Debian – Why is the Debian 9 (Stretch) Linux kernel not getting upgraded after ‘apt install’

I spent the better part of the month trying to install, reinstall, delete manually, and reinstall the latest linux-image-4.9.0-8 (or thereof) onto my Debian 9 (Stretch), but it will always (re)boot into that wrong version of Linux 3.16.0-5.

I even deleted the entire /boot directory content and reinstalled.

I have a standard Debian 9 installation into /dev/sda drive where /dev/sda1 is the /boot standalone partition.

My checklist:

• Checked the Debian Administration Handbook.
• No UEFI bootloader in hardware
• Turned off imageramfs option in /etc/kernel-img.conf
• No fancy kernel modules (not even NVIDIA nor ATI)
• Correctly used apt instead of apt-get

That is one puzzle system here that I've encountered myself.

The latest directory of /boot is:

$ ls -lat /boot
total 106000
drwxr-xr-x 23 root root     4096 Jan 17 12:25 ..
drwxr-xr-x  2 root root     4096 Jan 17 12:17 grub
drwxr-xr-x  3 root root     4096 Jan 17 12:17 .
-rw-r--r--  1 root root 19595458 Jan 17 12:17 initrd.img-4.9.0-8-amd64
-rw-r--r--  1 root root 19446192 Jan 17 12:08 initrd.img-4.9.0-5-amd64
-rw-r--r--  1 root root 19587298 Nov  7 13:58 initrd.img-4.9.0-7-amd64
-rw-r--r--  1 root root   186563 Oct 27 14:46 config-4.9.0-8-amd64
-rw-r--r--  1 root root  3195896 Oct 27 14:46 System.map-4.9.0-8-amd64
-rw-r--r--  1 root root  4232992 Oct 27 14:46 vmlinuz-4.9.0-8-amd64
-rw-r--r--  1 root root   186568 Aug 13 15:31 config-4.9.0-7-amd64
-rw-r--r--  1 root root  3192069 Aug 13 15:31 System.map-4.9.0-7-amd64
-rw-r--r--  1 root root  4232992 Aug 13 15:31 vmlinuz-4.9.0-7-amd64
-rw-r--r--  1 root root 19478453 Feb 19  2018 initrd.img-4.9.0-3-amd64
-rw-r--r--  1 root root   186473 Jan  4  2018 config-4.9.0-5-amd64
-rw-r--r--  1 root root  3185098 Jan  4  2018 System.map-4.9.0-5-amd64
-rw-r--r--  1 root root  4216608 Jan  4  2018 vmlinuz-4.9.0-5-amd64
-rw-r--r--  1 root root   186386 Sep 18  2017 config-4.9.0-3-amd64
-rw-r--r--  1 root root  3180929 Sep 18  2017 System.map-4.9.0-3-amd64
-rw-r--r--  1 root root  4204320 Sep 18  2017 vmlinuz-4.9.0-3-amd64

Noticed that there is no Linux 3.16.0-5 image/initramfs.

Yet executing uname always results in:

Linux arca 3.16.0-5-amd64 #1 SMP Debian 3.16.51-3+deb8u1 (2018-01-08)

The top-level directory content and their symbolic links are also correct:

# ls -lat /
total 112
drwxrwxrwt  14 root root 11264 Jan 17 13:15 tmp
drwxr-xr-x  33 root root  1080 Jan 17 12:46 run
drwxr-xr-x  19 root root  3480 Jan 17 12:45 dev
drwxr-xr-x 178 root root 12288 Jan 17 12:45 etc
dr-xr-xr-x  13 root root     0 Jan 17 12:44 sys
dr-xr-xr-x 195 root root     0 Jan 17 12:44 proc
drwx------  36 root root  4096 Jan 17 12:44 root
drwxr-xr-x  23 root root  4096 Jan 17 12:25 .
drwxr-xr-x  23 root root  4096 Jan 17 12:25 ..
drwxr-xr-x   3 root root  4096 Jan 17 12:17 boot
drwxr-xr-x   2 root root 12288 Jan 17 11:27 sbin
drwxrwxr-x   2 root root  4096 Jan 17 11:27 bin
lrwxrwxrwx   1 root root    29 Nov  7 13:56 initrd.img -> boot/initrd.img-4.9.0-8-amd64
lrwxrwxrwx   1 root root    29 Nov  7 13:56 initrd.img.crap -> boot/initrd.img-4.9.0-7-amd64
lrwxrwxrwx   1 root root    26 Nov  7 13:56 vmlinuz -> boot/vmlinuz-4.9.0-8-amd64
lrwxrwxrwx   1 root root    26 Nov  7 13:56 vmlinuz.crap.4.9.0.7 -> boot/vmlinuz-4.9.0-7-amd64
drwxr-xr-x   6 root root  4096 Oct 11 17:01 opt
drwxr-xr-x  20 root root  4096 Oct 10 16:52 lib
drwxr-xr-x   3 root root  4096 Oct 10 16:34 srv
drwxr-xr-x   8 root root  4096 Sep  5 13:34 home
drwxr-xr-x  13 root root  4096 Mar 17  2018 var
drwxr-xr-x   2 root root  4096 Mar 17  2018 lib64
drwxr-xr-x   7 root root  4096 Feb 19  2018 media
drwxr-xr-x   2 root root  4096 Feb 19  2018 debootstrap
drwxr-xr-x  10 root root  4096 May 16  2017 usr
drwxr-xr-x   2 root root  4096 Oct  8  2016 mnt
drwx------   2 root root 16384 Oct  8  2016 lost+found

Even boot partition sda1 for /boot is marked correctly.

# fdisk /dev/sda

Welcome to fdisk (util-linux 2.29.2).
Changes will remain in memory only, until you decide to write them.
Be careful before using the write command.


Command (m for help): p
Disk /dev/sda: 931.5 GiB, 1000204886016 bytes, 1953525168 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
Disklabel type: dos
Disk identifier: 0xfa4b1728

Device     Boot  Start        End    Sectors   Size Id Type
/dev/sda1  *      2048     499711     497664   243M 83 Linux
/dev/sda2       501758 1953523711 1953021954 931.3G  5 Extended
/dev/sda5       501760 1953523711 1953021952 931.3G 8e Linux LVM

Partition 2 does not start on physical sector boundary.

Command (m for help): quit