I’m documenting this mainly for myself, but if you’re ending up here based on a Google query, I hope it helps!
I tried to upgrade our Nexenta storage system (currently running 4.0.3FP3). After apt-get downloaded packages, I received this error:
Download complete and in download only mode
Upgrade is in progress. Please DO NOT interrupt...
Creating Upgrade Checkpoint...
Feb 03 19:13:23 EXCEPTION: FormatError: Failed to parse menu.lst: section content not complete
Uncaught exception from user code:
com.nexenta.nmu.FormatError: Failed to parse menu.lst: section content not complete
at /usr/perl5/5.12/lib/NZA/NMUUtil.pm line 731
NZA::NMUUtil::_mark_rootfs('syspool/rootfs-nmu-008', 0, '') called at /usr/perl5/5.12/lib/NZA/NMUUtil.pm line 817
NZA::NMUUtil::clone_rootfs() called at /usr/bin/nmu line 526
Nexenta tech support found that the issue was empty BOOTADM blocks in /syspool/boot/grub/menu.lst:
#---------- ADDED BY BOOTADM - DO NOT EDIT ----------
#---------------------END BOOTADM--------------------
The fix is to remove those and run bootadm update-archive -v.
If I understood correctly, the cause may have been using beadm destroy in the shell instead of setup appliance checkpoint ... in nmc.