Address issues related to testing with shinytest2 the examples (#1423)

# Pull Request

Attempts to fix
insightsengineering/coredev-tasks#536 on this
package.

1. system.file don't raise an error (but I need to check if it is empty
or it reports useful info).
2. When there is an error on a shiny session the test of the example
fails.
3. Many modules missed some package prefix or loaded (modules failed).  
4. Stop using `load_all` inside test-examples.
5. Checks all examples due to upstream issues being fixed since last
year.


For testing 2 create a new file and add a new file and document to add
this example:

```
#' Example failing
#' @export
#' @examples
#' app <- init(
#' data = teal_data(
#'   new_iris = transform(iris, id = seq_len(nrow(iris))),
#'   new_mtcars = transform(mtcars, id = seq_len(nrow(mtcars)))
#' ),
#' modules = modules(
#'   module(
#'     "Iris Sepal.Length histogram",
#'     server = function(input, output, session, data) {
#'       stop("yada") # 🔍 this will fail the app
#'     },
#'     ui = function(id, ...) {
#'       ns <- NS(id)
#'       plotOutput(ns("hist"))
#'     },
#'     datanames = "new_iris"
#'   )
#' )
#' )
#' if (interactive()) {
#'   shinyApp(app$ui, app$server)
#' }
module_error <- function() {}
```

Then for all check with `R CMD check` or `devtools::test(filter =
"examples")` from plain R session.

-------

Rstudio reports an error on some examples: 

```
  Error in .Call("rs_enqueClientEvent", type, data, PACKAGE = "(embedding)") : 
    "rs_enqueClientEvent" not available for .Call() for package "(embedding)"
```

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

Author: llrs-roche

R/tm_a_gee.R

@@ -165,10 +165,11 @@ template_a_gee <- function(output_table,
 #' {{ next_example }}
 #'
 #' @examples
-#' library(dplyr)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl
 #'   ADQS <- tmc_ex_adqs %>%
 #'     filter(ABLFL != "Y" & ABLFL2 != "Y") %>%

R/tm_a_mmrm.R

@@ -499,7 +499,6 @@ template_mmrm_plots <- function(fit_name,
 #' {{ next_example }}
 #'
 #' @examples
-#' library(dplyr)
 #'
 #' arm_ref_comp <- list(
 #'   ARMCD = list(
@@ -510,6 +509,8 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl
 #'   ADQS <- tmc_ex_adqs %>%
 #'     filter(ABLFL != "Y" & ABLFL2 != "Y") %>%

R/tm_g_barchart_simple.R

@@ -47,10 +47,12 @@
 #'
 #' @examples
 #' library(nestcolor)
-#' library(dplyr)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(formatters)
+#'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl %>%
 #'     mutate(ITTFL = factor("Y") %>%
 #'       with_label("Intent-To-Treat Population Flag"))

R/tm_g_ci.R

@@ -223,6 +223,8 @@ template_g_ci <- function(dataname,
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl
 #'   ADLB <- tmc_ex_adlb
 #' })
@@ -454,8 +456,7 @@ srv_g_ci <- function(id,
     )
 
     anl_q <- reactive({
-      data() %>%
-        teal.code::eval_code(as.expression(anl_inputs()$expr))
+      teal.code::eval_code(data(), as.expression(anl_inputs()$expr))
     })
 
     all_q <- reactive({

R/tm_g_forest_rsp.R

@@ -267,10 +267,12 @@ template_forest_rsp <- function(dataname = "ANL",
 #'
 #' @examples
 #' library(nestcolor)
-#' library(dplyr)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(formatters)
+#'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl
 #'   ADRS <- tmc_ex_adrs %>%
 #'     mutate(AVALC = d_onco_rsp_label(AVALC) %>%

R/tm_g_forest_tte.R

@@ -268,10 +268,12 @@ template_forest_tte <- function(dataname = "ANL",
 #'
 #' @examples
 #' library(nestcolor)
-#' library(dplyr)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(formatters)
+#'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl
 #'   ADTTE <- tmc_ex_adtte
 #'   ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")

R/tm_g_ipp.R

@@ -41,7 +41,6 @@ template_g_ipp <- function(dataname = "ANL",
                            ggplot2_args = teal.widgets::ggplot2_args(),
                            suppress_legend = FALSE,
                            add_avalu = TRUE) {
-
   checkmate::assert_string(dataname)
   checkmate::assert_string(paramcd)
   checkmate::assert_string(arm_var)
@@ -204,17 +203,18 @@ template_g_ipp <- function(dataname = "ANL",
 #'
 #' @examples
 #' library(nestcolor)
-#' library(dplyr)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(tern)
 #'   library(dplyr)
 #'   ADSL <- tmc_ex_adsl %>%
 #'     slice(1:20) %>%
-#'     tern::df_explicit_na()
+#'     df_explicit_na()
 #'   ADLB <- tmc_ex_adlb %>%
 #'     filter(USUBJID %in% ADSL$USUBJID) %>%
-#'     tern::df_explicit_na() %>%
+#'     df_explicit_na() %>%
 #'     filter(AVISIT != "SCREENING")
 #' })
 #' join_keys(data) <- default_cdisc_join_keys[names(data)]

R/tm_g_km.R

@@ -291,6 +291,8 @@ template_g_km <- function(dataname = "ANL",
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(dplyr)
+#'   library(teal.modules.clinical)
 #'   ADSL <- tmc_ex_adsl
 #'   ADTTE <- tmc_ex_adtte
 #' })

R/tm_g_lineplot.R

@@ -40,7 +40,6 @@ template_g_lineplot <- function(dataname = "ANL",
                                 title = "Line Plot",
                                 y_lab = "",
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-
   checkmate::assert_string(dataname)
   checkmate::assert_string(group_var)
   checkmate::assert_string(x)
@@ -237,11 +236,12 @@ template_g_lineplot <- function(dataname = "ANL",
 #'
 #' @examples
 #' library(nestcolor)
-#' library(dplyr)
-#' library(forcats)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(dplyr)
+#'   library(forcats)
 #'   ADSL <- tmc_ex_adsl
 #'   ADLB <- tmc_ex_adlb %>%
 #'     mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))

R/tm_g_pp_adverse_events.R

@@ -209,13 +209,13 @@ template_adverse_events <- function(dataname = "ANL",
 #'
 #' @examples
 #' library(nestcolor)
-#' library(dplyr)
 #'
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(teal.modules.clinical)
+#'   library(dplyr)
 #'   ADAE <- tmc_ex_adae
-#'   ADSL <- tmc_ex_adsl %>%
-#'     filter(USUBJID %in% ADAE$USUBJID)
+#'   ADSL <- filter(tmc_ex_adsl, USUBJID %in% ADAE$USUBJID)
 #' })
 #' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'