I do not believe this is a duplicate;  It is more likely a *packaging* issue.  The question remains for this bug, why does it only appear in the focal kernels;  but not Eoan or older?

And if someone could confirm whether or not the linux-generic or linux-modules generate this file and when (unpack, deb postinst, kernel install hook?)

Another reason why this isn't a duplicate as the error message is unrelated to the contents of the initrd, but rather when depmod -a -S is called (postins of linux-modules package).

On Eoan we can remove the file in question and regenerate the file with:

depmod -a -F /boot/System.map-5.3.0-40-generic;  

this command does not produce the error message on any release expect Focal.


# eoan

root@rharper-e1:~# cat /etc/issue
Ubuntu 19.10 \n \l

root@rharper-e1:~# dpkg --list | grep linux-
ii  linux-base                           4.5ubuntu2                             all          Linux image base package
ii  linux-firmware                       1.183.4                                all          Firmware for Linux kernel drivers
ii  linux-generic                        5.3.0.40.34                            amd64        Complete Generic Linux kernel and headers
ii  linux-headers-5.3.0-40               5.3.0-40.32                            all          Header files related to Linux kernel version 5.3.0
ii  linux-headers-5.3.0-40-generic       5.3.0-40.32                            amd64        Linux kernel headers for version 5.3.0 on 64 bit x86 SMP
ii  linux-headers-generic                5.3.0.40.34                            amd64        Generic Linux kernel headers
ii  linux-image-5.3.0-40-generic         5.3.0-40.32                            amd64        Signed kernel image generic
ii  linux-image-generic                  5.3.0.40.34                            amd64        Generic Linux kernel image
ii  linux-modules-5.3.0-40-generic       5.3.0-40.32                            amd64        Linux kernel extra modules for version 5.3.0 on 64 bit x86 SMP
ii  linux-modules-extra-5.3.0-40-generic 5.3.0-40.32                            amd64        Linux kernel extra modules for version 5.3.0 on 64 bit x86 SMP

root@rharper-e1:~# rm /lib/modules/5.3.0-40-generic/modules.builtin.bin 
root@rharper-e1:~# depmod -a -F /boot/System.map-5.3.0-40-generic  5.3.0-40-generic
root@rharper-e1:~# ls -al /lib/modules/5.3.0-40-generic/modules.builtin.bin 
-rw-r--r-- 1 root root 9943 Mar  2 15:03 /lib/modules/5.3.0-40-generic/modules.builtin.bin


# On focal this errors:
root@rharper-f1:~# cat /etc/issue
Ubuntu Focal Fossa (development branch) \n \l

root@rharper-f1:~# dpkg --list | grep linux-
ii  linux-5.4-headers-5.4.0-14           5.4.0-14.17                       all          Header files related to Linux kernel version 5.4.0
ii  linux-base                           4.5ubuntu2                        all          Linux image base package
ii  linux-firmware                       1.186                             all          Firmware for Linux kernel drivers
ii  linux-generic                        5.4.0.14.17                       amd64        Complete Generic Linux kernel and headers
ii  linux-headers-5.4.0-14-generic       5.4.0-14.17                       amd64        Linux kernel headers for version 5.4.0 on 64 bit x86 SMP
ii  linux-headers-generic                5.4.0.14.17                       amd64        Generic Linux kernel headers
ii  linux-image-5.4.0-14-generic         5.4.0-14.17                       amd64        Signed kernel image generic
ii  linux-image-generic                  5.4.0.14.17                       amd64        Generic Linux kernel image
ii  linux-modules-5.4.0-14-generic       5.4.0-14.17                       amd64        Linux kernel extra modules for version 5.4.0 on 64 bit x86 SMP
ii  linux-modules-extra-5.4.0-14-generic 5.4.0-14.17                       amd64        Linux kernel extra modules for version 5.4.0 on 64 bit x86 SMP
root@rharper-f1:~# ls -al /lib/modules/5.4.0-14-generic/modules.builtin.bin 
-rw-r--r-- 1 root root 10257 Mar  2 15:01 /lib/modules/5.4.0-14-generic/modules.builtin.bin
root@rharper-f1:~# set -o vi
root@rharper-f1:~# rm /lib/modules/5.4.0-14-generic/modules.builtin.bin 
root@rharper-f1:~# depmod -a -F /boot/System.map-5.4.0-14-generic 5.4.0-14-generic
depmod: ERROR: ../libkmod/libkmod.c:515 lookup_builtin_file() could not open builtin file '/lib/modules/5.4.0-14-generic/modules.builtin.bin'
depmod: ERROR: ../libkmod/libkmod.c:515 lookup_builtin_file() could not open builtin file '/lib/modules/5.4.0-14-generic/modules.builtin.bin'
depmod: ERROR: ../libkmod/libkmod.c:515 lookup_builtin_file() could not open builtin file '/lib/modules/5.4.0-14-generic/modules.builtin.bin'
depmod: ERROR: ../libkmod/libkmod.c:515 lookup_builtin_file() could not open builtin file '/lib/modules/5.4.0-14-generic/modules.builtin.bin'