raspberrypi-bootloader error during apt-get upgrade after restore form backup, how to fix?

Question

I recently restored a pi 3 from a backup. Before the incident that required the restore I had it booting from a USB SSD hard drive. To restore the operating system I simply copied the root directory of the SD card (using rsync -a with --delete-during) to the USB drive.

Next I tried apt-get update and apt-get upgrade. All went smoothly until I got an error like this:

Preparing to unpack .../raspberrypi-bootloader_1.20181112-1_armhf.deb ...
/boot appears to be NOOBS recovery partition. Applying fix.
Could not determine root partition
dpkg: error processing archive /var/cache/apt/archives/raspberrypi-bootloader_1.20181112-1_armhf.deb (--unpack):
 subprocess new pre-installation script returned error exit status 1
No diversion 'diversion of /boot/start.elf by rpikernelhack', none removed.
No diversion 'diversion of /boot/start_cd.elf by rpikernelhack', none removed.
No diversion 'diversion of /boot/start_db.elf by rpikernelhack', none removed.
No diversion 'diversion of /boot/start_x.elf by rpikernelhack', none removed.
No diversion 'diversion of /boot/fixup.dat by rpikernelhack', none removed.
No diversion 'diversion of /boot/fixup_cd.dat by rpikernelhack', none removed.
No diversion 'diversion of /boot/fixup_db.dat by rpikernelhack', none removed.
No diversion 'diversion of /boot/fixup_x.dat by rpikernelhack', none removed.
No diversion 'diversion of /boot/bootcode.bin by rpikernelhack', none removed.
No diversion 'diversion of /boot/LICENCE.broadcom by rpikernelhack', none removed.
Errors were encountered while processing:
 /var/cache/apt/archives/raspberrypi-bootloader_1.20181112-1_armhf.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

How can I fix this error and complete the upgrade?

When I made the restore from the SD card to the USB drive I used an rsync exclude file like this:

/proc/*
/sys/*
/dev/*
/boot/*
/tmp/*
/run/*
/mnt/*
/media/*

.bash_history
/etc/fake-hwclock.data
/var/lib/rpimonitor/stat/

But after this, I wasn't sure whether I needed to copy /boot, but decided to copy it over with sudo cp -r /boot/* /media/usbdrive/boot/.

Following this I set up my cmdline.txt and fstab etc to use the usb drive again instead of the SD after initial boot.

Some other things that might be relevant are

1) output of fdisk -l

pi@raspberrypi:~ $ sudo fdisk -l
Disk /dev/ram0: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram1: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram2: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram3: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram4: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram5: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram6: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram7: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram8: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram9: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram10: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram11: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram12: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram13: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram14: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/ram15: 4 MiB, 4194304 bytes, 8192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes


Disk /dev/mmcblk0: 14.9 GiB, 15931539456 bytes, 31116288 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x0004e623

Device         Boot   Start      End  Sectors  Size Id Type
/dev/mmcblk0p1         8192  3279296  3271105  1.6G  e W95 FAT16 (LBA)
/dev/mmcblk0p2      3279297 31116287 27836991 13.3G  5 Extended
/dev/mmcblk0p5      3284992  3350525    65534   32M 83 Linux
/dev/mmcblk0p6      3350528  3491839   141312   69M  c W95 FAT32 (LBA)
/dev/mmcblk0p7      3497984 31116287 27618304 13.2G 83 Linux


Disk /dev/sdb: 117.4 GiB, 126035288064 bytes, 246162672 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: gpt
Disk identifier: 909F2695-EDB4-4CDE-A258-7EE27E75BD77

Device     Start       End   Sectors   Size Type
/dev/sdb1   2048 246162638 246160591 117.4G Linux filesystem


Disk /dev/sda: 230.5 GiB, 247510073344 bytes, 483418112 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x00030033

Device     Boot Start       End   Sectors   Size Id Type
/dev/sda1  *     2048 483409919 483407872 230.5G 83 Linux

2) my fstab

pi@raspberrypi:~ $ cat /etc/fstab
proc            /proc           proc    defaults          0       0
/dev/mmcblk0p1  /boot           vfat    defaults          0       2
#PARTUUID=d96b7723-01  /boot           vfat    defaults          0       2
#PARTUUID=d96b7723-02  /               ext4    defaults,noatime  0       1
# The USB SSD  drive
PARTUUID=712ae4a6-73d8-4aca-9ec6-b6e507c95f74  /                 ext4    defaults,noatime                            0       1
# another USB flash drive
UUID=978cc26c-be1f-4318-b4c3-6b0448333b02      /media/usbflash0  ext4    defaults,nofail,noatime  0       0
# a swapfile is not a swap partition, no line here
#   use  dphys-swapfile swap[on|off]  for that

3) contents of /boot (on the usb drive, I copied this from sd card, should I have?)

pi@raspberrypi:~ $ ls /boot/
bcm2708-rpi-0-w.dtb  bcm2708-rpi-b-plus.dtb  bcm2709-rpi-2-b.dtb  bcm2710-rpi-cm3.dtb  defaults                 os        recovery7.img     recovery.elf                recovery.img  riscos-boot.bin
bcm2708-rpi-b.dtb    bcm2708-rpi-cm.dtb      bcm2710-rpi-3-b.dtb  BUILD-DATA           INSTRUCTIONS-README.txt  overlays  recovery.cmdline  RECOVERY_FILES_DO_NOT_EDIT  recovery.rfs

4) contents of sd card boot partition

pi@raspberrypi:~ $ sudo mkdir /media/sdboot
pi@raspberrypi:~ $ sudo mount /dev/mmcblk0p6 /media/sdboot/
pi@raspberrypi:~ $ ls /media/sdboot/
bcm2708-rpi-0-w.dtb  bcm2708-rpi-b-plus.dtb  bcm2709-rpi-2-b.dtb  bcm2710-rpi-cm3.dtb  cmdline.txt       cmdline.txt.usb  COPYING.linux  fixup.dat     fixup_x.dat  kernel7.img  LICENCE.broadcom  os_config.json  start_cd.elf  start.elf
bcm2708-rpi-b.dtb    bcm2708-rpi-cm.dtb      bcm2710-rpi-3-b.dtb  bootcode.bin         cmdline.txt.orig  config.txt       fixup_cd.dat   fixup_db.dat  issue.txt    kernel.img   LICENSE.oracle    overlays        start_db.elf  start_x.elf

3) my cmdline.txt in the sd card boot partition

pi@raspberrypi:~ $ cat /media/sdboot/cmdline.txt
dwc_otg.lpm_enable=0 console=serial0,115200 console=tty1 root=PARTUUID=712ae4a6-73d8-4aca-9ec6-b6e507c95f74 rootfstype=ext4 elevator=deadline fsck.repair=yes rootwait splash plymouth.ignore-serial-consoles max_usb_current=1

EDIT 1

When I originally set up the system, I used instructions very similar to these. This left me with a working SD card. It is the original SD card I am using as my 'backup'. I backed up my user data elsewhere.

Milliways · Answer 1 · 2019-01-17T23:38:07.150

It is unclear from your question HOW you did a backup/restore but I suspect can-a-raspberry-pi-be-used-to-create-a-backup-of-itself

goldilocks answer does not make it clear, but you should use sudo on both backup/restore.

There are a few other caveats - the backup is ONLY for restoration to the SAME SD Card (or a card with the same Disk Id and partition structure), and ONLY if the firmware/kernel are identical.

It was NOT designed for NOOBS (which you appear to be using) - although applied carefully could work. In particular this needs to be restored to the correct partition - which would be /dev/mmcblk0p7. NOTE attempting restoration to a working partition is unwise - so it would be to partition 7 on whatever device is used.

Your /etc/fstab and cmdline.txt are nonsense 712ae4a6-73d8-4aca-9ec6-b6e507c95f74 is NOT a PARTUUID (at least for MBR)!

The boot partition for Raspbian on NOOBS IS NOT /dev/mmcblk0p1 - this is the NOOBS boot partition.

You are using a GPT partition scheme which AFAIK is NOT SUPPORTED for boot.

You then seem to have compounded you problems by copying boot (although exactly from or to is unclear).

The bottom line is no one is going to be able to tell you how to fix it, or even if this is possible.

Your best bet would be to make a fresh installation. You could use the backup to recover your files. And I strongly suggest you DO NOT use NOOBS.

Well the 'backup' was just the initial flash of the SD card, originally I created the USB dirive image from this SD card. Now I basically want to repeat this, and thought I had. I don't know why you are saying the fstab is nonsense because it worked perfectly before the incident which required the backup, and after before I attempted the apt-get update. The reason the restore is required btw, is because of [this](https://unix.stackexchange.com/questions/494271/lots-of-dpkg-errors-when-doing-upgrade-on-raspian-how-to-fix) — crobar, Jan 18 '19 at 15:14
Oh, and you also mention `mmcblk0p1`, but I don't reference that, I reference `mmcblk0p6`, which is the SD card boot partition. That's why I showed my mount command. — crobar, Jan 18 '19 at 15:20
I added some info about how I set up the system to the question, with a link to the instructions, which also shows where the PARTUUID comes from. — crobar, Jan 18 '19 at 15:40
I've just see that I *do* reference `mmcblk0p1` in my `fstab`! Maybe this is the issue! — crobar, Jan 18 '19 at 15:42

raspberrypi-bootloader error during apt-get upgrade after restore form backup, how to fix?

1 Answers1