Fix broken pipelines (#280)

Fix #279

---------

Signed-off-by: Marcin <133694481+m7pr@users.noreply.github.com>
Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Co-authored-by: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>

.github/workflows/scheduled.yaml

@@ -83,6 +83,7 @@ jobs:
         insightsengineering/teal.transform
         insightsengineering/formatters
         insightsengineering/teal.code
+        insightsengineering/teal.slice
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets

DESCRIPTION

@@ -34,6 +34,7 @@ Imports:
     lifecycle (>= 0.2.0),
     shinyvalidate,
     teal.code (>= 0.4.1.9009),
+    teal.data (>= 0.3.0.9018),
     teal.logger (>= 0.2.0.9004),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
@@ -42,9 +43,7 @@ Imports:
 Suggests:
     knitr (>= 1.42),
     logger (>= 0.2.2),
-    nestcolor (>= 0.1.0),
     rmarkdown (>= 2.23),
-    teal.data (>= 0.3.0.9018),
     testthat (>= 3.1.5),
     withr (>= 2.0.0)
 Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny,
@@ -54,9 +53,8 @@ Config/Needs/verdepcheck: insightsengineering/osprey, rstudio/shiny,
     rstudio/shinyvalidate, insightsengineering/teal.code,
     insightsengineering/teal.logger, insightsengineering/teal.reporter,
     insightsengineering/teal.widgets, insightsengineering/tern,
-    tidyverse/tidyr, yihui/knitr, insightsengineering/nestcolor,
-    rstudio/rmarkdown, insightsengineering/teal.data, r-lib/testthat,
-    r-lib/withr
+    tidyverse/tidyr, yihui/knitr, rstudio/rmarkdown, 
+    insightsengineering/teal.data, r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US

NEWS.md

@@ -1,6 +1,8 @@
 # teal.osprey 0.1.16.9028
 
 * Removed `Show Warnings` modals from modules.
+* Moved `teal.data` from `Suggests` to `Imports`. 
+* Changed examples from `cdisc_data()` to `teal_data()`.
 
 ### Breaking Changes
 * Adapted all modules to use `teal_data` objects.

R/tm_g_ae_oview.R

@@ -16,9 +16,8 @@
 #' @export
 #'
 #' @examples
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
-#'     library(nestcolor)
 #'     ADSL <- rADSL
 #'     ADAE <- rADAE
 #'     add_event_flags <- function(dat) {

R/tm_g_ae_sub.R

@@ -18,7 +18,7 @@
 #'
 #' @examples
 #' # Example using stream (ADaM) dataset
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
 #'     ADSL <- rADSL
 #'     ADAE <- rADAE

R/tm_g_butterfly.R

@@ -41,10 +41,9 @@
 #'
 #' @examples
 #' # Example using stream (ADaM) dataset
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
 #'     library(dplyr)
-#'     library(nestcolor)
 #'     set.seed(23)
 #'     ADSL <- rADSL
 #'     ADAE <- rADAE

R/tm_g_events_term_id.R

@@ -18,9 +18,8 @@
 #' @author Molly He (hey59) \email{hey59@gene.com}
 #'
 #' @examples
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
-#'     library(nestcolor)
 #'     ADSL <- rADSL
 #'     ADAE <- rADAE
 #'   })

R/tm_g_heat_bygrade.R

@@ -34,10 +34,9 @@
 #' @export
 #'
 #' @examples
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
 #'     library(dplyr)
-#'     library(nestcolor)
 #'     ADSL <- rADSL %>% slice(1:30)
 #'     ADEX <- rADEX %>% filter(USUBJID %in% ADSL$USUBJID)
 #'     ADAE <- rADAE %>% filter(USUBJID %in% ADSL$USUBJID)

R/tm_g_patient_profile.R

@@ -60,9 +60,8 @@
 #' @export
 #'
 #' @examples
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
-#'     library(nestcolor)
 #'     ADSL <- rADSL
 #'     ADAE <- rADAE %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM))
 #'     ADCM <- rADCM %>% mutate(ASTDT = as.Date(ASTDTM), AENDT = as.Date(AENDTM))

R/tm_g_spiderplot.R

@@ -26,9 +26,8 @@
 #'
 #' @examples
 #' # Example using stream (ADaM) dataset
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
-#'     library(nestcolor)
 #'     ADSL <- rADSL
 #'     ADTR <- rADTR
 #'   })

R/tm_g_swimlane.R

@@ -36,17 +36,18 @@
 #'
 #' @examples
 #' # Example using stream (ADaM) dataset
-#' data <- cdisc_data() |>
-#'   within(library(dplyr)) |>
-#'   within(library(nestcolor)) |>
-#'   within(ADSL <- rADSL %>%
-#'     mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
-#'     filter(STRATA1 == "A" & ARMCD == "ARM A")) |>
-#'   within(ADRS <- rADRS %>%
-#'     filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
-#'     mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
-#'     rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
-#'     arrange(USUBJID))
+#' data <- teal_data() |>
+#'   within({
+#'     library(dplyr)
+#'     ADSL <- rADSL %>%
+#'       mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
+#'       filter(STRATA1 == "A" & ARMCD == "ARM A")
+#'     ADRS <- rADRS %>%
+#'       filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
+#'       mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
+#'       rbind(rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
+#'       arrange(USUBJID)
+#'   })
 #'
 #' datanames(data) <- c("ADSL", "ADRS")
 #' join_keys(data) <- default_cdisc_join_keys[datanames(data)]

R/tm_g_waterfall.R

@@ -47,9 +47,8 @@
 #' @author houx14 \email{houx14@gene.com}
 #'
 #' @examples
-#' data <- cdisc_data() |>
+#' data <- teal_data() |>
 #'   within({
-#'     library(nestcolor)
 #'     ADSL <- rADSL
 #'     ADRS <- rADRS
 #'     ADTR <- rADTR

staged_dependencies.yaml

@@ -33,7 +33,4 @@ upstream_repos:
   insightsengineering/formatters:
     repo: insightsengineering/formatters
     host: https://github.com
-  insightsengineering/nestcolor:
-    repo: insightsengineering/nestcolor
-    host: https://github.com
 downstream_repos: