Arch Linux

korimitsu

Member

Registered: 2016-08-14

Posts: 191

Help fixing packages issues

I have these issues with my packages, how can I fix them?

# pacman -Qkk | grep -E "missing|warning"
warning: ghc-libs: /usr/lib/ghc-9.2.8/lib/package.conf.d/package.cache (Modification time mismatch)
warning: ghc-libs: /usr/lib/ghc-9.2.8/lib/package.conf.d/package.cache (Size mismatch)
warning: ghc-libs: /usr/lib/ghc-9.2.8/lib/package.conf.d/package.cache (SHA256 checksum mismatch)
warning: intel-ucode: /boot/intel-ucode.img (Permissions mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Modification time mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Modification time mismatch)
warning: libutempter: /usr/lib/utempter/utempter (GID mismatch)
warning: libutempter: /usr/lib/utempter/utempter (Permissions mismatch)
warning: nodejs-nopt: /usr/bin/nopt (Permissions mismatch)
warning: shadow: /usr/bin/groupmems (GID mismatch)
warning: shadow: /usr/bin/groupmems (Permissions mismatch)
warning: systemd: /var/log/journal (GID mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (Modification time mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (Size mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (SHA256 checksum mismatch)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,726

Re: Help fixing packages issues

I don't see anything there that's a problem. Maybe the permissions mismatch on nodejs-nopt, what permissions are you seeing there?

loqs

Member

Registered: 2014-03-06

Posts: 18,885

Re: Help fixing packages issues

Are the changes not all expected due to the files being adjusted in post install scripts or by cache update scripts being run?

Last edited by loqs (2024-12-01 20:33:59)

korimitsu

Member

Registered: 2016-08-14

Posts: 191

Re: Help fixing packages issues

I've removed all affected packages except java with "sudo pacman -Rdd" and reinstalled still getting the errors:

$ # pacman -Qkk | grep -E "missing|warning"
warning: intel-ucode: /boot/intel-ucode.img (Permissions mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default (Modification time mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Symlink path mismatch)
warning: java-runtime-common: /usr/lib/jvm/default-runtime (Modification time mismatch)
warning: libutempter: /usr/lib/utempter/utempter (GID mismatch)
warning: libutempter: /usr/lib/utempter/utempter (Permissions mismatch)
warning: nodejs-nopt: /usr/bin/nopt (Permissions mismatch)
warning: shadow: /usr/bin/groupmems (GID mismatch)
warning: shadow: /usr/bin/groupmems (Permissions mismatch)
warning: systemd: /var/log/journal (GID mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (Modification time mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (Size mismatch)
warning: vlc: /usr/lib/vlc/plugins/plugins.dat (SHA256 checksum mismatch)

# stat /usr/bin/nopt
  File: /usr/bin/nopt -> ../lib/node_modules/nopt/bin/nopt.js
  Size: 36              Blocks: 0          IO Block: 4096   symbolic link
Device: 254,0   Inode: 60962263    Links: 1
Access: (0777/lrwxrwxrwx)  Uid: (    0/    root)   Gid: (    0/    root)

# stat /var/log/journal 
  File: /var/log/journal
  Size: 4096            Blocks: 16         IO Block: 4096   directory
Device: 254,0   Inode: 32899833    Links: 4
Access: (2755/drwxr-sr-x)  Uid: (    0/    root)   Gid: (  983/systemd-journal)

 stat /usr/lib/utempter/utempter
  File: /usr/lib/utempter/utempter
  Size: 14280           Blocks: 32         IO Block: 4096   regular file
Device: 254,0   Inode: 62278109    Links: 1
Access: (2755/-rwxr-sr-x)  Uid: (    0/    root)   Gid: (  997/    utmp)

# stat /boot/intel-ucode.img
  File: /boot/intel-ucode.img
  Size: 8139776         Blocks: 15904      IO Block: 4096   regular file
Device: 8,17    Inode: 14          Links: 1
Access: (0755/-rwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)

# stat /usr/bin/groupmems
  File: /usr/bin/groupmems
  Size: 43120           Blocks: 88         IO Block: 4096   regular file
Device: 254,0   Inode: 60962547    Links: 1
Access: (2750/-rwxr-s---)  Uid: (    0/    root)   Gid: (  958/  groups)

Last edited by korimitsu (2024-12-01 22:01:22)

loqs

Member

Registered: 2014-03-06

Posts: 18,885

Re: Help fixing packages issues

You do not distinguish between errors and warnings? You do not accept the explanation that the warnings you posted are all expected modifications?
Edit:

# stat /usr/bin/nopt
  File: /usr/bin/nopt -> ../lib/node_modules/nopt/bin/nopt.js
  Size: 36              Blocks: 0          IO Block: 4096   symbolic link
Device: 254,0   Inode: 60962263    Links: 1
Access: (0777/lrwxrwxrwx)  Uid: (    0/    root)   Gid: (    0/    root)

$ bsdtar -tvf /var/cache/pacman/cache/nodejs-nopt-7.2.1-1-any.pkg.tar.zst 
....
lrwxr-xr-x  0 root   root        0 Nov 29 12:48 usr/bin/nopt -> ../lib/node_modules/nopt/bin/nopt.js

symlinks do not have file modes. Possibly a pacman issue?

# stat /var/log/journal 
  File: /var/log/journal
  Size: 4096            Blocks: 16         IO Block: 4096   directory
Device: 254,0   Inode: 32899833    Links: 4
Access: (2755/drwxr-sr-x)  Uid: (    0/    root)   Gid: (  983/systemd-journal)

cat /usr/lib/tmpfiles.d/systemd.con
....
z /var/log/journal 2755 root systemd-journal - -

 stat /usr/lib/utempter/utempter
  File: /usr/lib/utempter/utempter
  Size: 14280           Blocks: 32         IO Block: 4096   regular file
Device: 254,0   Inode: 62278109    Links: 1
Access: (2755/-rwxr-sr-x)  Uid: (    0/    root)   Gid: (  997/    utmp)

https://gitlab.archlinux.org/archlinux/ … 1c49f7336e

# stat /boot/intel-ucode.img
  File: /boot/intel-ucode.img
  Size: 8139776         Blocks: 15904      IO Block: 4096   regular file
Device: 8,17    Inode: 14          Links: 1
Access: (0755/-rwxr-xr-x)  Uid: (    0/    root)   Gid: (    0/    root)

/boot is vfat?

# stat /usr/bin/groupmems
  File: /usr/bin/groupmems
  Size: 43120           Blocks: 88         IO Block: 4096   regular file
Device: 254,0   Inode: 60962547    Links: 1
Access: (2750/-rwxr-s---)  Uid: (    0/    root)   Gid: (  958/  groups)

https://gitlab.archlinux.org/archlinux/ … -/issues/2

Last edited by loqs (2024-12-02 00:05:51)

korimitsu

Member

Registered: 2016-08-14

Posts: 191

Re: Help fixing packages issues

/boot is vfat?

Yes the partition for /boot is vfat. I understand that the warnings are not that important.

loqs

Member

Registered: 2014-03-06

Posts: 18,885

Re: Help fixing packages issues

/boot is vfat?

Yes the partition for /boot is vfat. I understand that the warnings are not that important.

vfat does not support file permissions so assuming fmask=0022 all files on /boot have 0755 permissions including intel-ucode.img which pacman expects to have 0644 permissions hence the warning.

ReDress

Member

From: Nairobi

Registered: 2024-11-30

Posts: 289

Re: Help fixing packages issues

/boot is vfat?

Yes the partition for /boot is vfat. I understand that the warnings are not that important.

vfat does not support file permissions so assuming fmask=0022 all files on /boot have 0755 permissions including intel-ucode.img which pacman expects to have 0644 permissions hence the warning.

Seems to me like intel-microcode might have some very strong associations with gangsters :-(

korimitsu

Member

Registered: 2016-08-14

Posts: 191

Re: Help fixing packages issues

vfat does not support file permissions so assuming fmask=0022 all files on /boot have 0755 permissions including intel-ucode.img which pacman expects to have 0644 permissions hence the warning.

I guess they didn't account for that, or Arch's boot should not be installed in vfat?

Last edited by korimitsu (2024-12-02 17:48:48)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,726

Re: Help fixing packages issues

There's nothing to account for. It shows you things that are different, not that there's any kind of problem or anything like that. You're taking these warnings way, way too seriously, when they're simply an indicator.

Last edited by Scimmia (2024-12-02 17:54:43)

loqs

Member

Registered: 2014-03-06

Posts: 18,885

Re: Help fixing packages issues

I guess they didn't account for that

You could raise it as a pacman issue.

or Arch's boot should not be installed in vfat?

If you think the warning message is enough justification to change the file-system of /boot and the additional changes that involves to avoid breaking booting you can change it.

Each issue in your list so far has had a different root cause. With the only connection being they appear in # pacman -Qkk | grep -E "missing|warning" on your system which reduces the value of the thread to anyone else.