Technology Tales

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

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

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 in order 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

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

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

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.

Creating a VirtualBox virtual disk image using the Linux command line

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 part 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

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 of 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 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

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. The Linux distribution used is Debian so the instructions are relevant to that and maybe its derivatives such as Ubuntu, Linux Mint and their kind.

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 Citrix Receiver 13.0 in Ubuntu GNOME 13.10 64-bit

Installing the latest version of Citrix Receiver (13.0 at the time of writing) on 64-bit Ubuntu should be as simple as downloading the required DEB package and double-clicking on the file so that Ubuntu Software Centre can work its magic. Unfortunately, the 64-bit DEB file is faulty so that means that the Ubuntu community how-to guide for Citrix still is needed. In fact, any user of Linux Mint or another distro that uses Ubuntu as its base would do well to have a look at that Ubuntu link.

For sake of completeness, I still am going to let you in on the process that worked for me. Once the DEB file has been downloaded, the first task is to creating a temporary folder where the DEB file’s contents can be extracted:

mkdir ica_temp

With that in place, it then is time to do the extraction and it needs two commands with the second of these need to extract the control file while the first extracts everything else.

sudo dpkg-deb -x icaclient- ica_temp
sudo dpkg-deb --control icaclient- ica_temp/DEBIAN

It is the control file that has been the cause of all the bother because it refers to unavailable dependencies that it really doesn’t need anyway. To open the file for editing, issue the following command:

sudo gedit ica_temp/DEBIAN/control

Then change line 7 (it should begin with Depends:) to: Depends: libc6-i386 (>= 2.7-1), lib32z1, nspluginwrapper. There are other software packages in there that Ubuntu no longer supports and they are not needed anyway. With the edit made and the file saved, the next step is to build a new DEB package with the corrected control file:

dpkg -b ica_temp icaclient-modified.deb

Once you have the package, the next step is to install it using the following command:

sudo dpkg -i icaclient-modified.deb

If it fails, then you have missing dependencies and the following command should sort these before a re-run of the above command again:

sudo apt-get install libmotif4:i386 nspluginwrapper lib32z1 libc6-i386

With Citrix Receiver installed, there is one more thing that is needed before you can use it freely. This is to put Thawte security certificate files into /opt/Citrix/ICAClient/keystore/cacerts. What I had not realised until recently was that many of these already are in /usr/share/ca-certificates/mozilla and linking to them with the following command makes them available to Citrix receiver:

sudo ln -s /usr/share/ca-certificates/mozilla/* /opt/Citrix/ICAClient/keystore/cacerts/

Another approach is to download the Thawte certificates and extract the archive to /tmp/. From there they can be copied to /opt/Citrix/ICAClient/keystore/cacerts and I copied the Thawte Personal Premium certificate as follows:

sudo cp /tmp/Thawte Root Certificates/Thawte Personal Premium CA/Thawte Personal Premium CA.cer /opt/Citrix/ICAClient/keystore/cacerts/

Until I found out about what was in the Mozilla folder, I simply picked out the certificate mentioned in the Citrix error message and copied it over like the above. Of course, all of this may seem like a lot of work to those who are non-tinkerers and I have added a repaired 64-bit DEB package that incorporates all of the above and should not need any further intervention aside from installing it using GDebi, Ubuntu’s Software Centre, dpkg or anything else that does what’s needed.

A little look at Debian 7.0

Having a virtual machine with Debian 6 on there, I was interested to hear that Debian 7.0 is out. In another VM, I decided to give it a go. Installing it on there using the Net Install CD image took a little while but proved fairly standard with my choice of the GUI-based option. GNOME was the desktop environment with which I went and all started up without any real fuss after the installation was complete; it even disconnnected the CD image from the VM before rebooting, a common failing in many Linux operating installations that lands into the installation cycle again unless you kill the virtual machine.

Though the GNOME desktop looked familiar, a certain amount of conservatism reigned too since the version was 3.4.2. That was no bad thing since raiding the GNOME Extension site for a set of mature extensions was made all the more easy. In fact, a certain number of these was included in the standard installation anyway and the omission of a power off entry on the user menu was corrected as a matter of course without needing any intervention from this user. Adding to what already was there made for a more friendly desktop experience in a short period of time.

Debian’s variant of Firefox , Iceweasel, is version 10 so a bit of tweaking is needed to get the latest version. LibreOffice is there now too and it’s version 3.5 rather than 4. Shotwell too is the older 0.12 and not the 0.14 that is found in the likes of Ubuntu 13.04. As it happens, GIMP is about the only software with a current version and that is 2.8; a slower release cycle may be the cause of that though. All in all, the general sense is that older versions of current software are being included for the sake of stability and that is sensible too so I am not complaining very much about this at all.

The reason for not complaining is that the very reason for having a virtual machine with Debian 6 on there is to have Zinio and Dropbox available too. Adobe’s curtailment of support for Linux means that any application needing Adobe Air may not work on a more current Linux distribution. That affects Zinio so I’ll be retaining a Debian 6 instance for a while yet unless a bout of testing reveals that a move to the newer version is possible. As for Dropbox, I am sure that I can recall why I moved it onto Debian but it’s working well on there so I am in no hurry to move it over either. There are times when slower software development cycles are better…