easy-install.pth file
Installed /usr/local/lib/python3.2/dist-packages/patsy-0.2.1-py3.2.egg
Processing dependencies for patsy
Finished processing dependencies for patsy
Thanks to Jonathan Villemaire-Krajden who misled me while i was seeking a solution to show() in matplotlib, my statsmodels has broken.
I tried to reinstall statsmodels and now I get the following error:
easy_install3 -U statsmodels
Traceback (most recent call last):
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 449, in _build_master
ws.require(__requires__)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 742, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 643, in resolve
raise VersionConflict(dist, req) # XXX put more info here
pkg_resources.VersionConflict: (distribute 0.7.3 (/usr/local/lib/python3.2/dist-packages/distribute-0.7.3-py3.2.egg), Requirement.parse('distribute==0.6.24dev-r0'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/easy_install3", line 5, in <module>
from pkg_resources import load_entry_point
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 2837, in <module>
working_set = WorkingSet._build_master()
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 451, in _build_master
return cls._build_from_requirements(__requires__)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 464, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 799, in __init__
self.scan(search_path)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 829, in scan
self.add(dist)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 849, in add
dists.sort(key=operator.attrgetter('hashcmp'), reverse=True)
TypeError: unorderable types: NoneType() < str()
ra#ra-VGN-FZ19:~$ sudo easy_install3 -U statsmodels
Traceback (most recent call last):
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 449, in _build_master
ws.require(__requires__)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 742, in require
needed = self.resolve(parse_requirements(requirements))
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 643, in resolve
raise VersionConflict(dist, req) # XXX put more info here
pkg_resources.VersionConflict: (distribute 0.7.3 (/usr/local/lib/python3.2/dist-packages/distribute-0.7.3-py3.2.egg), Requirement.parse('distribute==0.6.24dev-r0'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/easy_install3", line 5, in <module>
from pkg_resources import load_entry_point
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 2837, in <module>
working_set = WorkingSet._build_master()
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 451, in _build_master
return cls._build_from_requirements(__requires__)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 464, in _build_from_requirements
dists = ws.resolve(reqs, Environment())
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 799, in __init__
self.scan(search_path)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 829, in scan
self.add(dist)
File "/usr/local/lib/python3.2/dist-packages/setuptools-5.1-py3.2.egg/pkg_resources.py", line 849, in add
dists.sort(key=operator.attrgetter('hashcmp'), reverse=True)
TypeError: unorderable types: NoneType() < str()
sudo pip3 install statsmodels
Downloading/unpacking statsmodels
Downloading statsmodels-0.5.0.tar.gz (5.5MB): 5.5MB downloaded
Running setup.py (path:/tmp/pip_build_root/statsmodels/setup.py) egg_info for package statsmodels
Traceback (most recent call last):
File "<string>", line 17, in <module>
File "/tmp/pip_build_root/statsmodels/setup.py", line 463, in <module>
check_dependency_versions(min_versions)
File "/tmp/pip_build_root/statsmodels/setup.py", line 109, in check_dependency_versions
from scipy.version import short_version as spversion
File "/usr/lib/python3/dist-packages/scipy/__init__.py", line 124, in <module>
pkgload(verbose=SCIPY_IMPORT_VERBOSE,postpone=True)
File "/usr/local/lib/python3.2/dist-packages/numpy/_import_tools.py", line 177, in __call__
for package_name in self._get_sorted_names():
File "/usr/local/lib/python3.2/dist-packages/numpy/_import_tools.py", line 114, in _get_sorted_names
for name in depend_dict.keys():
RuntimeError: dictionary changed size during iteration
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 17, in <module>
File "/tmp/pip_build_root/statsmodels/setup.py", line 463, in <module>
check_dependency_versions(min_versions)
File "/tmp/pip_build_root/statsmodels/setup.py", line 109, in check_dependency_versions
from scipy.version import short_version as spversion
File "/usr/lib/python3/dist-packages/scipy/__init__.py", line 124, in <module>
pkgload(verbose=SCIPY_IMPORT_VERBOSE,postpone=True)
File "/usr/local/lib/python3.2/dist-packages/numpy/_import_tools.py", line 177, in __call__
for package_name in self._get_sorted_names():
File "/usr/local/lib/python3.2/dist-packages/numpy/_import_tools.py", line 114, in _get_sorted_names
for name in depend_dict.keys():
RuntimeError: dictionary changed size during iteration
----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/statsmodels
Storing debug log for failure in /home/ra/.pip/pip.log

You are running statsmodels.py with Python 3, and almost certainly running ipython with Python 2.
When you install with pip it usesPython 2, and installs the packages in a different location than where Python 3 looks.
Either install nose using pip3 (if you have it installed - read here if not)
sudo pip3 install nose
or run your statsmodels.py with Python 2 (replace python3 with python on your first line):
#!/usr/bin/env python

Python GDAL: pip install --no-install GDAL fails

I am trying to install GDAL in virtual environment based on the various solutions out there.
However the download itself already fails:
$ pip install --no-install GDAL
Here is the pip.log
------------------------------------------------------------
/Users/test/venv/bin/pip run on Sun Jun 2 15:35:15 2013
Downloading/unpacking GDAL
Running setup.py egg_info for package GDAL
running egg_info
writing pip-egg-info/GDAL.egg-info/PKG-INFO
writing top-level names to pip-egg-info/GDAL.egg-info/top_level.txt
writing dependency_links to pip-egg-info/GDAL.egg-info/dependency_links.txt
warning: manifest_maker: standard file '-c' not found
Traceback (most recent call last):
File "<string>", line 16, in <module>
File "/Users/test/venv/build/GDAL/setup.py", line 267, in <module>
ext_modules = ext_modules )
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "<string>", line 14, in replacement_run
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/egg_info.py", line 259, in find_sources
mm.run()
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/egg_info.py", line 325, in run
self.add_defaults()
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/egg_info.py", line 361, in add_defaults
sdist.add_defaults(self)
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/sdist.py", line 211, in add_defaults
build_ext = self.get_finalized_command('build_ext')
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 312, in get_finalized_command
cmd_obj.ensure_finalized()
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
self.finalize_options()
File "/Users/test/venv/build/GDAL/setup.py", line 164, in finalize_options
self.gdaldir = self.get_gdal_config('prefix')
File "/Users/test/venv/build/GDAL/setup.py", line 144, in get_gdal_config
return fetch_config(option)
File "/Users/test/venv/build/GDAL/setup.py", line 97, in fetch_config
raise gdal_config_error, e""")
File "<string>", line 4, in <module>
__main__.gdal_config_error: [Errno 2] No such file or directory
Complete output from command python setup.py egg_info:
running egg_info
writing pip-egg-info/GDAL.egg-info/PKG-INFO
writing top-level names to pip-egg-info/GDAL.egg-info/top_level.txt
writing dependency_links to pip-egg-info/GDAL.egg-info/dependency_links.txt
warning: manifest_maker: standard file '-c' not found
Traceback (most recent call last):
File "<string>", line 16, in <module>
File "/Users/test/venv/build/GDAL/setup.py", line 267, in <module>
ext_modules = ext_modules )
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/core.py", line 152, in setup
dist.run_commands()
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "<string>", line 14, in replacement_run
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/egg_info.py", line 259, in find_sources
mm.run()
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/egg_info.py", line 325, in run
self.add_defaults()
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/egg_info.py", line 361, in add_defaults
sdist.add_defaults(self)
File "/Users/test/venv/lib/python2.7/site-packages/distribute-0.6.34-py2.7.egg/setuptools/command/sdist.py", line 211, in add_defaults
build_ext = self.get_finalized_command('build_ext')
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 312, in get_finalized_command
cmd_obj.ensure_finalized()
File "/usr/local/Cellar/python/2.7.5/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/cmd.py", line 109, in ensure_finalized
self.finalize_options()
File "/Users/test/venv/build/GDAL/setup.py", line 164, in finalize_options
self.gdaldir = self.get_gdal_config('prefix')
File "/Users/test/venv/build/GDAL/setup.py", line 144, in get_gdal_config
return fetch_config(option)
File "/Users/test/venv/build/GDAL/setup.py", line 97, in fetch_config
raise gdal_config_error, e""")
File "<string>", line 4, in <module>
__main__.gdal_config_error: [Errno 2] No such file or directory
----------------------------------------
Command python setup.py egg_info failed with error code 1 in /Users/test/venv/build/GDAL
Exception information:
Traceback (most recent call last):
File "/Users/test/venv/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/basecommand.py", line 139, in main
status = self.run(options, args)
File "/Users/test/venv/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/commands/install.py", line 266, in run
requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
File "/Users/test/venv/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/req.py", line 1057, in prepare_files
req_to_install.run_egg_info()
File "/Users/test/venv/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/req.py", line 236, in run_egg_info
command_desc='python setup.py egg_info')
File "/Users/test/venv/lib/python2.7/site-packages/pip-1.3.1-py2.7.egg/pip/util.py", line 662, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command python setup.py egg_info failed with error code 1 in /Users/test/venv/build/GDAL
What am I missing?

The workaround given by #user1738154 didn't work as expected for me so went ahead and installed GDAL using HomeBrew then using pip into my Virtual environment.
$ brew install gdal
(venv)$ pip install GDAL
Everything compiled and ran like a charm.

A workaround to that problem is to
Download GDAL Complete from this site
Install GDAL Complete.pkg
Go to /Library/Frameworks/GDAL.framework/Versions/1.10/ and copy all files in there
Go to your virtual environment's sites-packages /venv/lib/python2.7/site-packages and paste the copied files in there

after install gdal using these steps on host:
sudo apt-get install gdal-bin
sudo apt-get install libgdal-dev
After that use
pip install GDAL==$(gdal-config --version) --global-option=build_ext --global-option="-I/usr/include/gdal"
This should work like charm