Expanded FDA eCTD File Format Support for R Packages — A Milestone Achieved Through Industry–FDA Collaboration

A milestone! FDA expands accepted R file formats, resulting directly from joint work between industry and FDA through the R Consortium Submissions Working Group.
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R Consortium

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December 8, 2025

Expanded FDA eCTD File Format Support for R Packages — A Milestone Achieved Through Industry–FDA Collaboration

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, our only feasible option was to convert an R package into a plain text bundle using pkglite—functional, but not ideal.

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/