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Flatpak permission error #26

@Devcom439

Description

@Devcom439

Hello there. Yesterday I used this script to harden my Linux Mint system. Today, when I wanted to boot up my laptop and log in, I got an error that filled the entire screen reading

Error found when loading /etc/profile:
flatpak: error while loading shared libraries: libappstream.so.5: cannot open shared object file: Permission denied

As a result the session will not be configured correctly.
You should fix the problem as soon as feasible.

I'm new to Linux and I have absolutely no clue what to do. I tried running the verify_fortress.sh and PERM_diagnostic.sh, but they didn't give any clue as to how to fix this issue.

Because of this, my zen browser and fsearch apps don't open anymore and they aren't even listed anymore, but still installed.

I would highly appreciate it if someone could help me resolve this problem.

PERM_diagnostic.sh output:

ULTRA-DIAGNOSTIC REPORT
======================
Date: Sun Jun  7 03:33:48 PM CEST 2026

=== ROOT CHECK ===
✓ Running as root

=== BASIC COMMAND TEST ===
Testing if basic commands work...
✓ ls works
✓ cat works
✓ bash works

=== LIBSTDC++ SPECIFIC CHECK ===
Found: /usr/lib/i386-linux-gnu/libstdc++.so.6
lrwxrwxrwx 1 root root 19 Dec 18 22:36 /usr/lib/i386-linux-gnu/libstdc++.so.6 -> libstdc++.so.6.0.33
  File: /usr/lib/i386-linux-gnu/libstdc++.so.6 -> libstdc++.so.6.0.33
  Size: 19        	Blocks: 0          IO Block: 4096   symbolic link
Device: 259,2	Inode: 18498023    Links: 1
Access: (0777/lrwxrwxrwx)  Uid: (    0/    root)   Gid: (    0/    root)
Access: 2026-06-06 17:44:46.956506820 +0200
Modify: 2025-12-18 22:36:50.000000000 +0100
Change: 2026-06-06 17:44:34.621426749 +0200
 Birth: 2026-06-06 17:44:34.620426743 +0200
Can I read it as current user?
✓ YES - Readable
Parent directory permissions:
drwxr-xr-x 19 root root 20480 Jun  6 17:44 /usr/lib/i386-linux-gnu

=== ALL LIBRARY DIRECTORY PERMISSIONS ===
Directory: /lib
lrwxrwxrwx 1 root root 7 Jun  6 16:31 /lib -> usr/lib
Perms: 777 Owner: root:root
✓ Accessible (read+exec)

Directory: /lib64
lrwxrwxrwx 1 root root 9 Jun  6 16:31 /lib64 -> usr/lib64
Perms: 777 Owner: root:root
✓ Accessible (read+exec)

Directory: /usr/lib
drwxr-xr-x 116 root root 4096 Jun  6 22:51 /usr/lib
Perms: 755 Owner: root:root
✓ Accessible (read+exec)

Directory: /usr/lib64
drwxr-xr-x 2 root root 4096 Jun  6 16:57 /usr/lib64
Perms: 755 Owner: root:root
✓ Accessible (read+exec)

Directory: /lib/x86_64-linux-gnu
drwxr-xr-x 118 root root 118784 Jun  7 15:11 /lib/x86_64-linux-gnu
Perms: 755 Owner: root:root
✓ Accessible (read+exec)

Directory: /usr/lib/x86_64-linux-gnu
drwxr-xr-x 118 root root 118784 Jun  7 15:11 /usr/lib/x86_64-linux-gnu
Perms: 755 Owner: root:root
✓ Accessible (read+exec)

=== ALL MOUNT POINTS ===
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
udev on /dev type devtmpfs (rw,nosuid,relatime,size=15929188k,nr_inodes=3982297,mode=755,inode64)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,nodev,noexec,relatime,size=3195028k,mode=755,inode64)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
/dev/nvme0n1p2 on / type ext4 (rw,relatime,errors=remount-ro)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev,inode64)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k,inode64)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot)
none on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs (rw,relatime,fd=32,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=11323)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime)
hugetlbfs on /dev/hugepages type hugetlbfs (rw,nosuid,nodev,relatime,pagesize=2M)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run/shm type tmpfs (rw,nosuid,nodev,relatime,inode64)
/dev/nvme0n1p1 on /boot/efi type vfat (rw,relatime,fmask=0077,dmask=0077,codepage=437,iocharset=iso8859-1,shortname=mixed,errors=remount-ro)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run/user/1000 type tmpfs (rw,nosuid,nodev,relatime,size=3195024k,nr_inodes=798756,mode=700,uid=1000,gid=1000,inode64)
gvfsd-fuse on /run/user/1000/gvfs type fuse.gvfsd-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)

=== MOUNTS WITH NOEXEC ===
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,nodev,noexec,relatime,size=3195028k,mode=755,inode64)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k,inode64)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot)
none on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
devpts on /dev/pts type devpts (rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,nodev,noexec,relatime,size=3195028k,mode=755,inode64)
efivarfs on /sys/firmware/efi/efivars type efivarfs (rw,nosuid,nodev,noexec,relatime)
securityfs on /sys/kernel/security type securityfs (rw,nosuid,nodev,noexec,relatime)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k,inode64)
cgroup2 on /sys/fs/cgroup type cgroup2 (rw,nosuid,nodev,noexec,relatime,nsdelegate,memory_recursiveprot)
none on /sys/fs/pstore type pstore (rw,nosuid,nodev,noexec,relatime)
bpf on /sys/fs/bpf type bpf (rw,nosuid,nodev,noexec,relatime,mode=700)
debugfs on /sys/kernel/debug type debugfs (rw,nosuid,nodev,noexec,relatime)
mqueue on /dev/mqueue type mqueue (rw,nosuid,nodev,noexec,relatime)
tracefs on /sys/kernel/tracing type tracefs (rw,nosuid,nodev,noexec,relatime)
configfs on /sys/kernel/config type configfs (rw,nosuid,nodev,noexec,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,nosuid,nodev,noexec,relatime)
binfmt_misc on /proc/sys/fs/binfmt_misc type binfmt_misc (rw,nosuid,nodev,noexec,relatime)

=== /etc/fstab CONTENTS ===
# /etc/fstab: static file system information.
#
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point>   <type>  <options>       <dump>  <pass>
# / was on /dev/nvme0n1p2 during installation
UUID=9ff4146a-bf17-4289-92a8-bd3527fe43a0 /               ext4    errors=remount-ro 0       1
# /boot/efi was on /dev/nvme0n1p1 during installation
UUID=8C29-7780  /boot/efi       vfat    umask=0077      0       1
/swapfile                                 none            swap    sw              0       0
tmpfs /dev/shm tmpfs defaults,nodev,nosuid 0 0
tmpfs /run/shm tmpfs defaults,nodev,nosuid 0 0

=== LDCONFIG CHECK ===
Checking if libstdc++ is in ldconfig cache...
	libstdc++.so.6 (libc6,x86-64) => /lib/x86_64-linux-gnu/libstdc++.so.6
	libstdc++.so.6 (libc6) => /lib/i386-linux-gnu/libstdc++.so.6
	libstdc++.so.6 (libc6,x86-64) => /lib/x86_64-linux-gnu/libstdc++.so.6
	libstdc++.so.6 (libc6) => /lib/i386-linux-gnu/libstdc++.so.6

=== DIRECT LIBRARY LOAD TEST ===
Attempting to directly access library file...
✓ Can read library file directly

=== APPARMOR STATUS ===
apparmor module is loaded.
150 profiles are loaded.
150 profiles are in enforce mode.
   /usr/bin/irssi
   /usr/bin/man
   /usr/bin/pidgin
   /usr/bin/pidgin//sanitized_helper
   /usr/bin/totem
   /usr/bin/totem-audio-preview
   /usr/bin/totem-video-thumbnailer
   /usr/bin/totem//sanitized_helper
   /usr/lib/NetworkManager/nm-dhcp-client.action
   /usr/lib/NetworkManager/nm-dhcp-helper
   /usr/lib/connman/scripts/dhclient-script
   /usr/lib/cups/backend/cups-pdf
   /usr/lib/lightdm/lightdm-guest-session
   /usr/lib/lightdm/lightdm-guest-session//chromium
   /usr/sbin/cups-browsed
   /usr/sbin/cupsd
   /usr/sbin/cupsd//third_party
   /{,usr/}sbin/dhclient
   1password
   Discord
   MongoDB Compass
   QtWebEngineProcess
   apt-cacher-ng
   avahi-daemon
   balena-etcher
   brave
   buildah
   cam
   ch-checkns
   ch-run
   chrome
   crun
   devhelp
   dnsmasq
   dnsmasq//libvirt_leaseshelper
   element-desktop
   epiphany
   evolution
   firefox
   flatpak
   foliate
   geary
   github-desktop
   goldendict
   identd
   ipa_verify
   kchmviewer
   keybase
   klogd
   lc-compliance
   libcamerify
   libreoffice-oosplash
   libreoffice-senddoc
   libreoffice-soffice
   libreoffice-soffice//gpg
   libreoffice-xpdfimport
   linux-sandbox
   loupe
   lsb_release
   lxc-attach
   lxc-create
   lxc-destroy
   lxc-execute
   lxc-stop
   lxc-unshare
   lxc-usernsexec
   man_filter
   man_groff
   mdnsd
   mint-chromium
   mmdebstrap
   msedge
   nmbd
   notepadqq
   nscd
   nvidia_modprobe
   nvidia_modprobe//kmod
   obsidian
   opam
   opera
   pageedit
   php-fpm
   ping
   plasmashell
   plasmashell//QtWebEngineProcess
   podman
   polypane
   privacybrowser
   qcam
   qmapshack
   qutebrowser
   rootlesskit
   rpm
   rssguard
   rsyslogd
   runc
   samba-bgqd
   samba-dcerpcd
   samba-rpcd
   samba-rpcd-classic
   samba-rpcd-spoolss
   sbuild
   sbuild-abort
   sbuild-adduser
   sbuild-apt
   sbuild-checkpackages
   sbuild-clean
   sbuild-createchroot
   sbuild-destroychroot
   sbuild-distupgrade
   sbuild-hold
   sbuild-shell
   sbuild-unhold
   sbuild-update
   sbuild-upgrade
   scide
   signal-desktop
   slack
   slirp4netns
   smbd
   smbldap-useradd
   smbldap-useradd///etc/init.d/nscd
   steam
   stress-ng
   surfshark
   syslog-ng
   syslogd
   systemd-coredump
   tcpdump
   thunderbird
   toybox
   traceroute
   transmission-cli
   transmission-daemon
   transmission-gtk
   transmission-qt
   trinity
   tup
   tuxedo-control-center
   unix-chkpwd
   unprivileged_userns
   userbindmount
   uwsgi-core
   vdens
   virtiofsd
   vivaldi-bin
   vpnns
   vscode
   wike
   wpcom
0 profiles are in complain mode.
0 profiles are in prompt mode.
0 profiles are in kill mode.
0 profiles are in unconfined mode.
5 processes have profiles defined.
5 processes are in enforce mode.
   /usr/sbin/cups-browsed (1535) 
   /usr/sbin/cupsd (1322) 
   /usr/sbin/avahi-daemon (943) avahi-daemon
   /usr/sbin/avahi-daemon (1011) avahi-daemon
   /usr/sbin/rsyslogd (1121) rsyslogd
0 processes are in complain mode.
0 processes are in prompt mode.
0 processes are in kill mode.
0 processes are unconfined but have a profile defined.
0 processes are in mixed mode.

=== RECENT APPARMOR DENIALS ===

=== SELINUX CHECK ===
SELinux not installed

=== ACL CHECK ===
Checking ACLs on library directories...
ACLs for /lib:
getfacl: Removing leading '/' from absolute path names
# file: lib
# owner: root
# group: root
user::rwx
group::r-x
other::r-x

ACLs for /usr/lib:
getfacl: Removing leading '/' from absolute path names
# file: usr/lib
# owner: root
# group: root
user::rwx
group::r-x
other::r-x


=== NAMESPACE CHECK ===
Current namespaces:
total 0
lrwxrwxrwx 1 root root 0 Jun  7 15:33 cgroup -> cgroup:[4026531835]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 ipc -> ipc:[4026531839]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 mnt -> mnt:[4026531832]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 net -> net:[4026531833]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 pid -> pid:[4026531836]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 pid_for_children -> pid:[4026531836]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 time -> time:[4026531834]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 time_for_children -> time:[4026531834]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 user -> user:[4026531837]
lrwxrwxrwx 1 root root 0 Jun  7 15:33 uts -> uts:[4026531838]

=== LDD ON FIREFOX ===
firefox-esr not found

=== FIREFOX EXECUTION TEST ===

=== STRACE FIREFOX (if available) ===
strace not available or firefox not found

=== RECENT PERMISSION DENIED ERRORS ===
Jun 07 15:27:57 devbe-Lafite-Pro-15-AMD systemd[1393]: flatpak: error while loading shared libraries: libappstream.so.5: cannot open shared object file: Permission denied
Jun 07 15:28:04 devbe-Lafite-Pro-15-AMD systemd[1594]: flatpak: error while loading shared libraries: libappstream.so.5: cannot open shared object file: Permission denied
Jun 07 15:28:05 devbe-Lafite-Pro-15-AMD irqbalance[953]: Cannot change IRQ 77 affinity: Permission denied
Jun 07 15:28:05 devbe-Lafite-Pro-15-AMD irqbalance[953]: Cannot change IRQ 75 affinity: Permission denied

=== FORTRESS BACKUPS ===
No FORTRESS backups found

=== SUMMARY ===
This diagnostic report has been saved to: /tmp/ultra_diagnostic_20260607_153348.log

Please share this ENTIRE output.

Also saved to /root/ for safety

DIAGNOSTIC COMPLETE!
Log saved to: /tmp/ultra_diagnostic_20260607_153348.log

Please share ALL the output above, especially:
  1. Library directory permissions
  2. Mount output (any noexec?)
  3. ldd output for firefox
  4. strace output (if available)

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