Discover updates the system but when it finishes the system tray icon does not disappear, and if I reopen discover it cannot update, the preferences don't show the repositories list. If I run the sudo apt update command it tells me that /var/lib/apt/lists/lock could not be blocked.
This must be a different issue, I've just tested what you say and it worked. Something interesting would be to see why /var/lib/apt/lists/lock, maybe PackageKit crashed?
If I kill the PackageKit process, how do I know what error PackageKit makes?
Indeed, if I kill the PackageKit process it works again, how do I know what error PackageKit makes?
There's some tools you can use. You could attach to PackageKit with gdb and try to get a backtrace. If you are not familiar with gdb say so and I'll tell you the required commands. Something else to test would be to run the update with the "pkmon" tool and see what's the status and if there's something unexpected going on. You can paste here the output of pkmon up until PackageKit gets stuck and I'll see how to proceed. Thanks!
I run the update with "pkmon" tool and this is the status: It just freezes there at 99%. /1852_ddaaaccb status commit 08:55:09 PackageKit emit transaction-list-changed 08:55:09 PackageKit last: /1852_ddaaaccb 08:55:09 PackageKit last: /1853_dceedded 08:55:09 PackageKit current: /1852_ddaaaccb 08:55:09 PackageKit current: /1853_dceedded /1852_ddaaaccb allow_cancel 1 /1852_ddaaaccb status finished 08:55:09 PackageKit emit transaction-list-changed 08:55:09 PackageKit last: /1852_ddaaaccb 08:55:09 PackageKit last: /1853_dceedded 08:55:09 PackageKit current: /1853_dceedded 08:55:09 PackageKit emit removed: /1852_ddaaaccb 08:55:09 PackageKit removed: /1852_ddaaaccb Transactions: 1 /1853_dceedded /1852_ddaaaccb exit code: success Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] ' /1853_dceedded status setup Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] ' /1853_dceedded status loading-cache /1853_dceedded percentage 0 /1853_dceedded percentage 100 /1853_dceedded percentage 0 08:55:09 PackageKit emit updates-changed updates-changed 08:55:09 PackageKit emit transaction-list-changed 08:55:09 PackageKit last: /1853_dceedded 08:55:09 PackageKit current: /1853_dceedded 08:55:09 PackageKit current: /1854_acbeadcc 08:55:09 PackageKit emit added: /1854_acbeadcc 08:55:09 PackageKit added: /1854_acbeadcc Transactions: 1 /1853_dceedded 2 /1854_acbeadcc Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] 2 get-updates /1854_acbeadcc state[ready] exclusive[1] background[0] ' /1854_acbeadcc allow_cancel 1 /1854_acbeadcc percentage -1 08:55:09 PackageKit role now get-updates /1854_acbeadcc role get-updates /1854_acbeadcc status wait /1853_dceedded percentage 50 /1853_dceedded percentage 100 /1853_dceedded status refresh-cache /1853_dceedded status download /1853_dceedded percentage -1 /1853_dceedded percentage 0 08:55:10 PackageKit emit transaction-list-changed 08:55:10 PackageKit last: /1853_dceedded 08:55:10 PackageKit last: /1854_acbeadcc 08:55:10 PackageKit current: /1853_dceedded 08:55:10 PackageKit current: /1854_acbeadcc 08:55:10 PackageKit current: /1856_bbbbbbcb 08:55:10 PackageKit emit added: /1856_bbbbbbcb 08:55:10 PackageKit added: /1856_bbbbbbcb Transactions: 1 /1853_dceedded 2 /1854_acbeadcc 3 /1856_bbbbbbcb 08:55:10 PackageKit emit transaction-list-changed 08:55:10 PackageKit last: /1853_dceedded 08:55:10 PackageKit last: /1854_acbeadcc 08:55:10 PackageKit last: /1856_bbbbbbcb 08:55:10 PackageKit current: /1853_dceedded 08:55:10 PackageKit current: /1854_acbeadcc 08:55:10 PackageKit current: /1855_dacacceb 08:55:10 PackageKit current: /1856_bbbbbbcb 08:55:10 PackageKit emit added: /1855_dacacceb 08:55:10 PackageKit added: /1855_dacacceb Transactions: 1 /1853_dceedded 2 /1854_acbeadcc 3 /1856_bbbbbbcb 4 /1855_dacacceb Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] 2 get-updates /1854_acbeadcc state[ready] exclusive[1] background[0] 3 refresh-cache /1855_dacacceb state[ready] exclusive[1] background[0] 4 get-updates /1856_bbbbbbcb state[ready] exclusive[1] background[0] ' Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] 2 get-updates /1854_acbeadcc state[ready] exclusive[1] background[0] 3 refresh-cache /1855_dacacceb state[ready] exclusive[1] background[0] 4 get-updates /1856_bbbbbbcb state[ready] exclusive[1] background[0] ' /1856_bbbbbbcb allow_cancel 1 /1856_bbbbbbcb percentage -1 08:55:10 PackageKit role now get-updates /1856_bbbbbbcb role get-updates /1856_bbbbbbcb status wait /1855_dacacceb allow_cancel 1 /1855_dacacceb percentage -1 08:55:10 PackageKit role now refresh-cache /1855_dacacceb role refresh-cache /1855_dacacceb status wait 08:55:10 PackageKit emit updates-changed updates-changed 08:55:10 PackageKit emit transaction-list-changed 08:55:10 PackageKit last: /1853_dceedded 08:55:10 PackageKit last: /1854_acbeadcc 08:55:10 PackageKit last: /1856_bbbbbbcb 08:55:10 PackageKit last: /1855_dacacceb 08:55:10 PackageKit current: /1853_dceedded 08:55:10 PackageKit current: /1854_acbeadcc 08:55:10 PackageKit current: /1855_dacacceb 08:55:10 PackageKit current: /1856_bbbbbbcb 08:55:10 PackageKit current: /1857_dbceaacc 08:55:10 PackageKit emit added: /1857_dbceaacc 08:55:10 PackageKit added: /1857_dbceaacc Transactions: 1 /1853_dceedded 2 /1854_acbeadcc 3 /1856_bbbbbbcb 4 /1855_dacacceb 5 /1857_dbceaacc 08:55:10 PackageKit emit transaction-list-changed 08:55:10 PackageKit last: /1853_dceedded 08:55:10 PackageKit last: /1854_acbeadcc 08:55:10 PackageKit last: /1856_bbbbbbcb 08:55:10 PackageKit last: /1855_dacacceb 08:55:10 PackageKit last: /1857_dbceaacc 08:55:10 PackageKit current: /1853_dceedded 08:55:10 PackageKit current: /1854_acbeadcc 08:55:10 PackageKit current: /1855_dacacceb 08:55:10 PackageKit current: /1856_bbbbbbcb 08:55:10 PackageKit current: /1857_dbceaacc 08:55:10 PackageKit current: /1858_dccddeae 08:55:10 PackageKit emit added: /1858_dccddeae 08:55:10 PackageKit added: /1858_dccddeae Transactions: 1 /1853_dceedded 2 /1854_acbeadcc 3 /1856_bbbbbbcb 4 /1855_dacacceb 5 /1857_dbceaacc 6 /1858_dccddeae /1857_dbceaacc allow_cancel 1 /1857_dbceaacc percentage -1 08:55:10 PackageKit role now get-updates /1857_dbceaacc role get-updates /1857_dbceaacc status wait Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] 2 get-updates /1854_acbeadcc state[ready] exclusive[1] background[0] 3 refresh-cache /1855_dacacceb state[ready] exclusive[1] background[0] 4 get-updates /1856_bbbbbbcb state[ready] exclusive[1] background[0] 5 get-updates /1857_dbceaacc state[ready] exclusive[1] background[0] 6 get-updates /1858_dccddeae state[ready] exclusive[1] background[0] ' Daemon state: 'State: 0 update-packages /1852_ddaaaccb state[finished] exclusive[1] background[0] 1 refresh-cache /1853_dceedded state[running] exclusive[1] background[0] 2 get-updates /1854_acbeadcc state[ready] exclusive[1] background[0] 3 refresh-cache /1855_dacacceb state[ready] exclusive[1] background[0] 4 get-updates /1856_bbbbbbcb state[ready] exclusive[1] background[0] 5 get-updates /1857_dbceaacc state[ready] exclusive[1] background[0] 6 get-updates /1858_dccddeae state[ready] exclusive[1] background[0] ' /1858_dccddeae allow_cancel 1 /1858_dccddeae percentage -1 08:55:10 PackageKit role now get-updates /1858_dccddeae role get-updates /1858_dccddeae status wait /1853_dceedded percentage 29 /1853_dceedded percentage 99 /1853_dceedded percentage -1 /1853_dceedded percentage 95 /1853_dceedded percentage 99 /1853_dceedded percentage -1 /1853_dceedded percentage 26 /1853_dceedded percentage 27 /1853_dceedded percentage 85 /1853_dceedded percentage 99
Seems like a PackageKit issue. FWIW I've never seen or managed to reproduce the issue myself.
PackageKit just got a bunch of packages for Debian*. Make sure you use the stable version of the package.