Having problems booting into the system, presuming a problem with pacman

[Eragonvn]

I booted into the system a few days ago, but it hangs at the boot stage, as shown below:

Then I got advice to solve the problem on the Endeavor OS Telegram group, which is to refresh all download mirrors and update the whole system with the command ‘sudo pacman -Syyu’ but it seems that the problem is reoccurred again with pacman:

Until now, I still can’t logon. I’m looking forward to any help possible

[pebcak]

Perhaps you could try regenerating your mirrorlist before doing sudo pacman -Syyu again.

https://wiki.archlinux.org/title/Mirrors
https://wiki.archlinux.org/title/Reflector

Also have a look at the following post:

[FAQ] error: could not open file /var/lib/pacman/local/…/{desc,files,mtree}: No such file or directory

Your local package database and/or metadata may become corrupted if an update process is interrupted, for example if you hard power off during an update. Metadata corruption will generally manifest in a message similar to: error: could not open file /var/lib/pacman/local/$pkgname-$pkgver-$pkgrel/desc: No such file or directory error: could not open file /var/lib/pacman/local/$pkgname-$pkgver-$pkgrel/files: No such file or directory error: could not open file /var/lib/pacman/local/$pkgname-$pkg…

[anon11595408]

@Eragonvn

Until now, I still can’t logon. I’m looking forward to any help possible

Look at this thread, it is about China mirrors, and doing an offline-install.

[Eragonvn]

I have read the post and tried the solution, but seems like it didn’t work. Should I grab the ‘llvm’ package file and install it manually?

[pebcak]

@Eragonvn

seems like it didn’t work

Did you regenerate your mirrorlist?
Did you run sudo pacman -Syyu afterwards?
Did you get error messages and if so what messages?

[dalto]

You are working from the TTY at the moment. Have you checked to make sure you have a good network connection from the TTY?

[Shjim]

no need " sudo"

if look at screen shot usr root . usr already got warn " Avoid running yay as root/sudo

[Eragonvn]

I tried both with the TTY and chrooting into a live ISO. Both failed to rate mirrorlist

[Eragonvn]

@pebcak

Did you regenerate your mirrorlist?

Yes I did but it failed even when I set download-timeout to 10 secs

[root@EndeavourOS /]# sudo reflector --latest 8 --sort rate --download-timeout 10 --save /etc/pacman.d/mirrorlist
[2022-06-28 23:53:26] WARNING: failed to rate rsync download (rsync://arch.mirror.square-r00t.net/arch/community/os/x86_64/community.db): Download timed out after 10 second(s).
[2022-06-28 23:54:04] WARNING: failed to rate http(s) download (https://archlinux.thaller.ws/community/os/x86_64/community.db): Download timed out after 10 second(s).
[2022-06-28 23:54:14] WARNING: failed to rate rsync download (rsync://archlinux.thaller.ws/archlinux/community/os/x86_64/community.db): Download timed out after 10 second(s).
[2022-06-28 23:54:25] WARNING: failed to rate http(s) download (http://mirror.cyberbits.eu/archlinux/community/os/x86_64/community.db): Download timed out after 10 second(s).

@pebcak

Did you run sudo pacman -Syyu afterwards?

The error seem like the same when I tried both with TTY and chroot into a Live ISO

[root@EndeavourOS /]# sudo pacman -Syyu
:: Synchronizing package databases...
 core                                                                                                             156.4 KiB   166 KiB/s 00:01 [---------------------------------------------------------------------------------------] 100%
 extra                                                                                                           1717.9 KiB   329 KiB/s 00:05 [---------------------------------------------------------------------------------------] 100%
 community                                                                                                          6.7 MiB   608 KiB/s 00:11 [---------------------------------------------------------------------------------------] 100%
 multilib                                                                                                         170.6 KiB   163 KiB/s 00:01 [---------------------------------------------------------------------------------------] 100%
 endeavouros                                                                                                       33.5 KiB  25.6 KiB/s 00:01 [---------------------------------------------------------------------------------------] 100%
 kernel-lts                                                                                                        33.8 KiB  31.6 KiB/s 00:01 [---------------------------------------------------------------------------------------] 100%
:: Starting full system upgrade...
:: Replace cpufrequtils with community/cpupower? [Y/n] 
:: Replace kwayland-server with extra/kwin? [Y/n] 
resolving dependencies...
looking for conflicting packages...
error: could not open file /var/lib/pacman/local/llvm-13.0.1-3/files: No such file or directory
warning: could not fully load metadata for package llvm-13.0.1-3
error: failed to prepare transaction (invalid or corrupted package)

[dalto]

@Eragonvn

sudo reflector --latest 8 --sort rate --download-timeout 10 --save /etc/pacman.d/mirrorlist
[2022-06-28 23:53:26] WARNING: failed to rate rsync download (rsync://arch.mirror.square-r00t.net/arch/community/os/x86_64/community.db): Download timed out after 10 second(s).
[2022-06-28 23:54:04] WARNING: failed to rate http(s) download (https://archlinux.thaller.ws/community/os/x86_64/community.db): Download timed out after 10 second(s).
[2022-06-28 23:54:14] WARNING: failed to rate rsync download (rsync://archlinux.thaller.ws/archlinux/community/os/x86_64/community.db): Download timed out after 10 second(s).
[2022-06-28 23:54:25] WARNING: failed to rate http(s) download (http://mirror.cyberbits.eu/archlinux/community/os/x86_64/community.db): Download timed out after 10 second(s).

This output is normal. It just means that when it went throughit’s list, it failed to rate 4 of the mirrors.

[Eragonvn]

Oh that’s great But I suppose the

pacman -Syyu command does have problem right?

[Eragonvn]

Hi @pebcak could you please assist me with the issue?

[pebcak]

I am not sure what the current state of your system is.
If you are still having the same issue as in your OP, I’am afraid I don’t have more suggestions to make than the ones already made in my first reply.

[HMS_Endeavour]

Change it to

-p https --download-timeout 60 --verbose

I suggest verbose to get some information that may help you understand what is happening.
My connection is very poor and this helps me. I think its the increase download timeout.

[Eragonvn]

I have succeeded in updating the mirrors already. Now my main problem is that I can’t do a system-wide update successfully with the command pacman -Syyu

[fran]

Maybe a problem with gnupg keys? You can try the following:

sudo pacman -S archlinux-keyring endeavouros-keyring
sudo rm -r /etc/pacman.d/gnupg
sudo pacman-key --init
sudo pacman-key --populate archlinux endeavouros
sudo pacman-key --refresh-keys
sudo pacman -Sc
sudo pacman -Syyu

[Eragonvn]

error: kernel-lts: signature from "Jonathon Fernyhough <jonathon@m2x.dev>" is unknown trust
error: database 'kernel-lts' is not valid (invalid or corrupted database (PGP signature))

I got this error when trying the pacman -Syyu step again

[pebcak]

@Eragonvn

error: kernel-lts: signature from "Jonathon Fernyhough <jonathon@m2x.dev>" is unknown trust
error: database 'kernel-lts' is not valid (invalid or corrupted database (PGP signature))

You have added @jonathon’s kernel-lts repo to your /etc/pacman.conf but perhaps forgot to add the key-ID to your pacman keys.

Try the following:

sudo pacman-key --recv-keys 76C6E477042BFE985CC220BD9C08A255442FAFF0
sudo pacman-key --finger 76C6E477042BFE985CC220BD9C08A255442FAFF0
sudo pacman-key --lsign-key 76C6E477042BFE985CC220BD9C08A255442FAFF0

and then:

sudo pacman -Syyu

https://wiki.archlinux.org/title/Pacman/Package_signing#Adding_unofficial_keys

[Eragonvn]

@Eragonvn

llvm

llvm: /usr/lib/libLLVMBPFInfo.a exists in filesystem
llvm: /usr/lib/libLLVMBinaryFormat.a exists in filesystem
llvm: /usr/lib/libLLVMBitReader.a exists in filesystem
llvm: /usr/lib/libLLVMBitWriter.a exists in filesystem
llvm: /usr/lib/libLLVMBitstreamReader.a exists in filesystem
llvm: /usr/lib/libLLVMCFGuard.a exists in filesystem
llvm: /usr/lib/libLLVMCFIVerify.a exists in filesystem
llvm: /usr/lib/libLLVMCodeGen.a exists in filesystem
llvm: /usr/lib/libLLVMCore.a exists in filesystem
llvm: /usr/lib/libLLVMCoroutines.a exists in filesystem
llvm: /usr/lib/libLLVMCoverage.a exists in filesystem
llvm: /usr/lib/libLLVMDWARFLinker.a exists in filesystem
llvm: /usr/lib/libLLVMDWP.a exists in filesystem
llvm: /usr/lib/libLLVMDebugInfoCodeView.a exists in filesystem
llvm: /usr/lib/libLLVMDebugInfoDWARF.a exists in filesystem
llvm: /usr/lib/libLLVMDebugInfoGSYM.a exists in filesystem
llvm: /usr/lib/libLLVMDebugInfoMSF.a exists in filesystem
llvm: /usr/lib/libLLVMDebugInfoPDB.a exists in filesystem
llvm: /usr/lib/libLLVMDemangle.a exists in filesystem
llvm: /usr/lib/libLLVMDlltoolDriver.a exists in filesystem
llvm: /usr/lib/libLLVMExecutionEngine.a exists in filesystem
llvm: /usr/lib/libLLVMExegesis.a exists in filesystem
llvm: /usr/lib/libLLVMExegesisAArch64.a exists in filesystem
llvm: /usr/lib/libLLVMExegesisMips.a exists in filesystem
llvm: /usr/lib/libLLVMExegesisPowerPC.a exists in filesystem
llvm: /usr/lib/libLLVMExegesisX86.a exists in filesystem
llvm: /usr/lib/libLLVMExtensions.a exists in filesystem
llvm: /usr/lib/libLLVMFileCheck.a exists in filesystem
llvm: /usr/lib/libLLVMFrontendOpenACC.a exists in filesystem
llvm: /usr/lib/libLLVMFrontendOpenMP.a exists in filesystem
llvm: /usr/lib/libLLVMFuzzMutate.a exists in filesystem
llvm: /usr/lib/libLLVMGlobalISel.a exists in filesystem
llvm: /usr/lib/libLLVMHexagonAsmParser.a exists in filesystem
llvm: /usr/lib/libLLVMHexagonCodeGen.a exists in filesystem
llvm: /usr/lib/libLLVMHexagonDesc.a exists in filesystem
llvm: /usr/lib/libLLVMHexagonDisassembler.a exists in filesystem
llvm: /usr/lib/libLLVMHexagonInfo.a exists in filesystem
llvm: /usr/lib/libLLVMIRReader.a exists in filesystem
llvm: /usr/lib/libLLVMInstCombine.a exists in filesystem
llvm: /usr/lib/libLLVMInstrumentation.a exists in filesystem
llvm: /usr/lib/libLLVMInterfaceStub.a exists in filesystem
llvm: /usr/lib/libLLVMInterpreter.a exists in filesystem
llvm: /usr/lib/libLLVMJITLink.a exists in filesystem
llvm: /usr/lib/libLLVMLTO.a exists in filesystem
llvm: /usr/lib/libLLVMLanaiAsmParser.a exists in filesystem
llvm: /usr/lib/libLLVMLanaiCodeGen.a exists in filesystem
llvm: /usr/lib/libLLVMLanaiDesc.a exists in filesystem
llvm: /usr/lib/libLLVMLanaiDisassembler.a exists in filesystem
llvm: /usr/lib/libLLVMLanaiInfo.a exists in filesystem
llvm: /usr/lib/libLLVMLibDriver.a exists in filesystem
llvm: /usr/lib/libLLVMLineEditor.a exists in filesystem
llvm: /usr/lib/libLLVMLinker.a exists in filesystem
llvm: /usr/lib/libLLVMMC.a exists in filesystem
llvm: /usr/lib/libLLVMMCA.a exists in filesystem
llvm: /usr/lib/libLLVMMCDisassembler.a exists in filesystem
llvm: /usr/lib/libLLVMMCJIT.a exists in filesystem
llvm: /usr/lib/libLLVMMCParser.a exists in filesystem
llvm: /usr/lib/libLLVMMIRParser.a exists in filesystem
llvm: /usr/lib/libLLVMMSP430AsmParser.a exists in filesystem
llvm: /usr/lib/libLLVMMSP430CodeGen.a exists in filesystem
llvm: /usr/lib/libLLVMMSP430Desc.a exists in filesystem
llvm: /usr/lib/libLLVMMSP430Disassembler.a exists in filesystem
llvm: /usr/lib/libLLVMMSP430Info.a exists in filesystem
llvm: /usr/lib/libLLVMMipsAsmParser.a exists in filesystem
llvm: /usr/lib/libLLVMMipsCodeGen.a exists in filesystem
llvm: /usr/lib/libLLVMMipsDesc.a exists in filesystem
llvm: /usr/lib/libLLVMMipsDisassembler.a exists in filesystem
llvm: /usr/lib/libLLVMMipsInfo.a exists in filesystem
llvm: /usr/lib/libLLVMNVPTXCodeGen.a exists in filesystem
llvm: /usr/lib/libLLVMNVPTXDesc.a exists in filesystem

Okay now I got this llvm error while executing the command

[pebcak]

I think in this case you could try:

sudo pacman -Syu --overwrite '*'

For more info, see

[FAQ] Package installation says FILENAME exists in filesystem; “Failed to commit transaction (conflicting files)”

I can’t install or update a package because I get (something like) this: error: could not prepare transaction error: failed to commit transaction (conflicting files) libname: /insert/file/name/here exists in filesystem Errors occurred, no packages were upgraded. Why is this happening? The package manager, pacman , has detected an unexpected file already exists on disk. By design it will not overwrite files that already exist. This is a design feature, not a flaw - package managers are de…