From f15f9009f8ed4dec906b776f8228fa106ba590af Mon Sep 17 00:00:00 2001 From: Robert Devine <> Date: Mon, 12 Feb 2024 18:05:32 -0500 Subject: [PATCH 1/4] Refactored stray newline in the README file between the 2nd and 3rd bullets of the Latest News section. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 4c2018a..7dce484 100644 --- a/README.md +++ b/README.md @@ -32,7 +32,7 @@ The website is divide into 4 sections that will walk you through our efforts: * [Novo Nordisk's Journey to an R based FDA Submission](https://www.youtube.com/watch?v=t33dS17QHuA) - *Data scientists at Novo Nordisk, a leading pharmaceutical company in diabetes, obesity, and other chronic diseases, share details of their first FDA submission package featuring outputs and* [ADaM datasets](https://www.cdisc.org/standards/foundational/adam) *written exclusively in R.* -\n + * [Testing Containers and WebAssembly in Submissions to the FDA](https://pharmaverse.github.io/blog/posts/2024-02-01_containers_webassembly_submission/containers_and_webassembly_submissions.html) - *Blog post with short summary of the R Consortium FDA Pilots 1-4 Series and the ongoing efforts undertaken to evaluate new technologies for submissions to the Food and Drug Administration (FDA). These transformative approaches, including WebAssembly and containers, hold immense potential to transform the regulatory landscape and streamline the submission process.* From e7cf60f30c434f1acb9186a0fcc19357c2b48168 Mon Sep 17 00:00:00 2001 From: Robert Devine <> Date: Mon, 12 Feb 2024 18:50:54 -0500 Subject: [PATCH 2/4] Correct lintr trailing spaces lines 9-12 in pkgs4adrg.r --- submission/pkgs4adrg.r | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/submission/pkgs4adrg.r b/submission/pkgs4adrg.r index 007a2e6..e5b18e8 100644 --- a/submission/pkgs4adrg.r +++ b/submission/pkgs4adrg.r @@ -6,15 +6,15 @@ library(data.table) pkgloaded <- sessionInfo()$loadedOnly #get intial list of packages that were loaded pkgother <- sessionInfo()$otherPkgs #get initla list of packages that were also listed in the Session but may not have been used -loaded <- data.frame(rbindlist(pkgloaded, idcol = TRUE, fill=T)) %>% - select(Package, Title, Version, Description) %>% +loaded <- data.frame(rbindlist(pkgloaded, idcol = TRUE, fill=T)) %>% + select(Package, Title, Version, Description) %>% mutate(loaded='Y') -other <- data.frame(rbindlist(pkgother, idcol = TRUE, fill=T)) %>% - select(Package, Title, Version, Description) %>% +other <- data.frame(rbindlist(pkgother, idcol = TRUE, fill=T)) %>% + select(Package, Title, Version, Description) %>% mutate(loaded='N') pkgdesc <- bind_rows(loaded, other) # stacks all package data frames. # NOTE column 'loaded', from this data frame can be used to subset out packages not used and may not be needed for the adrg.pdf -# update path to save CSV in your local area. +# update path to save CSV in your local area. write.csv(pkgdesc, "/cloud/project/submission/pkgs4adrg.csv", row.names=FALSE) From 55eb6fbb5f1bf57b84251948651c102d6b4fab43 Mon Sep 17 00:00:00 2001 From: Robert Devine <> Date: Mon, 12 Feb 2024 19:08:36 -0500 Subject: [PATCH 3/4] Correct lintr infix operator spacing lines 9-EOF in pkgs4adrg.r --- submission/pkgs4adrg.r | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/submission/pkgs4adrg.r b/submission/pkgs4adrg.r index e5b18e8..6acf5cc 100644 --- a/submission/pkgs4adrg.r +++ b/submission/pkgs4adrg.r @@ -6,15 +6,15 @@ library(data.table) pkgloaded <- sessionInfo()$loadedOnly #get intial list of packages that were loaded pkgother <- sessionInfo()$otherPkgs #get initla list of packages that were also listed in the Session but may not have been used -loaded <- data.frame(rbindlist(pkgloaded, idcol = TRUE, fill=T)) %>% +loaded <- data.frame(rbindlist(pkgloaded, idcol = TRUE, fill = T)) %>% select(Package, Title, Version, Description) %>% - mutate(loaded='Y') -other <- data.frame(rbindlist(pkgother, idcol = TRUE, fill=T)) %>% + mutate(loaded = 'Y') +other <- data.frame(rbindlist(pkgother, idcol = TRUE, fill = T)) %>% select(Package, Title, Version, Description) %>% - mutate(loaded='N') + mutate(loaded = 'N') pkgdesc <- bind_rows(loaded, other) # stacks all package data frames. # NOTE column 'loaded', from this data frame can be used to subset out packages not used and may not be needed for the adrg.pdf # update path to save CSV in your local area. -write.csv(pkgdesc, "/cloud/project/submission/pkgs4adrg.csv", row.names=FALSE) +write.csv(pkgdesc, "/cloud/project/submission/pkgs4adrg.csv", row.names = FALSE) From d518039fa845201cfd5e28aba11071672b1a0597 Mon Sep 17 00:00:00 2001 From: Robert Devine <> Date: Mon, 12 Feb 2024 19:21:38 -0500 Subject: [PATCH 4/4] Correct lintr T or F and lintr single quote spacing lines 9-14 in pkgs4adrg.r --- submission/pkgs4adrg.r | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/submission/pkgs4adrg.r b/submission/pkgs4adrg.r index 6acf5cc..55fd9b3 100644 --- a/submission/pkgs4adrg.r +++ b/submission/pkgs4adrg.r @@ -6,12 +6,12 @@ library(data.table) pkgloaded <- sessionInfo()$loadedOnly #get intial list of packages that were loaded pkgother <- sessionInfo()$otherPkgs #get initla list of packages that were also listed in the Session but may not have been used -loaded <- data.frame(rbindlist(pkgloaded, idcol = TRUE, fill = T)) %>% +loaded <- data.frame(rbindlist(pkgloaded, idcol = TRUE, fill = TRUE)) %>% select(Package, Title, Version, Description) %>% - mutate(loaded = 'Y') -other <- data.frame(rbindlist(pkgother, idcol = TRUE, fill = T)) %>% + mutate(loaded = "Y") +other <- data.frame(rbindlist(pkgother, idcol = TRUE, fill = TRUE)) %>% select(Package, Title, Version, Description) %>% - mutate(loaded = 'N') + mutate(loaded = "N") pkgdesc <- bind_rows(loaded, other) # stacks all package data frames. # NOTE column 'loaded', from this data frame can be used to subset out packages not used and may not be needed for the adrg.pdf