Almalinux package update failure

tom9909

• May 24, 2023 18:17

Hi everyone, Has anyone else been having issues with their update upcp scripts on Almalinux? Any advise on best practices when it comes to these? I can skip-broken as suggested but not sure if I'd be missing critical package updates. [2023-05-24 21:15:34 +1000] Processing: Running update-packages [2023-05-24 21:15:34 +1000] - Processing command `/usr/local/cpanel/scripts/update-packages` [2023-05-24 21:15:35 +1000] [/usr/local/cpanel/scripts/update-packages] checkyum version 22.3 (excludes: bind-chroot) [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] Last metadata expiration check: 3:54:17 ago on Wed May 24 17:21:20 2023. [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] Error: [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] Problem 1: package shim-x64-15.6-1.el8.alma.1.x86_64 requires almalinux(kernel-sig-key) >= 202303, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - cannot install the best update candidate for package shim-x64-15.6-1.el8.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package kernel-core-4.18.0-477.10.1.el8_8.x86_64 is filtered out by exclude filtering [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] Problem 2: package grub2-efi-x64-1:2.02-148.el8.alma.x86_64 requires /boot/efi/EFI/almalinux/shimx64.efi, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package grub2-efi-x64-1:2.02-148.el8.alma.x86_64 conflicts with shim-x64 <= 15.6-1.el8.alma provided by shim-x64-15.6-1.el8.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package shim-x64-15.6-1.el8.alma.1.x86_64 requires almalinux(kernel-sig-key) >= 202303, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - cannot install the best update candidate for package grub2-efi-x64-1:2.02-142.el8_7.3.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package kernel-core-4.18.0-477.10.1.el8_8.x86_64 is filtered out by exclude filtering [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] Problem 3: package shim-x64-15.6-1.el8.alma.x86_64 requires /boot/efi/EFI/almalinux/grubx64.efi, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package grub2-efi-x64-1:2.02-148.el8.alma.x86_64 conflicts with shim-x64 <= 15.6-1.el8.alma provided by shim-x64-15.6-1.el8.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package grub2-efi-x64-1:2.02-142.el8_7.3.alma.x86_64 requires grub2-common = 1:2.02-142.el8_7.3.alma, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - problem with installed package shim-x64-15.6-1.el8.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - cannot install both grub2-common-1:2.02-148.el8.alma.noarch and grub2-common-1:2.02-142.el8_7.3.alma.noarch [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package shim-x64-15.6-1.el8.alma.1.x86_64 requires almalinux(kernel-sig-key) >= 202303, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - cannot install the best update candidate for package grub2-common-1:2.02-142.el8_7.3.alma.noarch [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package kernel-core-4.18.0-477.10.1.el8_8.x86_64 is filtered out by exclude filtering [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] Problem 4: package grub2-efi-x64-1:2.02-148.el8.alma.x86_64 requires /boot/efi/EFI/almalinux/shimx64.efi, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package grub2-efi-x64-1:2.02-148.el8.alma.x86_64 conflicts with shim-x64 <= 15.6-1.el8.alma provided by shim-x64-15.6-1.el8.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - problem with installed package grub2-efi-x64-1:2.02-142.el8_7.3.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package grub2-efi-x64-1:2.02-142.el8_7.3.alma.x86_64 requires grub2-tools = 1:2.02-142.el8_7.3.alma, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package grub2-tools-efi-1:2.02-148.el8.alma.x86_64 obsoletes grub2-tools < 1:2.02-148.el8.alma provided by grub2-tools-1:2.02-142.el8_7.3.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package shim-x64-15.6-1.el8.alma.1.x86_64 requires almalinux(kernel-sig-key) >= 202303, but none of the providers can be installed [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - cannot install the best update candidate for package grub2-tools-efi-1:2.02-142.el8_7.3.alma.x86_64 [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package kernel-core-4.18.0-477.10.1.el8_8.x86_64 is filtered out by exclude filtering [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] (try to add '--allowerasing' to command line to replace conflicting packages or '--skip-broken' to skip uninstallable packages or '--nobest' to use not only best candidate packages) [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] (XID zjt4fn) "/usr/bin/yum" reported error code "1" when it ended: [2023-05-24 21:15:38 +1000] E [/usr/local/cpanel/scripts/update-packages] The "/usr/local/cpanel/scripts/update-packages" command (process 3082839) reported error number 1 when it ended.

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  cPRex Jurassic Moderator

  • May 26, 2023 15:54

  Hey there! This is an issue with the OS packages themselves, and not related to a cPanel update. I did check a default cPanel system and confirmed that "shim" is not a package that is included or necessary for cPanel, so if you're not using that you may want to just try removing that specific package and then updating Yum again with the following commands: yum clean all yum makecache yum update
  Can you try that and see if that gets things working better for you?

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  bloatedstoat

  • May 26, 2023 22:45

  Hey tom9909, Did you resolve this mate? We're having similar issues with a newly provisioned server that has just had accounts migrated to it. I opened a forum thread myself on it.

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  tom9909

  • May 29, 2023 05:10

  Hey tom9909, Did you resolve this mate? We're having similar issues with a newly provisioned server that has just had accounts migrated to it. I opened a forum thread myself on it. Ours is a cPanel DNS only server, so no plugins or anything out of the defaults. Ill try the YUM clean suggestions from @cPRex now and see what happens overnight

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  bloatedstoat

  • May 29, 2023 05:13

  Thank you. Looking forward to getting to the bottom of this one. From scouring the internet it appears to be a repository issue, although this is conjecture at this stage. I've also opened a ticket with our server provider who installed the OS and have yet to hear back from them, as soon as that happens I'll update this thread. None of the commands cpRex provided worked for me.

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  tom9909

  • May 29, 2023 05:21

  Thank you. Looking forward to getting to the bottom of this one. From scouring the internet it appears to be a repository issue, although this is conjecture at this stage. I've also opened a ticket with our server provider who installed the OS and have yet to hear back from them, as soon as that happens I'll update this thread. None of the commands cpRex provided worked for me.

  
  I'm in agreeance that its a repository issue, although would have thought there would have been more people noting an issue on their forums and reddit - but there's nothing....

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  bloatedstoat

  • May 29, 2023 05:23

  I've just added to your AlmaLinux thread in the hope it'll bump. There are mentions of this issue out there on the internet with random solutions I am not game to try on a production server.

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  dpearson

  • May 29, 2023 22:57

  This is likely not a repository issue at all. The key is this - [2023-05-24 21:15:38 +1000] [/usr/local/cpanel/scripts/update-packages] - package kernel-core-4.18.0-477.10.1.el8_8.x86_64 is filtered out by exclude filtering If the kernel update has been excluded, then grub2 and shim should fail as they all rely on one another. Remove the kernel from the excluded updates (why it's excluded in the first place who knows) and I bet it works.

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  bloatedstoat

  • May 29, 2023 23:08

  Hello again, I've opened a support ticket #95068187 Tom do you have your UPCP log for the day before the issues started in your case? Worth pointing out here that I am running a CloudLinux 8 conversion from AlmaLinux 8 and not pure AlmaLinux 8.

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  tom9909

  • May 29, 2023 23:35

  Hello again, I've opened a support ticket #95068187 Tom do you have your UPCP log for the day before the issues started in your case? Worth pointing out here that I am running a CloudLinux 8 conversion from AlmaLinux 8 and not pure AlmaLinux 8.

  
  Hi, this is the update log prior to the issue occurring. ---------------------------------------------------------------------------------------------------- => Log opened from cPanel Update (upcp) - Slave (2863020) at Thu May 18 21:15:01 2023 [2023-05-18 21:15:01 +1000] Detected cron=1 (cron mode set from command line) [2023-05-18 21:15:01 +1000] 1% complete [2023-05-18 21:15:01 +1000] Running Standardized hooks [2023-05-18 21:15:01 +1000] 2% complete [2023-05-18 21:15:01 +1000] mtime on upcp is 1669125472 (Wed Nov 23 00:57:52 2022) ---------------------------------------------------------------------------------------------------- => Log opened from /usr/local/cpanel/scripts/updatenow (2863022) at Thu May 18 21:15:02 2023 [2023-05-18 21:15:02 +1000] Running version '11.110.0.5' of updatenow. [2023-05-18 21:15:02 +1000] Retrieved public key from vendor: cpanel, category: development, url: Log closed Thu May 18 21:15:38 2023 ---------------------------------------------------------------------------------------------------- => Log opened from cPanel Update (upcp) - Slave (2863020) at Thu May 18 21:15:38 2023 [2023-05-18 21:15:38 +1000] Pre Maintenance completed successfully [2023-05-18 21:15:38 +1000] 95% complete [2023-05-18 21:15:38 +1000] Running Standardized hooks [2023-05-18 21:15:38 +1000] 100% complete [2023-05-18 21:15:38 +1000] [2023-05-18 21:15:38 +1000] cPanel update completed [2023-05-18 21:15:38 +1000] A log of this update is available at /var/cpanel/updatelogs/update.2863020.1334414535.1671064356.log [2023-05-18 21:15:38 +1000] Removing upcp pidfile [2023-05-18 21:15:38 +1000] [2023-05-18 21:15:38 +1000] Completed all updates => Log closed Thu May 18 21:15:38 2023

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  tom9909

  • May 29, 2023 23:37

  and this is the log following: ---------------------------------------------------------------------------------------------------- => Log opened from cPanel Update (upcp) - Slave (2899489) at Fri May 19 21:15:02 2023 [2023-05-19 21:15:02 +1000] Detected cron=1 (cron mode set from command line) [2023-05-19 21:15:02 +1000] 1% complete [2023-05-19 21:15:02 +1000] Running Standardized hooks [2023-05-19 21:15:02 +1000] 2% complete [2023-05-19 21:15:02 +1000] mtime on upcp is 1669125472 (Wed Nov 23 00:57:52 2022) ---------------------------------------------------------------------------------------------------- => Log opened from /usr/local/cpanel/scripts/updatenow (2899491) at Fri May 19 21:15:03 2023 [2023-05-19 21:15:03 +1000] Running version '11.110.0.5' of updatenow. [2023-05-19 21:15:03 +1000] Retrieved public key from vendor: cpanel, category: development, url: Log closed Fri May 19 21:15:38 2023 ---------------------------------------------------------------------------------------------------- => Log opened from cPanel Update (upcp) - Slave (2899489) at Fri May 19 21:15:38 2023 [2023-05-19 21:15:38 +1000] E Pre Maintenance ended, however it did not exit cleanly (256). The following events were logged: "scripts/update-packages". Please check the logs for an indication of what happened [2023-05-19 21:15:38 +1000] 95% complete [2023-05-19 21:15:38 +1000] Running Standardized hooks [2023-05-19 21:15:38 +1000] 100% complete [2023-05-19 21:15:38 +1000] [2023-05-19 21:15:38 +1000] cPanel update completed [2023-05-19 21:15:38 +1000] A log of this update is available at /var/cpanel/updatelogs/update.2899489.1343054455.1671064357.log [2023-05-19 21:15:38 +1000] Removing upcp pidfile [2023-05-19 21:15:38 +1000] [2023-05-19 21:15:38 +1000] Completed all updates => Log closed Fri May 19 21:15:38 2023 => Log closed Fri May 19 21:15:39 2023

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  bloatedstoat

  • May 30, 2023 00:33

  Thanks Tom, Your log files, in particular the one preceding your issues are visibly benign. Mine has some really unusual entries in them that for some odd reason I am unable to include here, when I try the page goes white, has a little wheel spinning and that's where it stays. I'll see what cPanel has to say about it in the ticket response before doing anything else. Super frustrating, literally had this server less than a month.

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  bloatedstoat

  • May 30, 2023 01:38

  In my case the issue was a rogue repository serving outdated packages, CloudLinux Engineer found the issue within half hour of opening the ticket to its conclusion. Thank you for your time. The issue was with this automatically added repository: repo.cloudlinux.com_cloudlinux_8_BaseOS_x86_64_os_ It was causing the conflicts due to having outdated packages (because this is the BaseOS repo, which is for unregistered users). I removed the repo file, and "yum" can now complete the update: I suspect your issue Tom is the same thing, a repository with different packages. Hopefully someone at AlmaLinux can isolate it for you.

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  tom9909

  • May 30, 2023 02:07

  In my case the issue was a rogue repository serving outdated packages, CloudLinux Engineer found the issue within half hour of opening the ticket to its conclusion. Thank you for your time. The issue was with this automatically added repository: repo.cloudlinux.com_cloudlinux_8_BaseOS_x86_64_os_ It was causing the conflicts due to having outdated packages (because this is the BaseOS repo, which is for unregistered users). I removed the repo file, and "yum" can now complete the update: I suspect your issue Tom is the same thing, a repository with different packages. Hopefully someone at AlmaLinux can isolate it for you.

  
  Thanks for the assistance with this. Ill head over to the AlmaLinux forums and advise them there.

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  tom9909

  • May 31, 2023 00:50

  It appears that cPanel are excluding kernel updates for some reason. Running the following resolved the underlying issue. dnf clean all dnf update kernel Credit to Daniel Pearson over at the AlmaLinux forums for pointing this out.

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  2gendevs

  • June 12, 2023 12:08

  @tom9909's commands fix this error for us too. dnf clean all dnf update kernel

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