pipeline failures

pharmaverse · Jan 16, 2024 · 28f700d · 28f700d
1 parent 372aced
commit 28f700d
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Showing 5 changed files with 19 additions and 20 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -32,9 +32,9 @@ Depends: R (>= 4.1)
 Imports: 
     admiraldev,
     dplyr (>= 1.0.0),
-    purrr (>= 1.0.0),
-    rlang (>= 1.0.0),
-    stringr,
+    purrr (>= 0.3.3),
+    rlang (>= 0.4.4),
+    stringr (>= 1.4.0),
     tibble
 Suggests:
     knitr,

diff --git a/inst/create_cm_template.R b/inst/create_cm_template.R
@@ -14,13 +14,13 @@ library(dplyr)
 
 # Read Specification
 
-# sdtm_spec <- read_sdtm_spec(filename = "~/study/study_sdtm_spec.csv")
+sdtm_spec <- read_sdtm_spec(filename = "~/study/study_sdtm_spec.csv")
 
 study_ct <- read_study_ct(filename = "~/study/study_sdtm_ct.csv")
 
 # Read in raw data
 
-MD1 <- read_raw_data_csv(filename = "~/study/MD1.csv") |>
+md1 <- read_raw_data_csv(filename = "~/study/MD1.csv") |>
   # Derive oak_id_vars
   derive_oak_id_vars()
 

diff --git a/man/sdtm.oak-package.Rd b/man/sdtm.oak-package.Rd
diff --git a/vignettes/articles/algorithms.Rmd b/vignettes/articles/algorithms.Rmd
@@ -186,7 +186,8 @@ algorithms <- data.frame(
     ),
     paste("AE = 'Adverse Events' on early phase SAE form"),
     paste("EC = 'Exposure as Collected'")
-  )
+  ),
+  stringsAsFactors = TRUE
 )
 knitr::kable(algorithms)
 ```

diff --git a/vignettes/articles/study_sdtm_spec.Rmd b/vignettes/articles/study_sdtm_spec.Rmd
@@ -351,16 +351,8 @@ definition <- data.frame(
     "GROUP_BY",
     "ASSIGN_NO_CT",
     "ASSIGN_NO_CT"
-  )
-)
-# We do not want URLs to be activated since they are part of the longer API calls
-# and direct use is faulty.
-definition$Example_Values <- ifelse(
-  grepl("http", definition$Example_Values),
-  yes = paste0("`", definition$Example_Values, "`"),
-  no = definition$Example_Values
+  ),
+  stringsAsFactors = TRUE
 )
-
-knitr::kable(definition, col.names = gsub("_", " ", names(definition)))
+knitr::kable(definition)
 ```
-</div>