Debian | Technology Tales

What to do an error appears when using pip to install Python packages on Linux Mint 22

16^th December 2024

After upgrading to Linux Mint 22, the following message appeared when attempting to install Python packages using the pip command:

error: externally-managed-environment

× This environment is externally managed ╰─> To install Python packages system-wide, try apt install python3-xyz, where xyz is the package you are trying to install.

If you wish to install a non-Debian-packaged Python package, create a virtual environment using python3 -m venv path/to/venv. Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make sure you have python3-full installed.

If you wish to install a non-Debian packaged Python application, it may be easiest to use pipx install xyz, which will manage a virtual environment for you. Make sure you have pipx installed.

See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages. hint: See PEP 668 for the detailed specification.

This will frustrate anyone following how-tos on the web, so users will need to know about it. On something like Linux Mint, the repositories may not be as up-to-date as PyPI, so picking up the very latest version has its advantages. Thus, I initially used the unrecommended --break-system-packages switch to get things going as before, since doing never broke anything before. While the way of working feels like an overkill in some ways, using pipx probably is the way forward as long as things work as I want them to do.

There is wisdom in using virtual environments too, especially when AI models are involved. For most of what I get to do, that may be getting too elaborate. Then, deleting or renaming the message file in /usr/lib/python3.12/EXTERNALLY-MANAGED is tempting if that gets around things, as retrograde as that probably is. After all, I never broke anything before this message started to appear, possibly since my interests are data related.

Upgrading a web server from Debian 11 to Debian 12

25^th November 2024

While Debian 12 may be with us since the middle of 2023 and Debian 13 is due in the middle of next year, it has taken me until now to upgrade one of my web servers. The tardiness may have something to do with a mishap on another system that resulted in a rebuild, something to avoid it at all possible.

Nevertheless, I went and had a go with the aforementioned web server after doing some advance research. Thus, I can relate the process that you find here in the knowledge that it worked for me. Also, I will have it on file for everyone's future reference. The first step is to ensure that the system is up-to-date by executing the following commands:

sudo apt update sudo apt upgrade sudo apt dist-upgrade

Next, it is best to remove extraneous packages using these commands:

sudo apt --purge autoremove sudo apt autoclean

Once you have backed up important data and configuration files, you can move to the first step of the upgrade process. This involves changing the repository locations from what is there for bullseye (Debian 11) to those for bookworm (Debian 12). Issuing the following commands will accomplish this:

sudo sed -i 's/bullseye/bookworm/g' /etc/apt/sources.list sudo sed -i 's/bullseye/bookworm/g' /etc/apt/sources.list.d/*

In my case, I found the second of these to be extraneous since everything was included in the single file. Also, Debian 12 has added a new non-free repository called non-free-firmware. This can be added at this stage by manual editing of the above. In my case, I did it later because the warning message only began to appear at that stage.

Once the repository locations, it is time to update the package information using the following command:

sudo apt update

Then, it is time to first perform a minimal upgrade using the following command, that takes a conservative approach by updating existing packages without installing any new ones:

sudo apt upgrade --without-new-pkgs

Once that has completed, one needs to issue the following command to install new packages if needed for dependencies and even remove incompatible or unnecessary ones, as well as performing kernel upgrades:

sudo apt full-upgrade

Given all the changes, the completion of the foregoing commands' execution necessitates a system restart, which can be the most nerve-wracking part of the process when you are dealing with a remote server accessed using SSH. While, there are a few options for accomplishing this, here is one that is compatible with the upgrade cycle:

sudo systemctl reboot

Once you can log back into the system again, there is one more piece of housekeeping needed. This step not only removes redundant packages that were automatically installed, but also does the same for their configuration files, an act that really cleans up things. The command to execute is as follows:

sudo apt --purge autoremove

For added reassurance that the upgrade has completed, issuing the following command will show details like the operating system's distributor ID, description, release version and codename:

lsb_release -a

If you run the above commands as root, the sudo prefix is not needed, yet it is perhaps safer to execute them under a less privileged account anyway. The process needs the paying of attention to any prompts and questions about configuration files and service restarts if they arise. Nothing like that came up in my case, possibly because this web server serves flat files created using Hugo, avoiding the use of scripting and databases, which would add to the system complexity. Such a simple situation makes the use of scripting more of a possibility. The exercise was speedy enough for me too, though patience is of the essence should a 30–60 minute completion time be your lot, depending on your system and internet speed.

Resolving "repository doesn't support architecture i386" error when checking for updates to Brave Browser on Linux

7^th June 2024

Recently, I started to observe the following message when doing my usual update routine on Linux Mint (Debian, Ubuntu and their variants are likely affected as well):

N: Skipping acquire of configured file 'main/binary-i386/Packages' as repository 'https://brave-browser-apt-release.s3.brave.com stable InRelease' doesn't support architecture 'i386'

As the message suggests, there was something amiss with the repository set up for Brave, a browser that I added for extra privacy. Since Firefox remains the main one that I use, Brave is something that I have in hand for when I need it. Handily, its installation routine adds in repository information for keeping it up to date. However, there is an issue with what you find in /etc/apt/sources.list.d/brave-browser-release.list. By default, the line appears like thus:

deb [signed-by=/usr/share/keyrings/brave-browser-archive-keyring.gpg] https://brave-browser-apt-release.s3.brave.com/ stable main

To avoid the i386 error, it needs to look like this instead:

deb [signed-by=/usr/share/keyrings/brave-browser-archive-keyring.gpg arch=amd64] https://brave-browser-apt-release.s3.brave.com/ stable main

The difference between the tow is the presence of arch=amd64 in the second version. This stops the search for non-existent i386 files, the 32 bit version in other words. With Y2K2038 in the offing, the days of 32 bit computing architectures are numbered because there is a real limit to the magnitude of the dates that can be represented in any case. Thus, sticking with 64 bit ones is both the present for many and the future for all.

Upgrading from OpenMediaVault 6.x to OpenMediaVault 7.x

29^th May 2024

Having an older PC to upgrade, I decided to install OpenMediaVault on there a few years ago after adding in 6 TB and 4 TB hard drives for storage, a Gigabit network card to speed up backups and a new BeQuiet! power supply to make it quieter. It has been working smoothly since then, and the release of OpenMediaVault 7.x had me wondering how to move to it.

Usefully, I enabled an SSH service for remote logins and set up an account for anything that I needed to do. This includes upgrades, taking backups of what is on my NAS drives, and even shutting down the machine when I am done with what I need to do with it.

Using an SSH session, the first step was to switch to the administrator account and issue the following command to ensure that my OpenMediaVault 6.x installation was as up-to-date as it could be:

omv-update

Once that had completed what it needed to do, the next step was to do the upgrade itself with the following command:

omv-release-upgrade

With that complete, it was time to reboot the system, and I fired up the web administration interface and spotted a kernel update that I applied. Again, the system was restarted, and further updates were noticed and these were applied, again through the web interface. The whole thing is based on Debian 12.x, but I am not complaining as long as it quietly does exactly what I need of it. There was one slight glitch when doing an update after the changeover, and that was quickly sorted.

Later on, I ran into trouble because I had changed my broadband. Because the router address had changed, the system lost its access to the rest of the internet. The web interface also got disable and was issuing 502: Bad Gateway errors. The solution was to execute the following command with superuser privileges:

omv-salt stage run deploy

That took quite a while to run, though. After it completed, I needed to work out what the administrator credentials were. With that done, I could log in and update the network details as needed to restore external internet access. Since then, all has been well.

Using a BASH command to count the files in a directory

12^th March 2024

As part of my backup workflow, I maintain a machine running OpenMediaVault that I only power up when backups are to be performed. Typically, this often happens when I have new photography images to load, and I have a NAS that acts as an online backup system. The OpenMediaVault machine is a near-offline counterpart to the NAS for added safety.

Recently, I needed to check on the number of image files in a directory from an SSH session because of a need to create a new repository for 2024. Some files from this year had ended up in the 2023 one, and I needed to be sure that nothing from last year ended in the 2024 folder, or vice versa. Getting a file count from a trusted source was a quick way of doing exactly this.

Due to clumsiness with the NAS, I had to do this using the OpenMediaVault machine. While I could go mounting drives on an interim basis, it was quicker to work from a BASH session. The trick was to use the wc command for counting the lines output by an invocation of the ls command. An example follows:

ls -l | wc -l

The -l (as in l for Lima) switch forces wc to count lines, while the counterpart (same letter) for ls forces it to list the contents in long form, one item per line. Thus, counting the number of lines gets you the count of the number of files. The call to the ls command can be customised to add other things life the number of dot files, but the above was enough for my purposes. When the files in both 2023 directories matched, I was satisfied that all was in order.

Ensuring that Flatpak remains up to date on Linux Mint 19.2

25^th October 2019

The Flatpak concept offers a useful way of getting the latest version of software like LibreOffice or GIMP on Linux machines because repositories are managed conservatively when it comes to the versions of included software. Ubuntu has Snaps, which are similar in concept. Both options bundle dependencies with the packaged software so that its operation can use later versions of system libraries than what may be available with a particular distribution.

However, even Flatpak depends on what is available through the repositories for a distribution, as I found when a software update needed a version of the tool. The solution was to add PPA using the following command and agreeing to the prompts that arise (answering Y, in other words):

sudo add-apt-repository ppa:alexlarsson/flatpak

With the new PPA instated, the usual apt commands were used to update the Flatpak package and continue with the required updates. Since then, all has gone smoothly as expected.

Creating a VirtualBox virtual disk image using the Linux command line

9^th September 2019

Much of the past weekend was spent getting a working Debian 10 installation up and running in a VirtualBox virtual machine. Because I chose the Cinnamon desktop environment, the process was not as smooth as I would have liked, so a minimal installation was performed before I started to embellish as I liked. Along the way, I got to wondering if I could create virtual hard drives using the command line, and I found that something like the following did what was needed:

VBoxManage createmedium disk --filename <full path including file name without extension> -size <size in MiB> --format VDI --variant Standard

Most of the options are self-explanatory, apart from the one named variant. This defines whether the VDI file expands to the maximum size specified using the size parameter or is reserved with the size defined in that parameter. Two VDI files were created in this way and I used these to replace their Debian 8 predecessors and even to save a bit of space too. If you want, you can find out more in the user documentation, but this post hopefully gets you started anyway.

Lightening of desktop background images on Linux Mint Debian Edition running in Virtualbox

22^nd October 2018

After a recent upgrade to Linux Mint Debian Edition 3 in a VirtualBox virtual machine that I had running its predecessor, I began to notice that background images were being loaded with more washed out or faded colours. This happened at startup, so selecting another background image worked as intended until the same thing happened to that after a system restart.

This problem is not new and has affected the Cinnamon desktop in the main Linux Mint variant (the one that is based on Ubuntu) and issuing the following command in a terminal session is a suggested solution:

gsettings set org.cinnamon.muffin background-transition fade-in

In my case, that solved the problem and the desktop background image display is as it should be since I executed the above. All it took was a change to a system setting.

Compressing a VirtualBox VDI file for a Linux guest

6^th June 2016

In a previous posting, I talked about compressing a virtual hard disk for a Windows guest system running in VirtualBox on a Linux system. Since then, I have needed to do the same for a Linux guest following some housekeeping. Because the Linux distribution used is Debian, the instructions are relevant to that and maybe its derivatives such as Ubuntu, Linux Mint and their like.

While there are other alternatives like dd, I am going to stick with a utility named zerofree to overwrite the newly freed up disk space with zeroes to aid compression later on in the process for this and the first step is to install it using the following command:

apt-get install zerofree

Once that has been completed, the next step is to unmount the relevant disk partition. Luckily for me, what I needed to compress was an area that I reserved for synchronisation with Dropbox. If it was the root area where the operating system files are kept, a live distro would be needed instead. In any event, the required command takes the following form, with the mount point being whatever it is on your system (/home, for instance):

sudo umount [mount point]

With the disk partition unmounted, zerofree can be run by issuing a command that looks like this:

zerofree -v /dev/sdxN

Above, the -v switch tells zerofree to display its progress and a continually updating percentage count tells you how it is going. The /dev/sdxN piece is generic with the x corresponding to the letter assigned to the disk on which the partition resides (a, b, c or whatever) and the N is the partition number (1, 2, 3 or whatever; before GPT, the maximum was 4). Putting all this together, we get an example like /dev/sdb2.

Once, that had completed, the next step is to shut down the VM and execute a command like the following on the host Linux system ([file location/file name] needs to be replaced with whatever applies on your system):

VBoxManage modifyhd [file location/file name].vdi --compact

With the zero filling in place, there was a lot of space released when I tried this. While it would be nice for dynamic virtual disks to reduce in size automatically, I accept that there may be data integrity risks with those, so the manual process will suffice for now. It has not been needed that often anyway.

Installing FreeBSD in a VirtualBox Virtual Machine

2^nd March 2014

With UNIX being the basis of Linux, I have a soft spot for trying out any UNIX that can be installed on a PC. For a while, I had OpenSolaris on the go and even vaguely recall having a look at one of the BSD's. However, any recent attempt to install one of the latter, and there are quite a few around now, got stymied by some sort of kernel panic caused by using AMD CPU's. With the return to the Intel fold arising from the upgrade of my main home PC last year, it perhaps was time to try again.

The recent release of FreeBSD 10.0 was the cue and I downloaded a DVD image for a test installation in a VirtualBox virtual machine with 4 GB of memory and a 32 GB virtual hard drive attached (expanding storage was chosen so not all the allocated space has been taken so far). The variant of FreeBSD chosen was the 64-bit x86 one, and I set to installing it in there. Though not as pretty in appearance as those in various Linux distros, the installer was not that user unfriendly to me. Mind you, I have experience of installing Arch Linux, which might have acclimatised me somewhat.

Those installation screens ask about the keyboard mapping that you want, and I successfully chose one of the UK options. There was limited opportunity for adding extras, though there was a short list of a few from which I made some selections. Given that user account set up also was on offer, I would have been better off knowing what groups to assign for my personal user account to have to avoid needing to log in as root so often following system start up later. Otherwise, all the default options were sufficient.

When the installation process was complete, it was time to boot into the new system and all that was on offer was a command line log in session. After logging in as root, it was time to press pkg into service to get a desktop environment in place. The first step was to install X:

pkg install xorg

Then, it was time to install a desktop environment. While using XFCE or KDE were alternatives, I chose GNOME 2 due to familiarity and more extensive instructions on the corresponding FreeBSD handbook page. Issuing the following command added GNOME and all its helper applications:

pkg install gnome2

So that GNOME starts up at the next reboot, some extra steps are needed. The first of these is to add the following line into /etc/fstab:

proc /proc procfs rw 0 0

Then, two lines were needed in /etc/rc.conf:

gdm_enable="YES" gnome_enable="YES"

The first enables the GNOME display manager, while the second activates other GNOME programs that are needed for a desktop session to start. With each of these in place, I got a graphical login screen at the next boot time.

With FreeBSD being a VirtualBox Guest, it was time to consult the relevant FreeBSD manual page. Here, there are sections for a number of virtual machine tools, so a search was needed to find the one for VirtualBox. VirtualBox support for FreeBSD is incomplete in that there is no installation media for BSD systems, while Linux and Solaris are supported along with Windows. Therefore, it is over to the FreeBSD repositories for the required software:

pkg install virtualbox-ose-additions

Aside from the virtual machine session not capturing and releasing the mouse pointer automatically, that did everything that was needed, even if it was the open source edition of the drivers and their proprietary equivalents. To resolve the mouse pointer issue, I needed to temporarily disable the GNOME desktop session in /etc/rc.conf to drop to a console only session where xorg.conf could be generated using the following commands:

Xorg -configure cp xorg.conf.new /etc/xorg.conf

In the new xorg.conf file, the mouse section needs to be as follows:

Section "InputDevice" Identifier "Mouse0" Driver "vboxmouse" EndSection

If it doesn't look like the above, and it wasn't the case for me, then it needs changing. Also, any extra lines from the default set up also need removing, or the mouse will not function as it should. The ALT+F1 (for accessing GNOME menus) and ALT+F2 (for running commands) keyboard shortcuts then become crucial when your mouse is not working as it should and could avert a panic too; knowing that adjusting a single configuration file will resolve a problem when doing so is less accessible is not a good feeling as I discovered to my own cost. The graphics settings were fine by default, but here's what you should have in case it isn't for you:

Section "Device" ### Available Driver options are:- ### Values: <i>: integer, <f>: float, <bool>: "True"/"False", ### <string>: "String", <freq>: "<f> Hz/kHz/MHz" ### [arg]: arg optional Identifier "Card0" Driver "vboxvideo" VendorName "InnoTek Systemberatung GmbH" BoardName "VirtualBox Graphics Adapter" BusID "PCI:0:2:0" EndSection

The next step is to ensure that your HAL settings are as they should. I needed to create a file in /usr/local/etc/hal/fdi/policy called 90-vboxguest.fdi that contains the following:

<?xml version="1.0" encoding="utf-8"?>  <deviceinfo version="0.2"> <device> <match key="info.subsystem" string="pci"> <match key="info.product" string="VirtualBox guest Service"> <append key="info.capabilities" type="strlist">input</append> <append key="info.capabilities" type="strlist">input.mouse</append> <merge key="input.x11_driver" type="string">vboxmouse</merge> <merge key="input.device" type="string">/dev/vboxguest</merge> </match> </match> </device> </deviceinfo>

With all that set, it is time to ensure that the custom user account is added to the wheel and operator groups using this command:

pw user mod [user name] -G wheel operator

Executing the above as root means that the custom account can run the su command so that logging in as root at the start of a desktop session no longer is needed. That is what being in the wheel group allows, so anyone in the operator group can shut down or restart the system. Since both are facilities readily available on Linux, so I fancied having them in FreeBSD too.

Being able to switch to root in a terminal session meant that I could go on to add software like Firefox, LibreOffice, GIMP, EMACS, Geany, NetBeans, Banshee and so on. Though there may be a line of opinion that FreeBSD is a server operating system, all of these make it more than passable for serving as a desktop one too. There may be no package management GUI as such and the ones that come with GNOME do not work either, yet anyone familiar with command line working will get around that.

While FreeBSD may be conservative, that has its place too, and being able to build up a system one item at a time teaches far more than getting everything already sorted in one hit. So far, there is enough documentation to get me going, leaving me to see where else things go too. So far, the OS hasn't been that intimidating, which is good to see.

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