apt failing, normal fixes don't seem to help.

  • System Details:


    System Information
    Hostname
    piomv.[redacted]

    Version
    6.0.28-3 (Shaitan)

    Processor
    BCM2835

    Kernel
    Linux 5.15.32-v8+

    System time
    6/21/2022, 10:58:10 PM

    Uptime
    2 hours


    When I attempt to update, I get the following errors:


    From the UI:

    "500 - Internal Server Error

    File '/var/lib/openmediavault/apt/upgradeindex.json' contains invalid JSON: No error"


    From the CLI:

    *NOTE: The initial 4 commands were an attempt to try to "clean up" perhaps bad caching or something else after the initial update failed...but as you can see, no joy.

    root@piomv:/home/sysuser# apt-get clean

    root@piomv:/home/sysuser# rm -rf /var/lib/apt/lists/*

    root@piomv:/home/sysuser# apt-get clean

    root@piomv:/home/sysuser# apt-get update

    Get:1 file:/var/cache/openmediavault/archives InRelease

    Ign:1 file:/var/cache/openmediavault/archives InRelease

    Get:2 file:/var/cache/openmediavault/archives Release

    Ign:2 file:/var/cache/openmediavault/archives Release

    Get:3 file:/var/cache/openmediavault/archives Packages

    Ign:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Get:3 file:/var/cache/openmediavault/archives Packages

    Ign:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Get:3 file:/var/cache/openmediavault/archives Packages

    Ign:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Get:3 file:/var/cache/openmediavault/archives Packages

    Ign:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Get:3 file:/var/cache/openmediavault/archives Packages

    Ign:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Get:3 file:/var/cache/openmediavault/archives Packages

    Ign:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Get:3 file:/var/cache/openmediavault/archives Packages

    Get:4 file:/var/cache/openmediavault/archives Translation-en

    Ign:4 file:/var/cache/openmediavault/archives Translation-en

    Hit:5 https://openmediavault.github.io/packages shaitan InRelease

    Err:5 https://openmediavault.github.io/packages shaitan InRelease

    Splitting up /var/lib/apt/lists/openmediavault.github.io_packages_dists_shaitan_InRelease into data and signature failed

    Hit:6 https://openmediavault-plugin-…github.io/packages/debian shaitan InRelease

    Err:6 https://openmediavault-plugin-…github.io/packages/debian shaitan InRelease

    Splitting up /var/lib/apt/lists/openmediavault-plugin-developers.github.io_packages_debian_dists_shaitan_InRelease into data and signature failed

    Get:7 http://deb.debian.org/debian bullseye InRelease [116 kB]

    Hit:8 http://packages.openmediavault.org/public shaitan InRelease

    Get:9 http://archive.raspberrypi.org/debian bullseye InRelease [23.7 kB]

    Get:10 http://deb.debian.org/debian bullseye-updates InRelease [39.4 kB]

    Get:11 http://deb.debian.org/debian-security bullseye-security InRelease [44.1 kB]

    Get:12 http://httpredir.debian.org/debian bullseye-backports InRelease [44.2 kB]

    Get:13 https://download.docker.com/linux/debian bullseye InRelease [43.3 kB]

    Err:8 http://packages.openmediavault.org/public shaitan InRelease

    Splitting up /var/lib/apt/lists/packages.openmediavault.org_public_dists_shaitan_InRelease into data and signature failed

    Get:14 http://deb.debian.org/debian bullseye/main arm64 Packages [8070 kB]

    Get:15 http://deb.debian.org/debian bullseye/main armhf Packages [7944 kB]

    Get:16 http://deb.debian.org/debian bullseye/main Translation-en [6241 kB]

    Get:17 http://deb.debian.org/debian bullseye/contrib arm64 Packages [40.8 kB]

    Get:18 http://deb.debian.org/debian bullseye/contrib armhf Packages [40.2 kB]

    Get:19 http://deb.debian.org/debian bullseye/contrib Translation-en [46.9 kB]

    Get:20 http://deb.debian.org/debian bullseye/non-free arm64 Packages [69.6 kB]

    Get:21 http://deb.debian.org/debian bullseye/non-free armhf Packages [56.3 kB]

    Get:22 http://deb.debian.org/debian bullseye/non-free Translation-en [91.3 kB]

    Hit:23 http://deb.debian.org/debian bullseye-updates/main arm64 Packages

    Hit:24 http://deb.debian.org/debian bullseye-updates/main armhf Packages

    Get:25 http://deb.debian.org/debian bullseye-updates/main Translation-en [2343 B]

    Get:26 http://deb.debian.org/debian-security bullseye-security/main arm64 Packages [159 kB]

    Get:27 http://deb.debian.org/debian-security bullseye-security/main armhf Packages [161 kB]

    Get:28 http://deb.debian.org/debian-security bullseye-security/main Translation-en [99.8 kB]

    Get:29 https://download.docker.com/linux/debian bullseye/stable arm64 Packages [10.6 kB]

    Get:30 http://archive.raspberrypi.org/debian bullseye/main arm64 Packages [273 kB]

    Get:31 http://archive.raspberrypi.org/debian bullseye/main armhf Packages [281 kB]

    Err:23 http://deb.debian.org/debian bullseye-updates/main arm64 Packages

    Hash Sum mismatch

    Hashes of expected file:

    - Filesize:9834 [weak]

    - SHA256:b2ca2423e987d5024ee21c81bfb7c9e6efce30d81d112003c0b045fe9cea36fe

    Hashes of received file:

    - SHA256:cf8aa82c0ab9a31070d2920b14666d35b250211ff1d89a92a77420a2cdf9230a

    - Filesize:9834 [weak]

    Release file created at: Wed, 22 Jun 2022 20:32:22 +0000

    Err:24 http://deb.debian.org/debian bullseye-updates/main armhf Packages


    Traceback (most recent call last):

    File "/usr/sbin/omv-mkaptidx", line 124, in <module>

    cache = apt.cache.Cache()

    File "/usr/lib/python3/dist-packages/apt/cache.py", line 152, in __init__

    self.open(progress)

    File "/usr/lib/python3/dist-packages/apt/cache.py", line 214, in open

    self._cache = apt_pkg.Cache(progress)

    apt_pkg.Error: E:Unable to parse package file /var/lib/apt/lists/deb.debian.org_debian_dists_bullseye-updates_InRelease (1), E:The package lists or status file could not be parsed or opened.

    Reading package lists... Error!

    W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://openmediavault.github.io/packages shaitan InRelease: Splitting up /var/lib/apt/lists/openmediavault.github.io_packages_dists_shaitan_InRelease into data and signature failed

    W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://openmediavault-plugin-…github.io/packages/debian shaitan InRelease: Splitting up /var/lib/apt/lists/openmediavault-plugin-developers.github.io_packages_debian_dists_shaitan_InRelease into data and signature failed

    W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://packages.openmediavault.org/public shaitan InRelease: Splitting up /var/lib/apt/lists/packages.openmediavault.org_public_dists_shaitan_InRelease into data and signature failed

    E: Repository 'http://httpredir.debian.org/debian bullseye-backports InRelease' changed its 'Origin' value from '' to 'Debian Backports'

    E: Repository 'http://httpredir.debian.org/debian bullseye-backports InRelease' changed its 'Label' value from '' to 'Debian Backports'

    N: Repository 'http://httpredir.debian.org/debian bullseye-backports InRelease' changed its 'Suite' value from '' to 'bullseye-backports'

    E: Repository 'http://httpredir.debian.org/debian bullseye-backports InRelease' changed its 'Codename' value from '' to 'bullseye-backports'

    E: Repository 'http://httpredir.debian.org/debian bullseye-backports InRelease' changed its default priority for apt_preferences(5) from 500 to 100.

    N: This must be accepted explicitly before updates for this repository can be applied. See apt-secure(8) manpage for details.

    E: Unable to parse package file /var/lib/apt/lists/deb.debian.org_debian_dists_bullseye-updates_InRelease (1)

    E: The package lists or status file could not be parsed or opened.


    Any ideas? I have rebooted the system and did an fsck, which did find some problems, but I didn't see anything in the root partition.


    Kevin

  • Agricola

    Hat das Thema freigeschaltet.
    • Offizieller Beitrag

    What is the output of: sudo omv-aptclean

    omv 7.0-32 sandworm | 64 bit | 6.5 proxmox kernel

    plugins :: omvextrasorg 7.0 | kvm 7.0.9 | compose 7.0.9 | cputemp 7.0 | mergerfs 7.0.3


    omv-extras.org plugins source code and issue tracker - github


    Please try ctrl-shift-R and read this before posting a question.

    Please put your OMV system details in your signature.
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  • sudo omv-aptclean

    1. Cleaning apt cache files...


    2. Clearing available dpkg packages...


    3. Removing apt lists...

    rm: cannot remove '/var/lib/apt/lists/auxfiles': Structure needs cleaning

    rm: cannot remove '/var/lib/apt/lists/partial': Structure needs cleaning

    • Offizieller Beitrag

    How old is your sd card? It sure seems like it is starting to fail.

    omv 7.0-32 sandworm | 64 bit | 6.5 proxmox kernel

    plugins :: omvextrasorg 7.0 | kvm 7.0.9 | compose 7.0.9 | cputemp 7.0 | mergerfs 7.0.3


    omv-extras.org plugins source code and issue tracker - github


    Please try ctrl-shift-R and read this before posting a question.

    Please put your OMV system details in your signature.
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    • Offizieller Beitrag

    Its not old. I guess I can try to clone and replace.

    They can be bad from the start. Cloning won't work since you will just clone corrupted files to the new card.

    omv 7.0-32 sandworm | 64 bit | 6.5 proxmox kernel

    plugins :: omvextrasorg 7.0 | kvm 7.0.9 | compose 7.0.9 | cputemp 7.0 | mergerfs 7.0.3


    omv-extras.org plugins source code and issue tracker - github


    Please try ctrl-shift-R and read this before posting a question.

    Please put your OMV system details in your signature.
    Please don't PM for support... Too many PMs!

  • I'm going to try it anyway, if the problem is just with the apt /var/lib/apt/lists/* I'll just purge it. If it still is failing afterward, I'll bit the bullet and reinstall, which might be enough effort to just drop the whole thing :(

    • Offizieller Beitrag

    which might be enough effort to just drop the whole thing

    Drop OMV? This isn't an OMV issue. I'm guessing you just got a bad card from the start. Re-installing isn't hard. I have done it hundreds of times on an RPi.

    omv 7.0-32 sandworm | 64 bit | 6.5 proxmox kernel

    plugins :: omvextrasorg 7.0 | kvm 7.0.9 | compose 7.0.9 | cputemp 7.0 | mergerfs 7.0.3


    omv-extras.org plugins source code and issue tracker - github


    Please try ctrl-shift-R and read this before posting a question.

    Please put your OMV system details in your signature.
    Please don't PM for support... Too many PMs!

  • I have done it hundreds of times on an RPi.

    Ahh, I knew that you only here for the Pis, :D



    Its not old.

    ...

    If it still is failing afterward, I'll bit the bullet and reinstall, which might be enough effort to just drop the whole thing

    You won't believe the amount of times I've already installed RaspiOS/OMV on the Pis.

    And no, it's not difficult to have a "busted" SDcard.

    I can give you several of them that won't work anymore.

    Not only SDcards but also USB sticks.

  • It absolutely isn't an issue with omv at all. Im not planning on dumping the solution, I like it, its simple, and it doesn't take up much power or space. When I mean drop it, I'm talking about having to wait until a time where I'm not overbooked to solve it.

  • Also, its not the OS configuration and installation thats painful, its all the rsync and other post config items that are troublesome...again, not OMV at all. I'm using this as my backup from another nas, so I do want to solve it. I haven't had many SD cards fail, but the design does encourage failure. I've bought a "durable" version of sd, maybe that will be more reliable, not that the 400GB sd that is in there was cheap.

  • 400GB sd

    ???

    SD or SSD?

    If sd, why would you want a SDcard that big?

    A Pi with a 16/32Gb SDcard for OS/OMV is more than enough and way easier to clone.


    And to buy a 400Gb sdcard (never saw or heard about that size until now) must mean you don't have only the OS on it.

    So, the wear-and-tear might happened sooner.

  • Im actually using less than 4G, I used the 400G because I had one on hand and it wasn't removed from the package. Only the OS is on the SD card, all data is on the 18Tb USB disk. The new one I ordered was 128G, and I only bought that because it was $4 more than the 64G.


  • Can you post a link to where you bought that Sdcard?


    And don't take this wrong but, as a personal experience, when it comes to sdcard on Pis, bigger isn't better.

    The logic behinds this is:

    For backup, a couple of sdcards of 16gb will be cloned/flashes/rotated in less then 30m.

    You'll always have a failsafe backup of the OS.

    Do this every week or 2 and you won't sorry much.

  • Yeah, I bought it from amazon like above. I used h2testw to determine if it was "fake" before I used it.

    Ok, it seems a legit card and not some alienexpress knock-off.


    But, I insist with you: you're better off having 2 or 3 16Gb cards and do as I told before, use 1 and after everything is set, clone it to another and rotate them often.

    • Offizieller Beitrag

    Even having a real card doesn't prevent things writing too much to the card and prematurely wearing it out. Especially if you were using a large SD card like that for storage and doings lots of writes.

    omv 7.0-32 sandworm | 64 bit | 6.5 proxmox kernel

    plugins :: omvextrasorg 7.0 | kvm 7.0.9 | compose 7.0.9 | cputemp 7.0 | mergerfs 7.0.3


    omv-extras.org plugins source code and issue tracker - github


    Please try ctrl-shift-R and read this before posting a question.

    Please put your OMV system details in your signature.
    Please don't PM for support... Too many PMs!

  • All of the data that required writes was on the USB HD, no special setup for the SD, but I have accepted the failure. I am hoping the "durable" version I have ordered and should be here today will be a little more resilient.

  • I use this one's in 32Gb and haven't had a fail yet (the most used one is running LibreELEC for almost 2 years)

    Amazon.com: Cartão de Memória SanDisk Extreme microSD UHS-3 : Everything Else

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