I recently fixed my broken packages by deleting pulseaudio, since I cannot install any other packages that I needed for my research (I am using 20.04 btw). Deleting pulseaudio seems to solve my problem. I am now able to install other packages. It turns out that, after removing pulseaudio, I do not have any input and output to my sound device.

I even download the pulseaudio_13.99.1-1ubuntu3_amd64.deb and install it but failed due to this repeated error:

unable to make backup link of './usr/share/pulseaudio/alsa-mixer/paths/analog-output.conf.common' before installing new version: Operation not permitted

I have tried many methods all across the internet but failed. Any help will be appreciated.

Edit [12-29-21]

As I said above. I already deleted the pulseaudio and when trying to install it again, this is the error that always shows up:

This is the output when I try apt-cache policy pulseaudio:

Edit [12-30-21 | 1:12am]

After running snap as suggested by @nobody, I found the pulseaudio here:

Name                    Version                     Rev    Tracking         Publisher               Notes

bare                    1.0                         5      latest/stable    canonical✓              base

canonical-livepatch     10.1.2                      126    latest/stable    canonical✓              -

core                    16-2.52.1                   11993  latest/stable    canonical✓              core

core18                  20211028                    2253   latest/stable    canonical✓              base

core20                  20211129                    1270   latest/stable    canonical✓              base

evince                  41.3                        1008   latest/stable    ken-vandine             -

figma-linux             0.9.3                       149    latest/stable    youdonthavepermissiony  -

gnome-3-28-1804         3.28.0-19-g98f9e67.98f9e67  161    latest/stable    canonical✓              -

gnome-3-34-1804         0+git.3556cb3               77     latest/stable/…  canonical✓              -

gnome-3-38-2004         0+git.cd626d1               87     latest/stable    canonical✓              -

gtk-common-themes       0.1-59-g7bca6ae             1519   latest/stable/…  canonical✓              -

heroku                  v7.59.1                     4078   latest/stable    heroku✓                 classic

jupyter                 1.0.0                       6      latest/stable    projectjupyter✓         -

pdftk                   2.02-4                      9      latest/stable    smoser                  -

postman                 7.36.5                      133    latest/stable    postman-inc✓            -

pulseaudio              8.0-3                       9      latest/stable    canonical✓              -

simplescreenrecorder    0.1                         1      latest/stable    xiaoguo                 -

snap-store              3.38.0-66-gbd5b8f7          558    latest/stable/…  canonical✓              -

snapd                   2.53.4                      14295  latest/stable    canonical✓              snapd

telegram-desktop        3.3.1-beta-4-gffe420859     3492   latest/edge      telegram.desktop        -

utorrent                3.5.5.45828                 97     latest/stable    mmtrt                   -

wine-platform-3-stable  3.0.4                       14     latest/stable    mmtrt                   -

wine-platform-runtime   v1.0                        277    latest/stable    mmtrt                   -

zoom-client             5.9.1.1380                  167    latest/stable    ogra                    -

When i try sudo apt-get install pulseaudio this is the output looks like:

Reading package lists... Done

Building dependency tree       

Reading state information... Done

Suggested packages:

  pavumeter paman paprefs ubuntu-sounds

The following NEW packages will be installed:

  pulseaudio

0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.

2 not fully installed or removed.

Need to get 0 B/814 kB of archives.

After this operation, 4,645 kB of additional disk space will be used.

Selecting previously unselected package pulseaudio.

(Reading database ... 540571 files and directories currently installed.)

Preparing to unpack .../pulseaudio_1%3a13.99.1-1ubuntu3.13_amd64.deb ...

Unpacking pulseaudio (1:13.99.1-1ubuntu3.13) ...

dpkg: error processing archive /var/cache/apt/archives/pulseaudio_1%3a13.99.1-1ubuntu3.13_amd64.deb (--unpack):

 unable to make backup link of './usr/share/pulseaudio/alsa-mixer/paths/analog-output.conf.common' before installing new version: Operation not permitted

Errors were encountered while processing:

 /var/cache/apt/archives/pulseaudio_1%3a13.99.1-1ubuntu3.13_amd64.deb

E: Sub-process /usr/bin/dpkg returned an error code (1)

I think the pulseaudio installed via snap is not appearing or have some problem causing error to new installation. I'm not sure.

When I try sed -i s,//ph.archive,//archive,g /etc/apt/sources.list and sudo apt update as suggested by @nobody, this is the output looks like:

reymond@RMesuga:~$ sed -i s,//ph.archive,//archive,g  /etc/apt/sources.list

sed: couldn't open temporary file /etc/apt/sedeUQrNF: Permission denied

reymond@RMesuga:~$ sudo sed -i s,//ph.archive,//archive,g  /etc/apt/sources.list

[sudo] password for reymond: 

reymond@RMesuga:~$ sudo apt update

Ign:1 cdrom://Ubuntu 20.04.1 LTS _Focal Fossa_ - Release amd64 (20200731) focal InRelease

Err:2 cdrom://Ubuntu 20.04.1 LTS _Focal Fossa_ - Release amd64 (20200731) focal Release

  Please use apt-cdrom to make this CD-ROM recognized by APT. apt-get update cannot be used to add new CD-ROMs

Hit:3 http://dl.google.com/linux/chrome/deb stable InRelease

Hit:4 http://packages.microsoft.com/repos/edge stable InRelease                

Hit:5 http://packages.microsoft.com/repos/code stable InRelease                

Hit:6 https://packages.microsoft.com/repos/vscode stable InRelease             

Get:7 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]                

Hit:8 https://packages.microsoft.com/repos/ms-teams stable InRelease           

Hit:9 http://security.ubuntu.com/ubuntu focal-security InRelease               

Hit:10 http://ppa.launchpad.net/apandada1/droidcam/ubuntu focal InRelease      

Hit:11 http://archive.canonical.com/ubuntu focal InRelease                     

Hit:12 http://ppa.launchpad.net/git-core/ppa/ubuntu focal InRelease            

Hit:13 https://download.sublimetext.com apt/stable/ InRelease                  

Ign:14 http://ppa.launchpad.net/noobslab/icons2/ubuntu focal InRelease         

Get:15 http://archive.ubuntu.com/ubuntu focal-updates InRelease [114 kB] 

Get:16 http://archive.ubuntu.com/ubuntu focal-backports InRelease [108 kB]     

Ign:17 http://ppa.launchpad.net/octave/stable/ubuntu focal InRelease

Get:18 http://archive.ubuntu.com/ubuntu focal/main Sources [847 kB]      

Ign:19 http://ppa.launchpad.net/paolorotolo/droidcam/ubuntu focal InRelease   

Get:20 http://archive.ubuntu.com/ubuntu focal/restricted Sources [6,472 B]    

Get:21 http://archive.ubuntu.com/ubuntu focal/universe Sources [9,707 kB]

Hit:22 http://ppa.launchpad.net/scribus/ppa/ubuntu focal InRelease             

Ign:23 http://ppa.launchpad.net/snwh/pulp/ubuntu focal InRelease               

Err:24 http://ppa.launchpad.net/noobslab/icons2/ubuntu focal Release

  404  Not Found [IP: 91.189.95.85 80]

Err:25 http://ppa.launchpad.net/octave/stable/ubuntu focal Release             

  404  Not Found [IP: 91.189.95.85 80]

Get:26 http://archive.ubuntu.com/ubuntu focal/multiverse Sources [174 kB]      

Get:27 http://archive.ubuntu.com/ubuntu focal/main i386 Packages [718 kB]      

Err:28 http://ppa.launchpad.net/paolorotolo/droidcam/ubuntu focal Release      

  404  Not Found [IP: 91.189.95.85 80]

Get:29 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [970 kB]     

Get:30 http://archive.ubuntu.com/ubuntu focal/main Translation-en [506 kB]     

Err:31 http://ppa.launchpad.net/snwh/pulp/ubuntu focal Release                 

  404  Not Found [IP: 91.189.95.85 80]

Get:32 http://archive.ubuntu.com/ubuntu focal/main amd64 DEP-11 Metadata [494 kB]

Get:33 http://archive.ubuntu.com/ubuntu focal/main DEP-11 48x48 Icons [98.4 kB]

Get:34 http://archive.ubuntu.com/ubuntu focal/main DEP-11 64x64 Icons [163 kB] 

Get:35 http://archive.ubuntu.com/ubuntu focal/main DEP-11 64x64@2 Icons [15.8 kB]

Get:36 http://archive.ubuntu.com/ubuntu focal/main amd64 c-n-f Metadata [29.5 kB]

Get:37 http://archive.ubuntu.com/ubuntu focal/restricted i386 Packages [8,112 B]

Get:38 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [22.0 kB]

Get:39 http://archive.ubuntu.com/ubuntu focal/restricted Translation-en [6,212 B]

Get:40 http://archive.ubuntu.com/ubuntu focal/restricted amd64 c-n-f Metadata [392 B]

Get:41 http://archive.ubuntu.com/ubuntu focal/universe i386 Packages [4,642 kB]

Get:42 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [8,628 kB]

Get:43 http://archive.ubuntu.com/ubuntu focal/universe Translation-en [5,124 kB]

Get:44 http://archive.ubuntu.com/ubuntu focal/universe amd64 DEP-11 Metadata [3,603 kB]

Get:45 http://archive.ubuntu.com/ubuntu focal/universe DEP-11 48x48 Icons [3,016 kB]

Get:47 http://archive.ubuntu.com/ubuntu focal/universe DEP-11 64x64 Icons [7,794 kB]

Get:49 http://archive.ubuntu.com/ubuntu focal/universe DEP-11 64x64@2 Icons [44.3 kB]

Get:50 http://archive.ubuntu.com/ubuntu focal/universe amd64 c-n-f Metadata [265 kB]

Get:51 http://archive.ubuntu.com/ubuntu focal/multiverse i386 Packages [74.7 kB]

Get:52 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [144 kB]

Get:53 http://archive.ubuntu.com/ubuntu focal/multiverse Translation-en [104 kB]

Get:54 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 DEP-11 Metadata [48.4 kB]

Get:55 http://archive.ubuntu.com/ubuntu focal/multiverse DEP-11 48x48 Icons [23.1 kB]

Get:56 http://archive.ubuntu.com/ubuntu focal/multiverse DEP-11 64x64 Icons [192 kB]

Get:57 http://archive.ubuntu.com/ubuntu focal/multiverse DEP-11 64x64@2 Icons [214 B]

Get:58 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 c-n-f Metadata [9,136 B]

Get:59 http://archive.ubuntu.com/ubuntu focal-updates/restricted Sources [29.0 kB]

Get:60 http://archive.ubuntu.com/ubuntu focal-updates/multiverse Sources [19.0 kB]

Get:61 http://archive.ubuntu.com/ubuntu focal-updates/universe Sources [213 kB]

Get:62 http://archive.ubuntu.com/ubuntu focal-updates/main Sources [454 kB]    

Get:63 http://archive.ubuntu.com/ubuntu focal-updates/main i386 Packages [574 kB]

Get:64 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [1,400 kB]

Hit:46 https://packagecloud.io/github/git-lfs/ubuntu focal InRelease           

Get:65 http://archive.ubuntu.com/ubuntu focal-updates/main Translation-en [283 kB]

Get:66 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 DEP-11 Metadata [277 kB]

Get:67 http://archive.ubuntu.com/ubuntu focal-updates/main DEP-11 48x48 Icons [60.8 kB]

Get:68 http://archive.ubuntu.com/ubuntu focal-updates/main DEP-11 64x64 Icons [98.3 kB]

Get:69 http://archive.ubuntu.com/ubuntu focal-updates/main DEP-11 64x64@2 Icons [29 B]

Get:70 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 c-n-f Metadata [14.7 kB]

Get:71 http://archive.ubuntu.com/ubuntu focal-updates/restricted i386 Packages [21.8 kB]

Get:72 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [616 kB]

Get:73 http://archive.ubuntu.com/ubuntu focal-updates/restricted Translation-en [88.1 kB]

Get:74 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 c-n-f Metadata [528 B]

Get:75 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [884 kB]

Get:76 http://archive.ubuntu.com/ubuntu focal-updates/universe i386 Packages [654 kB]

Get:77 http://archive.ubuntu.com/ubuntu focal-updates/universe Translation-en [193 kB]

Get:78 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 DEP-11 Metadata [363 kB]

Get:79 http://archive.ubuntu.com/ubuntu focal-updates/universe DEP-11 48x48 Icons [219 kB]

Hit:48 https://packagecloud.io/slacktechnologies/slack/debian jessie InRelease 

Get:80 http://archive.ubuntu.com/ubuntu focal-updates/universe DEP-11 64x64 Icons [393 kB]

Get:81 http://archive.ubuntu.com/ubuntu focal-updates/universe DEP-11 64x64@2 Icons [29 B]

Get:82 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 c-n-f Metadata [19.9 kB]

Get:83 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [24.8 kB]

Get:84 http://archive.ubuntu.com/ubuntu focal-updates/multiverse i386 Packages [8,456 B]

Get:85 http://archive.ubuntu.com/ubuntu focal-updates/multiverse Translation-en [6,928 B]

Get:86 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 DEP-11 Metadata [944 B]

Get:87 http://archive.ubuntu.com/ubuntu focal-updates/multiverse DEP-11 48x48 Icons [1,865 B]

Get:88 http://archive.ubuntu.com/ubuntu focal-updates/multiverse DEP-11 64x64 Icons [2,498 B]

Get:89 http://archive.ubuntu.com/ubuntu focal-updates/multiverse DEP-11 64x64@2 Icons [29 B]

Get:90 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 c-n-f Metadata [616 B]

Get:91 http://archive.ubuntu.com/ubuntu focal-backports/main Sources [6,584 B] 

Get:92 http://archive.ubuntu.com/ubuntu focal-backports/universe Sources [4,624 B]

Get:93 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [42.0 kB]

Get:94 http://archive.ubuntu.com/ubuntu focal-backports/main i386 Packages [34.5 kB]

Get:95 http://archive.ubuntu.com/ubuntu focal-backports/main Translation-en [10.0 kB]

Get:96 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 DEP-11 Metadata [7,992 B]

Get:97 http://archive.ubuntu.com/ubuntu focal-backports/main DEP-11 48x48 Icons [6,977 B]

Get:98 http://archive.ubuntu.com/ubuntu focal-backports/main DEP-11 64x64 Icons [10.5 kB]

Get:99 http://archive.ubuntu.com/ubuntu focal-backports/main DEP-11 64x64@2 Icons [29 B]

Get:100 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 c-n-f Metadata [864 B]

Get:101 http://archive.ubuntu.com/ubuntu focal-backports/restricted amd64 c-n-f Metadata [116 B]

Get:102 http://archive.ubuntu.com/ubuntu focal-backports/universe i386 Packages [10.5 kB]

Get:103 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [18.9 kB]

Get:104 http://archive.ubuntu.com/ubuntu focal-backports/universe Translation-en [7,492 B]

Get:105 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 DEP-11 Metadata [11.3 kB]

Get:106 http://archive.ubuntu.com/ubuntu focal-backports/universe DEP-11 48x48 Icons [4,959 B]

Get:107 http://archive.ubuntu.com/ubuntu focal-backports/universe DEP-11 64x64 Icons [8,416 B]

Get:108 http://archive.ubuntu.com/ubuntu focal-backports/universe DEP-11 64x64@2 Icons [29 B]

Get:109 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 c-n-f Metadata [636 B]

Get:110 http://archive.ubuntu.com/ubuntu focal-backports/multiverse amd64 c-n-f Metadata [116 B]

Reading package lists... Done                                                  

E: The repository 'cdrom://Ubuntu 20.04.1 LTS _Focal Fossa_ - Release amd64 (20200731) focal Release' does not have a Release file.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.

W: Skipping acquire of configured file 'main/source/Sources' as repository 'https://packages.microsoft.com/repos/vscode stable InRelease' does not seem to provide it (sources.list entry misspelt?)

W: Skipping acquire of configured file 'Sources' as repository 'https://download.sublimetext.com apt/stable/ InRelease' does not seem to provide it (sources.list entry misspelt?)

E: The repository 'http://ppa.launchpad.net/noobslab/icons2/ubuntu focal Release' does not have a Release file.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.

E: The repository 'http://ppa.launchpad.net/octave/stable/ubuntu focal Release' does not have a Release file.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.

E: The repository 'http://ppa.launchpad.net/paolorotolo/droidcam/ubuntu focal Release' does not have a Release file.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.

E: The repository 'http://ppa.launchpad.net/snwh/pulp/ubuntu focal Release' does not have a Release file.

N: Updating from such a repository can't be done securely, and is therefore disabled by default.

N: See apt-secure(8) manpage for repository creation and user configuration details.



<strong>Edit [12-30-21 | 4:10 am]</strong><br>

All problems are SOLVED!!! Thanks to @nobody. To people who might be facing the same issue in the future, please check the accepted answer followed by the comments. The additional comments that she put there is is crucial part of the solution. Thanks again people especially to @nobody !!!