fix: remove cmdstanr:: from example, add skip guards for optional deps in tests

- Wrap TIGER example in dontrun and remove cmdstanr::cmdstan_path()
  call that was still triggering the undeclared import warning
- Update man/tiger.Rd to match
- Use data(skin, package='netZooR') in tests for robustness
- Add skip_if_not_installed() for edgeR and preprocessCore tests

Author: marouenbg

tests/testthat/test-yarn.R

@@ -97,55 +97,57 @@ test_that("checkMisAnnotation() returns coordinates without error", {
 # ---- Tests using the shipped skin dataset ----
 
 test_that("skin dataset loads and is an ExpressionSet", {
-  data(skin)
+  data(skin, package = "netZooR")
   expect_s4_class(skin, "ExpressionSet")
   expect_true(nrow(skin) > 0)
   expect_true(ncol(skin) > 0)
 })
 
 test_that("checkTissuesToMerge() works on skin data", {
-  data(skin)
+  data(skin, package = "netZooR")
   result <- checkTissuesToMerge(skin, "SMTS", "SMTSD", plotFlag = FALSE)
   expect_true(!is.null(result))
 })
 
 test_that("filterGenes() works on skin data", {
-  data(skin)
+  data(skin, package = "netZooR")
   filtered <- filterGenes(skin, labels = c("X", "Y", "MT"),
                           featureName = "chromosome_name")
   remaining <- Biobase::fData(filtered)[, "chromosome_name"]
   expect_true(!any(remaining %in% c("X", "Y", "MT")))
 })
 
 test_that("filterLowGenes() works on skin data", {
-  data(skin)
+  skip_if_not_installed("edgeR")
+  data(skin, package = "netZooR")
   filtered <- filterLowGenes(skin, "SMTSD")
   expect_true(nrow(filtered) <= nrow(skin))
 })
 
 test_that("filterMissingGenes() works on skin data", {
-  data(skin)
+  data(skin, package = "netZooR")
   filtered <- filterMissingGenes(skin)
   expect_s4_class(filtered, "ExpressionSet")
 })
 
 test_that("filterSamples() works on skin data", {
-  data(skin)
+  data(skin, package = "netZooR")
   filtered <- filterSamples(skin, ids = "Skin - Not Sun Exposed (Suprapubic)",
                             groups = "SMTSD")
   remaining <- Biobase::pData(filtered)[, "SMTSD"]
   expect_true(!any(remaining == "Skin - Not Sun Exposed (Suprapubic)"))
 })
 
 test_that("plotCMDS() works on skin data", {
-  data(skin)
+  data(skin, package = "netZooR")
   coords <- plotCMDS(skin, comp = 1:2, plotFlag = FALSE)
   expect_true(is.matrix(coords) || is.data.frame(coords))
   expect_equal(ncol(coords), 2)
 })
 
 test_that("normalizeTissueAware() works on skin data", {
-  data(skin)
+  skip_if_not_installed("preprocessCore")
+  data(skin, package = "netZooR")
   # Use a small subset for speed
   skinSub <- skin[1:100, ]
   normalized <- normalizeTissueAware(skinSub, "SMTSD",