Muon package manager gives error when trying to update

I run Lubuntu inside of VMware Fusion on a Mac. (I think this error is unrelated to the VM.)

When I try to update the system using Muon, it throws this error:
“An error occurred while applying changes:”
That’s all it says. Here’s some extra info:

lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 20.04.3 LTS
Release:        20.04
Codename:       focal

lshw and syslog are too big for this forum, but I can supply them if needed.

lscpu

Summary
Architecture:                    x86_64
CPU op-mode(s):                  32-bit, 64-bit
Byte Order:                      Little Endian
Address sizes:                   45 bits physical, 48 bits virtual
CPU(s):                          2
On-line CPU(s) list:             0,1
Thread(s) per core:              1
Core(s) per socket:              1
Socket(s):                       2
NUMA node(s):                    1
Vendor ID:                       GenuineIntel
CPU family:                      6
Model:                           158
Model name:                      Intel(R) Core(TM) i9-9900K CPU @ 3.60GHz
Stepping:                        13
CPU MHz:                         3600.000
BogoMIPS:                        7200.00
Hypervisor vendor:               VMware
Virtualization type:             full
L1d cache:                       64 KiB
L1i cache:                       64 KiB
L2 cache:                        512 KiB
L3 cache:                        32 MiB
NUMA node0 CPU(s):               0,1
Vulnerability Itlb multihit:     KVM: Vulnerable
Vulnerability L1tf:              Not affected
Vulnerability Mds:               Not affected
Vulnerability Meltdown:          Not affected
Vulnerability Spec store bypass: Mitigation; Speculative Store Bypass disabled via prctl and seccomp
Vulnerability Spectre v1:        Mitigation; usercopy/swapgs barriers and __user pointer sanitizatio
                                 n
Vulnerability Spectre v2:        Mitigation; Enhanced IBRS, IBPB conditional, RSB filling
Vulnerability Srbds:             Mitigation; TSX disabled
Vulnerability Tsx async abort:   Not affected
Flags:                           fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat p
                                 se36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm cons
                                 tant_tsc arch_perfmon nopl xtopology tsc_reliable nonstop_tsc cpuid
                                  pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcn
                                 t tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm a
                                 bm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ib
                                 rs_enhanced fsgsbase tsc_adjust bmi1 avx2 smep bmi2 invpcid rdseed 
                                 adx smap clflushopt xsaveopt xsavec xgetbv1 xsaves arat md_clear fl
                                 ush_l1d arch_capabilities

lsusb

Summary
Bus 001 Device 002: ID 0e0f:000b VMware, Inc. VMware Virtual USB Video Device                       
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub                                      
Bus 002 Device 004: ID 0e0f:0008 VMware, Inc. VMware Virtual USB Mouse                              
Bus 002 Device 003: ID 0e0f:0002 VMware, Inc. Virtual USB Hub                                       
Bus 002 Device 002: ID 0e0f:0003 VMware, Inc. Virtual Mouse                                         
Bus 002 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub

lscpi

Summary
00:00.0 Host bridge: Intel Corporation 440BX/ZX/DX - 82443BX/ZX/DX Host bridge (rev 01)
00:01.0 PCI bridge: Intel Corporation 440BX/ZX/DX - 82443BX/ZX/DX AGP bridge (rev 01)
00:07.0 ISA bridge: Intel Corporation 82371AB/EB/MB PIIX4 ISA (rev 08)
00:07.1 IDE interface: Intel Corporation 82371AB/EB/MB PIIX4 IDE (rev 01)
00:07.3 Bridge: Intel Corporation 82371AB/EB/MB PIIX4 ACPI (rev 08)
00:07.7 System peripheral: VMware Virtual Machine Communication Interface (rev 10)
00:0f.0 VGA compatible controller: VMware SVGA II Adapter
00:10.0 SCSI storage controller: Broadcom / LSI 53c1030 PCI-X Fusion-MPT Dual Ultra320 SCSI (rev 01)
00:11.0 PCI bridge: VMware PCI bridge (rev 02)
00:15.0 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.1 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.2 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.3 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.4 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.5 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.6 PCI bridge: VMware PCI Express Root Port (rev 01)
00:15.7 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.0 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.1 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.2 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.3 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.4 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.5 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.6 PCI bridge: VMware PCI Express Root Port (rev 01)
00:16.7 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.0 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.1 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.2 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.3 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.4 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.5 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.6 PCI bridge: VMware PCI Express Root Port (rev 01)
00:17.7 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.0 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.1 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.2 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.3 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.4 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.5 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.6 PCI bridge: VMware PCI Express Root Port (rev 01)
00:18.7 PCI bridge: VMware PCI Express Root Port (rev 01)
02:00.0 USB controller: VMware USB1.1 UHCI Controller
02:01.0 Ethernet controller: Intel Corporation 82545EM Gigabit Ethernet Controller (Copper) (rev 01)
02:02.0 Multimedia audio controller: Ensoniq ES1371/ES1373 / Creative Labs CT2518 (rev 02)
02:03.0 USB controller: VMware USB2 EHCI Controller
02:05.0 SATA controller: VMware SATA AHCI controller

Thank you for any help or insight.

I would jump to terminal (Ctrl+Alt+T) and run the commands from there, as the GUI alternative is to look at logs (start with apt or package logs), where as when executed at a terminal the output is directly in front of you.

sudo apt update

to ensure you’ve not added or made any corruption to your sources (ie. no warnings or errors appear)

and finally

sudo apt full-upgrade

to apply all upgrades to your system. A fully-upgraded focal (20.04) system will report itself as 20.04.4 (see https://lubuntu.me/focal-4-released/ or Ubuntu Fridge | Ubuntu 20.04.4 LTS Released) but installed systems upgraded to it in the week(s) before that date, with the 20.04.3 being changed to 20.04.4 about a week before (ie. after all upgrades had been applied).

2 Likes

sudo apt update
ran without errors.

sudo apt full-upgrade
gave me the following error:
E: dpkg was interrupted, you must manually run 'sudo dpkg --configure -a' to correct the problem.

I assume that is my next step?

1 Like

Yep.

The package command messages usually have great advice when problems are encountered. I’d use

sudo dpkg --configure -a

as my next command (99% of the time anyway) and again read the output (esp. if errors) to see if other suggestions are made.

FYI: in the ~1% where I think I know better, it’s usually as I realize I’d missed a command (that maybe led to the error in the first place), and thus may execute the missed command first, then execute what it suggests later :slight_smile:

2 Likes

sudo dpkg --configure -a
returned this message:

dpkg: error: parsing file '/var/lib/dpkg/updates/0000' near line 0:                                 
 field name 'ELF' must be followed by colon

I’m guessing the file got corrupted somehow.

There are a number of commands that could fix this issue, sorry it occurs so infrequently I’m not sure which is best, but most of what I’d try can be found in a link I’ll provide

Note: for the accepted & most up-voted answer; read it in relation to the actual question the user answers; ie. your error message doesn’t have 0045 so you won’t type that, but you can adjust that to match your error message if you understand me

1 Like

Fixed! Thank you!

For the benefit of the residents of the future, this is what I did:

I went to the directory of the offending file.
cd /var/lib/dpkg/updates

0000 was the offending file. I tried deleting it, but then 0001 was flagged as offending. So I just nuked everything in that directory (it was only four files).
sudo rm -rf *

Then I ran the command that the system originally suggested.
sudo dpkg --configure -a

It was happy with that, so I ran:
sudo apt update

That was also happy, so I ran:
sudo apt full-upgrade

That also ran happy. I then opened Muon and checked its opinion. It said my system was up to date.

3 Likes

Thank you for sharing what fixed it for you :slight_smile:

2 Likes

Ummm… I think I spoke too soon. I decided to reboot the system to prove that everything worked properly. It didn’t. Instead of fully booting, it stopped during its initializing. I have a lovely black screen that says:

[  1.829342] piix4_smbus 0000:0007.3: SMBus Host Controller not enabled!
[  2.431928] sd 32:0:0:0: [sda] Assuming drive3 cache: write through

BusyBox v1.30.1 (Ubuntu 1:1.30.1-4ubuntu6.4) built-in shell (ash)
Enter 'help' for a list of built-in commands.

(initramfs)_

If I see initramfs at boot time, I tend to stop trying to boot & just SysRqREISUB or safely reboot the machine and boot live media (eg. installation media) & perform file-system checks on my partitions (ie. fsck). I usually expect to see errors being detected, and fixes made in the messages, where by I can just reboot normally.

Notes: Lubuntu 21.10 & up don’t allow most SysRq commands, but it’ll work on your 20.04 system. I also don’t know your file-systems, and whilst fsck or file-system check will work on most, there are some file-systems where alternate commands are better (eg. xfs_check if using XFS, whilst fsck won’t damage a XFS file-system, it doesn’t do anything good either… so use the appropriate command for your file-system)

Like last time, I’ll provide a number of alternatives via an askubuntu link as what I do assumes you have installation media handy (which I always do).

3 Likes

I’m going to mark this as solved. The link you gave looks like it will work. The problem is that VMware is now locking up and crashing the Mac. I don’t know what its problem is. I’m going to nuke the application and the VMs then reinstall.

1 Like

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