[Howto] Three commands to update Fedora

These days using Fedora Workstation there are multiple commands necessary to update the entire software on the system: not everything is installed as RPMs anymore – and some systems hardly use RPMs at all anyway.

Fedora Logo Bubble

These days using Fedora Workstation there are multiple commands necessary to update the entire software on the system: not everything is installed as RPMs anymore – and some systems hardly use RPMs at all anyway.


In the past all updates of a Fedora system were easily applied with one single command:

$ yum update

Later on, yum was replaced by DNF, but the idea stayed the same:

$ dnf update

Simple, right? But not these days: Fedora recently added capabilities to install and manage code via other ways: Flatpak packages are not managed by DNF. Also, many firmware updates are managed via the dedicated management tool fwupd. And lost but not least, Fedora Silverblue does not support DNF at all.

GUI solution Gnome Software – one tool to rule them all…

To properly update your Fedora system you have to check multiple sources. But before we dive into detailed CLI commands there is a simple way to do that all in one go: The Gnome Software tool does that for you. It checks all sources and just provides the available updates in its single GUI:

The above screenshot highlights that Gnome Software just shows available updates and can manage those. The user does not even know where those come from.

If we have a closer look at the configured repositories in Gnome Software we see that it covers main Fedora repositories, 3rd party repositories, flatpaks, firmware and so on:

Using the GUI alone is sufficient to take care of all update routines. However, if you want to know and understand what happens underneath it is good to know the separate CLI commands for all kinds of software resources. We will look at them in the rest of the post.

System packages

Each and every system is made up at least of a basic set of software. The Kernel, a system for managing services like systemd, core libraries like libc and so on. With Fedora used as a Workstation system there are two ways to manage system packages, because there are two totally different spins of Fedora: the normal one, traditionally based on DNF and thus comprised out of RPM packages, and the new Fedora Silverblue, based on immutable ostree system images.

Traditional: DNF

Updating a RPM based system via DNF is easy:

$ dnf upgrade
[sudo] password for liquidat: 
Last metadata expiration check: 0:39:20 ago on Tue 18 Jun 2019 01:03:12 PM CEST.
Dependencies resolved.
 Package                      Arch       Version             Repository    Size
 kernel                       x86_64     5.1.9-300.fc30      updates       14 k
 kernel-core                  x86_64     5.1.9-300.fc30      updates       26 M
 kernel-modules               x86_64     5.1.9-300.fc30      updates       28 M
 kernel-modules-extra         x86_64     5.1.9-300.fc30      updates      2.1 M

This is the traditional way to keep a Fedora system up2date. It is used for years and well known to everyone.

And in the end it is analogue to the way Linux distributions are kept up2date for ages now, only the command differs from system to system (apt-get, etc.)

Silverblue: OSTree

With the recent rise of container technologies the idea of immutable systems became prominent again. With Fedora Silverblue there is an implementation of that approach as a Fedora Workstation spin.

[Unlike] other operating systems, Silverblue is immutable. This means that every installation is identical to every other installation of the same version. The operating system that is on disk is exactly the same from one machine to the next, and it never changes as it is used.

Silverblue’s immutable design is intended to make it more stable, less prone to bugs, and easier to test and develop. Finally, Silverblue’s immutable design also makes it an excellent platform for containerized apps as well as container-based software development development. In each case, apps and containers are kept separate from the host system, improving stability and reliability.


Since we are dealing with immutable images here, another tool to manage them is needed: OSTree. Basically OSTree is a set of libraries and tools which helps to manage images and snapshots. The idea is to provide a basic system image to all, and all additional software on top in sandboxed formats like Flatpak.

Unfortunately, not all tools can be packages as flatpak: especially command line tools are currently hardly usable at all as flatpak. Thus there is a way to install and manage RPMs on top of the OSTree image, but still baked right into it: rpm-ostreee. In fact, on Fedora Silverblue, all images and RPMs baked into it are managed by it.

Thus updating the system and all related RPMs needs the command rpm-ostreee update:

$ rpm-ostree update
⠂ Receiving objects: 98% (4653/4732) 4,3 MB/s 129,7 MB 
Receiving objects: 98% (4653/4732) 4,3 MB/s 129,7 MB... done
Checking out tree 209dfbe... done
Enabled rpm-md repositories: fedora-cisco-openh264 rpmfusion-free-updates rpmfusion-nonfree fedora rpmfusion-free updates rpmfusion-nonfree-updates
rpm-md repo 'fedora-cisco-openh264' (cached); generated: 2019-03-21T15:16:16Z
rpm-md repo 'rpmfusion-free-updates' (cached); generated: 2019-06-13T10:31:33Z
rpm-md repo 'rpmfusion-nonfree' (cached); generated: 2019-04-16T21:53:39Z
rpm-md repo 'fedora' (cached); generated: 2019-04-25T23:49:41Z
rpm-md repo 'rpmfusion-free' (cached); generated: 2019-04-16T20:46:20Z
rpm-md repo 'updates' (cached); generated: 2019-06-17T18:09:33Z
rpm-md repo 'rpmfusion-nonfree-updates' (cached); generated: 2019-06-13T11:00:42Z
Importing rpm-md... done
Resolving dependencies... done
Checking out packages... done
Running pre scripts... done
Running post scripts... done
Running posttrans scripts... done
Writing rpmdb... done
Writing OSTree commit... done
Staging deployment... done
Freed: 50,2 MB (pkgcache branches: 0)
  gcr 3.28.1-3.fc30 -> 3.28.1-4.fc30
  gcr-base 3.28.1-3.fc30 -> 3.28.1-4.fc30
  glib-networking 2.60.2-1.fc30 -> 2.60.3-1.fc30
  glib2 2.60.3-1.fc30 -> 2.60.4-1.fc30
  kernel 5.1.8-300.fc30 -> 5.1.9-300.fc30
  kernel-core 5.1.8-300.fc30 -> 5.1.9-300.fc30
  kernel-devel 5.1.8-300.fc30 -> 5.1.9-300.fc30
  kernel-headers 5.1.8-300.fc30 -> 5.1.9-300.fc30
  kernel-modules 5.1.8-300.fc30 -> 5.1.9-300.fc30
  kernel-modules-extra 5.1.8-300.fc30 -> 5.1.9-300.fc30
  plymouth 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-core-libs 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-graphics-libs 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-plugin-label 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-plugin-two-step 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-scripts 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-system-theme 0.9.4-5.fc30 -> 0.9.4-6.fc30
  plymouth-theme-spinner 0.9.4-5.fc30 -> 0.9.4-6.fc30
Run "systemctl reboot" to start a reboot

Desktop applications: Flatpak

Installing software – especially desktop related software – on Linux is a major pain for distributors, users and developers alike. One attempt to solve this is the flatpak format, see also Flatpak – a solution to the Linux desktop packaging problem.

Basically Flatpak is a distribution independent packaging format targeted at desktop applications. It does come along with sandboxing capabilities and the packages usually have hardly any dependencies at all besides a common set provided to all of them.

Flatpak also provide its own repository format thus Flatpak packages can come with their own repository to be released and updated independently of a distribution release cycle.

In fact, this is what happens with the large Flatpak community repository flathub.org: all packages installed from there can be updated via flathub repos fully independent from Fedora – which also means independent from Fedora security teams, btw….

So Flatpak makes developing and distributing desktop programs much easier – and provides a tool for that. Meet flatpak!

$ flatpak update
Looking for updates…

        ID                                            Arch              Branch            Remote            Download
 1. [✓] org.freedesktop.Platform.Locale               x86_64            1.6               flathub            1.0 kB / 177.1 MB
 2. [✓] org.freedesktop.Platform.Locale               x86_64            18.08             flathub            1.0 kB / 315.9 MB
 3. [✓] org.libreoffice.LibreOffice.Locale            x86_64            stable            flathub            1.0 MB / 65.7 MB
 4. [✓] org.freedesktop.Sdk.Locale                    x86_64            1.6               flathub            1.0 kB / 177.1 MB
 5. [✓] org.freedesktop.Sdk.Locale                    x86_64            18.08             flathub            1.0 kB / 319.3 MB


And there is firmware: the binary blobs that keep some of our hardware running and which is often – unfortunately – closed source.

A lot of Kernel related firmware is managed as system packages and thus part of the system image or packaged via RPM. But device related firmware (laptops, docking stations, and so on) is often only provided in Windows executable formats and difficult to handle.

Luckily, recently the Linux Vendor Firmware Service (LVFS) gained quite some traction as the default way for many vendors to make their device firmware consumable to Linux users:

The Linux Vendor Firmware Service is a secure portal which allows hardware vendors to upload firmware updates.

This site is used by all major Linux distributions to provide metadata for clients such as fwupdmgr and GNOME Software.


End users can take advantage of this with a tool dedicated to identify devices and manage the necessary firmware blobs for them: meet fwupdmgr!

$ fwupdmgr update                                                                                                                                                         No upgrades for 20L8S2N809 System Firmware, current is 0.1.31: 0.1.25=older, 0.1.26=older, 0.1.27=older, 0.1.29=older, 0.1.30=older
No upgrades for UEFI Device Firmware, current is 184.65.3590: 184.55.3510=older, 184.60.3561=older, 184.65.3590=same
No upgrades for UEFI Device Firmware, current is 0.1.13: 0.1.13=same
No releases found for device: Not compatible with bootloader version: failed predicate [BOT01.0[0-3]_* regex BOT01.04_B0016]

In the above example there were no updates available – but multiple devices are supported and thus were checked.

Forgot something? Gnome extensions…

The above examples cover the major ways to managed various bits of code. But they do not cover all cases, so for the sake of completion I’d like to highlight a few more here.

For example, Gnome extensions can be installed as RPM, but can also be installed via extensions.gnome.org. In that case the installation is done via a browser plugin.

The same is true for browser plugins themselves: they can be installed independently and extend the usage of the web browser. Think of the Chrome Web Store here, or Firefox Add-ons.


Keeping a system up2date was easier in the past – with a single command. However, at the same time that meant that those systems were limited by what RPM could actually deliver.

With the additional ways to update systems there is an additional burden on the system administrator, but at the same time there is much more software and firmware available these ways – code which was not available in the old RPM times at all. And with Silverblue an entirely new paradigm of system management is there – again something which would not have been the case with RPM at all.

At the same time it needs to be kept in mind that these are pure desktop systems – and there Gnome Software helps by being the single pane of glas.

So I fully understand if some people are a bit grumpy about the new needs for multiple tools. But I think the advantages by far outweigh the disadvantages.

So you think offline systems need no updates?

offlineOften customers run offline systems and claim that such machines do not need updates since they are offline. But this is a fallacy: updates do not only close security holes but also deliver bug fixes – and they can be crucial.


Recently a customer approached me with questions regarding an upgrade of a server. During the discussion, the customer mentioned that the system never got upgrades:

“It is an offline system, there is no need.”

That’s a common misconception. And a dangerous one.

Many people think that updates are only important to fix security issues, and that bugfixes are not really worth considering – after all, the machine works, right?


Software is never perfect. Errors happen. And while security issues might be uncomfortable, bugs in the program code can be a much more serious issue than “mere” security problems.

Example One: Xerox

To pick an example, almost each company out there has one type of system which hardly ever gets updated: copy machines. These days they are connected to the internet and can e-mail scanned documents. They are usually never updated, after all it just works, right?

In 2013 it was discovered that many Xerox WorkCentres had a serious software bug, causing them to alter scanned numbers. It took quite some weeks and analysis until finally a software update fixed the issue. During that time it turned out that the bug was at least 8 years old. So millions and millions of faulty scans have been produced over the years. In some cases the originals were destroyed in the meantime. It can hardly be estimated what impact that will have, but for sure it’s huge and will accompany us for a long time. And it was estimated that even today many scanners are still not patched – because it is not common to patch such systems. Offline, right?

So yes, a security issue might expose your data to the world. But it’s worse when the data is wrong to begin with.

Example two: Jails

Another example hit the news just recently: the US Washington State Department of Correction released inmates too early – due to a software bug. Again the software bug was present for years and years, releasing inmates too early all the time.

Example three: Valve

While Valve’s systems are often per definition online, the Valve Steam for Linux bug showed that all kinds of software can contain, well, all kinds of bugs: if you moved the folder of your Steam client, it could actually delete your entire (home) directory. Just like that. And again: this bug did not happen all the time, but only in certain situations and after quite some time.

# deletes your files when the variable is not set anymore
rm -rf "$STEAMROOT/"*

Example four: Office software

Imagine you have a bug in your calculating software – so that numbers are not processed or displayed correctly. The possible implications are endless. Two famous bugs which shows that bugfixes are worth considering are the MS Office multiplication bug from 2007 and the MS Office sum bug from a year later.

Example five: health

Yet another example surfaced in 2000 when a treatment planning system at a radiotherapy department was found to calculate wrong treatment times for patients and thus the patients were exposed to much more radiation than was good for them. It took quite some time until the bug was discovered – too lat for some patients whose

“deaths were probably radiation related”.


So, yes, security issues are harmful. They must be taken serious, and a solid and well designed security concept should be applied. Multiple layers, different zones, role based access, update often, etc.

But systems which are secured by air gaps need to be updated as well. The above mentioned examples do not show bugs in highly specific applications, but also in software components used in thousands and millions of machines. So administrators should at least spend few seconds reading into each update and check if its relevant. Otherwise you might ignore that you corrupt your data over years and years without realizing it – until its too late.