I’ve been able to reproduce the issue on cPanel accounts that are low on storage space.
ex:
- vhost has 2gb
- 1.8gb used
- toolkit update takes 250mb
- account isn’t able to function due to being out of storage space
The only solution I’ve found is manually deleting these folders.
Another...
I'm on a cPanel server, but was finding the same problem on one of my client's installs. I'm not 100% certain that this is it yet, and I also couldn't tell you how this happened... but, I just noticed that the /public_html folder had 755 permissions assigned to it. That's the only difference...