Right, then they should have been rebuilt after the transaction. What's in /usr/src/?

In /usr/src/ I have:
- vboxhost-5.0.14_OSE (community-testing/virtualbox-host-dkms)
- phc-intel-0.3.2 (https://aur.archlinux.org/packages/phc-intel)
- compal-laptop-0.2.10 (http://eko.one.pl/?p=compal-laptop merged with intree module by myself)

Yes, it should rebuild all DKMS added modules after the transaction, but the 70-dkms-remove.hook *removes* all modules from DKMS before the transaction. So afterwards there are no modules to install anymore because they were removed in the first place. I guess the modules should only be *uninstalled* before a kernel update so that they are still registered in DKMS.

Yes, 70-dkmd-remove removes the modules, then 70-dkms-install rebuilds them post-transaction. Seems to work fine for me.

Then how does this happen?

[root@zepto ~]# pacman -Q dkms virtualbox-host-dkms phc-intel
dkms 2.2.0.3+git151023-5
virtualbox-host-dkms 5.0.14-3
phc-intel 0.3.2.12.19-2
[root@zepto ~]# dkms status
compal-laptop, 0.2.10, 4.4.2-1-ARCH, x86_64: installed
phc-intel, 0.3.2, 4.4.2-1-ARCH, x86_64: installed
vboxhost, 5.0.14_OSE, 4.4.2-1-ARCH, x86_64: installed
[root@zepto ~]# ls -l /var/lib/dkms/
total 4
drwxr-xr-x 1 root root 64 Feb 28 13:44 compal-laptop
-rw-r--r-- 1 root root 6 Feb 21 13:06 dkms_dbversion
drwxr-xr-x 1 root root 62 Feb 28 13:43 phc-intel
drwxr-xr-x 1 root root 72 Feb 28 13:45 vboxhost
[root@zepto ~]# find /usr/lib/modules/ -name vboxdrv.ko -o -name phc-intel.ko -o -name compal-laptop.ko
/usr/lib/modules/4.4.2-1-ARCH/kernel/misc/vboxdrv.ko
/usr/lib/modules/4.4.2-1-ARCH/extra/phc-intel.ko
/usr/lib/modules/4.4.2-1-ARCH/updates/compal-laptop.ko
[root@zepto ~]# pacman -Su
:: Starting full system upgrade...
resolving dependencies...
looking for conflicting packages...

Package (2) Old Version New Version Net Change

testing/linux 4.4.2-1 4.4.3-1 -0.12 MiB
testing/linux-headers 4.4.2-1 4.4.3-1 0.00 MiB

Total Installed Size: 108.02 MiB
Net Upgrade Size: -0.12 MiB

:: Proceed with installation? [Y/n]
(2/2) checking keys in keyring [######################] 100%
(2/2) checking package integrity [######################] 100%
(2/2) loading package files [######################] 100%
(2/2) checking for file conflicts [######################] 100%
(2/2) checking available disk space [######################] 100%
:: Running pre-transaction hooks...
(1/1) Remove DKMS modules
:: Processing package changes...
(1/2) upgrading linux [######################] 100%
>>> Updating module dependencies. Please wait ...
>>> Generating initial ramdisk, using mkinitcpio. Please wait...
==> Building image from preset: /etc/mkinitcpio.d/linux.preset: 'default'
-> -k /boot/vmlinuz-linux -c /etc/mkinitcpio.conf -g /boot/initramfs-linux.img
==> Starting build: 4.4.3-1-ARCH
-> Running build hook: [systemd]
==> Generating module dependencies
==> Creating lz4-compressed initcpio image: /boot/initramfs-linux.img
==> Image generation successful
(2/2) upgrading linux-headers [######################] 100%
:: Running post-transaction hooks...
(1/1) Install DKMS modules
[root@zepto ~]# dkms status
[root@zepto ~]# ls -l /var/lib/dkms/
total 4
-rw-r--r-- 1 root root 6 Feb 21 13:06 dkms_dbversion
[root@zepto ~]# find /usr/lib/modules/ -name vboxdrv.ko -o -name phc-intel.ko -o -name compal-laptop.ko
[root@zepto ~]#

This appears to be an issue with /usr/lib/dkms/alpm-hook; when headers are removed/installed it checks /var/lib/dkms/*/*/source for which modules it needs to remove/install.

/var/lib/dkms is populated when the removal version of the hook runs, but it's empty when it tries to reinstall the modules so we end up with no modules.

You can easily reproduce the issue by removing and then reinstalling linux-headers.

ok, this is happening when you have only one kernel installed. Others kernels prevent un-registering of modules in /var/lib/dkms/ and make things apparently works.

Should be fixed in dkms-2.2.0.3+git151023-6. Could you confirm all is ok?

It now works for me with one kernel and virtualbox-host-dkms as the only DMKS modules on the system.