Virtualenv causing setuptools error - virtualenv

I am having trouble running a virtualenv, and I keep getting this same error code: "setuptools pip wheel failed with error code 1"
I saw some pages talking about how this is a discrepancy between different versions of setuptools, but I've uninstalled and reinstalled virtualenv and setuptools in several versions to no results. Does anyone know what's happening here?
Roberts-MacBook-Air:script Rob$ virtualenv venv
New python executable in venv/bin/python
Installing setuptools, pip, wheel...
Complete output from command /Users/Rob/Seedstages/script/venv/bin/python -c "import sys, pip; sys...d\"] + sys.argv[1:]))" setuptools pip wheel:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/Rob/anaconda/lib/python2.7/site-packages/virtualenv_support/pip-7.1.2-py2.py3-none-any.whl/pip/__init__.py", line 13, in <module>
File "/Users/Rob/anaconda/lib/python2.7/site-packages/virtualenv_support/pip-7.1.2-py2.py3-none-any.whl/pip/utils/__init__.py", line 15, in <module>
File "/Users/Rob/anaconda/lib/python2.7/zipfile.py", line 6, in <module>
import io
File "/Users/Rob/anaconda/lib/python2.7/io.py", line 51, in <module>
import _io
ImportError: dlopen(/Users/Rob/Seedstages/script/venv/lib/python2.7/lib-dynload/_io.so, 2): Symbol not found: __PyErr_ReplaceException
Referenced from: /Users/Rob/Seedstages/script/venv/lib/python2.7/lib-dynload/_io.so
Expected in: dynamic lookup
----------------------------------------
...Installing setuptools, pip, wheel...done.
Traceback (most recent call last):
File "/Users/Rob/anaconda/bin/virtualenv", line 11, in <module>
sys.exit(main())
File "/Users/Rob/anaconda/lib/python2.7/site-packages/virtualenv.py", line 832, in main
symlink=options.symlink)
File "/Users/Rob/anaconda/lib/python2.7/site-packages/virtualenv.py", line 1004, in create_environment
install_wheel(to_install, py_executable, search_dirs)
File "/Users/Rob/anaconda/lib/python2.7/site-packages/virtualenv.py", line 969, in install_wheel
'PIP_NO_INDEX': '1'
File "/Users/Rob/anaconda/lib/python2.7/site-packages/virtualenv.py", line 910, in call_subprocess
% (cmd_desc, proc.returncode))
OSError: Command /Users/Rob/Seedstages/script/venv/bin/python -c "import sys, pip; sys...d\"] + sys.argv[1:]))" setuptools pip wheel failed with error code 1
Roberts-MacBook-Air:script Rob$

I would say that Anaconda causes the conflict, though to be more specific, it appears as if Anaconda's virtualenv is the problem. Running which virtualenv on my macbook (where I'm having the same problem) yields /Users/me/anaconda/bin/virtualenv while running it on the linux system I just tested this on yields /usr/local/bin/virtualenv.
So, on OS X, I downloaded virtualenv using /usr/local/bin/pip install virtualenv. This doesn't create a virtualenv binary (or it didn't for me) in the PATH folders, so I had to type this painfully long command:
sudo /usr/local/bin/python ... {the path to virtualenv.py in the system python's site-packages folder} new_env
And that did it. But that's ridiculous. No one wants to do that - even creating links would still be hacking it when you don't need to.
According to the ContinuumIO github page on this very subject, the virtualenv env and source /bin/activate commands are replaced with conda create -n env python=2.7 and source activate env.
Tested on my macbook (running Anaconda2 v4 on OS Yosemite) and it worked out.

Related

How can I import libraries in PythonAnywhere and use them in a Python notebook?

I'm both updating and installing packages/libaries, but are only able to use them through the Python3.6 console.
10:40 ~ $ pip3.6 install -U --user scikit-learn
Requirement already up-to-date: scikit-learn in ./.local/lib/python3.6/site-packages
Requirement already up-to-date: numpy>=1.11.0 in ./.local/lib/python3.6/site-packages (from scikit-learn)
Requirement already up-to-date: joblib>=0.11 in ./.local/lib/python3.6/site-packages (from scikit-learn)
Requirement already up-to-date: scipy>=0.17.0 in ./.local/lib/python3.6/site-packages (from scikit-learn)
When using pip install it fails with :
10:40 ~ $ pip install -U --user scikit-learn
Collecting scikit-learn
Using cached https://files.pythonhosted.org/packages/18/28/5a48b00599b476875415b97bdfdb3849bafb31183c1d785501dbc8a77aa2/scikit-learn-0.22.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-JYw8w1/scikit-learn/setup.py", line 47, in <module>
import sklearn
File "sklearn/__init__.py", line 81, in <module>
from . import __check_build # noqa: F401
File "sklearn/__check_build/__init__.py", line 46, in <module>
raise_build_error(e)
File "sklearn/__check_build/__init__.py", line 41, in raise_build_error
%s""" % (e, local_dir, ''.join(dir_content).strip(), msg))
ImportError: No module named _check_build
___________________________________________________________________________
Contents of sklearn/__check_build:
__init__.py _check_build.pyx __init__.pyc
setup.py
___________________________________________________________________________
It seems that scikit-learn has not been built correctly.
If you have installed scikit-learn from source, please do not forget
to build the package before using it: run `python setup.py install` or
`make` in the source directory.
It appears that you are importing a local scikit-learn source tree. For
this, you need to have an inplace install. Maybe you are in the source
directory and you need to try from another location.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-JYw8w1/scikit-learn/
If you've installed a package using pip3.6, make sure that your kernel version for your notebook is 3.6 -- if it's (say) 3.7, then it won't work, because each version of Python has its own separate set of installed modules.
I imported the notebook, and forgot to change Kernel Python3.6. It was still on Python3. Changed notebook to 3.6, and the it used the updated libary's-
When you run pip on PythonAnywhere, outside virtual environment, it installs packages for python2. The latest version of scikit-learn to work with python2 is 0.20.4. So, install it with pip install scikit-learn==0.20.4
You tried to install 0.22.1 with python2.

Rasa NLU installation issue

I had rasa nlu version 0.12.3 installed. I had some issues and uninstalled rasa nlu and other requirements using
pip uninstall rasa_nlu
pip uninstall -r requirements.txt
Now when I am installing rasa nlu again using pip install rasa_nlu
I see below messages in the terminal
Error processing line 1 of /Users/uername/anaconda3/lib/python3.6/site-packages/matplotlib-2.0.2-py3.6-nspkg.pth:
Traceback (most recent call last):
File "/Users/username/anaconda3/lib/python3.6/site.py", line 168, in addpackage
exec(line)
File "<string>", line 1, in <module>
File "<frozen importlib._bootstrap>", line 557, in module_from_spec
AttributeError: 'NoneType' object has no attribute 'loader'
Remainder of file ignored
There are more messages regarding installation and the final message is
Found existing installation: greenlet 0.4.12
Cannot uninstall 'greenlet'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
And it turns out that rasa nlu is not installed. I know that the nlu is not installed because when I check the nlu version with below command
python -c "import rasa_nlu; print(rasa_nlu.__version__);"
I get error
Error processing line 1 of /Users/username/anaconda3/lib/python3.6/site-packages/matplotlib-2.0.2-py3.6-nspkg.pth:
Traceback (most recent call last):
File "/Users/username/anaconda3/lib/python3.6/site.py", line 168, in addpackage
exec(line)
File "<string>", line 1, in <module>
File "<frozen importlib._bootstrap>", line 557, in module_from_spec
AttributeError: 'NoneType' object has no attribute 'loader'
Remainder of file ignored
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'rasa_nlu'
Turns out the problem was happening due to a distutils installed project which the pip install couldn't uninstall before installation.
So I had to use --ignore-installed
In short, below command solved the problem
sudo pip install --ignore-installed rasa_nlu
If you want to uninstall python package which is part of distutils, you can manually remove the folder from 'site-packages' folder. If it is Anaconda distribution, it will be in following folder. I suggest to cut the folder and paste it somewhere else for the backup purpose.
In windows:
C:\Users\\AppData\Local\Continuum\Anaconda3\Lib\site-packages
I'm sure Linux will have similar folder structure.
Following 2 items needs to be removed.
Folder [package version no.]
File - [package>.egg-info]
As mentioned in Rasa's official documentation, Install it with
pip3 install rasa-x --extra-index-url https://pypi.rasa.com/simple
It will install Rasa X and Rasa. It works great.
pip3 install rasa-x -U --extra-index-url https://pypi.rasa.com/simple
installation guide

Geodjango Exception when importing django.contrib.gis.gdal: OSError: /usr/lib/libgdal.so.1: undefined symbol: sqlite3_column_table_name

I have followed the tutorial for installing Geodjango on my Ubuntu 14.04. I am using Django 1.10 and Python 3.5, postgres-9.6 and postgis 2.3.
I have checked here and here, but found no solution.
In a newly installed ubuntu 14.04 Virtual Machine, it worked.
But in my installation, when I tried making migrations, I got:
OSError: /usr/lib/libgdal.so.1: undefined symbol: sqlite3_column_table_name
Investigating a bit further, I tried simply:
from django.contrib.gis import gdal
And got:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/__init__.py", line 49, in <module>
from django.contrib.gis.gdal.driver import Driver # NOQA
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/driver.py", line 5, in <module>
from django.contrib.gis.gdal.prototypes import ds as vcapi, raster as rcapi
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/prototypes/ds.py", line 9, in <module>
from django.contrib.gis.gdal.libgdal import GDAL_VERSION, lgdal
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/site-packages/django/contrib/gis/gdal/libgdal.py", line 48, in <module>
lgdal = CDLL(lib_path)
File "/home/pv/anaconda3/envs/dj110py35/lib/python3.5/ctypes/__init__.py", line 347, in __init__
self._handle = _dlopen(self._name, mode)
OSError: /usr/lib/libgdal.so.1: undefined symbol: sqlite3_column_table_name
Is there any suggestions on how I could repair my setup?
UPDATE
It seems to be a problema with my conda environment. When I started using a pip virtualenv, the problem did not arise anymore. I am not answering the question, because I could not find the solution, only a workaround. But rebuilding the environment with pip virtualenv works.
In conda environment: conda install -c conda-forge gdal=2.2.1
In django settings.py:
GDAL_LIBRARY_PATH = '<HOME>/anaconda3/envs/<env_name>/lib/libgdal.so'
I was having this issue as well and the specifying
GDAL_LIBRARY_PATH = <HOME>/anaconda3/envs/<env_name>/lib/libgdal.so
(in project.settings or os.environ.setdefault) led to
libicui18n.so.56: cannot open shared object file: No such file or directory.
The fix that worked for me was to upgrade icu:
conda install -c conda-forge icu=58
Upgrading icu lead to some changes in other package versions as well (qt downgraded from 5.6.2-4 to 5.6.2-3, the rest upgraded).
I simply run under my conda environment:
conda install gdal
Guy de Carufel's solution did not work for me, though he pointed to a correct direction, thanks
Have you built SQLite from source? Then, you forgot to enable Column metadata. Recompile SQLite with
CFLAGS="-DSQLITE_ENABLE_COLUMN_METADATA=1" ./configure
make
sudo make install
Have fun using the cutting edge SQLite.
Reference - https://www.sqlite.org/compile.html#enable_column_metadata

upgrading scipy in mac

I want to upgrade scipy. and I used pip install scipy --upgrade to do this, but here is error, how should I fix this?
Installing collected packages: scipy
Found existing installation: scipy 0.13.0b1
DEPRECATION: Uninstalling a distutils installed project (scipy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
Uninstalling scipy-0.13.0b1:
Exception:
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/basecommand.py", line 215, in main
status = self.run(options, args)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/commands/install.py", line 342, in run
prefix=options.prefix_path,
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py", line 778, in install
requirement.uninstall(auto_confirm=True)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py", line 754, in uninstall
paths_to_remove.remove(auto_confirm)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_uninstall.py", line 115, in remove
renames(path, new_path)
File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py", line 267, in renames
shutil.move(old, new)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 302, in move
copy2(src, real_dst)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 131, in copy2
copystat(src, dst)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 103, in copystat
os.chflags(dst, st.st_flags)
OSError: [Errno 1] Operation not permitted: '/var/folders/7x/1ly_pjjd3g50632kc7mc68n00000gn/T/pip-a37H18-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy-0.13.0b1-py2.7.egg-info'
Python version 2.7.10
Mac version 10.12.04
I tried to install face_recognition, then display the same problem.
sudo pip install face_recognition
try use:
sudo pip install --upgrade scipy --ignore-installed six

orange3-associate install fails, other add-ons install without issue

Install error for Orang3-Associate add-on on a Windows7 PC
Command:
pip install Orange3-Associate (same result from UI Options - Add-Ons)
Error:
Collecting Orange3-Associate
Using cached Orange3-Associate-0.1.1.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 20, in <module>
File "C:\cygwin64\tmp\pip-build-nzb1zehp\Orange3-Associate\setup.py", line 32, in <module>
long_description=open(path.join(path.dirname(__file__), 'README.md')).re ad(),
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\cygwin64\\tmp\\ pip-build-nzb1zehp\\Orange3-Associate\\README.md'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in C:\cygwin64\tmp\p ip-build-nzb1zehp\Orange3-Associate
Add-ons DataFusion and Text successfully installed.
Thanks. This was a bug in Orange3-Associate 0.1.1. It is hopefully fixed in 0.1.2, already available through pip or Options | Add-ons.