From the log, the following command
apt-get-noninteractive --yes --no-install-recommends install libc6-dev bsdmainutils gcc fasttrack-archive-keyring
For unknown reason results in:
The following packages will be REMOVED:
qubes-core-agent qubes-core-agent-networking qubes-gui-agent
qubes-input-proxy-sender qubes-mgmt-salt-vm-connector qubes-usb-proxy
qubes-vm-dependencies qubes-whonix qubes-whonix-shared-packages-recommended
qubes-whonix-workstation salt-common salt-ssh systemcheck whonix-firewall
The further debug, you’d need to either manually run the commands the build script would be running (look at
/usr/sbin/release-upgrade) would be to edit the script and append
i.e. make that
apt-get-noninteractive --yes --no-install-recommends install libc6-dev bsdmainutils gcc fasttrack-archive-keyring qubes-whonix-workstation
Might also be a good idea to remove the “–yes”. I.e.
apt-get-noninteractive --no-install-recommends install libc6-dev bsdmainutils gcc fasttrack-archive-keyring qubes-whonix-workstation
By removing the “–yes” you could abort before any above mentioned packages are installed. Removing the “–yes” everywhere in the script might be a good idea as well.
You could replace the experiment
The abstract task: you need to find out which package dependency of a custom installed package is created a conflict so APT decides to remove
qubes-vm-dependencies instead of the custom installed package.
Not too easy to debug in Qubes. Time consuming. Since you cannot snapshot a VM and easily restore at least not as far as I know.