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I upgraded Debian 8 to 9 yesterday. The system now boots without a graphical UI and mdadm complains that

mdadm: Found some drive for an array that is already active: /dev/md0
mdadm: giving up

I have run e2fsck on my drives, the filesystem is alright. I tried using a new mdadm.conf (using the output from a --scan) but it didn't work.

It is a bit worrying that the GUI is missing.

Is there something about kernel 4.9 that I am missing?

Thanks for your help...!

Edit:

After some more looking around, sudo dpkg-reconfigure linux-image-4.9.0-3-amd64 gives the following error:

/etc/kernel/postinst.d/dkms:
Error! Bad return status for module build on kernel: 4.9.0-3-amd64 (x86_64)
Consult /var/lib/dkms/virtualbox/4.3.36/build/make.log for more information.
/etc/kernel/postinst.d/initramfs-tools:
update-initramfs: GEnerating /boot/initrd.img-4.9.0-3-amd64
W: initramfs-tools configuration sets RESUME=UUID=XXXX....
W but no matching swap device is available.
[ xx] EXT4-fs error (device md0): ext4_iget:4627: inode #32513: comm zz-update-grub: bad extended attribute block 2182084667

EDIT 2: I fixed the virtualbox dkms issue. Now the main problem is this:

W: initramfs-tools configuration sets RESUME=UUID=XXXX....
W but no matching swap device is available.

Existing documentation on the web is not 100% clear... will update if I get anything working.

EDIT 3: I regenerated a new UUID for my swap partition and edited /etc/initramfs-tools/conf.d/resume accordingly. This resolved the RESUME=UUID error. However now I have the same [ xx] EXT4-fs error (device md0): ext4_iget:4627: inode #32513: comm zz-update-grub: bad extended attribute block 2182084667 error to worry about.

EDIT 4: Fixed that last EXT4-fs error by booting to a livecd, assembling the raid array and repairing the filesystem with fdisk.

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