Udoo will not boot after apt-get upgrade

Discussion in 'UDOO NEO' started by lazerdye, Nov 9, 2015.

  1. feesma

    feesma New Member

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    Hi, apt-get update and upgrade works now. Udoo is rebooting. Thx.
     
  2. sieler

    sieler New Member

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    Still does not work for me.

    Note: I'm assuming you did not build a new .img file. I'm still using
    3131047936 Oct 28 16:48 udoobuntu_neo_v2.0beta3.img

    apt-get update / apt-get upgrade still gets error in same place.

    After that, reboot fails in same way. Here's console output, with some lines deleted to get under the 10,000 char limit of this forum.


    Welcome to Ubuntu 14.04.3 LTS (GNU/Linux 3.14.28-udooneo-04196-gb15f827 armv7l)

    * Documentation: https://help.ubuntu.com/

    The programs included with the Ubuntu system are free software;
    the exact distribution terms for each program are described in the
    individual files in /usr/share/doc/*/copyright.

    Ubuntu comes with ABSOLUTELY NO WARRANTY, to the extent permitted by
    applicable law.

    udooer@udooneo:~$ sudo su -
    [sudo] password for udooer:
    root@udooneo:~# apt-get update
    Ign http://ports.ubuntu.com trusty InRelease
    Get:1 http://repository.udoo.org udoobuntu InRelease [2,094 B]
    Get:2 http://ports.ubuntu.com trusty-updates InRelease [64.4 kB]
    Get:3 http://repository.udoo.org udoobuntu/main armhf Packages [32.4 kB]
    Get:4 http://ports.ubuntu.com trusty-security InRelease [64.4 kB]
    Ign http://repository.udoo.org udoobuntu/main Translation-en
    Hit http://ports.ubuntu.com trusty Release.gpg
    Get:5 http://ports.ubuntu.com trusty-updates/main armhf Packages [577 kB]
    Get:6 http://ports.ubuntu.com trusty-updates/universe armhf Packages [322 kB]
    Get:7 http://ports.ubuntu.com trusty-updates/multiverse armhf Packages [9,755 B]
    ...
    Get:16 http://ports.ubuntu.com trusty-security/universe Translation-en [69.6 kB]
    Hit http://ports.ubuntu.com trusty Release
    Hit http://ports.ubuntu.com trusty/main armhf Packages
    Hit http://ports.ubuntu.com trusty/universe armhf Packages
    Hit http://ports.ubuntu.com trusty/multiverse armhf Packages
    Hit http://ports.ubuntu.com trusty/main Translation-en
    Hit http://ports.ubuntu.com trusty/multiverse Translation-en
    Hit http://ports.ubuntu.com trusty/universe Translation-en
    Fetched 2,304 kB in 26s (87.4 kB/s)
    Reading package lists... Done

    root@udooneo:~# time apt-get upgrade
    Reading package lists... Done
    Building dependency tree
    Reading state information... Done
    Calculating upgrade... Done
    The following packages will be upgraded:
    arduino arduino-core arduino-core-udooneo gir1.2-vte-2.90 indicator-session
    krb5-locales libdrm-dev libdrm-exynos1 libdrm-freedreno1 libdrm-nouveau2
    libdrm-omap1 libdrm-radeon1 libdrm2 libgssapi-krb5-2 libido3-0.1-0
    libk5crypto3 libkrb5-3 libkrb5support0 libnautilus-extension1a libnspr4
    libnss3 libnss3-nssdb libpoppler-glib8 libpoppler44 libvte-2.90-9
    libvte-2.90-common libxml2 linux-firmware-image-3.14.28-udooneo
    linux-image-3.14.28-udooneo nautilus-data poppler-utils python-libxml2
    udooneo-bluetooth unity-settings-daemon unzip xserver-common
    xserver-xorg-core xserver-xorg-dev
    The following packages will be DOWNGRADED:
    linux-dtb-3.14.28-udooneo
    38 upgraded, 0 newly installed, 1 downgraded, 0 to remove and 0 not upgraded.
    Need to get 41.6 MB of archives.
    After this operation, 2,185 kB disk space will be freed.
    Do you want to continue? [Y/n] y
    Get:1 http://repository.udoo.org/ udoobuntu/main libdrm-dev armhf 2.4.60-2~ubuntu14.04.2-udoo [139 kB]
    Get:2 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main libk5crypto3 armhf 1.12+dfsg-2ubuntu5.2 [75.9 kB]
    Get:3 http://repository.udoo.org/ udoobuntu/main libdrm2 armhf 2.4.60-2~ubuntu14.04.2-udoo [26.8 kB]
    Get:4 http://repository.udoo.org/ udoobuntu/main libdrm-radeon1 armhf 2.4.60-2~ubuntu14.04.2-udoo [27.9 kB]
    Get:8 http://repository.udoo.org/ udoobuntu/main libdrm-freedreno1 armhf 2.4.60-2~ubuntu14.04.2-udoo [19.6 kB]
    ...
    Get:29 http://repository.udoo.org/ udoobuntu/main xserver-xorg-dev armhf 2:1.15.1-0ubuntu2.7udoo [290 kB]
    Get:30 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main indicator-session armhf 12.10.5+14.04.20151021.1-0ubuntu1 [91.1 kB]
    Get:31 http://repository.udoo.org/ udoobuntu/main arduino all 1.6.5-r3ubuntu4 [12.0 MB]
    Get:32 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main libnautilus-extension1a armhf 1:3.10.1-0ubuntu9.11 [50.2 kB]
    Get:33 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main nautilus-data all 1:3.10.1-0ubuntu9.11 [50.7 kB]
    Get:34 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main poppler-utils armhf 0.24.5-2ubuntu4.3 [102 kB]
    Get:35 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main python-libxml2 armhf 2.9.1+dfsg1-3ubuntu4.5 [123 kB]
    Get:36 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main unity-settings-daemon armhf 14.04.0+14.04.20151012-0ubuntu1 [452 kB]
    Get:37 http://ports.ubuntu.com/ubuntu-ports/ trusty-updates/main unzip armhf 6.0-9ubuntu1.5 [151 kB]
    Get:38 http://repository.udoo.org/ udoobuntu/main arduino-core all 1.6.5-r3ubuntu4 [13.9 MB]
    Get:39 http://repository.udoo.org/ udoobuntu/main arduino-core-udooneo all 1.6.5-r3ubuntu4 [803 kB]
    Fetched 41.6 MB in 40s (1,020 kB/s)
    Extracting templates from packages: 100%
    (Reading database ... 105557 files and directories currently installed.)
    Preparing to unpack .../libk5crypto3_1.12+dfsg-2ubuntu5.2_armhf.deb ...
    Unpacking libk5crypto3:armhf (1.12+dfsg-2ubuntu5.2) over (1.12+dfsg-2ubuntu5.1) ...
    ...
    Preparing to unpack .../indicator-session_12.10.5+14.04.20151021.1-0ubuntu1_armhf.deb ...
    Unpacking indicator-session (12.10.5+14.04.20151021.1-0ubuntu1) over (12.10.5+14.04.20151008-0ubuntu1) ...
    Preparing to unpack .../libnautilus-extension1a_1%3a3.10.1-0ubuntu9.11_armhf.deb ...
    Unpacking libnautilus-extension1a (1:3.10.1-0ubuntu9.11) over (1:3.10.1-0ubuntu9.9) ...
    Preparing to unpack .../linux-image-3.14.28-udooneo_04206-g9e7d486_armhf.deb ...
    Unpacking linux-image-3.14.28-udooneo (04206-g9e7d486) over (04196-gb15f827) ...
    dpkg: error processing archive /var/cache/apt/archives/linux-image-3.14.28-udooneo_04206-g9e7d486_armhf.deb (--unpack):
    trying to overwrite '/boot/dts/imx6sx-udoo-neo-hdmi.dtb', which is also in package linux-dtb-3.14.28-udooneo 04196-gb15f827
    dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
    dpkg: warning: downgrading linux-dtb-3.14.28-udooneo from 04196-gb15f827 to 1.0-1
    Preparing to unpack .../linux-dtb-3.14.28-udooneo_1.0-1_all.deb ...
    Unpacking linux-dtb-3.14.28-udooneo (1.0-1) over (04196-gb15f827) ...
    Preparing to unpack .../linux-firmware-image-3.14.28-udooneo_04204-ge2a34ed_armhf.deb ...
    Unpacking linux-firmware-image-3.14.28-udooneo (04204-ge2a34ed) over (04196-gb15f827) ...
    Preparing to unpack .../nautilus-data_1%3a3.10.1-0ubuntu9.11_all.deb ...
    Unpacking nautilus-data (1:3.10.1-0ubuntu9.11) over (1:3.10.1-0ubuntu9.9) ...
    Preparing to unpack .../poppler-utils_0.24.5-2ubuntu4.3_armhf.deb ...
    Unpacking poppler-utils (0.24.5-2ubuntu4.3) over (0.24.5-2ubuntu4.2) ...
    Preparing to unpack .../python-libxml2_2.9.1+dfsg1-3ubuntu4.5_armhf.deb ...
    Unpacking python-libxml2 (2.9.1+dfsg1-3ubuntu4.5) over (2.9.1+dfsg1-3ubuntu4.4) ...
    Preparing to unpack .../udooneo-bluetooth_1.2_armhf.deb ...
    UIM SYSFS Node Found at /sys/./devices/soc0/kim.21/install
    Stopping uim-sysfs daemon.
    Unpacking udooneo-bluetooth (1.2) over (1.1) ...
    Preparing to unpack .../unity-settings-daemon_14.04.0+14.04.20151012-0ubuntu1_armhf.deb ...
    Unpacking unity-settings-daemon (14.04.0+14.04.20151012-0ubuntu1) over (14.04.0+14.04.20150825-0ubuntu2) ...
    Preparing to unpack .../unzip_6.0-9ubuntu1.5_armhf.deb ...
    Unpacking unzip (6.0-9ubuntu1.5) over (6.0-9ubuntu1.3) ...
    Preparing to unpack .../xserver-common_2%3a1.15.1-0ubuntu2.7udoo_all.deb ...
    Unpacking xserver-common (2:1.15.1-0ubuntu2.7udoo) over (2:1.15.1-0ubuntu2.7) ...
    Preparing to unpack .../xserver-xorg-core_2%3a1.15.1-0ubuntu2.7udoo_armhf.deb ...
    Unpacking xserver-xorg-core (2:1.15.1-0ubuntu2.7udoo) over (2:1.15.1-0ubuntu2.7) ...
    Preparing to unpack .../xserver-xorg-dev_2%3a1.15.1-0ubuntu2.7udoo_armhf.deb ...
    Unpacking xserver-xorg-dev (2:1.15.1-0ubuntu2.7udoo) over (2:1.15.1-0ubuntu2.7) ...
    Preparing to unpack .../arduino_1.6.5-r3ubuntu4_all.deb ...
    Unpacking arduino (1.6.5-r3ubuntu4) over (1.6.5-r3ubuntu3) ...
    Preparing to unpack .../arduino-core_1.6.5-r3ubuntu4_all.deb ...
    Unpacking arduino-core (1.6.5-r3ubuntu4) over (1.6.5-r3ubuntu3) ...
    Preparing to unpack .../arduino-core-udooneo_1.6.5-r3ubuntu4_all.deb ...
    Unpacking arduino-core-udooneo (1.6.5-r3ubuntu4) over (1.6.5-r3ubuntu3) ...
    Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
    Processing triggers for libglib2.0-0:armhf (2.40.2-0ubuntu1) ...
    Processing triggers for hicolor-icon-theme (0.13-1) ...
    Processing triggers for shared-mime-info (1.2-0ubuntu3) ...
    Processing triggers for gconf2 (3.2.6-0ubuntu2) ...
    Processing triggers for ureadahead (0.100.0-16) ...
    Processing triggers for mime-support (3.54ubuntu1.1) ...
    Processing triggers for gnome-menus (3.10.1-0ubuntu2) ...
    Processing triggers for desktop-file-utils (0.22-1ubuntu1) ...
    Errors were encountered while processing:
    /var/cache/apt/archives/linux-image-3.14.28-udooneo_04206-g9e7d486_armhf.deb
    E: Sub-process /usr/bin/dpkg returned an error code (1)

    real 2m53.934s
    user 0m37.450s
    sys 0m20.510s
    root@udooneo:~# sync
    root@udooneo:~# shutdown -h now

    I waited a bit, then cycled the power. Doesn't come up.
     
  3. feesma

    feesma New Member

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    I've run sudo apt-get update and apt-get upgrade twice before reboot:
    After the first upgrade this error was throwed:

    /var/cache/apt/archives/linux-image-3.14.28-udooneo_04206-g9e7d486_armhf.deb
    E: Sub-process /usr/bin/dpkg returned an error code (1)

    The second time I run update and upgrade the error was gone. After this I rebooted the Udoo Board with:
    sudo reboot

    Hope this will help!
     
  4. Marcelo Duarte Trevisani

    Marcelo Duarte Trevisani New Member

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    I tried what you did but the udoo neo still doesnt work after the upgrade
     
    sieler likes this.
  5. Xykon

    Xykon Member

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    I used dist-upgrade instead of upgrade just out of habit... MicroUSB services don't work anymore (no serial console/msd/network)

    Only way to get to the udoo neo again is via wired Ethernet cable... and that seems to be extremely slow.

    Edit:
    When I go to the configuration interface and do the "first configuration" it doesn't show any Wifi networks... and doesn't let me continue.

    Edit2:
    So after the upgrade I check with "cat /proc/version" it gives me 3.14.28-udooneo-04206-g9e7d486
    But when I check /boot I have:
    config-3.14.28-udooneo-04208-g7b269fc
    docs
    dts
    initrd.img-3.14.28-udooneo-04196-gb15f827
    m4clean.fw
    m4startup.fw
    quickstart.html
    System.map-3.14.28-udooneo-04208-g7b269fc
    System Volume Information
    uEnv.txt
    zImage

    Also creating a new initrd fails (which might be the reason for missing Wifi/USB support):
    root@udooneo:~# update-initramfs -ck all
    update-initramfs: Generating /boot/initrd.img-3.14.28-udooneo-04196-gb15f827
    grep: /boot/config-3.14.28-udooneo-04196-gb15f827: No such file or directory
    WARNING: missing /lib/modules/3.14.28-udooneo-04196-gb15f827
    Device driver support needs thus be built-in linux image!
    depmod: ERROR: could not open directory /lib/modules/3.14.28-udooneo-04196-gb15f827: No such file or directory
    depmod: FATAL: could not search modules: No such file or directory
    depmod: WARNING: could not open /tmp/mkinitramfs_VKmAZJ/lib/modules/3.14.28-udooneo-04196-gb15f827/modules.order: No such file or directory
    depmod: WARNING: could not open /tmp/mkinitramfs_VKmAZJ/lib/modules/3.14.28-udooneo-04196-gb15f827/modules.builtin: No such file or directory

    I guess there is something wrong with the upgraded kernel image... need to look into this more.

    Edit3:
    I tried to install the kernel package manually from /var/cache/apt/archive but it fails with the following error:

    root@udooneo:/var/cache/apt/archives# dpkg -i linux-image-3.14.28-udooneo_04208-g7b269fc_armhf.deb
    (Reading database ... 105493 files and directories currently installed.)
    Preparing to unpack linux-image-3.14.28-udooneo_04208-g7b269fc_armhf.deb ...
    Unpacking linux-image-3.14.28-udooneo (04208-g7b269fc) over (04208-g7b269fc) ...
    dpkg: error processing archive linux-image-3.14.28-udooneo_04208-g7b269fc_armhf.deb (--install):
    unable to make backup link of `./boot/System.map-3.14.28-udooneo-04208-g7b269fc' before installing new version: Operation not permitted
    dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
    Errors were encountered while processing:
    linux-image-3.14.28-udooneo_04208-g7b269fc_armhf.deb

    Obviously that's because the boot partition is fat and doesn't support symlinks.
     
    Last edited: Nov 19, 2015
  6. Xykon

    Xykon Member

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    I think I found the problem... when you do an upgrade you install linux-image-3.14.28-udooneo_04208-g7b269fc_armhf.deb

    If you look at dpkg -L linux-image-3.14.28-udooneo you can find that modules are installed in /lib/modules/3.14.28-udooneo-04208-g7b269fc

    But the kernel (zImage) that is installed with this package seems to be 3.14.28-udooneo-04206-g9e7d486

    Either the kernel file /boot/zImage isn't correctly replaced or there is an outdated kernel binary in the package.

    Update: I removed the kernel package, checked that /boot/zImage had been deleted (and that /boot was properly mounted) and re-installed the kernel package. After a reboot I'm still at kernel version 3.14.28-udooneo-04206-g9e7d486

    Update2: A quick (but dirty) fix for this is to (all as root, sudo su -) "cd /lib/modules" after running apt-get upgrade and "ln -s 3.14.28-udooneo-04208-g7b269fc 3.14.28-udooneo-04206-g9e7d486"
    I ran "depmod -a" and "update-initramfs -ck 3.14.28-udooneo-04206-g9e7d486" after that as well though it might not be necessary. Now udoo boots back with USB support but I'm getting some errors like "timeout 'accelerometer /devices/virtual/input/input2'". I'm not sure it's actually a good idea to upgrade right now...
     
    Last edited: Nov 20, 2015
    sieler likes this.
  7. mparkes

    mparkes New Member

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    I can confirm this just happened to me.

    I originally thought the reason it wouldn't boot was that I ran "sudo rfkill unblock wifi" but after finding this thread I can confirm I ran the apt-get upgrade command about an hour earlier.

    Not a good idea to upgrade right now.
     
    sieler likes this.
  8. Xykon

    Xykon Member

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    If you have Ethernet or serial console (not the onboard USB but a USB <-> Uart converter) you can recover by following the steps I outlined above.
     
  9. sieler

    sieler New Member

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    apt-get upgrade works with beta 5. (i.e., I can successfully reboot after apt-get upgrade (and, it no longer get errors, either).)

    (Note: as of 2015-11-20, the sourceforge version of beta5 img was bad (about 719 MBS),
    but the EU version was good (810 or so MBs). unzipped img file should be: 2703228928 bytes (2,578 MBs)
     
    Chris Dickerson likes this.
  10. Chris Dickerson

    Chris Dickerson New Member

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    Confirming, I was able to apt-get upgrade without issue on beta 5. Also on the sourceforge img I downloaded 3 times and was corrupted every time, EU img is good.
     
    sieler likes this.
  11. JackSilb

    JackSilb Active Member

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    Upate and Upgrade worked for me.
    Not much happened in terms of Upgrade.
    V2 Beta 5
    -Jack
     
    sieler likes this.
  12. Andrea Rovai

    Andrea Rovai Well-Known Member

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    @Chris Dickerson @sieler yeah, we uploaded a corrupted image, it's been substituted now, please check the SHA-1 and eventually reflash the Micro SD.
    Cheers
     

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