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FCP-INDI / C-PAC

Configurable Pipeline for the Analysis of Connectomes
https://fcp-indi.github.io/
GNU Lesser General Public License v3.0
62 stars 40 forks source link

CPAC 1.0.1 Install Script Alters Grub Configuration and Kernel Headers? #626

Closed nimzodisaster closed 6 years ago

nimzodisaster commented 7 years ago

I'm not sure it is a problem but I'm getting nervous. I ran this cd /tmp ; git clone https://github.com/FCP-INDI/C-PAC.git ; cd C-PAC ; python setup.py install ;

and the installer script seemed to start messing with my linux kernel and grub configuration! I would not have expected that.

Full and lengthy message below `Removing linux-image-extra-4.4.0-21-generic (4.4.0-21.37) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Error! Your kernel headers for kernel 4.4.0-21-generic cannot be found. Please install the linux-headers-4.4.0-21-generic package, or use the --kernelsourcedir option to tell DKMS where it's located Error! Your kernel headers for kernel 4.4.0-21-generic cannot be found. Please install the linux-headers-4.4.0-21-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic update-initramfs: Generating /boot/initrd.img-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found linux image: /boot/vmlinuz-4.4.0-21-generic Found initrd image: /boot/initrd.img-4.4.0-21-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-21-generic (4.4.0-21.37) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-21-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-22-generic (4.4.0-22.40) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Error! Your kernel headers for kernel 4.4.0-22-generic cannot be found. Please install the linux-headers-4.4.0-22-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic update-initramfs: Generating /boot/initrd.img-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-22-generic (4.4.0-22.40) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic dkms: removing: bbswitch 0.8 (4.4.0-22-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-22-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-22-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-24-generic (4.4.0-24.43) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Error! Your kernel headers for kernel 4.4.0-24-generic cannot be found. Please install the linux-headers-4.4.0-24-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic update-initramfs: Generating /boot/initrd.img-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-24-generic (4.4.0-24.43) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic dkms: removing: bbswitch 0.8 (4.4.0-24-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-24-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-24-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-28-generic (4.4.0-28.47) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Error! Your kernel headers for kernel 4.4.0-28-generic cannot be found. Please install the linux-headers-4.4.0-28-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic update-initramfs: Generating /boot/initrd.img-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-28-generic (4.4.0-28.47) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic dkms: removing: bbswitch 0.8 (4.4.0-28-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-28-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-28-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-31-generic (4.4.0-31.50) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Error! Your kernel headers for kernel 4.4.0-31-generic cannot be found. Please install the linux-headers-4.4.0-31-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic update-initramfs: Generating /boot/initrd.img-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-31-generic (4.4.0-31.50) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic dkms: removing: bbswitch 0.8 (4.4.0-31-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-31-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-31-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-34-generic (4.4.0-34.53) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Error! Your kernel headers for kernel 4.4.0-34-generic cannot be found. Please install the linux-headers-4.4.0-34-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic update-initramfs: Generating /boot/initrd.img-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-34-generic (4.4.0-34.53) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic dkms: removing: bbswitch 0.8 (4.4.0-34-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-34-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-34-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-36-generic (4.4.0-36.55) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Error! Your kernel headers for kernel 4.4.0-36-generic cannot be found. Please install the linux-headers-4.4.0-36-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic update-initramfs: Generating /boot/initrd.img-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-36-generic (4.4.0-36.55) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic dkms: removing: bbswitch 0.8 (4.4.0-36-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-36-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-36-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-38-generic (4.4.0-38.57) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Error! Your kernel headers for kernel 4.4.0-38-generic cannot be found. Please install the linux-headers-4.4.0-38-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic update-initramfs: Generating /boot/initrd.img-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-38-generic (4.4.0-38.57) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic dkms: removing: bbswitch 0.8 (4.4.0-38-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-38-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-38-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-42-generic (4.4.0-42.62) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Error! Your kernel headers for kernel 4.4.0-42-generic cannot be found. Please install the linux-headers-4.4.0-42-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic update-initramfs: Generating /boot/initrd.img-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-42-generic (4.4.0-42.62) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic dkms: removing: bbswitch 0.8 (4.4.0-42-generic) (x86_64)

-------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-42-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-42-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing nifti-bin (2.0.0-2) ... Removing openjdk-8-doc (8u111-b14-2ubuntu0.16.04.2) ... Removing openjdk-8-jdk:amd64 (8u111-b14-2ubuntu0.16.04.2) ... Removing openjdk-8-jdk-headless:amd64 (8u111-b14-2ubuntu0.16.04.2) ... Removing qhull-bin (2015.2-1) ... Removing xserver-xorg-legacy (2:1.18.4-0ubuntu0.2) ... Removing ant (1.9.6-1ubuntu1) ... Removing antlr3 (3.5.2-4) ... Removing libstringtemplate4-java (4.0.8-2) ... Removing libantlr3-runtime-java (3.5.2-4) ... Removing libcommons-logging-java (1.2-1+build1) ... Removing libcommons-parent-java (39-3) ... Removing libapache-pom-java (10-2build1) ... Removing libapr1:amd64 (1.5.2-3) ... Removing libgeronimo-jpa-2.0-spec-java (1.1-2) ... Removing aspectj (1.8.8-1) ... Removing libaspectj-java (1.8.8-1) ... Removing libgeronimo-osgi-support-java (1.1-1) ... Removing libosgi-compendium-java (5.0.0-3) ... Removing libosgi-core-java (6.0.0-1) ... Removing libosgi-annotation-java (6.0.0-1) ... Removing libosgi-foundation-ee-java (4.2.0-2) ... Removing libservlet3.1-java (8.0.32-1ubuntu1.2) ... Processing triggers for man-db (2.7.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu5) ... [ Tue Dec 13 11:58:40 PST 2016 ] Installing miniconda! --2016-12-13 11:58:40-- http://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh Resolving repo.continuum.io (repo.continuum.io)... 104.16.18.10, 104.16.19.10, 2400:cb00:2048:1::6810:130a, ... Connecting to repo.continuum.io (repo.continuum.io)|104.16.18.10|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh [following] --2016-12-13 11:58:40-- https://repo.continuum.io/miniconda/Miniconda-3.8.3-Linux-x86_64.sh Connecting to repo.continuum.io (repo.continuum.io)|104.16.18.10|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 23521627 (22M) [application/octet-stream] Saving to: ‘Miniconda-3.8.3-Linux-x86_64.sh’

`

jpellman commented 7 years ago

Assuming that you are using 'cpac_install.sh', the install script runs 'apt-get upgrade' before it installs anything else if you are running an Ubuntu Linux system. This will upgrade the kernel as well as other packages at the system level if possible (i.e., if run as the superuser). This is indeed behavior that you would not expect if you were just running it with the '-p' flag, so we should change this.

On Tue, Dec 13, 2016 at 3:11 PM, Joshua Lee notifications@github.com wrote:

I'm not sure it is a problem but I'm getting nervous. I ran this cd /tmp git clone https://github.com/FCP-INDI/C-PAC.git cd C-PAC python setup.py install

and the installer script seemed to start messing with my linux kernel and grub configuration! I would not have expected that.

Full and lengthy message below `Removing linux-image-extra-4.4.0-21-generic (4.4.0-21.37) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Error! Your kernel headers for kernel 4.4.0-21-generic cannot be found. Please install the linux-headers-4.4.0-21-generic package, or use the --kernelsourcedir option to tell DKMS where it's located Error! Your kernel headers for kernel 4.4.0-21-generic cannot be found. Please install the linux-headers-4.4.0-21-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic update-initramfs: Generating /boot/initrd.img-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found linux image: /boot/vmlinuz-4.4.0-21-generic Found initrd image: /boot/initrd.img-4.4.0-21-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-21-generic (4.4.0-21.37) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-21-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-22-generic (4.4.0-22.40) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Error! Your kernel headers for kernel 4.4.0-22-generic cannot be found. Please install the linux-headers-4.4.0-22-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic update-initramfs: Generating /boot/initrd.img-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-22-generic (4.4.0-22.40) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic dkms: removing: bbswitch 0.8 (4.4.0-22-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-22-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-22-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-22-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-24-generic (4.4.0-24.43) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Error! Your kernel headers for kernel 4.4.0-24-generic cannot be found. Please install the linux-headers-4.4.0-24-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic update-initramfs: Generating /boot/initrd.img-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-24-generic (4.4.0-24.43) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic dkms: removing: bbswitch 0.8 (4.4.0-24-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-24-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-24-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-24-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-28-generic (4.4.0-28.47) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Error! Your kernel headers for kernel 4.4.0-28-generic cannot be found. Please install the linux-headers-4.4.0-28-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic update-initramfs: Generating /boot/initrd.img-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-28-generic (4.4.0-28.47) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic dkms: removing: bbswitch 0.8 (4.4.0-28-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-28-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-28-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-28-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-31-generic (4.4.0-31.50) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Error! Your kernel headers for kernel 4.4.0-31-generic cannot be found. Please install the linux-headers-4.4.0-31-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic update-initramfs: Generating /boot/initrd.img-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-31-generic (4.4.0-31.50) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic dkms: removing: bbswitch 0.8 (4.4.0-31-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-31-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-31-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-31-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-34-generic (4.4.0-34.53) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Error! Your kernel headers for kernel 4.4.0-34-generic cannot be found. Please install the linux-headers-4.4.0-34-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic update-initramfs: Generating /boot/initrd.img-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-34-generic (4.4.0-34.53) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic dkms: removing: bbswitch 0.8 (4.4.0-34-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-34-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-34-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-34-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-36-generic (4.4.0-36.55) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Error! Your kernel headers for kernel 4.4.0-36-generic cannot be found. Please install the linux-headers-4.4.0-36-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic update-initramfs: Generating /boot/initrd.img-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-36-generic (4.4.0-36.55) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic dkms: removing: bbswitch 0.8 (4.4.0-36-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-36-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-36-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-36-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-38-generic (4.4.0-38.57) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Error! Your kernel headers for kernel 4.4.0-38-generic cannot be found. Please install the linux-headers-4.4.0-38-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic update-initramfs: Generating /boot/initrd.img-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-38-generic (4.4.0-38.57) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic dkms: removing: bbswitch 0.8 (4.4.0-38-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-38-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-38-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-38-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-42-generic (4.4.0-42.62) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Error! Your kernel headers for kernel 4.4.0-42-generic cannot be found. Please install the linux-headers-4.4.0-42-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic update-initramfs: Generating /boot/initrd.img-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-42-generic (4.4.0-42.62) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic dkms: removing: bbswitch 0.8 (4.4.0-42-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-42-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
    • Deleting from: /lib/modules/4.4.0-42-generic/updates/dkms/
  • Original module
    • No original module was found for this module on this kernel.
    • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-42-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing nifti-bin (2.0.0-2) ... Removing openjdk-8-doc (8u111-b14-2ubuntu0.16.04.2) ... Removing openjdk-8-jdk:amd64 (8u111-b14-2ubuntu0.16.04.2) ... Removing openjdk-8-jdk-headless:amd64 (8u111-b14-2ubuntu0.16.04.2) ... Removing qhull-bin (2015.2-1) ... Removing xserver-xorg-legacy (2:1.18.4-0ubuntu0.2) ... Removing ant (1.9.6-1ubuntu1) ... Removing antlr3 (3.5.2-4) ... Removing libstringtemplate4-java (4.0.8-2) ... Removing libantlr3-runtime-java (3.5.2-4) ... Removing libcommons-logging-java (1.2-1+build1) ... Removing libcommons-parent-java (39-3) ... Removing libapache-pom-java (10-2build1) ... Removing libapr1:amd64 (1.5.2-3) ... Removing libgeronimo-jpa-2.0-spec-java (1.1-2) ... Removing aspectj (1.8.8-1) ... Removing libaspectj-java (1.8.8-1) ... Removing libgeronimo-osgi-support-java (1.1-1) ... Removing libosgi-compendium-java (5.0.0-3) ... Removing libosgi-core-java (6.0.0-1) ... Removing libosgi-annotation-java (6.0.0-1) ... Removing libosgi-foundation-ee-java (4.2.0-2) ... Removing libservlet3.1-java (8.0.32-1ubuntu1.2) ... Processing triggers for man-db (2.7.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu5) ... [ Tue Dec 13 11:58:40 PST 2016 ] Installing miniconda! --2016-12-13 11:58:40-- http://repo.continuum.io/ miniconda/Miniconda-3.8.3-Linux-x86_64.sh Resolving repo.continuum.io (repo.continuum.io)... 104.16.18.10, 104.16.19.10, 2400:cb00:2048:1::6810:130a, ... Connecting to repo.continuum.io (repo.continuum.io)|104.16.18.10|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://repo.continuum.io/miniconda/Miniconda-3.8.3- Linux-x86_64.sh [following] --2016-12-13 11:58:40-- https://repo.continuum.io/ miniconda/Miniconda-3.8.3-Linux-x86_64.sh Connecting to repo.continuum.io (repo.continuum.io)|104.16.18.10|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 23521627 (22M) [application/octet-stream] Saving to: ‘Miniconda-3.8.3-Linux-x86_64.sh’

`

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nimzodisaster commented 7 years ago

I half suspected that was what was going on, and in this circumstance, relieved.

I do have a concern about the install script at present.

Since C-PAC depends on a lot of other packages (e.g. FSL, ANTs, c3d, AFNI, etc) it is totally reasonable to want to standardize the versions of those packages which are used to help ensure C-PAC works well. Since my server is only analyzing data in C-PAC this is great. However! Many clusters are shared environments, and some even share the same user account; upgrading FSL, FreeSurfer, ANTs for everyone will not be desirable since different software version often produce different results, which is especially problematic for in-progress studies. If CPAC alters the $PATH, or the .bashrc, or replaces an older package with a different version, then researchers may get a nasty surprise. So, I'm wondering to what extent are the C-PAC dependencies separated from the rest of the research environment?

ccraddock commented 7 years ago

Please remove the apt-get upgrade altogether.

Sent from my iPhone

On Dec 13, 2016, at 3:55 PM, John Pellman notifications@github.com wrote:

Assuming that you are using 'cpac_install.sh', the install script runs 'apt-get upgrade' before it installs anything else if you are running an Ubuntu Linux system. This will upgrade the kernel as well as other packages at the system level if possible (i.e., if run as the superuser). This is indeed behavior that you would not expect if you were just running it with the '-p' flag, so we should change this.

On Tue, Dec 13, 2016 at 3:11 PM, Joshua Lee notifications@github.com wrote:

I'm not sure it is a problem but I'm getting nervous. I ran this cd /tmp git clone https://github.com/FCP-INDI/C-PAC.git cd C-PAC python setup.py install

and the installer script seemed to start messing with my linux kernel and grub configuration! I would not have expected that.

Full and lengthy message below `Removing linux-image-extra-4.4.0-21-generic (4.4.0-21.37) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Error! Your kernel headers for kernel 4.4.0-21-generic cannot be found. Please install the linux-headers-4.4.0-21-generic package, or use the --kernelsourcedir option to tell DKMS where it's located Error! Your kernel headers for kernel 4.4.0-21-generic cannot be found. Please install the linux-headers-4.4.0-21-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic update-initramfs: Generating /boot/initrd.img-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found linux image: /boot/vmlinuz-4.4.0-21-generic Found initrd image: /boot/initrd.img-4.4.0-21-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-21-generic (4.4.0-21.37) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-21-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-21-generic /boot/vmlinuz-4.4.0-21-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-22-generic (4.4.0-22.40) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Error! Your kernel headers for kernel 4.4.0-22-generic cannot be found. Please install the linux-headers-4.4.0-22-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic update-initramfs: Generating /boot/initrd.img-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found linux image: /boot/vmlinuz-4.4.0-22-generic Found initrd image: /boot/initrd.img-4.4.0-22-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-22-generic (4.4.0-22.40) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic dkms: removing: bbswitch 0.8 (4.4.0-22-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-22-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-22-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-22-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-22-generic /boot/vmlinuz-4.4.0-22-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-24-generic (4.4.0-24.43) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Error! Your kernel headers for kernel 4.4.0-24-generic cannot be found. Please install the linux-headers-4.4.0-24-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic update-initramfs: Generating /boot/initrd.img-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found linux image: /boot/vmlinuz-4.4.0-24-generic Found initrd image: /boot/initrd.img-4.4.0-24-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-24-generic (4.4.0-24.43) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic dkms: removing: bbswitch 0.8 (4.4.0-24-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-24-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-24-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-24-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-24-generic /boot/vmlinuz-4.4.0-24-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-28-generic (4.4.0-28.47) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Error! Your kernel headers for kernel 4.4.0-28-generic cannot be found. Please install the linux-headers-4.4.0-28-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic update-initramfs: Generating /boot/initrd.img-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found linux image: /boot/vmlinuz-4.4.0-28-generic Found initrd image: /boot/initrd.img-4.4.0-28-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-28-generic (4.4.0-28.47) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic dkms: removing: bbswitch 0.8 (4.4.0-28-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-28-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-28-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-28-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-28-generic /boot/vmlinuz-4.4.0-28-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-31-generic (4.4.0-31.50) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Error! Your kernel headers for kernel 4.4.0-31-generic cannot be found. Please install the linux-headers-4.4.0-31-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic update-initramfs: Generating /boot/initrd.img-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found linux image: /boot/vmlinuz-4.4.0-31-generic Found initrd image: /boot/initrd.img-4.4.0-31-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-31-generic (4.4.0-31.50) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic dkms: removing: bbswitch 0.8 (4.4.0-31-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-31-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-31-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-31-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-31-generic /boot/vmlinuz-4.4.0-31-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-34-generic (4.4.0-34.53) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Error! Your kernel headers for kernel 4.4.0-34-generic cannot be found. Please install the linux-headers-4.4.0-34-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic update-initramfs: Generating /boot/initrd.img-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found linux image: /boot/vmlinuz-4.4.0-34-generic Found initrd image: /boot/initrd.img-4.4.0-34-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-34-generic (4.4.0-34.53) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic dkms: removing: bbswitch 0.8 (4.4.0-34-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-34-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-34-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-34-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-34-generic /boot/vmlinuz-4.4.0-34-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-36-generic (4.4.0-36.55) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Error! Your kernel headers for kernel 4.4.0-36-generic cannot be found. Please install the linux-headers-4.4.0-36-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic update-initramfs: Generating /boot/initrd.img-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found linux image: /boot/vmlinuz-4.4.0-36-generic Found initrd image: /boot/initrd.img-4.4.0-36-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-36-generic (4.4.0-36.55) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic dkms: removing: bbswitch 0.8 (4.4.0-36-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-36-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-36-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-36-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-36-generic /boot/vmlinuz-4.4.0-36-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-38-generic (4.4.0-38.57) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Error! Your kernel headers for kernel 4.4.0-38-generic cannot be found. Please install the linux-headers-4.4.0-38-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic update-initramfs: Generating /boot/initrd.img-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found linux image: /boot/vmlinuz-4.4.0-38-generic Found initrd image: /boot/initrd.img-4.4.0-38-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-38-generic (4.4.0-38.57) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic dkms: removing: bbswitch 0.8 (4.4.0-38-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-38-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-38-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-38-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-38-generic /boot/vmlinuz-4.4.0-38-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-extra-4.4.0-42-generic (4.4.0-42.62) ... run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Error! Your kernel headers for kernel 4.4.0-42-generic cannot be found. Please install the linux-headers-4.4.0-42-generic package, or use the --kernelsourcedir option to tell DKMS where it's located run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic update-initramfs: Generating /boot/initrd.img-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/pm-utils 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/update-notifier 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found linux image: /boot/vmlinuz-4.4.0-42-generic Found initrd image: /boot/initrd.img-4.4.0-42-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing linux-image-4.4.0-42-generic (4.4.0-42.62) ... Examining /etc/kernel/prerm.d. run-parts: executing /etc/kernel/prerm.d/dkms 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic dkms: removing: bbswitch 0.8 (4.4.0-42-generic) (x86_64) -------- Uninstall Beginning -------- Module: bbswitch Version: 0.8 Kernel: 4.4.0-42-generic (x86_64)

Status: Before uninstall, this module version was ACTIVE on this kernel.

bbswitch.ko:

  • Uninstallation
  • Deleting from: /lib/modules/4.4.0-42-generic/updates/dkms/
  • Original module
  • No original module was found for this module on this kernel.
  • Use the dkms install command to reinstall any previous module version.

depmod....

DKMS: uninstall completed. Examining /etc/kernel/postrm.d . run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic update-initramfs: Deleting /boot/initrd.img-4.4.0-42-generic run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.4.0-42-generic /boot/vmlinuz-4.4.0-42-generic Generating grub configuration file ... Found linux image: /boot/vmlinuz-4.4.0-53-generic Found initrd image: /boot/initrd.img-4.4.0-53-generic Found linux image: /boot/vmlinuz-4.4.0-51-generic Found initrd image: /boot/initrd.img-4.4.0-51-generic Found linux image: /boot/vmlinuz-4.4.0-47-generic Found initrd image: /boot/initrd.img-4.4.0-47-generic Found linux image: /boot/vmlinuz-4.4.0-45-generic Found initrd image: /boot/initrd.img-4.4.0-45-generic Found memtest86+ image: /boot/memtest86+.elf Found memtest86+ image: /boot/memtest86+.bin Found Windows 7 (loader) on /dev/sda1 done Removing nifti-bin (2.0.0-2) ... Removing openjdk-8-doc (8u111-b14-2ubuntu0.16.04.2) ... Removing openjdk-8-jdk:amd64 (8u111-b14-2ubuntu0.16.04.2) ... Removing openjdk-8-jdk-headless:amd64 (8u111-b14-2ubuntu0.16.04.2) ... Removing qhull-bin (2015.2-1) ... Removing xserver-xorg-legacy (2:1.18.4-0ubuntu0.2) ... Removing ant (1.9.6-1ubuntu1) ... Removing antlr3 (3.5.2-4) ... Removing libstringtemplate4-java (4.0.8-2) ... Removing libantlr3-runtime-java (3.5.2-4) ... Removing libcommons-logging-java (1.2-1+build1) ... Removing libcommons-parent-java (39-3) ... Removing libapache-pom-java (10-2build1) ... Removing libapr1:amd64 (1.5.2-3) ... Removing libgeronimo-jpa-2.0-spec-java (1.1-2) ... Removing aspectj (1.8.8-1) ... Removing libaspectj-java (1.8.8-1) ... Removing libgeronimo-osgi-support-java (1.1-1) ... Removing libosgi-compendium-java (5.0.0-3) ... Removing libosgi-core-java (6.0.0-1) ... Removing libosgi-annotation-java (6.0.0-1) ... Removing libosgi-foundation-ee-java (4.2.0-2) ... Removing libservlet3.1-java (8.0.32-1ubuntu1.2) ... Processing triggers for man-db (2.7.5-1) ... Processing triggers for libc-bin (2.23-0ubuntu5) ... [ Tue Dec 13 11:58:40 PST 2016 ] Installing miniconda! --2016-12-13 11:58:40-- http://repo.continuum.io/ miniconda/Miniconda-3.8.3-Linux-x86_64.sh Resolving repo.continuum.io (repo.continuum.io)... 104.16.18.10, 104.16.19.10, 2400:cb00:2048:1::6810:130a, ... Connecting to repo.continuum.io (repo.continuum.io)|104.16.18.10|:80... connected. HTTP request sent, awaiting response... 301 Moved Permanently Location: https://repo.continuum.io/miniconda/Miniconda-3.8.3- Linux-x86_64.sh [following] --2016-12-13 11:58:40-- https://repo.continuum.io/ miniconda/Miniconda-3.8.3-Linux-x86_64.sh Connecting to repo.continuum.io (repo.continuum.io)|104.16.18.10|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 23521627 (22M) [application/octet-stream] Saving to: ‘Miniconda-3.8.3-Linux-x86_64.sh’

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jpellman commented 7 years ago

Done.

jpellman commented 7 years ago

Hi @nimzodisaster ,

Many clusters are shared environments, and some even share the same user account; upgrading FSL, FreeSurfer, ANTs for everyone will not be desirable since different software version often produce different results, which is especially problematic for in-progress studies.

This is the kind of scenario where you might want to consider a container-based system. Services such as Docker and Singularity allow you to isolate specific versions of these dependencies from the rest of the system and completely control the ecosystem that your pipeline runs in without affecting other users. I might have mentioned this earlier, but C-PAC has a pre-configured Docker environment that can run pipelines without installing any dependencies on your server (see here). We're working towards having a similar pre-configured setup available for Singularity as well.

Another frequently employed strategy for keeping conflicting versions of software packages separate include using environmental modules, which allows you to swap out different versions of various libraries and binaries.

So, I'm wondering to what extent are the C-PAC dependencies separated from the rest of the research environment?

With respect to the C-PAC install script in particular you can do a local installation that will install dependencies in your home directory and not affect other users. Dependencies that operate at the system-level (such as the libxp library used by AFNI) cannot be installed when doing a local install so you'd still need someone with superuser privileges to install these. To the extent that it is possible, though, the local installation will put copies of AFNI/FSL/ANTS/Miniconda in your home directory and update your individual user's .bashrc file. Note that FSL cannot be installed in Debian-based distributions through sources other than Neurodebian, and as such still requires superuser privileges to install.

The syntax for running the local install is:

./cpac_install.sh -l

nimzodisaster commented 7 years ago

Thanks John for your thoughtful reply.

These are several of the reasons I'm excited by containerization technology for science research applications. Admittedly, as compute capabilities continue to expand, even using whole virtual instances of Linux to isolate environments is a workable solution. I thought about trying the C-PAC Docker container, but is it still only capable of doing preprocessing? .

On Wed, Dec 14, 2016 at 1:50 PM, John Pellman notifications@github.com wrote:

Hi @nimzodisaster https://github.com/nimzodisaster ,

Many clusters are shared environments, and some even share the same user account; upgrading FSL, FreeSurfer, ANTs for everyone will not be desirable since different software version often produce different results, which is especially problematic for in-progress studies.

This is the kind of scenario where you might want to consider a container-based system. Services such as Docker and Singularity allow you to isolate specific versions of these dependencies from the rest of the system and completely control the ecosystem that your pipeline runs in without affecting other users. I might have mentioned this earlier, but C-PAC has a pre-configured Docker environment that can run pipelines without installing any dependencies on your server (see here https://github.com/BIDS-Apps/CPAC). We're working towards having a similar pre-configured setup available for Singularity as well.

Another frequently employed strategy for keeping conflicting versions of software packages separate include using environmental modules http://modules.sourceforge.net/, which allows you to swap out different versions of various libraries and binaries.

So, I'm wondering to what extent are the C-PAC dependencies separated from the rest of the research environment?

With respect to the C-PAC install script in particular you can do a local installation that will install dependencies in your home directory and not affect other users. Dependencies that operate at the system-level (such as the libxp library used by AFNI) cannot be installed when doing a local install so you'd still need someone with superuser privileges to install these. To the extent that it is possible, though, the local installation will put copies of AFNI/FSL/ANTS/Miniconda in your home directory and update your individual user's .bashrc file. Note that FSL cannot be installed in Debian-based distributions through sources other than Neurodebian, and as such still requires superuser privileges to install.

The syntax for running the local install is:

./cpac_install.sh -l

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sgiavasis commented 6 years ago

Hi @nimzodisaster,

We do have a C-PAC Docker container image available, and it can run both individual and group-level analyses. More information is available here: https://github.com/BIDS-Apps/CPAC

Best, Steve