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Thread: problems with updating the system

  1. #1
    Join Date
    Mar 2013
    Posts
    48

    Default problems with updating the system

    Hi all,

    I'm trying to update my system but I'm having the problem pasted below. This happens for about a month now. Any ideas on how to fix this?

    Thanks!

    Code:
    ➜  applications  sudo zypper cleanroot's password:
    All repositories have been cleaned up.
    ➜  applications  sudo zypper dup
    Warning: You are about to do a distribution upgrade with all enabled repositories. Make sure these repositories are compatible before you continue. See 'man zypper' for more information about this command.
    Loading repository data...
    Reading installed packages...
    Computing distribution upgrade...
    
    The following 3 packages are going to be upgraded:
      dkms-nvidia python-pycrypto x11-video-nvidia 
    
    3 packages to upgrade.
    Overall download size: 382.8 KiB. After the operation, additional 182.0 KiB will be used.
    Continue? [y/n/? shows all options] (y): y
    Retrieving package dkms-nvidia-331.49-1.1.x86_64                                                                                                                                                            (1/3),   6.6 KiB (  513 B unpacked)
    Retrieving: dkms-nvidia-331.49-1.1.x86_64.rpm ...........................................................................................................................................................................................[done]
    Retrieving package x11-video-nvidia-331.49-1.1.x86_64                                                                                                                                                       (2/3),   9.8 KiB (  495 B unpacked)
    Retrieving: x11-video-nvidia-331.49-1.1.x86_64.rpm ......................................................................................................................................................................................[done]
    Retrieving package python-pycrypto-2.6-3.1.2.x86_64                                                                                                                                                       (3/3), 366.3 KiB (  2.0 MiB unpacked)
    Retrieving: python-pycrypto-2.6-3.1.2.x86_64.rpm ..........................................................................................................................................................................[done (481.3 KiB/s)]
    (1/3) Installing: dkms-nvidia-331.49-1.1 ...............................................................................................................................................................................................[error]
    Installation of dkms-nvidia-331.49-1.1 failed:
    Error: Subprocess failed. Error: RPM failed: Error in checksums 256293698 71803884
    error: %pre(dkms-nvidia-331.49-1.1.x86_64) scriptlet failed, exit status 254
    error: dkms-nvidia-331.49-1.1.x86_64: install failed
    error: dkms-nvidia-331.38-2.1.x86_64: erase skipped
    
    
    Abort, retry, ignore? [a/r/i] (a): i
    (2/3) Installing: x11-video-nvidia-331.49-1.1 ..........................................................................................................................................................................................[error]
    Installation of x11-video-nvidia-331.49-1.1 failed:
    Error: Subprocess failed. Error: RPM failed: Error in checksums 256293698 71803884
    error: %pre(x11-video-nvidia-331.49-1.1.x86_64) scriptlet failed, exit status 254
    error: x11-video-nvidia-331.49-1.1.x86_64: install failed
    error: x11-video-nvidia-331.38-3.1.x86_64: erase skipped
    
    
    Abort, retry, ignore? [a/r/i] (a): i
    (3/3) Installing: python-pycrypto-2.6-3.1.2 ............................................................................................................................................................................................[error]
    Installation of python-pycrypto-2.6-3.1.2 failed:
    Error: Subprocess failed. Error: RPM failed: error: unpacking of archive failed on file /usr/lib64/python2.7/site-packages/pycrypto-2.6-py2.7.egg-info: cpio: rename failed - Is a directory
    error: python-pycrypto-2.6-3.1.2.x86_64: install failed
    error: python-pycrypto-2.5-7.1.1.x86_64: erase skipped
    
    
    Abort, retry, ignore? [a/r/i] (a): i
    There are some running programs that use files deleted by recent upgrade. You may wish to restart some of them. Run 'zypper ps' to list these programs. ➜  applications  

  2. #2

    Default Re: problems with updating the system

    Quote Originally Posted by osa1 View Post
    Code:
    ➜  applications  sudo zypper cleanroot's password:
    All repositories have been cleaned up.
    ➜  applications  sudo zypper dup
    Warning: You are about to do a distribution upgrade with all enabled repositories. Make sure these repositories are compatible before you continue. See 'man zypper' for more information about this command.
    Why are you doing a distribution upgrade?
    You should use "zypper up" to update your system, except if you're running Factory or Tumbleweed. But in that case you would be posting to the wrong forum...

    Or do you mean to upgrade your openSUSE version to a newer one?
    You should have mentioned that. It's adviseable to disable _all_ additional repos in that case.

    Code:
    (1/3) Installing: dkms-nvidia-331.49-1.1 ...............................................................................................................................................................................................[error]
    Installation of dkms-nvidia-331.49-1.1 failed:
    Error: Subprocess failed. Error: RPM failed: Error in checksums 256293698 71803884
    error: %pre(dkms-nvidia-331.49-1.1.x86_64) scriptlet failed, exit status 254
    error: dkms-nvidia-331.49-1.1.x86_64: install failed
    error: dkms-nvidia-331.38-2.1.x86_64: erase skipped
    
    
    Abort, retry, ignore? [a/r/i] (a): i
    (2/3) Installing: x11-video-nvidia-331.49-1.1 ..........................................................................................................................................................................................[error]
    Installation of x11-video-nvidia-331.49-1.1 failed:
    Error: Subprocess failed. Error: RPM failed: Error in checksums 256293698 71803884
    error: %pre(x11-video-nvidia-331.49-1.1.x86_64) scriptlet failed, exit status 254
    error: x11-video-nvidia-331.49-1.1.x86_64: install failed
    error: x11-video-nvidia-331.38-3.1.x86_64: erase skipped
    Apparently something went wrong with the nvidia driver download. The checksum is wrong.
    Remove the downloaded file:
    Code:
    sudo rm /usr/src/NVIDIA*.run
    Then try the update again.

    Code:
    (3/3) Installing: python-pycrypto-2.6-3.1.2 ............................................................................................................................................................................................[error]
    Installation of python-pycrypto-2.6-3.1.2 failed:
    Error: Subprocess failed. Error: RPM failed: error: unpacking of archive failed on file /usr/lib64/python2.7/site-packages/pycrypto-2.6-py2.7.egg-info: cpio: rename failed - Is a directory
    error: python-pycrypto-2.6-3.1.2.x86_64: install failed
    error: python-pycrypto-2.5-7.1.1.x86_64: erase skipped
    Remove that directory and the update should install fine:
    Code:
    sudo rm -r /usr/lib64/python2.7/site-packages/pycrypto-2.6-py2.7.egg-info
    That's a limitation of rpm that it cannot change a directory to a file or symlink. (apparently the package you have installed includes a directory of that name, but the newer one has a file/symlink of the same name)
    Last edited by wolfi323; 19-Apr-2014 at 11:41.

  3. #3
    Join Date
    Mar 2013
    Posts
    48

    Default Re: problems with updating the system

    Thanks, this solved the problem. But now optirun is not working:

    Code:
    ➜  ~  optirun glxgears
    [  193.300445] [ERROR]Cannot access secondary GPU - error: [XORG] (EE) NVIDIA(0): Failed to initialize the NVIDIA kernel module. Please see the
    
    
    [  193.300514] [ERROR]Aborting because fallback start is disabled.
    Where should I ask this?

  4. #4

    Default Re: problems with updating the system

    Quote Originally Posted by osa1 View Post
    Code:
    [  193.300445] [ERROR]Cannot access secondary GPU - error: [XORG] (EE) NVIDIA(0): Failed to initialize the NVIDIA kernel module. Please see the
    Seems like the nvidia kernel module is not installed now.
    Did you get any other error when installing dkms-nvidia?

    Try to install it again and post the output:
    Code:
    sudo zypper in -f dkms-nvidia

  5. #5
    Join Date
    Mar 2013
    Posts
    48

    Default Re: problems with updating the system

    Here:


    Code:
    
    ➜  ~  sudo zypper install -f dkms-nvidia
    root's password:
    Loading repository data...
    Reading installed packages...
    Forcing installation of 'dkms-nvidia-331.49-1.1.x86_64' from repository 'Overman79'.
    Resolving package dependencies...
    
    
    The following package is going to be reinstalled:
      dkms-nvidia 
    
    
    1 package to reinstall.
    Overall download size: 6.6 KiB. No additional space will be used or freed after the operation.
    Continue? [y/n/? shows all options] (y): y
    Retrieving package dkms-nvidia-331.49-1.1.x86_64                                                                                                                                                            (1/1),   6.6 KiB (  513 B unpacked)
    Retrieving: dkms-nvidia-331.49-1.1.x86_64.rpm ...........................................................................................................................................................................................[done]
    (1/1) Installing: dkms-nvidia-331.49-1.1 ................................................................................................................................................................................................[done]
    Additional rpm output:
    check sums and md5 sums are ok
    + '[' -x /usr/sbin/dkms ']'
    + /usr/sbin/dkms add -m nvidia -v 331.49-1.1 --rpm_safe_upgrade
    Error! DKMS tree already contains: nvidia-331.49-1.1
    You cannot add the same module/version combo more than once.
    + /usr/sbin/dkms build -m nvidia -v 331.49-1.1
    Module nvidia/331.49-1.1 already built for kernel 3.11.10-7-desktop/4
    + /usr/sbin/dkms install -m nvidia -v 331.49-1.1
    
    
    nvidia:
    Running module version sanity check.
     - Original module
       - Found /lib/modules/3.11.10-7-desktop/updates/nvidia.ko
       - Storing in /var/lib/dkms/nvidia/original_module/3.11.10-7-desktop/x86_64/
       - Archiving for uninstallation purposes
     - Installation
       - Installing to /lib/modules/3.11.10-7-desktop/updates//
    Adding any weak-modules
    
    
    Kernel image:   /boot/vmlinuz-3.11.6-4-desktop
    Initrd image:   /boot/initrd-3.11.6-4-desktop
    KMS drivers:     i915
    Root device:    /dev/disk/by-id/ata-Corsair_Force_GT_123979170000201101CF-part2 (/dev/sda2) (mounted on / as ext4)
    Resume device:  /dev/disk/by-id/ata-Corsair_Force_GT_123979170000201101CF-part1 (/dev/sda1)
    Microcode: Adding Intel microcode 06-3a-09
    Kernel Modules: thermal_sys thermal processor fan drm nvidia scsi_dh scsi_dh_rdac scsi_dh_emc scsi_dh_hp_sw scsi_dh_alua video button i2c-algo-bit drm_kms_helper i915 xhci-hcd hid-logitech-dj hid-holtek-kbd hid-lenovo-tpkbd hid-ortek hid-roccat hid-roccat-common hid-roccat-arvo hid-roccat-isku hid-samsung ohci-pci libcrc32c xor zlib_deflate raid6_pq btrfs crc32c-intel 
    Features:       acpi intel_microcode kms plymouth block usb btrfs resume.userspace resume.kernel
    
    
    depmod....
    
    
    Backing up initrd-3.11.10-7-desktop to /boot/initrd-3.11.10-7-desktop.old-dkms
    Making new initrd-3.11.10-7-desktop
    (If next boot fails, revert to initrd-3.11.10-7-desktop.old-dkms image)
    Error! Unable to find valid kernel file under 
    /boot for kernel version 3.11.10-7-desktop
    
    
    -------- Uninstall Beginning --------
    Module:  nvidia
    Version: 331.49-1.1
    Kernel:  3.11.10-7-desktop (x86_64)
    -------------------------------------
    
    
    Status: Before uninstall, this module version was ACTIVE on this kernel.
    Removing any linked weak-modules
    
    
    nvidia.ko:
     - Uninstallation
       - Deleting from: /lib/modules/3.11.10-7-desktop/updates//
     - Original module
       - Archived original module found in the DKMS tree
       - Moving it to: /lib/modules/3.11.10-7-desktop/updates//
    depmod....
    
    
    Backing up initrd-3.11.10-7-desktop to /boot/initrd-3.11.10-7-desktop.old-dkms
    Making new initrd-3.11.10-7-desktop
    (If next boot fails, revert to initrd-3.11.10-7-desktop.old-dkms image)
    Error! Unable to find valid kernel file under 
    /boot for kernel version 3.11.10-7-desktop
    : There was a problem remaking your initrd.  You must manually remake it
    before booting into this kernel.
    
    
    Removing original_module from DKMS tree for kernel 3.11.10-7-desktop (x86_64)
    
    
    DKMS: uninstall completed.
    Error! Problems with mkinitrd detected.  Automatically uninstalling this module.
    DKMS: Install Failed (mkinitrd problems).  Module rolled back to built state.
    + popd
    
    
    
    
    ➜  ~

  6. #6

    Default Re: problems with updating the system

    This seems to be the problem:
    Quote Originally Posted by osa1 View Post
    Code:
    Making new initrd-3.11.10-7-desktop
    (If next boot fails, revert to initrd-3.11.10-7-desktop.old-dkms image)
    Error! Unable to find valid kernel file under 
    /boot for kernel version 3.11.10-7-desktop
    : There was a problem remaking your initrd.  You must manually remake it
    before booting into this kernel.
    Strange that it wouldn't find a valid kernel file.

    Do you maybe have a separate /boot partition that's full possibly?
    Code:
    df -h /boot
    Does it work if you call "mkinitrd" manually, as the message suggests?

  7. #7
    Join Date
    Mar 2013
    Posts
    48

    Default Re: problems with updating the system

    I don't know about boot partition, I'm using openSUSE with default installation settings:

    Code:
    
    ➜  ~  df -h /boot
    Filesystem      Size  Used Avail Use% Mounted on
    /dev/sda2        20G   15G  4.3G  77% /
    Manually calling mkinitrd did not make any change.

  8. #8

    Default AW: Re: problems with updating the system

    Quote Originally Posted by osa1 View Post
    Code:
    
    ➜  ~  df -h /boot
    Filesystem      Size  Used Avail Use% Mounted on
    /dev/sda2        20G   15G  4.3G  77% /
    Should be enough free space.

    Manually calling mkinitrd did not make any change.
    Ok, but did you get any error message?

    Maybe try to remove dkms-nvidia and then install it again?
    Code:
    sudo rpm -e --nodeps dkms-nvidia
    sudo zypper in dkms-nvidia

  9. #9
    Join Date
    Mar 2013
    Posts
    48

    Default Re: problems with updating the system

    No, I didn't get any errors:


    Code:
    
    
    linux-axly:/home/omer # mkinitrd
    
    
    Kernel image:   /boot/vmlinuz-3.11.10-7-desktop
    Initrd image:   /boot/initrd-3.11.10-7-desktop
    KMS drivers:     i915
    Root device:    /dev/disk/by-id/ata-Corsair_Force_GT_123979170000201101CF-part2 (/dev/sda2) (mounted on / as ext4)
    Resume device:  /dev/disk/by-id/ata-Corsair_Force_GT_123979170000201101CF-part1 (/dev/sda1)
    Microcode: Adding Intel microcode 06-3a-09
    Kernel Modules: thermal_sys thermal processor fan drm nvidia scsi_dh scsi_dh_rdac scsi_dh_emc scsi_dh_hp_sw scsi_dh_alua video button i2c-algo-bit drm_kms_helper i915 xhci-hcd hid-logitech-dj hid-holtek-kbd hid-lenovo-tpkbd hid-ortek hid-roccat hid-roccat-common hid-roccat-arvo hid-roccat-isku hid-samsung ohci-pci libcrc32c xor zlib_deflate raid6_pq btrfs crc32c-intel 
    Features:       acpi intel_microcode kms plymouth block usb btrfs resume.userspace resume.kernel
    
    
    Kernel image:   /boot/vmlinuz-3.11.6-4-desktop
    Initrd image:   /boot/initrd-3.11.6-4-desktop
    KMS drivers:     i915
    Root device:    /dev/disk/by-id/ata-Corsair_Force_GT_123979170000201101CF-part2 (/dev/sda2) (mounted on / as ext4)
    Resume device:  /dev/disk/by-id/ata-Corsair_Force_GT_123979170000201101CF-part1 (/dev/sda1)
    Microcode: Adding Intel microcode 06-3a-09
    Kernel Modules: thermal_sys thermal processor fan drm nvidia scsi_dh scsi_dh_rdac scsi_dh_emc scsi_dh_hp_sw scsi_dh_alua video button i2c-algo-bit drm_kms_helper i915 xhci-hcd hid-logitech-dj hid-holtek-kbd hid-lenovo-tpkbd hid-ortek hid-roccat hid-roccat-common hid-roccat-arvo hid-roccat-isku hid-samsung ohci-pci libcrc32c xor zlib_deflate raid6_pq btrfs crc32c-intel 
    Features:       acpi intel_microcode kms plymouth block usb btrfs resume.userspace resume.kernel

    Also, removing dkms-nvidia and then installing again did not work(failed with same problems).

  10. #10

    Default AW: Re: problems with updating the system

    Quote Originally Posted by osa1 View Post
    Also, removing dkms-nvidia and then installing again did not work(failed with same problems).
    Hm, I never used dkms (or bumblebee) myself.

    But in another thread where I tried to help, we got the same error message:
    https://forums.opensuse.org/showthre...87#post2627987

    Apparently what fixed it there in the end was:
    Code:
    zypper in -f kernel-desktop
    zypper in -f dkms-nvidia
    So try that please, but uninstall dkms-nvidia first..

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