URGENT HELP NEEDED! a bunch of things broke after an update

[premier69]

hi

i just installed the 500mb worth of updates Discover told me about, i then rebooted and since all kinds of hell broke lose.

for example: my firefox got factory reset, addons, settings, EVERYTHING got reset. same with Thunderbird
no programs in the Favorites tab in the start menu launcher is there anymore, all cleared. programs like Nixnote2 will now not launch at all, same with peazip. when i start the terminal it now says bash-5.1$

nothing about my username or pc name.

when i start the computer i get a fedora list before it boots the OS, I’ve tried those different entries, no luck.

[update] i have fixed nixnote and peazip but KRun or whatever it’s called (alt+space) doesn’t work.

what actually happened? everything was fine before.

[dalto]

@premier69

KRun or whatever it’s called (alt+space) doesn’t work.

I had this problem recently. In system settings under shortcuts if you search for krunner, see if you have two entries for it. If you do, move the hotkeys from one entry to the other.

@premier69

for example: my firefox got factory reset, addons, settings, EVERYTHING got reset. same with Thunderbird
no programs in the Favorites tab in the start menu launcher is there anymore, all cleared. programs like Nixnote2 will now not launch at all, same with peazip. when i start the terminal it now says bash-5.1$

It sounds to me like something happened to the dot files in your home directory. Either the permissions became broken or they were deleted/corrupted. That being said, I don’t think normal updates would have made changes to your directory.

[premier69]

hmm, is it possible to find evidence to your theory? because I’m doubting my system now, a bit nervous to even breath on my computer. this issue was the type of fuckery i previously only would have expected from Manjaro or Windows.

Does the system keep logs of updates?

[dalto]

@premier69

hmm, is it possible to find evidence to your theory?

I would start by checking the permissions on all the files in your home directory including the hidden files.

@premier69

Does the system keep logs of updates?

You could check dnf history or the file /var/log/dnf.rpm/log

[premier69]

ok, will check. any clue on the meaning of Konsole now looking like this when i start it and also if matters to the functionality of the system? i seem to be able to do everything i did before in the terminal.

i am currently looking in my home dir and had hidden files shown, i can’t see any .bashrc file, is there supposed to be one? i am looking at an unrelated video and at Linux vs Windows File System Structure Compared! - YouTube on 10:01 minutes in the video he is talking about that file and i can’t find it on my fedora system although he is using Mint.

[vgaetera (Vladislav Grigoryev)]

Check the output:

getent passwd ${USER}; ls -l -a -Z ${HOME}{,/..}

[premier69]

@vgaetera

getent passwd ${USER}; ls -l -a -Z ${HOME}{,/..}

bash-5.1$ getent passwd ${USER}; ls -l -a -Z ${HOME}{,/..}
premier69:x:1000:1000:Lee Hughes:/home/premier69:/bin/bash
/home/premier69:
total 53
drwx------.  1 premier69 premier69 unconfined_u:object_r:user_home_dir_t:s0  862 29 jun 13.17  .
drwxr-xr-x.  1 root      root      system_u:object_r:home_root_t:s0           18  4 maj 02.09  ..
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      648 29 jun 13.08  .aMule
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      224 19 jun 13.46  Applications
-rw-------.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0     8813 29 jun 13.18  .bash_history
drwxr-xr-x.  1 premier69 premier69 system_u:object_r:cache_home_t:s0        3628 29 jun 13.11  .cache
drwxrwxr-x.  1 premier69 premier69 unconfined_u:object_r:config_home_t:s0   3842 29 jun 13.21  .config
-rw-r--r--.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0     3695  6 apr 19.49  cproton.sh
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       20 18 maj 14.35  Desktop
-rw-------.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       98 29 jun 13.16  .directory
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       88 12 jun 18.48  Documents
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       12 22 jun 17.20  .doombringer
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       20  6 maj 18.37  Downloads
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      222 15 jun 13.48  .factorio
-rw-r--r--.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      110 11 maj 17.34  .fonts.conf
drwxrwxr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      348  5 jun 18.24  gamemode
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      100 22 jun 13.55  Games
drwx------.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        8 16 maj 08.32  .gnome
drwx------.  1 premier69 premier69 unconfined_u:object_r:gpg_secret_t:s0      44  4 maj 09.18  .gnupg
-rw-r--r--.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      246 28 jun 16.37  .gtkrc-2.0
-rw-r--r--.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      322 28 jun 16.37  .gtkrc-2.0-kde4
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       26 17 jun  2020  .icons
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:config_home_t:s0     80  6 maj 15.38  .kde
-rw-------.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       20 16 jun 08.03  .lesshst
drwx------.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       56  4 maj 09.17  .librewolf
drwxr-xr-x.  1 premier69 premier69 system_u:object_r:gconf_home_t:s0          10  3 maj 20.11  .local
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:mozilla_home_t:s0    72 28 jun 14.04  .mozilla
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:mplayer_home_t:s0    12 18 apr  2019  .mplayer
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:audio_home_t:s0       0  3 maj 20.11  Music
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        0  6 maj 18.56  None
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       86  5 jun 18.41  .pcloud
drwxr-xr-x. 14 premier69 premier69 system_u:object_r:fusefs_t:s0            4096 22 apr 15.07  pCloudDrive
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       76 28 jun 16.39  .PeaZip
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        0 12 maj 12.55  Pictures
drwx------.  1 premier69 premier69 unconfined_u:object_r:home_cert_t:s0       10  3 maj 20.45  .pki
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       20  9 maj 14.06  .projectM
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        0  3 maj 20.11  Public
drwx------.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       42  1 jun 15.04  .putty
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:snappy_home_t:s0    188 28 jun 17.11  snap
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      252 28 jun 23.50  .steam
lrwxrwxrwx.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       34 28 jun 19.08  .steampath -> /home/premier69/.steam/sdk32/steam
lrwxrwxrwx.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       32 28 jun 19.08  .steampid -> /home/premier69/.steam/steam.pid
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      680 28 jun 14.01  TEMP
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        0  3 maj 20.11  Templates
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      138  3 maj 21.19  .themes
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:mozilla_home_t:s0   340 28 jun 14.33  .thunderbird
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        6  3 maj 21.11  .var
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0        0  3 maj 20.11  Videos
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0       52 11 maj 16.43 'VirtualBox VMs'
-rw-r--r--.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      308 24 jun 15.55  .wget-hsts
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:wine_home_t:s0      126 28 jun 13.35  .wine
drwxrwxr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      178  4 maj 08.31  wl-clipboard
-rw-------.  1 premier69 premier69 unconfined_u:object_r:xdm_home_t:s0        67 28 jun 16.37  .xsession-errors
drwxr-xr-x.  1 premier69 premier69 unconfined_u:object_r:user_home_t:s0      104 31 maj 06.23  .youtube-dl-gui

/home/premier69/..:
total 0
drwxr-xr-x. 1 root      root      system_u:object_r:home_root_t:s0          18  4 maj 02.09 .
dr-xr-xr-x. 1 root      root      system_u:object_r:root_t:s0              258 28 jun 16.44 ..
drwx------. 1 premier69 premier69 unconfined_u:object_r:user_home_dir_t:s0 862 29 jun 13.17 premier69
bash-5.1$

[vgaetera (Vladislav Grigoryev)]

Looks like you are the only user and there are some files/dirs in the user profile with much earlier modification dates, so it seems that only a few other files/dirs have been implicated.

You can restore shell settings like this:

cp -f -a /etc/skel/. ~; exit

Also check your mount parameters:

mount

[premier69]

it worked, resetting the terminal.

[premier69@fedora ~]$ mount
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime,seclabel)
devtmpfs on /dev type devtmpfs (rw,nosuid,seclabel,size=8123532k,nr_inodes=2030883,mode=755,inode64)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,seclabel,inode64)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,seclabel,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,nodev,seclabel,size=3272328k,nr_inodes=819200,mode=755,inode64)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,seclabel,nsdelegate,memory_recursiveprot)
pstore on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime,seclabel)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
none on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
/dev/nvme0n1p3 on / type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=257,subvol=/root)
selinuxfs on /sys/fs/selinux type selinuxfs (rw,nosuid,noexec,relatime)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=31,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=15921)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime,seclabel)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime,seclabel)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,relatime,seclabel,pagesize=2M)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime,seclabel)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)
tmpfs on /tmp type tmpfs (rw,nosuid,nodev,seclabel,nr_inodes=409600,inode64)
/dev/nvme0n1p3 on /home type btrfs (rw,relatime,seclabel,compress=zstd:1,ssd,space_cache,subvolid=256,subvol=/home)
/dev/nvme0n1p2 on /boot type ext4 (rw,relatime,seclabel)
/dev/nvme0n1p1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=ascii,shortname=winnt,errors=remount-ro)
/var/lib/snapd/snaps/gnome-3-34-1804_66.snap on /var/lib/snapd/snap/gnome-3-34-1804/66 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/anbox_186.snap on /var/lib/snapd/snap/anbox/186 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/guiscrcpy_256.snap on /var/lib/snapd/snap/guiscrcpy/256 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/bitwarden_50.snap on /var/lib/snapd/snap/bitwarden/50 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/bitwarden_49.snap on /var/lib/snapd/snap/bitwarden/49 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-34-1804_72.snap on /var/lib/snapd/snap/gnome-3-34-1804/72 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/snap-store_542.snap on /var/lib/snapd/snap/snap-store/542 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/snapd_12057.snap on /var/lib/snapd/snap/snapd/12057 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/dev/sda1 on /8TB type ext4 (rw,relatime,seclabel)
/var/lib/snapd/snaps/core20_975.snap on /var/lib/snapd/snap/core20/975 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/scrcpy_274.snap on /var/lib/snapd/snap/scrcpy/274 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-38-2004_39.snap on /var/lib/snapd/snap/gnome-3-38-2004/39 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/snapd_12159.snap on /var/lib/snapd/snap/snapd/12159 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/core20_1026.snap on /var/lib/snapd/snap/core20/1026 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/gnome-3-28-1804_145.snap on /var/lib/snapd/snap/gnome-3-28-1804/145 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/core_11187.snap on /var/lib/snapd/snap/core/11187 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/gtk-common-themes_1515.snap on /var/lib/snapd/snap/gtk-common-themes/1515 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/gtk2-common-themes_13.snap on /var/lib/snapd/snap/gtk2-common-themes/13 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/core18_2074.snap on /var/lib/snapd/snap/core18/2074 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/snap-store_547.snap on /var/lib/snapd/snap/snap-store/547 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/scrcpy_276.snap on /var/lib/snapd/snap/scrcpy/276 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/var/lib/snapd/snaps/core18_2066.snap on /var/lib/snapd/snap/core18/2066 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw,relatime)
tmpfs on /run/snapd/ns type tmpfs (rw,nosuid,nodev,seclabel,size=3272328k,nr_inodes=819200,mode=755,inode64)
nsfs on /run/snapd/ns/anbox.mnt type nsfs (rw)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,seclabel,size=1636164k,nr_inodes=409041,mode=700,uid=1000,gid=1000,inode64)
eiskaltdcpp-qt-2.2.10-689-x86_64.AppImage on /tmp/.mount_eiskalKS8uca type fuse.eiskaltdcpp-qt-2.2.10-689-x86_64.AppImage (ro,nosuid,nodev,relatime,user_id=1000,group_id=1000)
pcloud on /tmp/.mount_pcloud5Htnls type fuse.pcloud (ro,nosuid,nodev,relatime,user_id=1000,group_id=1000)
pCloud.fs on /home/premier69/pCloudDrive type fuse (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
portal on /run/user/1000/doc type fuse.portal (rw,nosuid,nodev,relatime,user_id=1000,group_id=1000)
nsfs on /run/snapd/ns/bitwarden.mnt type nsfs (rw)
nsfs on /run/snapd/ns/guiscrcpy.mnt type nsfs (rw)
nsfs on /run/snapd/ns/scrcpy.mnt type nsfs (rw)
/var/lib/snapd/snaps/core_11316.snap on /var/lib/snapd/snap/core/11316 type squashfs (ro,nodev,relatime,context=system_u:object_r:snappy_snap_t:s0,x-gdu.hide)
/dev/sdc1 on /run/media/premier69/USB STICK type fuseblk (rw,nosuid,nodev,relatime,user_id=0,group_id=0,default_permissions,allow_other,blksize=4096,uhelper=udisks2)
[premier69@fedora ~]$ 

yes, i am the only user, also, please elaborate on “there are some files/dirs in the user profile with much earlier modification dates, so it seems that only a few other files/dirs have been implicated.”

[vgaetera (Vladislav Grigoryev)]

Faulty storage or a partially corrupted filesystem can explain those missing files.
You can verify the RPM database integrity to isolate the issue:

sudo rpm -V -a | sort -t / -k 2

In addition, I think it’s a good idea to make a backup.

[premier69]

sudo rpm -V -a | sort -t / -k 2

OK, done. I have backups, i had to restore a lot after yesterdays issue. i don’t understand what caused this because i haven’t done anything i know of that would damage the system.

is this all that can be done now? is the system “good”? or is it basically held together with duct tape and a prayer?