Options For Installing Scikit-learn
Solution 1:
First, you should definitely upgrade pip, as the current version is 6.1.1. Run
pip install --upgrade pip
to do that. I wouldn't necessarily trust what man pip has to say, as it may be for an ancient version of pip. Instead, use the docs here.
-U and --upgrade are the same thing. --user is separate.
You don't need to worry about the prefix thing, or distutils.cfg. You'd know if you have them, because it's something you'd have to set up manually. So, just try running
pip install scikit-learn -U --userafter you've upgraded pip, and hopefully everything will go smoothly.
If you're on a Linux or Unix system (like OS X), or you have the GNU command-line tools installed on Windows, and you want pip to upgrade all of your packages, this command should work in bash:
pip list | awk '{print $1}' | while read -r package; do sudo -H pip install -U "$package"; done
pip list prints out the name and version of each package installed (and, at least on my Ubuntu 14.10 system, that includes everything, system- or pip-installed), along with its version number in parentheses. awk '{print $1}' splits each line on whitespace, and returns the first field (the package name). The while loop reads each incoming line (the package name) and calls sudo -H pip install -U packagename, which will look to see if the package is up-to-date, and if not it will upgrade it. I'm assuming system packages like those installed by Ubuntu won't be upgraded, as they're not listed in PyPI, but I killed the command before I found out.
Solution 2:
One option is to install Anaconda, which will allow you to easily install scikit-learn
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