This happened because of the /var/run -> /run transition in progress. /var/run used to be a directory and is now a symlink.
Partman creates /target/var/lock and /target/var/run as soon as the disks are formatted. When the file copy routine gets around to these directories, it assumes they were files or symlinks and tries to unlink them, but fails because they're directories.
I've committed a fix to trunk to rmdir the directories when this happens, but another way to fix it would be to remove the code in partman from creating /target/var/lock and /target/var/run in the first place.
This happened because of the /var/run -> /run transition in progress. /var/run used to be a directory and is now a symlink.
Partman creates /target/var/lock and /target/var/run as soon as the disks are formatted. When the file copy routine gets around to these directories, it assumes they were files or symlinks and tries to unlink them, but fails because they're directories.
I've committed a fix to trunk to rmdir the directories when this happens, but another way to fix it would be to remove the code in partman from creating /target/var/lock and /target/var/run in the first place.