This post has been updated to more accurately characterize pkglite’s role in regulatory submissions. We regret any impression that pkglite was merely a stopgap solution: it remains a principled, peer-reviewed approach that continues to serve the community well.
Over the past several years, the R Consortium Regulatory Submission Working Group has conducted multiple pilots to explore and validate the use of R in regulatory submissions. One recurring challenge surfaced early in our work:
How should sponsors submit non-public R packages—especially those containing proprietary information—to the FDA?
For security reasons, FDA’s eCTD portal historically allowed only a highly restricted set of file formats. As a result, standard R package formats such as compressed files were not accepted. In Pilot 1 and Pilot 2, we used pkglite to convert R packages into a plain text bundle. This approach, documented in a peer-reviewed paper in Clinical Trials, proved highly effective: the FDA reviewer successfully reproduced our analysis results by following the instructions in the Analysis Data Reviewer’s Guide (ADRG). The pkglite workflow offers distinct advantages: human-readable output, full transparency, easy version control, and language-agnostic design, that remain valuable regardless of which file formats the eCTD gateway accepts.
A Milestone: FDA Expands Accepted R File Formats
Resulting directly from joint work between industry and FDA through the R Consortium Submissions Working Group
We are pleased to share that the FDA has expanded its list of acceptable file formats to better support R workflows.
This update—found in the August 2025 revision of the FDA eCTD Technical Conformance Guide (link to guidance)—was directly informed by multi-year collaboration between industry partners and FDA reviewers participating in the R Consortium Regulatory Submission Working Group.
Through joint pilots, repeated feedback, and hands-on testing, FDA colleagues gained deeper visibility into how R packages are used and what formats are needed to preserve functionality and reproducibility.
The 2025-08-20 update includes:
Section 9.3 – Updated references
Newly accepted Modeling & Simulation file types:
.rds, .rdb, .rdx, .rdata / .rda, .md, .rd (for delivering R packages)
Expanded permissible use of:
.zip and .html (for delivering full R packages)
This means:
Sponsors can now submit non-public R packages directly as a .zip file.
This significantly reduces friction for organizations that rely on internal or proprietary R packages as part of their submission workflows.
Recommendation: Open-Source When Possible
Although submitting proprietary R packages is now easier, the Working Group continues to strongly recommend that organizations open-source their R packages whenever feasible.
Reasons include:
Reproducibility
Public repositories (e.g., CRAN, GitHub) allow FDA reviewers and other users to retrieve, install, and verify dependencies reliably.
Transparency in dependency handling
Open-source packages minimize hidden or fragile dependency structures, supporting long-term reproducibility.
Trust and community validation
Open-source tools benefit from broader testing, feedback, and shared maintenance.
Sustainability
Packages with a public footprint are more likely to be updated and maintained over time, benefiting the entire community.
In summary, while the updated guidance provides much-needed flexibility, open-source remains the most reliable path for transparency, reproducibility, and trust.
Looking Ahead
This guidance update reflects what can be achieved when industry experts and FDA reviewers work collaboratively to improve regulatory science infrastructure. The R Consortium Submissions Working Group will continue strengthening this partnership to ensure that R-based analysis workflows remain secure, reproducible, and reviewer-friendly. To learn more about the working group, visit: https://rconsortium.github.io/submissions-wg/