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I use debian squeeze, and upgraded the kernel with the latest source from kernel.org (2.6.38). Everything is fine, except when I try to upgrade software/security, it also try to update the linux kernel (to linux-image-2.6.32-5-amd64).
My current kernel, from apt-cache,
linux-image-2.6.38-amd64 - Linux kernel binary image for version 2.6.38-amd64
apt-get upgrade --show-upgraded
The following packages will be upgraded:
base-files console-setup desktop-base gdm3 gedit gedit-common git gnome-screensaver google-chrome-stable ia32-libs keyboard-configuration libnautilus-extension1 libnm-glib-vpn1 libnm-glib2 libnm-util1 libpulse-mainloop-glib0
libpulse0 linux-base linux-image-2.6.32-5-amd64 linux-libc-dev nautilus nautilus-data network-manager python python-minimal sudo sun-java6-bin sun-java6-jdk sun-java6-jre ttf-liberation usb-modeswitch-data xserver-common
xserver-xephyr xserver-xorg-core xserver-xorg-video-intel
35 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 159 MB/182 MB of archives.
Pin linux-image-2.6.32-5-amd64 to its current version (search apt pinning), or uninstall it? But I don't see a problem with having a 2.6.32 kernel and a 2.6.38 kernel installed. You seem to have properly built the 2.6.38 kernel as a .deb and installed it that way, so letting apt upgrade the 2.6.32 kernel should be harmless. Just check that 2.6.38 remains the default choice in grub after.