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How can I completely uninstall/remove cygwin? I don't think it is as simple as deleting C:\cygwin. Maybe alter registry?

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The developers give fairly detailed instructions on how to remove the software:

How do I uninstall all of Cygwin?

Setup has no automatic uninstall facility. The recommended method to remove all of Cygwin is as follows:

  1. If you have any Cygwin services running, remove by repeating the instructions in http://cygwin.com/faq/faq.html#faq.setup.uninstall-service for all services that you installed. Common services that might have been installed are sshd, cron, cygserver, inetd, apache, postgresql, and so on.

  2. Stop the X11 server if it is running, and terminate any Cygwin programs that might be running in the background. Exit the command prompt and ensure that no Cygwin processes remain. Note: If you want to save your mount points for a later reinstall, first save the output of mount -m as described at http://cygwin.com/cygwin-ug-net/using-utils.html#mount.

  3. Delete the Cygwin root folder and all subfolders. If you get an error that an object is in use, then ensure that you've stopped all services and closed all Cygwin programs. If you get a 'Permission Denied' error then you will need to modify the permissions and/or ownership of the files or folders that are causing the error. For example, sometimes files used by system services end up owned by the SYSTEM account and not writable by regular users.

    The quickest way to delete the entire tree if you run into this problem is to change the ownership of all files and folders to your account. To do this in Windows Explorer, right click on the root Cygwin folder, choose Properties, then the Security tab. If you are using Windows XP Home or Simple File Sharing, you will need to boot into Safe Mode to access the Security tab. Select Advanced, then go to the Owner tab and make sure your account is listed as the owner. Select the 'Replace owner on subcontainers and objects' checkbox and press Ok. After Explorer applies the changes you should be able to delete the entire tree in one operation. Note that you can also achieve this in Cygwin by typing chown -R user / or by using other tools such as CACLS.EXE.

  4. Delete the Cygwin shortcuts on the Desktop and Start Menu, and anything left by setup.exe in the download directory. However, if you plan to reinstall Cygwin it's a good idea to keep your setup.exe download directory since you can reinstall the packages left in its cache without redownloading them.

  5. If you added Cygwin to your system path, you should remove it unless you plan to reinstall Cygwin to the same location. Similarly, if you set your CYGWIN environment variable system-wide and don't plan to reinstall, you should remove it.

  6. Finally, if you want to be thorough you can delete the registry tree Software\Cygwin under HKEY_LOCAL_MACHINE and/or HKEY_CURRENT_USER. However, if you followed the directions above you will have already removed everything important. Typically only the installation directory has been stored in the registry at all.

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I originally found these instructions at the source that John T linked to and tried them on Windows 7. They didn't work for me. Has anyone gotten them to work on Windows 7? I wasn't able to delete the C:\Cygwin directory, even after booting into safe mode with a command prompt. –  Ben McCormack Aug 6 '11 at 13:39
    
Thanks, this worked for me. Every couple of years I get to a point where I think cygwin might be useful and that it can't be as useless as I remember it (today I wanted to do a bit of Lisp hacking). Then after installing it and wasting about two hours because nothing works and there is no documentation I get this horrible feeling of deja vu and remember that it is virus-like in its difficulty to remove from your machine. Ubuntu under VMWARE seems like a much better option. –  user81238 Jan 21 '12 at 11:03
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I had to do more than just change the owner in order to delete, I also had to change the permissions to be more permissive (basically let everyone have full access). This is the permissions tab next to the owner tab. Cygwin: not even once. –  mrmagooey Oct 2 '13 at 3:33
    
The command you indicate (chown -R user /) is NOT the equivalent of changing ownership of the Cygwin folder. It will modify the ownership of ALL files on the filesystem. –  piwi Feb 7 at 9:17
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C:\>takeown /r /d y /f cygwin

C:\>icacls cygwin /t /grant Everyone:F

C:\cygwin\bin>.\cygrunsrv.exe -E sshd

C:\cygwin\bin>.\cygrunsrv.exe -R sshd

Delete the folder c:\cygwin and all its sub-folders. it works for me

Be aware that windows commands like takeown are depending on the locale, i.e. option /d y works only in english systems. In german system one needs to use /d j to work (without hint in the english help, *facepalm* microsoft)

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Yes, install Linux on USB. I use Fedora 15.

After following the instructions above, boot Linux up and delete the folder.

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Why would this work better than just deleting it from within windows? –  Simon Sheehan Jan 14 '12 at 18:08
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I had trouble in deleting Cygwin folder and I have traversed the entire directory structure and deleted each sub-folder. This is really painful, but no other choice.

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