Update Related Issue, Software & Updates not working

Question

I'm using Ubuntu 20.04.3. LTS. Software & Update app is not working on my system. I don't care as I prefer terminal for updates. But, I don't know how to remove unused repositores (I added FDM repository earlier and I no longer use FDM, but its repository is still present).

Even it doesn't bother me. My issue is a notification related to update error. I have pasted the message below.

An error occured, please run Package Manager from the right-click menu or apt-get in a terminal to see what is wrong. The error message was: 'Error: Opening the cache (E: cannot open /var/lib/apt/lists/ppa.launchpad.net_alex-p_tesseract-ocr-devel_ubuntu_dists_focal_InRelease -fopen (13: Permission denied), E: The package lists or means that your installed packages have unmed dependencies Show updates Show notifications Preferences

That's that notification that I'm getting all the time. I am facing no problem while updating my system using sudo apt-get upgrade command.

I just want to get rid of this notification and to fix the Software & Updates app not opening issue.

Here is the output of apt-get

amartya@amartya-Pavilion-15t-cs200:~$ apt-get
apt 2.0.6 (amd64)
Usage: apt-get [options] command
apt-get [options] install|remove pkg1 [pkg2 ...]
apt-get [options] source pkg1 [pkg2 ...]
apt-get is a command line interface for retrieval of packages
and information about them from authenticated sources and
for installation, upgrade and removal of packages together
with their dependencies.
Most used commands:
update - Retrieve new lists of packages
upgrade - Perform an upgrade
install - Install new packages (pkg is libc6 not libc6.deb)
reinstall - Reinstall packages (pkg is libc6 not libc6.deb)
remove - Remove packages
purge - Remove packages and config files
autoremove - Remove automatically all unused packages
dist-upgrade - Distribution upgrade, see apt-get(8)
dselect-upgrade - Follow dselect selections
build-dep - Configure build-dependencies for source packages
satisfy - Satisfy dependency strings
clean - Erase downloaded archive 
autoclean - Erase old downloaded archive files
check - Verify that there are no broken dependencies
source - Download source archives
download - Download the binary package into the current directory
changelog - Download and display the changelog for the given package
See apt-get(8) for more information about the available commands.
Configuration options and syntax is detailed in apt.conf(5).
Information about how to configure sources can be found in sources.list(5).
Package and version choices can be expressed via apt_preferences(5).
Security details are available in apt-secure(8).
                                        This APT has Super Cow Powers.

Here is the output of sudo apt update

amartya@amartya-Pavilion-15t-cs200:~$ sudo apt update
[sudo] password for amartya: 
Hit:1 http://in.archive.ubuntu.com/ubuntu focal InRelease
Get:2 http://in.archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB]                          
Hit:3 http://dl.google.com/linux/chrome/deb stable InRelease                                        
Get:4 http://in.archive.ubuntu.com/ubuntu focal-backports InRelease [101 kB]                        
Hit:5 http://ppa.launchpad.net/alex-p/tesseract-ocr-devel/ubuntu focal InRelease                    
Get:6 http://in.archive.ubuntu.com/ubuntu focal-security InRelease [114 kB]                         
Get:7 http://in.archive.ubuntu.com/ubuntu focal-updates/main i386 Packages [536 kB]                 
Hit:8 http://ppa.launchpad.net/daniruiz/flat-remix/ubuntu focal InRelease                           
Get:9 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [1,214 kB]              
Hit:10 https://debrepo.freedownloadmanager.org bionic InRelease                                     
Get:11 https://repo.protonvpn.com/debian stable InRelease [2,519 B]                                 
Hit:12 http://ppa.launchpad.net/deadsnakes/ppa/ubuntu focal InRelease                     
Get:13 http://in.archive.ubuntu.com/ubuntu focal-updates/main amd64 DEP-11 Metadata [282 kB]
Get:14 http://in.archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [855 kB]           
Get:15 http://in.archive.ubuntu.com/ubuntu focal-updates/universe amd64 DEP-11 Metadata [352 kB]    
Hit:16 http://ppa.launchpad.net/flexiondotorg/cpu-x/ubuntu focal InRelease              
Get:17 http://in.archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 DEP-11 Metadata [944 B]
Get:18 http://in.archive.ubuntu.com/ubuntu focal-backports/universe amd64 DEP-11 Metadata [10.4 kB] 
Get:19 http://in.archive.ubuntu.com/ubuntu focal-security/main amd64 DEP-11 Metadata [27.6 kB]      
Get:20 http://in.archive.ubuntu.com/ubuntu focal-security/universe amd64 DEP-11 Metadata [61.3 kB]  
Get:21 http://in.archive.ubuntu.com/ubuntu focal-security/multiverse amd64 DEP-11 Metadata [2,464 B]
Hit:22 http://ppa.launchpad.net/gns3/ppa/ubuntu focal InRelease                                     
Hit:23 http://ppa.launchpad.net/micahflee/ppa/ubuntu focal InRelease
Fetched 3,673 kB in 3s (1,137 kB/s)                
Reading package lists... Done
Building dependency tree       
Reading state information... Done
All packages are up to date.

Here is the file permission

amartya@amartya-Pavilion-15t-cs200:~$ sudo ls -l /var/lib/apt/lists/ppa.launchpad.net_alex-p_tesseract-ocr-devel_ubuntu_dists_focal_InRelease
-rw-r--r-- 1 root root 17583 Aug 25 02:10 /var/lib/apt/lists/ppa.launchpad.net_alex-p_tesseract-ocr-devel_ubuntu_dists_focal_InRelease

Here is the output of history |grep add-apt

amartya@amartya-Pavilion-15t-cs200:~$ history |grep add-apt
 1281  sudo add-apt-repository ppa:flexiondotorg/cpu-x
 1305  sudo add-apt-repository ppa:gns3/ppa
 1318  sudo add-apt-repository ppa:micahflee/ppa
 1827  sudo add-apt-repository ppa:alex-p/tesseract-ocr-devel
 1997  history |grep add-apt
 2003  history |grep add-apt

Answer 1

Error: Opening the cache (E: cannot open /var/lib/apt/lists/ppa.launchpad.et_alex-p__tesseract-ocr-devel__ubuntu__dists__focal_-InRelease-fopen (13: Permission denied)

check the file permissions on the file

sudo ls -l /var/lib/apt/lists/ppa.launchpad.et_alex-p__tesseract-ocr-devel__ubuntu__dists__focal_-InRelease-fopen

that should tell you who owns it, and why there are permission issues.

I don't know how to remove unused repositores (I added FDM repository earlier ...

how did you add it? command line or via GUI? It's a good idea to remove repos that you no longer use.

if you installed via command line:

history |grep add-apt

depending on how long ago it was, this may show you the command used to add it, and you can look for the reverse of this command via Google.

worst case scenario, you can always edit the repos file directly. here is another question that is related to yours: How to remove a repository?