There is an easy way (The Hines' way) for updating/installing your Cygwin distribution and keeping neuron working:
Step 1. Close all applications
Step 2. Run Cygwin's setup.exe to update Cygwin
Step 3. Reboot
Step 4. Uninstall Neuron
Step 5. Install Neuron
The best test to see if it worked out fine is to try to run mknrndll to build a nrnmech.dll. Neuron (nrniv.exe) sometimes works when mknrndll doesn't.
If this failed and mknrndll doesn't work on your mod-files and complains about cygwin1.dll versions, either because you never came accross this good advice or you did not see the point and tried otherwise, there is the (DON'T TRY THIS AT HOME) unpolished solution (Raj's way).
!Warning: Editing the registry can have serious negative consequences for operation of your computer/operating system!
Step 0: Become Administrator
Step 1: Uninstall Cygwin
Step 2: Uninstall Neuron
Step 3: Delete Cygwin from the registry using regedit (in
HKEY_CURRENT_USER\Software\Cygnus Solutions and in
HKEY_LOCAL_MACHINE\Software\Cygnus Solutions)
Step 4: Install Cygwin
Step 5: Install Neuron.
!Warning: Editing the registry can have serious negative consequences for operation of your computer/operating system!