error on apt-get dist-upgrade related to boot image [SOLVED]

changer · 2016-01-12 16:05:32

I keep getting the same errors when trying to run apt-get dist-upgrade.

NOTE: the two raids (/dev/md/newblack:2 and 3) are not related to booting. So hopefully those warnings can just be ignored. I did check the output of running /usr/share/mdadm/mkconf, and it seemed to just contain default values. My /etc/mdadm/mdadm.conf has the info needed for my raids containing system files and home directory. So i left that as is.

The other errors I'm getting all seem to be related to not having /lib/live/boot, which I confirmed does not exist.

Here is what I'm getting:

$ sudo apt-get dist-upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n] Y
Setting up linux-image-3.16.0-4-amd64 (3.16.7-ckt20-1+deb8u2) ...
/etc/kernel/postinst.d/initramfs-tools:
update-initramfs: Generating /boot/initrd.img-3.16.0-4-amd64
cp: cannot stat ‘/lib/live/boot’: No such file or directory
W: mdadm: the array /dev/md/newblack:3 with UUID 939ba052:5c073d0c:XXXXXXXXX
W: mdadm: is currently active, but it is not listed in mdadm.conf. if
W: mdadm: it is needed for boot, then YOUR SYSTEM IS NOW UNBOOTABLE!
W: mdadm: please inspect the output of /usr/share/mdadm/mkconf, compare
W: mdadm: it to /etc/mdadm/mdadm.conf, and make the necessary changes.
W: mdadm: the array /dev/md/newblack:2 with UUID f612ba9b:0819e90a:XXXXXXXXX
W: mdadm: is currently active, but it is not listed in mdadm.conf. if
W: mdadm: it is needed for boot, then YOUR SYSTEM IS NOW UNBOOTABLE!
W: mdadm: please inspect the output of /usr/share/mdadm/mkconf, compare
W: mdadm: it to /etc/mdadm/mdadm.conf, and make the necessary changes.
live-boot: corecp: cannot stat ‘/lib/live/boot’: No such file or directory
E: /usr/share/initramfs-tools/hooks/live failed with return 1.
update-initramfs: failed for /boot/initrd.img-3.16.0-4-amd64 with 1.
run-parts: /etc/kernel/postinst.d/initramfs-tools exited with return code 1
Failed to process /etc/kernel/postinst.d at /var/lib/dpkg/info/linux-image-3.16.0-4-amd64.postinst line 634, <STDIN> line 2.
dpkg: error processing package linux-image-3.16.0-4-amd64 (--configure):
 subprocess installed post-installation script returned error exit status 2
Errors were encountered while processing:
 linux-image-3.16.0-4-amd64
E: Sub-process /usr/bin/dpkg returned an error code (1)

Last edited by changer (2016-03-05 14:08:02)

Head_on_a_Stick · 2016-01-12 18:35:57

Can we see the output of:

cat /etc/apt/sources.list{,.d/*}; apt-cache policy

changer · 2016-03-01 03:28:43

cat /etc/apt/sources.list{,.d/*}; apt-cache policy
deb http://ftp.us.debian.org/debian/ jessie main contrib 
deb http://security.debian.org/ jessie/updates main contrib 
deb http://ftp.us.debian.org/debian/ jessie-updates main contrib 
deb http://pkg.bunsenlabs.org/debian bunsen-hydrogen mainPackage files:
 100 /var/lib/dpkg/status
     release a=now
 500 http://pkg.bunsenlabs.org/debian/ bunsen-hydrogen/main amd64 Packages
     release o=bunsenlabs,n=bunsen-hydrogen,l=bunsenlabs,c=main
     origin pkg.bunsenlabs.org
 500 http://ftp.us.debian.org/debian/ jessie-updates/main Translation-en
 500 http://ftp.us.debian.org/debian/ jessie-updates/contrib Translation-en
 500 http://ftp.us.debian.org/debian/ jessie-updates/contrib amd64 Packages
     release o=Debian,a=stable-updates,n=jessie-updates,l=Debian,c=contrib
     origin ftp.us.debian.org
 500 http://ftp.us.debian.org/debian/ jessie-updates/main amd64 Packages
     release o=Debian,a=stable-updates,n=jessie-updates,l=Debian,c=main
     origin ftp.us.debian.org
 500 http://security.debian.org/ jessie/updates/main Translation-en
 500 http://security.debian.org/ jessie/updates/contrib Translation-en
 500 http://security.debian.org/ jessie/updates/contrib amd64 Packages
     release v=8,o=Debian,a=stable,n=jessie,l=Debian-Security,c=contrib
     origin security.debian.org
 500 http://security.debian.org/ jessie/updates/main amd64 Packages
     release v=8,o=Debian,a=stable,n=jessie,l=Debian-Security,c=main
     origin security.debian.org
 500 http://ftp.us.debian.org/debian/ jessie/main Translation-en
 500 http://ftp.us.debian.org/debian/ jessie/contrib Translation-en
 500 http://ftp.us.debian.org/debian/ jessie/contrib amd64 Packages
     release v=8.3,o=Debian,a=stable,n=jessie,l=Debian,c=contrib
     origin ftp.us.debian.org
 500 http://ftp.us.debian.org/debian/ jessie/main amd64 Packages
     release v=8.3,o=Debian,a=stable,n=jessie,l=Debian,c=main
     origin ftp.us.debian.org
Pinned packages:

Head_on_a_Stick · 2016-03-01 07:51:37

Try:

sudo chmod -x /usr/share/initramfs-tools/hooks/live

then `apt-get dist-upgrade`

changer · 2016-03-04 18:14:36

EDIT: Okay, first I assumed it was +x, so I didn't understand my results below. Then I realized it probably should be +x. So I tried that. Seems to work. Thanks!

I did sudo chmod -x on that file, and I now have:

total 124K
drwxr-xr-x 2 root root 4.0K Feb 24 19:58 .
drwxr-xr-x 7 root root 4.0K Oct 25 10:55 ..
-rwxr-xr-x 1 root root 2.7K Dec 18  2014 amd64_microcode
-rwxr-xr-x 1 root root  378 Mar  1  2015 busybox
-rwxr-xr-x 1 root root 1014 Jan 22  2015 cryptgnupg
-rwxr-xr-x 1 root root  451 Jan 22  2015 cryptkeyctl
-rwxr-xr-x 1 root root 1.6K Jan 22  2015 cryptopenct
-rwxr-xr-x 1 root root 1.5K Jan 22  2015 cryptopensc
-rwxr-xr-x 1 root root  913 Jan 22  2015 cryptpassdev
-rwxr-xr-x 1 root root  16K Jan 22  2015 cryptroot
-rwxr-xr-x 1 root root  472 Jan 17  2015 dmsetup
-rwxr-xr-x 1 root root 2.5K Mar  1  2015 fsck
-rwxr-xr-x 1 root root  230 Jan 21 09:38 fuse
-rwxr-xr-x 1 root root 4.3K Jan 29  2015 intel_microcode
-rwxr-xr-x 1 root root 1.3K Mar  1  2015 keymap
-rwxr-xr-x 1 root root  686 Mar  1  2015 klibc
-rwxr-xr-x 1 root root  424 Sep 26  2014 kmod
-rw-r--r-- 1 root root 4.8K Dec 10  2014 live
-rwxr-xr-x 1 root root  770 Jan 17  2015 lvm2
-rwxr-xr-x 1 root root 6.8K Dec 28 06:59 mdadm
-rwxr-xr-x 1 root root  304 May 26  2015 ntfs_3g
-rwxr-xr-x 1 root root 1.3K Mar  1  2015 resume
-rwxr-xr-x 1 root root 1.3K Feb  1  2011 thermal
-rwxr-xr-x 1 root root 1.9K Nov 21 11:00 udev
-rwxr-xr-x 1 root root 1.2K Jul 27  2014 zz-busybox

apt-get dist-upgrade still gives the same errors though and seems to not be updating mdadm

Last edited by changer (2016-03-04 18:18:05)

changer · 2016-03-04 18:32:59

So after doing the above:

sudo chmod +x /usr/share/initramfs-tools/hooks/live
sudo apt-get dist-upgrade

The update finished without error. But on reboot I am now stuck in emergency mode.
This happens after a message of:

A start job is running for dev-disk-by\<numbers>\<more numbers>.device [1min 30s]

It counts down for 90 seconds, then boots into emergency mode command line.

Don't know what to do from there.

Last edited by changer (2016-03-04 18:33:15)

damo · 2016-03-04 18:41:06

You get a similar error when the UUID of a partition has been changed and /etc/fstab doesn't reflect it, if that is what is being used (eg a new install in /dev/sda2 creates a new swap, but the fstab in /dev/sda1 still has the old value).

Perhaps check the device ID's by running gparted in a Live session, and checking the appropriate files for your setup.

changer · 2016-03-04 19:06:02

Thanks. I commented out an unrequired disk in fstab and can boot regularly now.

However, I am missing two of my raid devices on boot now. The two required for boot are showing (boot and filesystem) but the other two are not. So I did:

mdadm -A /dev/md2 /dev/sda3 /dev/sdb3
mdadm -A /dev/md3 /dev/sda4 /dev/sda4

Now all raids are available. In attempt to make this stick I ran:

update-initramfs -u

This returned the same errors from my original post:
cp: cannot stat '/lib/live/boot': No such file or directory
etc, etc

/usr/share/initramfs-tools/hooks/live is set to rwxr-xr-x

So I seem to be back at my original post here.

xaos52 · 2016-03-04 19:32:24

^I don't know how the 'live' entry in /usr/share/initramfs-tools/hooks got there in the first place, but it should not be there at all. Perhaps you installed your system by copying things from the live boot to the installed system, not by booting from the live system and selecting the install entry.

I would remove the 'live' hook.

Head_on_a_Stick · 2016-03-04 21:26:15

xaos52 wrote:

I would remove the 'live' hook.

+1

I was attempting to simply disable the hook by making it non-executable but clearly that doesn't work.

Just (re)move it instead.

changer · 2016-03-04 22:29:37

I deleted /usr/share/initramfs-tools/hooks/live
then when I run update-initramfs -u the first error is gone, but the mdadm errors are still there.

Then I noticed there is an /etc/mdadm/mdadm.conf, but I was editing /etc/mdadm.conf
So I added my other two raids definitions to /etc/mdadm/mdadm.conf as well.
I ran update-initramfs -u and got no errors!
Thought I was in good shape until I rebooted. Then I get a message telling me that two disks (with the same UUID) are competing for /dev/md0, which is my boot disk
This is followed by:

Reading all physical volumes. this may take a while...
No volume groups found
No volume groups found
[...]
ALERT! /dev/md1 does not exist. [which is my root file system]

I'm guessing I should have deleted /etc/mdadm.conf, and having both is causing this duplicate error?
So I can boot to a live CD and change that, but how do I run update-initramfs on that system without being able to boot into it?

Head_on_a_Stick · 2016-03-04 22:41:51

changer wrote:

how do I run update-initramfs on that system without being able to boot into it?

From the live system, assemble your arrays then use:

sudo -i
mount /dev/sdXY /mnt
for i in /proc /sys /dev;do mount --bind $i /mnt$i;done
chroot /mnt /bin/bash
source /etc/profile
update-initramfs -u
exit
umount -R /mnt
exit

Replace "XY" with the drive letter and the partition number of your root partition.

I have no experience of RAID so you may have to fill in the gaps a bit.

damo · 2016-03-04 22:46:50

changer wrote:

...
So I can boot to a live CD and change that, but how do I run update-initramfs on that system without being able to boot into it?

You can chroot into an installation from a Live session. This method should still work for you I think: How to chroot into #! on disk when you can not boot via grub

Edit: Ninja'd by HoaS. Again!

Last edited by damo (2016-03-04 22:47:28)

changer · 2016-03-05 00:30:25

So I was able to chroot in doing something like this:

fdisk -l
cryptsetup luksOpen /dev/md125 xxx
pvdisplay
lvdisplay
mount /dev/bunsen/root /mnt
mount /dev/bunsen/home /mnt/home
mount /dev/md127 /mnt/boot
mount --bind /dev /mnt/dev
mount --bind /sys /mnt/sys
mount --bind /proc /mnt/proc
chroot /mnt
vim /etc/mdadm/mdadm.conf

I realized the problem was that I had run:

sudo sh -c 'mdadm --detail --scan >> /etc/mdadm/mdadm.conf'

This appended the instructions for all 4 of my raids, but I already had 2 listed. So when I rebooted mdadm could not build the two that were duplicated, which were my boot and filesystem. So rather than delete /etc/mdadm.conf (as I suggest above) I just got rid of those duplicates in /etc/mdadm/mdadm.conf

Then, still in the chroot, I ran:

update-initramfs -u

RETURNED THIS:
cryptsetup:WARNING: invalid line in /etc/crypttab for abc

Turns out I had to unmount everything and open the LUKS device using the same device name listed in /etc/crypttab. I also rebuilt all the raids to correspond with the numbers I use in my real system.

Then I reran update-initramfs -u
I got no errors!
Now I can reboot. I can also run update-initramfs -u in my booted system with no more errors.

Original problem finally solved. I did learn some stuff.

damo · 2016-03-05 07:25:57

changer wrote:

....
Original problem finally solved. I did learn some stuff.

Good news

If you could edit the title of your first post and add [SOLVED], it might help others searching for answers

#1 2016-01-12 16:05:32

error on apt-get dist-upgrade related to boot image [SOLVED]

#2 2016-01-12 18:35:57

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#3 2016-03-01 03:28:43

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#4 2016-03-01 07:51:37

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#5 2016-03-04 18:14:36

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#6 2016-03-04 18:32:59

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#7 2016-03-04 18:41:06

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#8 2016-03-04 19:06:02

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#9 2016-03-04 19:32:24

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#10 2016-03-04 21:26:15

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#11 2016-03-04 22:29:37

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#12 2016-03-04 22:41:51

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#13 2016-03-04 22:46:50

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#14 2016-03-05 00:30:25

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

#15 2016-03-05 07:25:57

Re: error on apt-get dist-upgrade related to boot image [SOLVED]

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