Hello moocan
The warning is almost certainly there for a good reason.
Linux file systems and disk usage are worth understanding (at least a little).
- The number GB of disk space you have free is not important.
- What is important is the percentage (%) of the total disk space that is free.
I presume you are using ext4 as your filesystem (please correct me if you are using another file system). In this case you need to know that:
- Under some circumstances, a filesystem’s performance can begin to degrade when a filesystem is more than 80%-90% full. It is a good idea to take any corrective action before your filesystems reach this level, rather than waiting until they are completely full.
- The operating system generally holds back some amount of space in each filesystem, allocatable only by the superuser (usually 10%, although Linux uses 5% by default, so-called "reserved blocks"). A filesystem may appear to use over 100% of the available space when it has tapped into this reserve.
To find out the percentage of disk space you have remaining you may either use GUI tools or command-line (in a terminal) tools.
GUI (graphical user interface)
- Open the program "Mate System Monitor".
- Go to the tab "File Systems". Here you will see the information you need.
Command-line
The df -k command produces a report that describes all the filesystems, their total capacities, and the amount of free space available on each one (reporting sizes in KB).
The three directories/partitions of your disk that are important regarding the amount of disk-space used are:
/ (the root directory)
/boot (the boot directory)
/home (your "home" directory, where all your files are saved)
Note that the "snap"-packaged software installed on your computer behaves in a special way and will show up as 100% of that specific filesystem (e.g. /snap/software-boutique). You can ignore the "snap" messages.
References:
- Essential System Administration, 3rd Edition, Author Æleen Frisch, Publisher O’Reilly Media, 2009, ISBN:9780596103286
- How Linux Works: What Every Superuser Should Know, Author Brian Ward Publisher No Starch Press, 2014, ISBN:9781593276454
Does this help? 
