Written by Sebastià Barceló, Malte Stein, and Angelo Tinazzi

Open source has been a leitmotif in our industry for many years now, but its adoption poses a number of challenges. At Cytel, our journey into open source began a couple of years ago. Since then, we have focused on building a dedicated Statistical Computing Environment (SCE), defining new processes, and developing new tools to support these processes. Additionally, we also contributed to industry initiatives such as the R {admiral}.

This year, PHUSE-EU will feature a dedicated stream, Open-Source Technology, where presenters will share their experience with open-source technology adoption. In this spirit of collaboration, we will be contributing with two presentations, both addressing critical aspects:

• The co-existence of R and SAS in the same SCE
• The risk assessment of R packages

Integrating RStudio POSIT and SAS in the same environment

Our new SCE integrates RStudio POSIT and SAS Grid across both Windows and Linux servers. The integration was designed to create a unified and efficient environment for data analytics, leveraging both SAS and POSIT’s capabilities.

The integration was complex and presented several obstacles and surprises along the way. For instance, we encountered compatibility issues, particularly around data access and permissions. To address these, we implemented dual protocol drive, enabling real-time data sharing across platforms, and the use of Git as a version control system, which allows us to maintain and publish content in Connect in a more robust and secure way.

Additional challenges in managing this SCE include balancing security with usability for internal and external access to POSIT Connect and optimizing R package management.

Figure 1 illustrates the final infrastructure.

R packages risk assessment

Installing and using R packages in the SCE requires assessing the risks associated using these packages. These packages are typically accessed through CRAN, the primary source for R packages developed by various organizations and individuals. Risk assessment is especially critical in industries like pharmaceuticals, where strong compliance requirements (e.g., GxP), necessitate that packages are well maintained, documented, and, after all, reliable.

A key aspect of the risk assessment is the collection of packages metadata, enabling us to classify and assess the reliability of all potential packages we will want to make available in our SCE.

At Cytel, we applied a comprehensive assessment approach by extracting metadata from R packages. We began by evaluating various techniques, such as APIs and web scraping, and compared our approach with the R riskmetric package. This comparison highlighted limitations in conventional methods, which often only address the latest package version. As a result, we enhanced our metadata extraction process.

Interested in learning more?

If you are attending the PHUSE-EU in Strasbourg from November 10–13, do not miss Sebastià and Malte’s poster and presentation, where the co-existence of R and SAS and our approach to extracting metadata from R packages will be discussed in more detail:

“Bridging Platforms: Integrating RStudio POSIT and SAS Grid in the Same Environment”

Cytel presenters: Sebastià Barceló and Malte Stein

Tuesday, November 12, at 5:30 p.m. (Poster Session – PP28)

“Unveiling R Package Risk Assessment: A Comparative Analysis of Metadata Extraction”

Cytel presenters: Malte Stein and Sebastià Barceló

Wednesday, November 13, at 1:30 p.m. (Open-Source Technology Stream – OS14)

Angelo Tinazzi will moderate the Scripts, Macros and Automation stream, which will also cover some open-source experiences from other organizations.

Cytel will be at Booth #6! We hope to see you there!

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