Pandaboard (Rev A2) ARM/OMAP4 upgrade to 12.10 from 12.04 fails

Tried to upgrade a 12.04 (Precise) Ubuntu-Server install running on an OMAP4 Pandaboard (rev A2) to 12.10 (Quantal) using:

do-release-upgrade -d

Upgrade appeared to proceed normally, but once the system had rebooted, I found a number of problems that were not present in the previous releases.

NOTE: This particular system was installed on a 8GB SDHC card 6 months ago using the following 12.04 omap4-armhf image:

http://cdimage.ubuntu.com/releases/12.04/release/ubuntu-12.04-preinstalled-server-armhf+omap4.img.gz

And that prior to upgrading the system was completely up-to-date (i.e. apt-get update ; apt-get dist-upgrade ; reboot).

NOTE2: I notice that in dmesg, the board is being detected as a OMAP4430 ES2.2, but the A2 revision actually has the ES2.1 silicon, I don't know if this perhaps is a contributing factor (see http://omappedia.org/wiki/PandaBoard_Revisions).

NOTE3: I should point out that the root filesystem (ext4) has been [force] checked with fsck and there are no issues; also there is no encryption in use.

1) mongod now fails to start with:

[ 1147.582946] Alignment trap: not handling instruction ed900a00 at [<00156400>]
[ 1147.591156] Unhandled fault: alignment exception (0x011) at 0x01b69f63

...

Thu Nov 8 10:57:22 Backtrace:
0x180b9c 0x34d95e 0x34dae4 0xb6c1e9f0
 mongod(_ZN5mongo15printStackTraceERSo+0xf) [0x180b9c]
 mongod(_ZN5mongo10abruptQuitEi+0x99) [0x34d95e]
 mongod(_ZN5mongo24abruptQuitWithAddrSignalEiP7siginfoPv+0x6b) [0x34dae4]
 /lib/arm-linux-gnueabihf/libc.so.6(__default_rt_sa_restorer_v2+0) [0xb6c1e9f0]

2) Serial console is now broken after upgrade:

The flash-kernel utility seemed to add the following preEnv.txt:

bootargs=ro quiet splash root=UUID=...

But this overrides the proper bootargs in boot.scr:

setenv bootargs ro elevator=noop vram=40M mem=456M@0x80000000 mem=512M@0xA0000000 root=UUID=... fixrtc quiet splash console=ttyO2,115200n8

Which causes /etc/init/serial.conf to fail to start a getty for the console as it inspects /proc/cmdline looking for "console=", which it no longer finds because /proc/cmdline now contains the contents of preEnv.txt.

Because preEnv.txt uses 'quiet', the last thing you see at the console while booting is:

## Booting kernel from Legacy Image at 80000000 ...
   Image Name: kernel 3.5.0-213-omap4
   Image Type: ARM Linux Kernel Image (uncompressed)
   Data Size: 4276896 Bytes = 4.1 MiB
   Load Address: 80008000
   Entry Point: 80008000
   Verifying Checksum ... OK
## Loading init Ramdisk from Legacy Image at 81600000 ...
   Image Name: ramdisk 3.5.0-213-omap4
   Image Type: ARM Linux RAMDisk Image (gzip compressed)
   Data Size: 5903851 Bytes = 5.6 MiB
   Load Address: 00000000
   Entry Point: 00000000
   Verifying Checksum ... OK
   Loading Kernel Image ... OK
OK

Starting kernel ...

Uncompressing Linux... done, booting the kernel.

There is no more output after this! The workaround for this was to mount the boot partition mmcblk0p1 and rename preEnv.txt (although now u-boot complains that preEnv.txt is missing).

3) System will no longer reboot

Running the command /sbin/reboot causes the system to shutdown but then hang (and NOT restart), power must be removed, or the reset button pressed to get a restart.

Once the system "stops" the status LEDs (STATUS1 and STATUS2) are both lit, as are both of the ethernet link/activity LEDs.

4) Previously unseen "abnormal" messages in dmesg output:

I'm now seeing "abnormal" messages in the dmesg output that I didn't see with previous releases (I don't know if these are significant issues or not!).

[ 10.550048] init: plymouth main process (246) killed by ABRT signal
[ 10.553527] init: plymouth-splash main process (449) terminated with status 2
...
[ 13.749603] init: failsafe main process (514) killed by TERM signal
...
[ 14.306884] init: plymouth-stop pre-start process (827) terminated with statu
...
error: unexpectedly disconnected from boot status daemon