WIP 771 fix failed pipelines (#789)

Fixes #771 - revdepcheck 🆗 https://github.com/insightsengineering/teal.modules.general/actions/runs/11162906687 - rhub 🌮 WIP https://github.com/insightsengineering/teal.modules.general/actions/runs/11211837075/job/31161572229 This fixes R-hub and revdepcheck checks
insightsengineering · Oct 7, 2024 · d9fd08b · d9fd08b
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Showing 12 changed files with 41 additions and 26 deletions.
diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
@@ -56,6 +56,19 @@ jobs:
       )
     name: revdepcheck ↩️
     uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
+    with:
+      lookup-refs: |
+        insightsengineering/roxy.shinylive
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/tern
+        insightsengineering/rtables
   rhub:
     if: >
       github.event_name == 'schedule' || (
@@ -66,10 +79,12 @@ jobs:
     uses: insightsengineering/r.pkg.template/.github/workflows/rhub.yaml@main
     with:
       lookup-refs: |
+        insightsengineering/roxy.shinylive
         insightsengineering/teal
         insightsengineering/teal.transform
         insightsengineering/teal.code
         insightsengineering/teal.data
+        insightsengineering/teal.slice
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -81,7 +81,7 @@ Suggests:
 VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
-    rstudio/shiny, insightsengineering/teal,
+    rstudio/shiny, insightsengineering/teal, 
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
     rstudio/DT, tidyverse/forcats, r-lib/scales, daattali/shinyjs,
     shinyTree/shinyTree, rstudio/shinyvalidate, dreamRs/shinyWidgets,

diff --git a/vignettes/teal-modules-general.Rmd b/vignettes/teal-modules-general.Rmd
@@ -39,7 +39,7 @@ See [package functions / modules](https://insightsengineering.github.io/teal.mod
 ### Example application
 
 A simple application featuring the `tm_variable_browser()` module:
-```{r app, message = FALSE, results = "hide"}
+```{r app, message = FALSE, results = "hide", eval = requireNamespace("sparkline", quietly = TRUE)}
 # load libraries
 library(teal.modules.general)
 library(teal.widgets)
@@ -78,7 +78,7 @@ shinyApp(app$ui, app$server)
 
 ### Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("app"),
   knitr::knit_code$get("shinyapp")
@@ -88,7 +88,7 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
 
@@ -146,7 +146,7 @@ In a `teal` app, data and modules are decoupled. In the app above:
 - The app developer specified the module and assigned it to the `modules` argument.
 - The `init` function took these arguments and returned a list containing `ui` and `server` object, which can be demonstrated by running:
 
-```{r, indent = "     "}
+```{r, indent = "     ", eval = requireNamespace("sparkline", quietly = TRUE)}
 class(app)
 names(app)
 ```

diff --git a/vignettes/using-association-plot.Rmd b/vignettes/using-association-plot.Rmd
@@ -304,7 +304,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -316,6 +316,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-bivariate-plot.Rmd b/vignettes/using-bivariate-plot.Rmd
@@ -630,7 +630,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -642,6 +642,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-cross-table.Rmd b/vignettes/using-cross-table.Rmd
@@ -147,7 +147,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -159,6 +159,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-data-table.Rmd b/vignettes/using-data-table.Rmd
@@ -117,7 +117,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -129,6 +129,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-outliers-module.Rmd b/vignettes/using-outliers-module.Rmd
@@ -198,7 +198,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -210,6 +210,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-regression-plots.Rmd b/vignettes/using-regression-plots.Rmd
@@ -277,7 +277,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -289,6 +289,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-response-plot.Rmd b/vignettes/using-response-plot.Rmd
@@ -386,7 +386,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -398,6 +398,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-scatterplot-matrix.Rmd b/vignettes/using-scatterplot-matrix.Rmd
@@ -165,7 +165,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -177,6 +177,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```
diff --git a/vignettes/using-scatterplot.Rmd b/vignettes/using-scatterplot.Rmd
@@ -21,7 +21,7 @@ various types of datasets using the scatter plot module `tm_g_scatterplot()`:
 
 ## 1 - Load libraries
 
-```{r library, echo=TRUE, message=FALSE, warning=FALSE, results="hide"}
+```{r library, echo=TRUE, message=FALSE, warning=FALSE, results="hide", eval = requireNamespace("ggpmics") && requireNamespace("ggExtra") && requireNamespace("colourpicker")}
 library(teal.modules.general) # used to create the app
 library(dplyr) # used to modify data sets
 library(ggpmisc)
@@ -38,7 +38,7 @@ Inside this app 4 datasets will be used
 3. `ADTTE` A long data set with time to event data
 4. `ADLB` A long data set with lab measurements for each subject
 
-```{r data, echo=TRUE, message=FALSE, warning=FALSE, results="hide"}
+```{r data, echo=TRUE, message=FALSE, warning=FALSE, results="hide", eval = requireNamespace("ggpmics") && requireNamespace("ggExtra") && requireNamespace("colourpicker")}
 data <- teal_data()
 data <- within(data, {
   ADSL <- teal.modules.general::rADSL %>%
@@ -64,7 +64,7 @@ create an app. The data will be handed over using `teal.data::teal_data()`. The
 itself will be constructed by multiple calls of `tm_g_scatterplot()` using different
 combinations of data sets.
 
-```{r app, echo=TRUE, message=FALSE, warning=FALSE, results="hide"}
+```{r app, echo=TRUE, message=FALSE, warning=FALSE, results="hide", eval = requireNamespace("ggpmics") && requireNamespace("ggExtra") && requireNamespace("colourpicker")}
 # configuration for the single wide datasets
 mod1 <- tm_g_scatterplot(
   label = "Single wide dataset",
@@ -381,7 +381,7 @@ shinyApp(app$ui, app$server, options = list(height = 1024, width = 1024))
 
 ## 5 - Try it out in Shinylive
 
-```{r shinylive_url, echo = FALSE, results = 'asis'}
+```{r shinylive_url, echo = FALSE, results = 'asis', eval = requireNamespace("roxy.shinylive", quietly = TRUE)}
 code <- paste0(c(
   knitr::knit_code$get("library"),
   knitr::knit_code$get("data"),
@@ -393,6 +393,6 @@ url <- roxy.shinylive::create_shinylive_url(code)
 cat(sprintf("[Open in Shinylive](%s)\n\n", url))
 ```
 
-```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
+```{r shinylive_iframe, echo = FALSE, out.width = '150%', out.extra = 'style = "position: relative; z-index:1"', eval = requireNamespace("roxy.shinylive", quietly = TRUE) && knitr::is_html_output() && identical(Sys.getenv("IN_PKGDOWN"), "true")}
 knitr::include_url(url, height = "800px")
 ```