Ubuntu – Conda update : Permission issues

ipythonpythonxubuntu

I have a frequent issue with python packages, in this case with conda updating packages:

ipython update

user:~$ conda update ipython

Proceed ([y]/n)? y

Fetching packages … Error: Could not open
u'/home/user/anaconda/pkgs/ipython-2.3.1-py27_0.tar.bz2.part' for
writing (seek).00 B/s

ipython notebook update

user:~$ pip install "ipython[notebook]"

–upgrade Downloading/unpacking
ipython[notebook] from
https://pypi.python.org/packages/2.7/i/ipython/ipython-2.3.1-py27-none-any.whl#md5=14b9c7c5280ded28777559c434947573
Downloading ipython-2.3.1-py27-none-any.whl (2.8MB): 2.8MB downloaded
…

OSError: [Errno 13] Permission denied:
'/usr/lib/python2.7/dist-packages/ipython-1.2.1.egg-info'

Storing debug log for failure in /home/user/.pip/pip.log

conda update setuptools

user:~$ conda update setuptools

Fetching package metadata: .. …
Proceed ([y]/n)? y

Fetching packages … Error: Could not open
u'/home/user/anaconda/pkgs/setuptools-7.0-py27_0.tar.bz2.part' for
writing (seek).0 B/s user:~$Fetching package metadata: .. …

Possible Hint:

This could be related to other issue accessing these packages from python script:

https://stackoverflow.com/questions/27413162/some-python-modules-available-only-with-sudo-others-only-without

Any ideas?

Best Answer

Have you tried to reinstall it? It worked directly for me on one machine and on a VM I had to do a link from ~/anaconda/bin/conda to /usr/local/bin to get it to work. You can do a hardlink with sudo ln ~/anaconda/bin/conda /usr/local/bin/

Related Solutions

Ubuntu – Permission denied when trying to run pip install ipython

You can have both the default version of IPython from the default Ubuntu repositories and IPython 2.3.1 installed at the same time.

Install IPython from the default Ubuntu repositories using the following command:

 sudo apt-get install ipython ipython3 # ipython is available in 18.04 and earlier

Install IPython 2.3.1 in a virtual environment. virtualenv allows you to create a sandboxed and isolated environment where Python packages can be installed without interfering with other packages on the same machine. Install Python virtual environment creator (virtualenv):
```
 sudo apt-get install python-virtualenv virtualenv 
```
Set up a virtual environment for Python (Information about virtualenv basic usage), activate your Python virtual environment from the terminal, and then install the current version of IPython using pip install.
```
 pip install --user ipython 
```

This is working on my Ubuntu 14.04 using IPython from the default Ubuntu repositories and IPython 2.3.0 installed inside a Python virtual environment (virtualenv).

Ubuntu – the difference between pip and conda

conda is a package management tool for installing scientific and analytical computing packages, which may be written in Python or other programming languages. conda also creates a virtual environment, like python-virtualenv does. conda is the package manager of Anaconda. Anaconda is a free Python distribution provided by Continuum Analytics, which includes over 195 of the most popular Python packages for science, math, engineering and data analysis, almost all of which are also available in the default Ubuntu repositories. Anaconda is known for making a big mess out of the default paths for many Python modules in Linux. For these reasons I don't recommend Anaconda for new Linux users.

pip is a general purpose Python package installer. In addition, python-pip and python3-pip are in the default Ubuntu repositories. In most cases you would choose pip instead of conda if you want to install a Python package management application. To create a Python virtual environment without installing conda, you can install python-virtualenv from the Ubuntu Software Center.

pip and conda use different packaging formats so they do not operate interchangeably, but you can use both tools side by side.

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