Minutes 2023-08-04 – R Submissions Working Group

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Minutes

The meeting was recorded and the video is available.

HyeSoo Cho reported that she is working with the Pilot 2 re-submission and that it looks good.
HyeSoo expects that the final on this pilot submission will be available at the end of August.
Everyone recognized and thanked Eric Nantz for the sustained and last-minute efforts to get the submission out.

Paul Schuette brought the attention of the group to section 4.i.2.10 of the Study Data Technical Conformance Guide - Technical Specification Document and noted that .r and .zip files are listed as acceptable file formats for submissions.
After some discussion, the WG decided not to use pkglite to wrap the R code as has been done in previous submissions, but to use .r files for the code. (Note that the FDA is unable to use .R internally.)
Paul noted that the FDA desires submission materials to be applicable for at least six years after submission. This triggered a discussion about possibility of using .zip files to transmit the proprietary packages, instead of pulling them from public GitHub repos as been done so far.
In the end, the WG decided to stick with using GitHub repos for Pilot 3 as there is currently no apparent advantage testing the .zip file method at this time.
Joel Laxama reported that preparations for Pilot 3 are going well, and that a submission using .r files could be made in early September.
The WG thought it best to wait for the report of Pilot 2 before submitting Pilot 3.

Eric reported that thanks to the contributions form the Appsilon team significant progress has been made on using both mechanisms for packaging R submissions: Containers and Webassembly.
Appsilon has a prototype submission using Podman container technology working and has confirmed that it does not cause files to be written to the hard-drive.
Eric and the Appsilon engineers also have a very preliminary prototype of using Webassembly to wrap a small Shiny app working.
Posit engineers have contributed webr expertise.
Eric is optimistic about having Pilot submissions based on at least one, and possibly both, of these technologies ready by the end of the year.

Action

Paul will confer with the proper FDA authorities to determine what preparations need to be undertaken by the FDA to use the Podman containers.
Eric will invite an Appsilon representative to come to a future meeting of this working group

The R Foundation SummeR Bay Area R Meetup was held at San Jose State University on July 21. Ning Leng reports that:

The 50 plus attendees indicated that quite a few Bay Area companies are moving towards using R in preclinical and genomics research.
Representatives from several small CROs attended the meeting.
R Consortium recognition was not good among this group.

Action

Eric will submit an abstract to speak about Pilot 3 and Pilot 4 at the R/Pharma virtual conference to be held in on October 24 - 26.
Paul will be presenting at both at the PHUSE/FDA CSS 2023 conference on September 18 -20 and the ASA Biopharmaaceutical Section Regulatory-Industry statistics Workshop to be held in Rockville, MD on September 27 - 29 and intends to use the activities of this working group as a case study.
Ning suggests that it would be very nice if the RC could hold and R Adoption Webinar in the November time frame to describe the Pilot 2 and Pilot 3 submissions.

Action:

Paul will check with FDA authorities to see whether it is appropriate for the R Consortium to publicize his speaking opportunities on social media.
JBR will work with the RC Community development committee to make preparations for the promoting the speaking activities and setting up the webinar.

The next meeting of the Submissions working group will be at 9AM PST on Friday, September 1st.