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Help!! my install has broken and it cant get up

loki_asguardian

New member
Sep 24, 2020
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Hi all,
I am getting pretty scared I might need to start from scratch with a new install. If there is a way to fix my current install, I would love some advice.
Here is what happened:
I am running :
///////*767//////////////// OS: Pop!_OS 20.10 x86_64
//////7676767676*////////////// Kernel: 5.11.0-7620-generic
/////76767//7676767////////////// Uptime: 8 mins
/////767676///*76767/////////////// Packages: 3021 (dpkg), 17 (flatpak)
///////767676///76767.///7676*/////// Shell: bash 5.0.17
/////////767676//76767///767676//////// Resolution: 2560x1440
//////////76767676767////76767///////// DE: GNOME
///////////76767676//////7676////////// WM: Mutter
////////////,7676,///////767/////////// WM Theme: Pop
/////////////*7676///////76//////////// Theme: Pop-dark [GTK2/3]
///////////////7676//////////////////// Icons: Pop [GTK2/3]
///////////////7676///767//////////// Terminal: gnome-terminal
//////////////////////'//////////// CPU: Intel i7-6950X (20) @ 4.000GHz
//////.7676767676767676767,////// GPU: NVIDIA GeForce GTX 1080 Ti
/////767676767676767676767///// Memory: 2074MiB / 128735MiB
///////////////////////////
/////////////////////
Up to now it has been rock solid for a year. Recently, however I was running into a weird issue where zoom would not work and I would need to reinstall it after every restart (a bit annoying and probably unrelated to what is happening now). But, about a week later I tried to open my zoom recording from the class I TA in order to edit it before I post it on the class website. I could not play the video because my system could not find nor install gstreamer and related pacs. I tried to upgrade and that failed. I tried to clean the repos and reconfig dpkg which also failed. Finally, I tried the system recommended sudo apt --fix-broken install and was greeted to this laundry list of broken packages which the system does not let me reinstall due to mutual dependencies:
sudo apt --fix-broken install
[sudo] password for loki:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Correcting dependencies... Done
The following packages were automatically installed and are no longer required:
alien at bsdmainutils calendar debugedit libclang-cpp11 libclang1-10
libfakeroot libfl2 libkf5syntaxhighlighting-data libkf5syntaxhighlighting5
libllvm10 libncurses5 libomp-11-dev libomp5-11 libpfm4
libqt5designercomponents5 libqt5positioning5 libqt5quicktest5 libqt5sensors5
libqt5serialport5 libqt5webchannel5 libqt5webkit5 libqt5xmlpatterns5
librpmbuild8 librpmsign8 libtinfo5 libz3-4 libz3-dev llvm-11 llvm-11-dev
llvm-11-runtime llvm-11-tools lsb-security ncal pax python3-pygments
qdoc-qt5 qhelpgenerator-qt5 qml-module-qtgraphicaleffects qml-module-qtqml
qml-module-qtqml-models2 qml-module-qtquick-controls
qml-module-qtquick-layouts qml-module-qtquick-window2 qmlscene qt3d5-doc
qt5-assistant qt5-doc qtattributionsscanner-qt5 qtbase5-doc qtcharts5-doc
qtconnectivity5-doc qtcreator-data qtcreator-doc qtdatavisualization5-doc
qtdeclarative5-dev-tools qtdeclarative5-doc qtgraphicaleffects5-doc
qtlocation5-doc qtmultimedia5-doc qtnetworkauth5-doc qtquickcontrols2-5-doc
qtquickcontrols5-doc qtscript5-doc qtscxml5-doc qtsensors5-doc
qtserialbus5-doc qtserialport5-doc qtsvg5-doc qttools5-dev-tools
qttools5-doc qtvirtualkeyboard5-doc qtwayland5-doc qtwebchannel5-doc
qtwebengine5-doc qtwebsockets5-doc qtwebview5-doc qtx11extras5-doc
qtxmlpatterns5-dev-tools qtxmlpatterns5-doc rpm
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
avahi-daemon avahi-utils lib32gcc-s1 lib32stdc++6 libavahi-client3
libavahi-client3:i386 libavahi-common-data libavahi-common-data:i386
libavahi-common3 libavahi-common3:i386 libavahi-core7 libavahi-glib1
libc6:i386 libc6-i386 libclang-11-dev libclang-common-11-dev libclang-dev
libcrypt1:i386 libnss-nis:i386 libnss-nisplus:i386 libroken18-heimdal:i386
locales-all
Suggested packages:
glibc-doc:i386 locales:i386
The following packages will be REMOVED:
language-pack-ar language-pack-ar-base language-pack-de
language-pack-de-base language-pack-en language-pack-en-base
language-pack-es language-pack-es-base language-pack-fr
language-pack-fr-base language-pack-gnome-ar language-pack-gnome-ar-base
language-pack-gnome-de language-pack-gnome-de-base language-pack-gnome-en
language-pack-gnome-en-base language-pack-gnome-es
language-pack-gnome-es-base language-pack-gnome-fr
language-pack-gnome-fr-base language-pack-gnome-it
language-pack-gnome-it-base language-pack-gnome-ja
language-pack-gnome-ja-base language-pack-gnome-pt
language-pack-gnome-pt-base language-pack-gnome-ru
language-pack-gnome-ru-base language-pack-gnome-zh-hans
language-pack-gnome-zh-hans-base language-pack-gnome-zh-hant
language-pack-gnome-zh-hant-base language-pack-it language-pack-it-base
language-pack-ja language-pack-ja-base language-pack-pt
language-pack-pt-base language-pack-ru language-pack-ru-base
language-pack-zh-hans language-pack-zh-hans-base language-pack-zh-hant
language-pack-zh-hant-base libreoffice-help-es libreoffice-l10n-es locales
lsb-core ubuntu-minimal
The following NEW packages will be installed:
lib32gcc-s1 lib32stdc++6 libc6:i386 libc6-i386 libclang-11-dev
libclang-common-11-dev libclang-dev libcrypt1:i386 libnss-nis:i386
libnss-nisplus:i386 libroken18-heimdal:i386 locales-all
The following packages will be upgraded:
avahi-daemon avahi-utils libavahi-client3 libavahi-client3:i386
libavahi-common-data libavahi-common-data:i386 libavahi-common3
libavahi-common3:i386 libavahi-core7 libavahi-glib1
10 upgraded, 12 newly installed, 49 to remove and 10 not upgraded.
3 not fully installed or removed.
Need to get 0 B/43.2 MB of archives.
After this operation, 247 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Preconfiguring packages ...
(Reading database ... 346695 files and directories currently installed.)
Preparing to unpack .../libc6_2.32-0ubuntu3_i386.deb ...
Unpacking libc6:i386 (2.32-0ubuntu3) ...
dpkg: error processing archive /var/cache/apt/archives/libc6_2.32-0ubuntu3_i386.
deb (--unpack):
trying to overwrite shared '/usr/share/doc/libc6/NEWS.Debian.gz', which is diff
erent from other instances of package libc6:i386
Errors were encountered while processing:
/var/cache/apt/archives/libc6_2.32-0ubuntu3_i386.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)

What should I do!!??
Thanks in advance for any suggestions you may have.
 

derpOmattic

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What do your apt sources look like?

Can you show the contents or output of each of the following lines:

cat /etc/apt/sources.list

cd /etc/apt/ && ls

cd sources.list.d && ls

cat pop-os-apps.sources

cat system.sources

cat pop-os-ppa.list

That last one may vary in name slightly depending, but it should say whether it is pointing to groovy or hirsute. See here.
 
Last edited:

loki_asguardian

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Sep 24, 2020
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Here's what I have :
cat /etc/apt/sources.list
## This file is deprecated in Pop!_OS.
## See `man deb822` and /etc/apt/sources.list.d/system.sources.
etc/apt$ ls
apt.conf.d preferences.d sources.list~ trusted.gpg trusted.gpg.d
auth.conf.d sources.list sources.list.d trusted.gpg~

brave-browser-release.list pop-os-apps.sources
cybermax-dexter-ubuntu-sdl2-backport-focal.list pop-os-ppa.list
google-earth-pro.list skype-stable.list
home:stevenpusser.list slack.list
kelleyk-ubuntu-emacs-focal.list system.sources
mendeleydesktop.list vscode.list
micahflee-ubuntu-ppa-focal.list

X-Repolib-Name: Pop_OS Apps
Enabled: yes
Types: deb
URIs: http://apt.pop-os.org/proprietary
Suites: groovy
Components: main

cat system.sources
X-Repolib-Name: Pop_OS System Sources
Enabled: yes
Types: deb deb-src
URIs: http://us.archive.ubuntu.com/ubuntu/
Suites: groovy groovy-security groovy-updates groovy-backports
Components: main restricted universe multiverse
X-Repolib-Default-Mirror: http://us.archive.ubuntu.com/ubuntu/

## This file was generated by pop-upgrade
#
## X-Repolib-Name: Pop_OS PPA
deb http://ppa.launchpad.net/system76/pop/ubuntu groovy main
deb-src http://ppa.launchpad.net/system76/pop/ubuntu groovy main
 

derpOmattic

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cat /etc/apt/sources.list
## This file is deprecated in Pop!_OS.
## See `man deb822` and /etc/apt/sources.list.d/system.sources.
This is fine - exactly how it should be.


etc/apt$ ls
apt.conf.d preferences.d sources.list~ trusted.gpg trusted.gpg.d
auth.conf.d sources.list sources.list.d trusted.gpg~
Same here - Looks OK.


brave-browser-release.list pop-os-apps.sources
cybermax-dexter-ubuntu-sdl2-backport-focal.list pop-os-ppa.list
google-earth-pro.list skype-stable.list
home:stevenpusser.list slack.list
kelleyk-ubuntu-emacs-focal.list system.sources
mendeleydesktop.list vscode.list
micahflee-ubuntu-ppa-focal.list
I'm assuming the above is /etc/apt/sources.list.d && ls. Normally, all Person Package Archives (PPAs) and third-party repositories are disabled when updating to a new release of the operating system. This helps keep upgrades simpler and prevents PPAs that haven't been properly updated for the new release from breaking the upgrade. Everything in the above list needs to be moved or deleted except the three files mentioned below.
pop-os-apps.sources system.sources pop-os-ppa.list
The easiest way to remove them if you're not familiar with a terminal is with Repoman. I believe you should remove them because of the trouble you're having, but there is another choice under better circumstances.


Do a restart.

Once they're deleted, try the commands to fix the package manager - run them one at a time;

Code:
sudo apt clean
sudo apt update -m
sudo dpkg --configure -a
sudo apt install -f
sudo apt full-upgrade
sudo apt autoremove --purge
And repair Flatpak.
Code:
flatpak repair --user   
flatpak uninstall --unused
sudo flatpak repair --system
If you get this far, run the commands to update the repos in preparation for the release upgrade;

sudo apt update && sudo apt full-upgrade --allow-downgrades

Also update Flatpak;

Code:
flatpak update 
flatpak update --appstream
flatpak update --user
If all has gone well to this point things are looking great, and you could try to run the release.;

pop-upgrade release upgrade


If you have any trouble with that, I'd edit the sources manually then rerun the release command. Use Nano if your unfamiliar with editors. You'll need administrative privileges as well, so it would be sudo nano /etc/apt/sources.list.d/pop-os-apps.sources If you were already in the right directory you could forego the full path. Anyway, what you need to do is substitute the word hirsute in every instance where your says groovy. To save change sin Nano use ctrl + s. To exit Nano use ctrl + x.

/pop-os-apps.sources

Code:
X-Repolib-Name: Pop_OS Applications
Enabled: yes
Types: deb
URIs: http://apt.pop-os.org/proprietary
Suites: hirsute
Components: main
/system.sources
Code:
X-Repolib-Name: Pop_OS System Sources
Enabled: yes
Types: deb deb-src
URIs: http://us.archive.ubuntu.com/ubuntu/
Suites: hirsute hirsute-security hirsute-updates hirsute-backports
Components: main restricted universe multiverse
X-Repolib-Default-Mirror: http://us.archive.ubuntu.com/ubuntu/
/system76-ubuntu-pop-hirsute.list (Yours is pop-os-ppa.list)
Code:
deb http://ppa.launchpad.net/system76/pop/ubuntu/ hirsute main
deb-src http://ppa.launchpad.net/system76/pop/ubuntu/ hirsute main
Ok, once you've edited sources to point at hirsute, try the upgrade again.
 
Last edited:

loki_asguardian

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Sep 24, 2020
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@derpOmattic Thanks for the the advice. The sudo apt clean, sudo apt update -m, sudo dpkg --configure -a. sudo apt install -f, sudo apt full-upgrade, and sudo apt autoremove --purge was one of the first things I tried but I hadn't moved the PPAs. Per your advice I moved them and restarted, but got the same set of errors while trying to repair the package manager. Here's what I get when I try to configure dpkg:
sudo dpkg --configure -a
dpkg: dependency problems prevent configuration of locales:
locales depends on libc-bin (>> 2.33); however:
Version of libc-bin on system is 2.32-0ubuntu3.

dpkg: error processing package locales (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of libfakeroot:amd64:
libfakeroot:amd64 depends on libc6 (>= 2.14); however:
Package libc6:amd64 is not installed.

dpkg: error processing package libfakeroot:amd64 (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent processing triggers for libc-bin:
libc-bin depends on libc6 (>> 2.32); however:
Package libc6:amd64 is not installed.
libc-bin depends on libc6 (<< 2.33); however:
Package libc6:amd64 is not installed.

dpkg: error processing package libc-bin (--configure):
dependency problems - leaving triggers unprocessed
dpkg: dependency problems prevent processing triggers for man-db:
man-db depends on libc6 (>= 2.28); however:
Package libc6:amd64 is not installed.

dpkg: error processing package man-db (--configure):
dependency problems - leaving triggers unprocessed
dpkg: dependency problems prevent processing triggers for desktop-file-utils:
desktop-file-utils depends on libc6 (>= 2.7); however:
Package libc6:amd64 is not installed.

dpkg: error processing package desktop-file-utils (--configure):
dependency problems - leaving triggers unprocessed
Errors were encountered while processing:
locales
libfakeroot:amd64
libc-bin
man-db
desktop-file-utils


Any kind of upgrade is also still blocked by the same missing/broken packages in my original post.
What should I try next?
Edit: By the way here is what happens when I try to reinstall libc:
udo apt reinstall libc6:amd64
[sudo] password for loki:
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: The package libc6 needs to be reinstalled, but I can't find an archive for it
Just install (rather than reinstall) or libc6 by itself without the :amd64 gives the same result.....
edit again:
A similar issue was reported on Ask Ubuntu and their solution was to downgrade libc6 https://askubuntu.com/questions/1315906/unmet-dependencies-libc6-the-package-system-is-broken
I am a bit nervous to try that because I don't know If I have the exact same issue and I don't want to make the problem worse. Also I worry downgrading may cause further issues for the release upgrade.
 
Last edited:

derpOmattic

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Try sudo apt --fix-broken install. It's a bit of a mess. Make sure you have back ups of anything important before trying any kind of upgrade, or anything to do with kernels or BIOS. A good general practice.

If that doesn't work, try using the following command for each package it's complaining about.

sudo dpkg --force-remove-reinstreq --purge --force-depends <package-name>

Where I have <package-name>, just substitute and remove the arrows. eg;

sudo dpkg --force-remove-reinstreq --purge --force-depends libfakeroot:amd64

You could run all of them in one command, but I want to easily see if any of them fail.
 
Last edited:

loki_asguardian

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Try sudo apt --fix-broken install. It's a bit of a mess. Make sure you have back ups of anything important before trying any kind of upgrade, or anything to do with kernels or BIOS. A good general practice.
I tried that too and it gave the same issue; it couldn't reinstall libc6.
 

loki_asguardian

New member
Sep 24, 2020
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Try sudo apt --fix-broken install. It's a bit of a mess. Make sure you have back ups of anything important before trying any kind of upgrade, or anything to do with kernels or BIOS. A good general practice.

If that doesn't work, try using the following command for each package it's complaining about.

sudo dpkg --force-remove-reinstreq --purge --force-depends <package-name>

Where I have <package-name>, just substitute and remove the arrows. eg;

sudo dpkg --force-remove-reinstreq --purge --force-depends libfakeroot:amd64

You could run all of them in one command, but I want to easily see if any of them fail.
It also throws an error:
sudo dpkg --force-remove-reinstreq --purge --force-depends libc6:amd64
[sudo] password for loki:
dpkg: libc6:amd64: dependency problems, but removing anyway as you requested:
zlib1g:amd64 depends on libc6 (>= 2.14).
zip depends on libc6 (>= 2.14).
zenity depends on libc6 (>= 2.4).
yelp depends on libc6 (>= 2.4).
xz-utils depends on libc6 (>= 2.17).
xxd depends on libc6 (>= 2.3.4).
And 100s of other things that depend on that package.... then:


dpkg: warning: overriding problem because --force enabled:
dpkg: warning: package is in a very bad inconsistent state; you should
reinstall it before attempting a removal
(Reading database ... 346695 files and directories currently installed.)
Removing libc6:amd64 (2.32-0ubuntu3) ...
dpkg (subprocess): unable to execute installed libc6:amd64 package post-removal script (/var/lib/dpkg/info/libc6:amd64.postrm): No such file or directory
dpkg: error processing package libc6:amd64 (--purge):
installed libc6:amd64 package post-removal script subprocess returned error exit status 2
dpkg: libc-bin: dependency problems, but processing triggers anyway as you requested:
libc-bin depends on libc6 (>> 2.32); however:
Package libc6:amd64 is not installed.
libc-bin depends on libc6 (<< 2.33); however:
Package libc6:amd64 is not installed.

Processing triggers for libc-bin (2.32-0ubuntu3) ...
dpkg (subprocess): unable to execute installed libc-bin package post-installation script (/var/lib/dpkg/info/libc-bin.postinst): No such file or directory
dpkg: error processing package libc-bin (--purge):
installed libc-bin package post-installation script subprocess returned error exit status 2
dpkg: error: error executing hook 'if { test "$DPKG_HOOK_ACTION" = add-architecture || test "$DPKG_HOOK_ACTION" = remove-architecture; } && test -x /usr/share/pkgconf-dpkghook; then /usr/share/pkgconf-dpkghook update; fi', exit code -1

Edit: Runing that also seemed to kill bash! any command I now run says this:
ls
bash: /usr/bin/ls: No such file or directory
sudo
bash: /usr/bin/sudo: No such file or directory
etc
 
Last edited:

derpOmattic

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Well, that was one step away from the nuclear option. It's a mess. At times like this the devs usually recommend a "refresh install" from the recovery partition or USB.

A refresh install will give you a clean system, but preserve your $HOME folder. You could then do sudo apt update && sudo apt full-upgrade before running the release upgrade command. Almost nuke and pave. Honestly , I would have done this a long time ago, but I do have back ups, dot files and install scripts to make a new install painless.
 

loki_asguardian

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Well, that was one step away from the nuclear option. It's a mess. At times like this the devs usually recommend a "refresh install" from the recovery partition or USB.

A refresh install will give you a clean system, but preserve your $HOME folder. You could then do sudo apt update && sudo apt full-upgrade before running the release upgrade command. Almost nuke and pave. Honestly , I would have done this a long time ago, but I do have back ups, dot files and install scripts to make a new install painless.
Will I have to reinstall applications? I am scared nuking some proprietary software which we have run out of licenses for. Can I try copying libc6 back into the root directory from the recovery partition into the boot drive?
 

derpOmattic

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Will I have to reinstall applications? I am scared nuking some proprietary software which we have run out of licenses for. Can I try copying libc6 back into the root directory from the recovery partition into the boot drive?
Oof. That makes things hard. Sure you can try. It may be those software that are causing the trouble though.
 
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loki_asguardian

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Oof. That makes things hard. Sure you can try. It may be those software that are causing the trouble though.
Yeah I think dpkg --force-remove-reinstreq --purge --force-depends killed it. It wont boot anymore and when I try to chroot into the boot drive from the recovery partition, it says '/bin/bash': No such file or directory. I am currently on stage one of grief: denial. I am hoping to work through the other stages overnight and work my way to acceptance then I will refresh the install :(. Thanks for the suggestions.
 

loki_asguardian

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Yeah It was super painless too. It didn't nuke my containerized software, and even my browser tabs were still there!
 

derpOmattic

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Yeah It was super painless too. It didn't nuke my containerized software, and even my browser tabs were still there!
I know right. Using recovery or something like Timeshift snapshot is rather painless. With recovery, it will delete your installed .deb packages, but it leaves your $HOME alone, which means your config files are waiting there for when you reinstall the software. Flatapks and containers aren't touched usually. I'm always ready to "nuke and pave", but it isn't something you can recommend to others straight up if they're not set up for it.
 
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