TOPIC: APT
SAS Packages: Revolutionising code sharing in the SAS ecosystem
26th July 2025In the world of statistical programming, SAS has long been the backbone of data analysis for countless organisations worldwide. Yet, for decades, one of the most significant challenges facing SAS practitioners has been the efficient sharing and reuse of code. Knowledge and expertise have often remained siloed within individual developers or teams, creating inefficiencies and missed opportunities for collaboration. Enter the SAS Packages Framework (SPF), a solution that changes how SAS professionals share, distribute and utilise code across their organisations and the broader community.
The Problem: Fragmented Knowledge and Complex Dependencies
Anyone who has worked extensively with SAS knows the frustration of trying to share complex macros or functions with colleagues. Traditional code sharing in SAS has been plagued by several issues:
- Dependency nightmares: A single macro often relies on dozens of utility macros working behind the scenes, making it nearly impossible to share everything needed for the code to function properly
- Version control chaos: Keeping track of which version of which macro works with which other components becomes an administrative burden
- Platform compatibility issues: Code that works on Windows might fail on Linux systems and vice versa
- Lack of documentation: Without proper documentation and help systems, even the most elegant code becomes unusable to others
- Knowledge concentration: Valuable SAS expertise remains trapped within individuals rather than being shared with the broader community
These challenges have historically meant that SAS developers spend countless hours reinventing the wheel, recreating functionality that already exists elsewhere in their organisation or the wider SAS community.
The Solution: SAS Packages Framework
The SAS Packages Framework, developed by Bartosz Jabłoński, represents a paradigm shift in how SAS code is organised, shared and deployed. At its core, a SAS package is an automatically generated, single, standalone zip file containing organised and ordered code structures, extended with additional metadata and utility files. This solution addresses the fundamental challenges of SAS code sharing by providing:
- Functionality over complexity: Instead of worrying about 73 utility macros working in the background, you simply share one file and tell your colleagues about the main functionality they need to use.
- Complete self-containment: Everything needed for the code to function is bundled into one file, eliminating the "did I remember to include everything?" problem that has plagued SAS developers for years.
- Automatic dependency management: The framework handles the loading order of code components and automatically updates system options like
cmplib=andfmtsearch=for functions and formats. - Cross-platform compatibility: Packages work seamlessly across different operating systems, from Windows to Linux and UNIX environments.
Beyond Macros: A Spectrum of SAS Functionality
One of the most compelling aspects of the SAS Packages Framework is its versatility. While many code-sharing solutions focus solely on macros, SAS packages support a wide range of SAS functionality:
- User-defined functions (both FCMP and CASL)
- IML modules for matrix programming
- PROC PROTO C routines for high-performance computing
- Custom formats and informats
- Libraries and datasets
- PROC DS2 threads and packages
- Data generation code
- Additional content such as documentation PDF's
This comprehensive approach means that virtually any SAS functionality can be packaged and shared, making the framework suitable for everything from simple utility macros to complex analytical frameworks.
Real-World Applications: From Pharmaceutical Research to General Analytics
The adoption of SAS packages has been particularly notable in the pharmaceutical industry, where code quality, validation and sharing are critical concerns. The PharmaForest initiative, led by PHUSE Japan's Open-Source Technology Working Group, exemplifies how the framework is being used to revolutionise pharmaceutical SAS programming. PharmaForest offers a collaborative repository of SAS packages specifically designed for pharmaceutical applications, including:
- OncoPlotter: A comprehensive package for creating figures commonly used in oncology studies
- SAS FAKER: Tools for generating realistic test data while maintaining privacy
- SASLogChecker: Automated log review and validation tools
- rtfCreator: Streamlined RTF output generation
The initiative's philosophy perfectly captures the spirit of the SAS Packages Framework: "Through SAS packages, we want to actively encourage sharing of SAS know-how that has often stayed within individuals. By doing this, we aim to build up collective knowledge, boost productivity, ensure quality through standardisation and energise our community".
The SASPAC Archive: A Growing Ecosystem
The establishment of SASPAC (SAS Packages Archive) represents the maturation of the SAS packages ecosystem. This dedicated repository serves as the official home for SAS packages, with each package maintained as a separate repository complete with version history and documentation. Some notable packages available through SASPAC include:
- BasePlus: Extends BASE SAS with functionality that many developers find themselves wishing was built into SAS itself. With 12 stars on GitHub, it's become one of the most popular packages in the archive.
- MacroArray: Provides macro array functionality that simplifies complex macro programming tasks, addressing a long-standing gap in SAS's macro language capabilities.
- SQLinDS: Enables SQL queries within data steps, bridging the gap between SAS's powerful data step processing and SQL's intuitive query syntax.
- DFA (Dynamic Function Arrays): Offers advanced data structures that extend SAS's analytical capabilities.
- GSM (Generate Secure Macros): Provides tools for protecting proprietary code while still enabling sharing and collaboration.
Getting Started: Surprisingly Simple
Despite the capabilities, getting started with SAS packages is fairly straightforward. The framework can be deployed in multiple ways, depending on your needs. For a quick test or one-time use, you can enable the framework directly from the web:
filename packages "%sysfunc(pathname(work))";
filename SPFinit url "https://raw.githubusercontent.com/yabwon/SAS_PACKAGES/main/SPF/SPFinit.sas";
%include SPFinit;
For permanent installation, you simply create a directory for your packages and install the framework:
filename packages "C:SAS_PACKAGES";
%installPackage(SPFinit)
Once installed, using packages becomes as simple as:
%installPackage(packageName)
%helpPackage(packageName)
%loadPackage(packageName)
Developer Benefits: Quality and Efficiency
For SAS developers, the framework offers numerous advantages that go beyond simple code sharing:
- Enforced organisation: The package development process naturally encourages better code organisation and documentation practices.
- Built-in testing: The framework includes testing capabilities that help ensure code quality and reliability.
- Version management: Packages include metadata such as version numbers and generation timestamps, supporting modern DevOps practices.
- Integrity verification: The framework provides tools to verify package authenticity and integrity, addressing security concerns in enterprise environments.
- Cherry-picking: Users can load only specific components from a package, reducing memory usage and namespace pollution.
The Future of SAS Code Sharing
The growing adoption of SAS packages represents more than just a new tool, it signals a fundamental shift towards a more collaborative and efficient SAS ecosystem. The framework's MIT licensing and 100% open-source nature ensure that it remains accessible to all SAS users, from individual practitioners to large enterprise installations. This democratisation of advanced code-sharing capabilities levels the playing field and enables even small teams to benefit from enterprise-grade development practices.
As the ecosystem continues to grow, with contributions from pharmaceutical companies, academic institutions and individual developers worldwide, the SAS Packages Framework is proving that the future of SAS programming lies not in isolated development, but in collaborative, community-driven innovation.
For SAS practitioners looking to modernise their development practices, improve code quality and tap into the collective knowledge of the global SAS community, exploring SAS packages isn't just an option, it's becoming an essential step towards more efficient and effective statistical programming.
What to do an error appears when using pip to install Python packages on Linux Mint 22
16th December 2024After 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
25th November 2024While 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.
What to do when a GPG signature becomes invalid for a package repository on Linux Mint
12th September 2024During a package update on my main Linux system, I encountered the following kind of error message:
An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: https://cli.github.com/packages stable InRelease: The following signatures were invalid: EXPKEYSIG <GPG Key> GitHub CLI
The message indicated a problem with the GPG signature verification for the GitHub CLI repository. The cause was that the signature for the repository was invalid, preventing the package manager from updating the repository's index files. The first step then was to remove the invalid GPG key using the following command:
sudo apt-key del <GPG Key>
With the invalid GPG key removed, the next step is to add the new GPG key for the GitHub CLI repository by issuing the following command:
curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | sudo tee /usr/share/keyrings/githubcli-archive-keyring.gpg > /dev/null
Once I had the new GPG key, I was able to use my usual system update process without any problem. The error message was gone, and updates and upgrades proceeded as intended.
Resolving "repository doesn't support architecture i386" error when checking for updates to Brave Browser on Linux
7th June 2024Recently, 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.
Getting rid of the "Get more security upgrades through Ubuntu Pro with 'esm-apps' enabled" message when performing a system update
15th April 2024Not so long ago, I got the above message while running sudo apt upgrade on an Ubuntu Server system. This was not the first time that this kind of thing happened to me, so I started searching the web for a solution. You do get to see complaints about advertising, but these are never useful.
Accordingly, here are some possible ways of remediating the situation:
- Execute the following commands to disable the responsible services, renaming the configuration file to prevent it from being used (deleting or editing the configuration file to remove the unwanted content are other options):
sudo systemctl mask apt-news.servicesudo systemctl mask esm-cache.servicesudo mv /etc/apt/apt.conf.d/20apt-esm-hook.conf
/etc/apt/apt.conf.d/20apt-esm-hook.conf.disabled - Alternatively, simply remove the
ubuntu-advantage-toolspackage, which contains the/etc/apt/apt.conf.d/20apt-esm-hook.conffile. - Another option is to remove the
ubuntu-pro-clientpackage. - Lastly, there also is the possibility of enabling ESM, though that was not desirable for me.
In my case, it may have been the penultimate option on the list that I chose. In any case, I was rid of the unwanted message.
Fixing an Ansible warning about boolean type conversion
27th October 2022My primary use for Ansible is doing system updates using the inbuilt apt module. Recently, I updated my main system to Linux Mint 21 and a few things like Ansible stopped working. Removing instances that I had added with pip3 sorted the problem, but I then ran playbooks manually, only for various warning messages to appear that I had not noticed before. What follows below is one of these.
[WARNING]: The value True (type bool) in a string field was converted to u'True' (type string). If this does not look like what you expect, quote the entire value to ensure it does not change.
The message is not so clear in some ways, not least because it had me looking for a boolean value of True when it should have been yes. A search on the web revealed something about the apt module that surprised me.: the value of the upgrade parameter is a string, when others like it take boolean values of yes or no. Thus, I had passed a bareword of yes when it should have been declared in quotes as "yes". To my mind, this is an inconsistency, but I have changed things anyway to get rid of the message.
Ensuring that Flatpak remains up to date on Linux Mint 19.2
25th October 2019The 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.
Upgrading avahi-dnsconfd on Ubuntu
18th April 2018This is how I got around a problem that occurred when I was updating a virtualised Ubuntu 16.04 instance that I have. My usual way to do this is using apt-get or apt from the command line and the process halted because a pre-removal script for the upgrade of avahi-dnsconf failed. The cause was its failure to disable the avahi daemon beforehand, so I needed to execute the following command before repeating the operation:
sudo systemctl disable avahi-daemon
Once the upgrade had completed, then it was time to re-enable the service using the following command:
sudo systemctl enable avahi-daemon
Ideally, this would be completed without such manual intervention. As it happens, there is a bug report for the unexpected behaviour. Hopefully, it will be sorted soon, but these steps will fix things for now.
Trying out a new way to upgrade Linux Mint in situ while going from 17.3 to 18.1
19th March 2017There was a time when the only recommended way to upgrade Linux Mint from one version to another was to do a fresh installation with back-ups of data and a list of the installed applications created from a special tool.
Even so, it never stopped me doing my own style of in situ upgrade, though some might see that as a risky option. More often than not, that actually worked without causing major problems in a time when Linux Mint releases were more tightly tied to Ubuntu's own six-monthly cycle.
Linux Mint releases now align with Ubuntu's Long Term Support (LTS) editions. This means major changes occur only every two years, with minor releases in between. These minor updates are delivered through Linux Mint's Update Manager, making the process simple. Upgrades are not forced, so you can decide when to upgrade, as all main and interim versions receive the same extended support. The recommendation is to avoid upgrading unless something is broken on your installation.
For a number of reasons, I stuck with that advice by sticking on my main machine with Linux Mint 17.3 instead of upgrading to Linux Mint 18. The fact that I broke things on another machine using an older method of upgrading provided even more encouragement.
However, I subsequently discovered another means of upgrading between major versions of Linux Mint that had some endorsement from the project. There still are warnings about testing a live DVD version of Linux Mint on your PC first and backing up your data beforehand. Another task is ensuring that you are upgraded from a fully up-to-date Linux Mint 17.3 installation.
When you are ready, you can install mintupgrade using the following command:
sudo apt-get install mintupgrade
When that is installed, there is a sequence of tasks that you need to do. The first of these is to simulate an upgrade to test for the appearance of untoward messages and resolve them. Repeating any checking, until all is well, gets a recommendation. The command is as follows:
mintupgrade check
Once you are happy that the system is ready, the next step is to download the updated packages so they are on your machine ahead of their installation. Only then should you begin the upgrade process. The two commands that you need to execute are below:
mintupgrade download
mintupgrade upgrade
After these complete, restart your system. In my case, the process worked well, with only my PHP installation requiring attention. I resolved a clash between different versions of the scripting interpreter by removing the older one, as PHP 7 is best kept for testing. Apart from reinstalling VMware Player and upgrading from version 18 to 18.1, I had almost nothing else to do and experienced minimal disruption. This is fortunate as I rely heavily on my main PC. The alternative of a full installation would have left me sorting things out for several days afterwards because I use a customised selection of software.