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Whonix 15 to 16 upgrade fails, Terminal crashes, Qube still running

I’ve updated all my Whonix Qubes from 15 to 16 except for 1. And I’d like to avoid rebuilding it from scratch.

I followed the instructions for upgrading, including all the sanity checks and was in the midst of “release-upgrade” when it crashed. This has happened 2 times now. But I have not been watching it when it actually happens. I just come back and my Terminal is gone. I can’t launch the Terminal or xterm. And qvm-ls reports the qube is still running.

If I shut it down it will not boot anymore. This is the second attempt on this Qube. I have not yet shut it down in case there is anything you can suggest I try first.

Hopefully I can help you track down the problem.

Thanks.

p.s. One other piece of info. I can still access the nginx server running on this qube via a browser but I get the default nginx message as if the website data is no longer there, which is strange.

You can append log output to a file log by appending the following command.

&> log

Also output before the crash might be useful. There’s a small chance due to user modifications (installed packages) that some Qubes specific package gets removed during release which is required.

Can be debugged as if it was happening with a Debian based VM. → Information Booster might be Available!

Config files were reset by package default. Mentioned on the release upgrade instructions wiki page.

didn’t get help in the qubes forum, so i set up an ssh connection and ran release-upgrade from there, here is the last output i got before it disconnected:

Preparing to unpack …/udisks2_2.9.2-2_amd64.deb …
Unpacking udisks2 (2.9.2-2) over (2.8.1-4) …
(Reading database … 92835 files and directories currently installed.)
Removing policykit-1-gnome (0.105-7) …
Removing policykit-1 (0.105-25) …
Removing libpam-systemd:amd64 (241-7~deb10u8) …
Removing libqt4-declarative:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-designer:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-help:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-xmlpatterns:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-network:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-scripttools:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-script:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-sql:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-svg:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-test:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqtdbus4:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqt4-xml:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing libqtgui4:amd64 (4:4.8.7+dfsg-18+deb10u1) …
Removing qubes-whonix (1:16.5-1) …
Removing ‘diversion of /usr/share/qubes-updates-cache/errors/ERR_INVALID_URL to /usr/share/qubes-updates-cache/errors/ERR_INVALID_URL.anondist-orig by qubes-whonix’
Removing ‘diversion of /usr/share/tinyproxy/default.html to /usr/share/tinyproxy/default.html.anondist-orig by qubes-whonix’
Removing ‘diversion of /usr/lib/qubes/qubes-setup-dnat-to-ns to /usr/lib/qubes/qubes-setup-dnat-to-ns.anondist-orig by qubes-whonix’
Removing ‘diversion of /etc/qubes-rpc/qubes.SetDateTime to /etc/qubes-rpc/qubes.SetDateTime.anondist-orig by qubes-whonix’
Removing ‘diversion of /etc/qubes-rpc/qubes.SyncNtpClock to /etc/qubes-rpc/qubes.SyncNtpClock.anondist-orig by qubes-whonix’
Removing qubes-core-agent-networking (4.0.62-1+deb10u1) …
Removing qubes-vm-dependencies (4.0.11-1+deb10u1) …
Removing qubes-gui-agent (4.0.38-1+deb10u1) …
client_loop: send disconnect: Broken pipe

This is the main issue which should not be happening. Removal of several Qubes packages.

The log is too short to know why this is happening. Complete log required.

Yeah, I noticed that. Didn’t look good. Here’s the full log:

So far nothing wrong with that part of the log. The log is incomplete. It stops with:

Get:221 tor+https://deb.debian.org/

as well as it stops at a different point.

Most likely reason for incomplete log: Qubes global clipboard copy/paste has a maximum size. Unspecific to Whonix. → Information Booster might be Available!

Complete log required.

Sorry, missed that. Here’s the full version:

From the log, the following command

apt-get-noninteractive --yes --no-install-recommends install libc6-dev bsdmainutils gcc fasttrack-archive-keyring

For unknown reason results in:

The following packages will be REMOVED:
kicksecure-desktop-applications-xfce
qubes-core-agent qubes-core-agent-networking qubes-gui-agent
qubes-input-proxy-sender qubes-mgmt-salt-vm-connector qubes-usb-proxy
qubes-vm-dependencies qubes-whonix qubes-whonix-shared-packages-recommended
qubes-whonix-workstation salt-common salt-ssh systemcheck whonix-firewall
whonix-shared-packages-dependencies-cli
whonix-shared-packages-recommended-cli
whonix-workstation-shared-packages-shared-meta

The further debug, you’d need to either manually run the commands the build script would be running (look at /usr/sbin/release-upgrade) would be to edit the script and append qubes-whonix-workstation.

i.e. make that

apt-get-noninteractive --yes --no-install-recommends install libc6-dev bsdmainutils gcc fasttrack-archive-keyring qubes-whonix-workstation

Might also be a good idea to remove the “–yes”. I.e.

apt-get-noninteractive --no-install-recommends install libc6-dev bsdmainutils gcc fasttrack-archive-keyring qubes-whonix-workstation

By removing the “–yes” you could abort before any above mentioned packages are installed. Removing the “–yes” everywhere in the script might be a good idea as well.

You could replace the experiment qubes-whonix-workstation by qubes-vm-dependencies.

The abstract task: you need to find out which package dependency of a custom installed package is created a conflict so APT decides to remove qubes-whonix-workstation / qubes-vm-dependencies instead of the custom installed package.

Not too easy to debug in Qubes. Time consuming. Since you cannot snapshot a VM and easily restore at least not as far as I know.

Here is what I tried:

I copied /usr/sbin/release-upgrade and in the copy I deleted everything form the install line you suggest changing above down. Then I ran that script, doing everything before the problem occurs.

Then I tried installing each of those items manually one by one.

sudo apt-get --no-install-recommends libc6-dev

Says it will remove the qubes/whonix packages. So I say ‘n’ and don’t install. I go through and install the other 3 packages no problem.

I went back and tried installing libc6-def again. I get the same result, it wants to remove qubes-core-agent, etc. It was to upgrade 156, install 43 and remove 56 packages.

If I try running

sudo apt-get --no-install-recommends libc6-dev qubes-whonix-workstation

I get:

user@host:/usr/sbin$ sudo apt-get --no-install-recommends install libc6-dev qubes-whonix-workstation
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 qubes-whonix-workstation : Depends: qubes-whonix-shared-packages-recommended but it is not going to be installed
E: Unable to correct problems, you have held broken packages.

So I ran:

sudo apt install qubes-whonix-shared-packages-recommended

Then I try installing libc6-def and qubes-whonix-workstation again. I get a similar message but the unmet dependency is now “qubes-mgmt-salt-vm-connector”

I’m going to stop here for now and see what you think of this. Should I keep installing the unmet dependencies?

Yes, please. You’ve got the correct mindset. Don’t do insecure stuff (installing unsigned packages, saying yes to strong warnings) (you didn’t do that) but do keep shuffling around with the packages. To fix or work around this, we need to figure out the the package conflict which APT is unable to resolve.

I installed qubes-mgmt-salt-vm-connector, tried installing libc6-dev and qubes-whonix-workstation. It wouldn’t let me because qubes-mgmt-salt-vm-connector is dependent on salt-ssh.

I tried
sudo apt install salt-ssh

And I got the same list as above I think. It wants to upgrade 158, install 46 and remove 53 packages including qubes-whonix, qubes-whonix-workstation, etc. So then I did:

user@host:/usr/sbin$ sudo apt install salt-ssh libc6-dev qubes-whonix-workstation
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following packages were automatically installed and are no longer required:
  cpp-8 gir1.2-gdesktopenums-3.0 gir1.2-gnomedesktop-3.0 gir1.2-notify-0.7 gir1.2-soup-2.4
  gnome-desktop3-data gnome-settings-daemon-common gnome-shell-common
  gstreamer1.0-pulseaudio iio-sensor-proxy libasan5 libaudio2 libdouble-conversion1
  libgeoclue-2-0 libgeocode-glib0 libgnome-desktop-3-17 libgweather-3-15
  libgweather-common libhiredis0.14 libicu57 libisl19 libmng1 libnm0
  libpulse-mainloop-glib0 libpython2.7 libupower-glib3 mutter-common python3-xcffib
  python3.7-minimal qdbus qdbus-qt5 qtchooser qtcore4-l10n upower xserver-xorg-input-qubes
  xserver-xorg-video-dummyqbs
Use 'sudo apt autoremove' to remove them.
The following additional packages will be installed:
  bubblewrap cython3 gnome-settings-daemon-common gsettings-desktop-schemas
  iio-sensor-proxy init libapt-pkg-perl libapt-pkg6.0 libblockdev-utils2 libblockdev2
  libc-bin libc-dev-bin libc-devtools libc-l10n libc6 libcbor0 libcrypt-dev libcrypt1
  libcryptsetup12 libdbd-mysql-perl libdbi-perl libdouble-conversion3 libfcgi-perl
  libfcgi0ldbl libffi7 libfido2-1 libfile-fnmatch-perl libfreetype6 libgdk-pixbuf-2.0-0
  libgdk-pixbuf-xlib-2.0-0 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common
  libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin libgnutls-dane0 libgnutls30
  libharfbuzz0b libhogweed6 libhtml-parser-perl libicu67 libintl-perl libintl-xs-perl
  libjson-c5 libjson-glib-1.0-0 libjson-glib-1.0-common libkpathsea6 libldb2
  liblist-moreutils-perl liblist-moreutils-xs-perl liblocale-gettext-perl liblz4-1
  libmaxminddb0 libmd4c0 libmount1 libmpdec3 libnet-ssleay-perl libnettle8
  libnginx-mod-http-auth-pam libnginx-mod-http-cache-purge libnginx-mod-http-dav-ext
  libnginx-mod-http-echo libnginx-mod-http-fancyindex libnginx-mod-http-geoip
  libnginx-mod-http-geoip2 libnginx-mod-http-headers-more-filter
  libnginx-mod-http-image-filter libnginx-mod-http-lua libnginx-mod-http-ndk
  libnginx-mod-http-perl libnginx-mod-http-subs-filter libnginx-mod-http-uploadprogress
  libnginx-mod-http-upstream-fair libnginx-mod-http-xslt-filter libnginx-mod-mail
  libnginx-mod-nchan libnginx-mod-stream libnginx-mod-stream-geoip
  libnginx-mod-stream-geoip2 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0
  libperl5.32 libproc-processtable-perl libptexenc1 libpython3-stdlib libpython3.9
  libpython3.9-minimal libpython3.9-stdlib libqt5core5a libqt5dbus5 libqt5designer5
  libqt5gui5 libqt5help5 libqt5network5 libqt5printsupport5 libqt5sql5 libqt5svg5
  libqt5test5 libqt5widgets5 libqt5xdgiconloader3 libqt5xml5 libqubesdb libreadline8
  libseccomp2 libselinux1 libsmbclient libsnappy1v5 libsodium23 libstdc++6 libsynctex2
  libtalloc2 libtasn1-6 libtdb1 libteckit0 libterm-readkey-perl libtevent0 libtexlua53
  libtexluajit2 libtext-charwidth-perl libtext-iconv-perl libtirpc-common libtirpc-dev
  libtirpc3 libudev1 libudisks2-0 libwbclient0 libwebpmux3 libx11-6 libx11-xcb1 libxau6
  libxcb-xinput0 libxxhash0 libzstd1 locales manpages manpages-dev nginx-common
  nginx-extras openssh-client openssh-server openssh-sftp-server p11-kit-modules perl
  perl-base perl-modules-5.32 python-matplotlib-data python3 python3-apt python3-cairo
  python3-cbor python3-cffi-backend python3-dbus python3-distutils python3-geoip
  python3-gi python3-gi-cairo python3-kiwisolver python3-ldb python3-lib2to3
  python3-libapparmor python3-lz4 python3-markupsafe python3-matplotlib python3-minimal
  python3-msgpack python3-nacl python3-nautilus python3-numpy python3-pil python3-psutil
  python3-pycryptodome python3-pyqt5 python3-pyqt5.sip python3-pyx python3-qubesdb
  python3-sip python3-snappy python3-talloc python3-tk python3-twisted-bin python3-ubjson
  python3-wsaccel python3-yaml python3-zmq python3-zope.interface python3.9
  python3.9-minimal qdbus qdbus-qt5 qubes-core-agent-nautilus qubes-pdf-converter ranger
  runit-helper salt-common samba-libs tex-common texlive-base texlive-binaries
  texlive-latex-base udev udisks2 xen-utils-common
Suggested packages:
  cython-doc glibc-doc libclone-perl libmldbm-perl libnet-daemon-perl
  libsql-statement-perl dns-root-data libdata-dump-perl mmdb-bin qt5-image-formats-plugins
  qtwayland5 fcgiwrap nginx-doc ssl-cert keychain libpam-ssh monkeysphere ssh-askpass
  molly-guard ufw perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl
  libtap-harness-archive-perl python3-doc python3-venv python3-apt-dbg python-apt-doc
  python-dbus-doc python3-dbus-dbg dvipng ffmpeg inkscape python-matplotlib-doc
  python3-cairocffi python3-gobject python3-nose python3-scipy python3-tornado
  texlive-extra-utils texlive-latex-extra ttf-staypuft python-nacl-doc gfortran
  python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python-pil-doc
  python3-pil-dbg python-psutil-doc python3-pyqt5-dbg python3-pyx-doc
  texlive-fonts-recommended tix python3-tk-dbg python3-twisted-bin-dbg python3.9-venv
  python3.9-doc binfmt-support atool caca-utils unoconv python3-mako salt-doc debhelper
  perl-tk xzdec texlive-latex-base-doc btrfs-progs f2fs-tools libblockdev-mdraid2 mdadm
  nilfs-tools reiserfsprogs udftools udisks2-bcache udisks2-btrfs udisks2-lvm2
  udisks2-zram xfsprogs
Recommended packages:
  python3-dev apt libfcgi-bin libgdk-pixbuf2.0-bin qttranslations5-l10n
  qt5-gtk-platformtheme libqt5sql5-sqlite | libqt5sql5-mysql | libqt5sql5-odbc
  | libqt5sql5-psql | libqt5sql5-tds | libqt5sql5-ibase python3-olefile python3-croniter
  dvisvgm dosfstools eject exfat-utils
The following packages will be REMOVED:
  gcc-8 gnome-settings-daemon gnome-tweaks libgcc-8-dev libldb1 libpython-stdlib
  libqt4-dbus libqt4-declarative libqt4-designer libqt4-help libqt4-network libqt4-script
  libqt4-scripttools libqt4-sql libqt4-svg libqt4-test libqt4-xml libqt4-xmlpatterns
  libqtassistantclient4 libqtcore4 libqtdbus4 libqtgui4 nginx perl-modules-5.24 python
  python-enum34 python-gi python-minimal python-nautilus python-qt4 python-sip
  python-talloc python3-systemd python3-tornado4 python3.7 qubes-gui-agent
  qubes-vm-dependencies
The following NEW packages will be installed:
  libapt-pkg6.0 libc-devtools libcbor0 libcrypt-dev libcrypt1 libdouble-conversion3
  libfcgi0ldbl libffi7 libfido2-1 libgdk-pixbuf-2.0-0 libgdk-pixbuf-xlib-2.0-0 libhogweed6
  libicu67 libjson-c5 libldb2 liblist-moreutils-xs-perl libmaxminddb0 libmd4c0 libmpdec3
  libnettle8 libnginx-mod-http-geoip2 libnginx-mod-stream-geoip libnginx-mod-stream-geoip2
  libnsl-dev libnsl2 libnss-nis libnss-nisplus libperl5.32 libpython3.9
  libpython3.9-minimal libpython3.9-stdlib libreadline8 libtirpc-common libtirpc-dev
  libtirpc3 libxcb-xinput0 manpages manpages-dev perl-modules-5.32 python3-ldb
  python3-nautilus python3-pycryptodome python3-pyqt5.sip python3-talloc python3-zmq
  python3.9 python3.9-minimal qdbus-qt5 runit-helper
The following packages will be upgraded:
  bubblewrap cython3 gnome-settings-daemon-common gsettings-desktop-schemas
  iio-sensor-proxy init libapt-pkg-perl libblockdev-utils2 libblockdev2 libc-bin
  libc-dev-bin libc-l10n libc6 libc6-dev libcryptsetup12 libdbd-mysql-perl libdbi-perl
  libfcgi-perl libfile-fnmatch-perl libfreetype6 libgdk-pixbuf2.0-0
  libgdk-pixbuf2.0-common libgirepository-1.0-1 libglib2.0-0 libglib2.0-bin
  libgnutls-dane0 libgnutls30 libharfbuzz0b libhtml-parser-perl libintl-perl
  libintl-xs-perl libjson-glib-1.0-0 libjson-glib-1.0-common libkpathsea6
  liblist-moreutils-perl liblocale-gettext-perl liblz4-1 libmount1 libnet-ssleay-perl
  libnginx-mod-http-auth-pam libnginx-mod-http-cache-purge libnginx-mod-http-dav-ext
  libnginx-mod-http-echo libnginx-mod-http-fancyindex libnginx-mod-http-geoip
  libnginx-mod-http-headers-more-filter libnginx-mod-http-image-filter
  libnginx-mod-http-lua libnginx-mod-http-ndk libnginx-mod-http-perl
  libnginx-mod-http-subs-filter libnginx-mod-http-uploadprogress
  libnginx-mod-http-upstream-fair libnginx-mod-http-xslt-filter libnginx-mod-mail
  libnginx-mod-nchan libnginx-mod-stream libp11-kit0 libproc-processtable-perl libptexenc1
  libpython3-stdlib libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5
  libqt5network5 libqt5printsupport5 libqt5sql5 libqt5svg5 libqt5test5 libqt5widgets5
  libqt5xdgiconloader3 libqt5xml5 libqubesdb libseccomp2 libselinux1 libsmbclient
  libsnappy1v5 libsodium23 libstdc++6 libsynctex2 libtalloc2 libtasn1-6 libtdb1 libteckit0
  libterm-readkey-perl libtevent0 libtexlua53 libtexluajit2 libtext-charwidth-perl
  libtext-iconv-perl libudev1 libudisks2-0 libwbclient0 libwebpmux3 libx11-6 libx11-xcb1
  libxau6 libxxhash0 libzstd1 locales nginx-common nginx-extras openssh-client
  openssh-server openssh-sftp-server p11-kit-modules perl perl-base python-matplotlib-data
  python3 python3-apt python3-cairo python3-cbor python3-cffi-backend python3-dbus
  python3-distutils python3-geoip python3-gi python3-gi-cairo python3-kiwisolver
  python3-lib2to3 python3-libapparmor python3-lz4 python3-markupsafe python3-matplotlib
  python3-minimal python3-msgpack python3-nacl python3-numpy python3-pil python3-psutil
  python3-pyqt5 python3-pyx python3-qubesdb python3-sip python3-snappy python3-tk
  python3-twisted-bin python3-ubjson python3-wsaccel python3-yaml python3-zope.interface
  qdbus qubes-core-agent-nautilus qubes-pdf-converter qubes-whonix-workstation ranger
  salt-common salt-ssh samba-libs tex-common texlive-base texlive-binaries
  texlive-latex-base udev udisks2 xen-utils-common
159 upgraded, 49 newly installed, 37 to remove and 1014 not upgraded.
Need to get 146 MB of archives.
After this operation, 19.5 MB of additional disk space will be used.
Do you want to continue? [Y/n] 

I hit “n”. It seems to list some important things for removal still like qubes-gui-agent.

1 Like

Try to install qubes-vm-dependencies only. For now. Removal of qubes-whonix-workstation would be acceptable in the debugging process as long as no important Qubes packages such as qubes-gui-agent are removed. Would be interesting if qubes-vm-dependencies could be re-installed including all the packages which qubes-vm-dependencies Depends: on. See also:

apt-cache show qubes-vm-dependencies

Maybe some Qubes package recently changed dependencies and somehow became incompatible (packaging conflict) during the buster → bullseye upgrade? The same might be happening attempting to upgrade Qubes Debian buster → bullseye?

user@host:/usr/sbin$ sudo apt install qubes-vm-dependencies
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following package was automatically installed and is no longer required:
  gstreamer1.0-pulseaudio
Use 'sudo apt autoremove' to remove it.
Recommended packages:
  qubes-vm-recommended
The following packages will be upgraded:
  qubes-vm-dependencies
1 upgraded, 0 newly installed, 0 to remove and 1178 not upgraded.
Need to get 2,252 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 https://deb.qubes-os.org/r4.0/vm bullseye/main amd64 qubes-vm-dependencies amd64 4.0.11-1+deb11u1 [2,252 B]
Fetched 2,252 B in 7s (307 B/s)            
(Reading database ... 92027 files and directories currently installed.)
Preparing to unpack .../qubes-vm-dependencies_4.0.11-1+deb11u1_amd64.deb ...
Unpacking qubes-vm-dependencies (4.0.11-1+deb11u1) over (4.0.11-1+deb10u1) ...
Setting up qubes-vm-dependencies (4.0.11-1+deb11u1) ...
Scanning processes...                                           
Scanning candidates...                                          
Scanning linux images...                                        

No services need to be restarted.

No containers need to be restarted.

No user sessions are running outdated binaries.

Then as it recommended I tried:

user@host:/usr/sbin$ sudo apt install qubes-vm-recommended
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 cython3 : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
           Recommends: python3-dev but it is not going to be installed
 libsmbclient : Depends: samba-libs (= 2:4.13.5+dfsg-2) but it is not going to be installed
 python3 : PreDepends: python3-minimal (= 3.7.3-1) but 3.9.2-3 is to be installed
           Depends: python3.7 (>= 3.7.3-1~) but it is not going to be installed
           Depends: libpython3-stdlib (= 3.7.3-1) but 3.9.2-3 is to be installed
 python3-apt : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-cairo : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-cbor : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-cffi-backend : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-dbus : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-distutils : Depends: python3:any (>= 3.9.1-0~)
 python3-dnf : Depends: python3-gpg but it is not going to be installed
               Depends: python3-rpm (>= 4.14.0-1~) but it is not going to be installed
               Recommends: deltarpm but it is not installable
 python3-geoip : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-gi : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-gi-cairo : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-hawkey : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-kiwisolver : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-lib2to3 : Depends: python3:any (>= 3.9.1-0~)
 python3-libapparmor : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-libcomps : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-libdnf : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-lz4 : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-markupsafe : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-matplotlib : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-msgpack : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-numpy : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-pil : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
               Recommends: python3-olefile but it is not going to be installed
 python3-psutil : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-pyqt5.sip : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-pyx : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-qubesdb : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-snappy : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-talloc : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-tk : Depends: python3 (>= 3.9.1-0~) but 3.7.3-1 is to be installed
 python3-tornado : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-twisted-bin : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-ubjson : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-unbound : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-wsaccel : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-yaml : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-zmq : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 python3-zope.interface : Depends: python3 (>= 3.9~) but 3.7.3-1 is to be installed
 qubes-vm-recommended : Depends: network-manager (>= 0.8.1-1) but it is not going to be installed
                        Depends: network-manager-gnome but it is not going to be installed
                        Depends: qubes-core-agent-network-manager but it is not going to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.
user@host:/usr/sbin$ 

Is that expected?

Not expected.

Try.

sudo apt install qubes-vm-recommended network-manager network-manager-gnome qubes-core-agent-network-manager

And/or add/drop any number of packages from that.

I am working on this:
https://github.com/Whonix/whonix-legacy/blob/master/usr/sbin/release-upgrade

release-upgrade command version 1.5 is available now. It’s provided by the whonix-legacy package which has been uploaded to all Whonix 15 / buster repositories. How to check release-upgrade command version version number is documented on the usual documentation wiki page for this release upgrade Release Upgrade Whonix 15 to Whonix 16 - Whonix.

In-place release upgrade should be fixed - but it assumes a non-broken APT state. So if you had created a VM snapshot (or clone or backup) before release upgrade attempt, you’re in luck now, revert to snapshot, perform a standard upgrade to get the updated/fixed release-upgrade and retry the release upgrade process.

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