fix expect_error warning about the error class

tests/testthat/GatingHierarchy-testSuite.R

@@ -8,10 +8,10 @@ test_that(".isCompensated",
 test_that("getNodeInd ",{
 
       #invalid numeric indexing
-      expect_error(flowWorkspace:::.getNodeInd(gh, 2), "string")
+      expect_error(flowWorkspace:::.getNodeInd(gh, 2), "string", class = "Rcpp::not_compatible")
 
       #invalid node name
-      expect_error(flowWorkspace:::.getNodeInd(gh, "singlet"), "singlet not found")
+      expect_error(flowWorkspace:::.getNodeInd(gh, "singlet"), "singlet not found", class = "std::domain_error")
 
       #valid unique node name
       expect_equal(flowWorkspace:::.getNodeInd(gh, "singlets"), 3)
@@ -29,10 +29,10 @@ test_that("getNodeInd ",{
       expect_equal(flowWorkspace:::.getNodeInd(gh, "CD8/38- DR+"), 15)
 
       #non-unqiue partial path
-      expect_error(flowWorkspace:::.getNodeInd(gh, "/38- DR+"), "not found")
+      expect_error(flowWorkspace:::.getNodeInd(gh, "/38- DR+"), "not found", class = "std::domain_error")
 
       #non-unique node name indexing
-      expect_error(flowWorkspace:::.getNodeInd(gh, "38- DR+"), "is ambiguous within the gating tree")
+      expect_error(flowWorkspace:::.getNodeInd(gh, "38- DR+"), "is ambiguous within the gating tree", class = "std::domain_error")
 
       #dealing with root
       expect_equal(flowWorkspace:::.getNodeInd(gh, "/not debris"), 2)
@@ -214,9 +214,9 @@ test_that("gs_pop_get_parent",{
 
       expect_equal(gs_pop_get_parent(gh, "not debris/singlets"), "/not debris")
 
-      expect_error(gs_pop_get_parent(gh, "singlet"), "singlet not found")
+      expect_error(gs_pop_get_parent(gh, "singlet"), "singlet not found", class = "std::domain_error")
 
-      expect_error(gs_pop_get_parent(gh, "root"), "0 :parent not found!")
+      expect_error(gs_pop_get_parent(gh, "root"), "0 :parent not found!", class = "std::domain_error")
 
     })
 
@@ -228,9 +228,9 @@ test_that("gs_pop_get_children",{
       expect_equal(gs_pop_get_children(gh, "singlets"), "/not debris/singlets/CD3+")
 
 
-      expect_error(gs_pop_get_children(gh, "singlet"), "singlet not found")
+      expect_error(gs_pop_get_children(gh, "singlet"), "singlet not found", class = "std::domain_error")
 
-      expect_error(gs_pop_get_children(gh, "38- DR+"), "ambiguous")
+      expect_error(gs_pop_get_children(gh, "38- DR+"), "ambiguous", class = "std::domain_error")
 
       expect_equal(gs_pop_get_children(gh, "CD4/38- DR+"), character(0))
 
@@ -244,9 +244,9 @@ test_that("gs_pop_get_children",{
 
 test_that(".getPopStat",{
 
-      expect_error(flowWorkspace:::.getPopStat(gh, 3), "string")
+      expect_error(flowWorkspace:::.getPopStat(gh, 3), "string", class = "Rcpp::not_compatible")
 
-      expect_error(flowWorkspace:::.getPopStat(gh, "singlet"), "not found")
+      expect_error(flowWorkspace:::.getPopStat(gh, "singlet"), "not found", class = "std::domain_error")
 
       expect_equal(flowWorkspace:::.getPopStat(gh, "singlets"), list(openCyto = c(percent = 9.487789e-01, count = 8.702200e+04)
                                             , xml = c(percent = 9.488988e-01, count = 8.703300e+04)
@@ -270,7 +270,7 @@ test_that("gh_pop_get_proportion",{
 
       expect_equal(gh_pop_get_proportion(gh, "singlets", xml = TRUE), 0.9488988, tol = 1e-7)
 
-      expect_error(gh_pop_get_proportion(gh, "singlet"), "singlet not found")
+      expect_error(gh_pop_get_proportion(gh, "singlet"), "singlet not found", class = "std::domain_error")
     })      
 
 test_that("gh_pop_get_count",{
@@ -281,7 +281,7 @@ test_that("gh_pop_get_count",{
 
       expect_equal(gh_pop_get_stats(gh, "singlets", xml = TRUE)[[2]], 87033)
 
-      expect_error(gh_pop_get_stats(gh, "singlet"), "singlet not found")
+      expect_error(gh_pop_get_stats(gh, "singlet"), "singlet not found", class = "std::domain_error")
     })      
 
 

tests/testthat/GatingSetList-testSuite.R

@@ -14,7 +14,7 @@ test_that("GatingSetList constructor", {
       #different colnames
       chnnls <- colnames(gs_cyto_data(gs_clone))
       chnnls[1] <- "FSC-H" 
-      expect_error(colnames(gs_cyto_data(gs_clone)) <- chnnls, "already")
+      expect_error(colnames(gs_cyto_data(gs_clone)) <- chnnls, "already", class = "std::domain_error")
       chnnls[1] <- "F" 
       colnames(gs_cyto_data(gs_clone)) <- chnnls
       expect_error(GatingSetList(list(gs, gs_clone)), "colnames of flowSets don't match")
@@ -181,7 +181,7 @@ test_that("save_gslist /load_gslist", {
       expect_true(setequal(list.files(tmp), expectRes))
 
       # can't cp the h5 file to the dest tmp since it is already present
-      expect_error(save_gslist(gslist, tmp), regexp = "File exists")
+      expect_error(save_gslist(gslist, tmp), regexp = "File exists", class = "boost::filesystem::filesystem_error")
       # set cdf flag to skip h5
       expect_message(save_gslist(gslist, tmp, cdf = "skip"), regexp = "Done")
       expect_true(setequal(list.files(tmp), expectRes))

tests/testthat/cytoframe-suite.R

@@ -60,7 +60,7 @@ test_that("write permission", {
   rm(cf1)
   invisible(gc())
   cf2 <- load_cytoframe_from_h5(h5file)
-  expect_error(exprs(cf2)[1,1] <- 2, "read-only")
+  expect_error(exprs(cf2)[1,1] <- 2, "read-only", class = "std::domain_error")
   cf_unlock(cf2)
   exprs(cf2)[1,1] <- 2
   expect_equivalent(exprs(cf2)[1,1], 2)
@@ -87,8 +87,8 @@ test_that("lock", {
   expect_equivalent(exprs(cf1)[1,1], 3)
   #lock it
   cf_lock(cf1)
-  expect_error(exprs(cf1)[1,1] <- 4, "read-only")
-  expect_error(keyword(cf1)[["TUBE NAME"]] <- "dd", "read-only")
+  expect_error(exprs(cf1)[1,1] <- 4, "read-only", class = "std::domain_error")
+  expect_error(keyword(cf1)[["TUBE NAME"]] <- "dd", "read-only", class = "std::domain_error")
   expect_equivalent(exprs(cf1)[1,1], 3)
   cf_unlock(cf1)
   exprs(cf1)[1,1] <- 4
@@ -134,8 +134,8 @@ test_that("exprs<-", {
   expect_true(all(exprs(cf1)[1:10, 1:10] == 0))
   expect_false(all(exprs(cf)[1:10, 1:10] == 0))
 
-  expect_error(exprs(cf1) <- exprs(cf1)[1:10, ] , "size")
-  expect_error(exprs(cf1) <- exprs(cf1)[, 1:2] , "size")
+  expect_error(exprs(cf1) <- exprs(cf1)[1:10, ] , "size", class = "std::domain_error")
+  expect_error(exprs(cf1) <- exprs(cf1)[, 1:2] , "size", class = "std::domain_error")
 
 })
 
@@ -169,7 +169,7 @@ test_that("colnames<-", {
       #TODO:change the order of colnames
       coln <- colnames(cf1)
       cf2 <- cf1[, coln[2:1]]
-      expect_error(colnames(cf2) <- newColNames, "colname already exists")
+      expect_error(colnames(cf2) <- newColNames, "colname already exists", class = "std::domain_error")
       cf_swap_colnames(cf2, "c1", "c2")
       expect_equivalent(unlist(keyword(cf2)[c("$P1N", "$P2N")]), rev(newColNames))
     })

tests/testthat/test-add.R

@@ -159,7 +159,7 @@ test_that("add factor vector", {
   expect_equal(gh_pop_get_count(gs[[1]], "clusterA_Q5"),0)
 
   expect_error(gs_pop_add(gs, fac.list, parent = "rectangle", name = "clusterA")
-               , "exist")
+               , "exist", class = "std::domain_error")
 
   #retrieve clustering results
   expect_error(gh_get_cluster_labels(gs[[1]], "rectangle", "cluster"), "No clustering results")

tests/testthat/test-archive.R

@@ -23,7 +23,7 @@ test_that("save GatingSet to archive",
       expect_that(gs, is_a("GatingSet"))
       expect_setequal(colnames(pData(gs)), colnames(pd))
       expect_message(save_gs(gs, path = tmp), "Done")
-      expect_error(save_gs(gs[1], path = tmp), "doesn't match")
+      expect_error(save_gs(gs[1], path = tmp), "doesn't match", class = "std::domain_error")
 
       cdf <- list.files(tmp, ".h5", full.names = TRUE)
       expect_equal(identifier(gs), id)
@@ -33,10 +33,10 @@ test_that("save GatingSet to archive",
       #restore id
       identifier(gs) <- id
       file.copy(cdf, file.path(tmp, "redundant.nc"))
-      expect_error(save_gs(gs, path = tmp), "Not a valid")
+      expect_error(save_gs(gs, path = tmp), "Not a valid", class = "std::domain_error")
 
-      expect_error(colnames(gs_cyto_data(gs))[1] <- "dd" , "read-only")
-      expect_error(exprs(get_cytoframe_from_cs(gs_cyto_data(gs), 1))[1,1] <- 0, "read-only")
+      expect_error(colnames(gs_cyto_data(gs))[1] <- "dd" , "read-only", class = "std::domain_error")
+      expect_error(exprs(get_cytoframe_from_cs(gs_cyto_data(gs), 1))[1,1] <- 0, "read-only", class = "std::domain_error")
 
     })
 ## it is placed here because trans may get cleared later on by cloning process

tests/testthat/test-compensate.R

@@ -22,11 +22,11 @@ test_that("compensate & transform a GatingSet", {
 
       # unmatched names
       names(comp)[1] <- "dd"
-      expect_error(compensate(gs, comp), regexp = "compensation not found")
+      expect_error(compensate(gs, comp), regexp = "compensation not found", class = "std::domain_error")
 
       #unmatched length
       comp <- comp[1:3]
-      expect_error(compensate(gs, comp), regexp = "compensation not found ")
+      expect_error(compensate(gs, comp), regexp = "compensation not found ", class = "std::domain_error")
 
       #modify comp[5]
       comp <- sapply(sampleNames(gs), function(sn)comp.mat, simplify = FALSE)

tests/testthat/test-cytoset.R

@@ -175,7 +175,7 @@ test_that("sampleNames<-", {
       is_equal_flowFrame(cs[sn][[1]], nc[[1]])
 
       newNames <- c("s2", "s2")
-      expect_error(sampleNames(nc) <- newNames, "exists")
+      expect_error(sampleNames(nc) <- newNames, "exists", class = "std::range_error")
 
       #replace the single subsetted fs
       nc <- nc["s2"]
@@ -203,7 +203,7 @@ test_that("colnames<-", {
       colnames(nc) <- newColNames
       newColNames <- rev(newColNames)
       expect_equivalent(unlist(keyword(nc[[1]])[c("$P1N", "$P2N")]), newColNames)
-      expect_error(colnames(nc) <- newColNames, "colname already exists")
+      expect_error(colnames(nc) <- newColNames, "colname already exists", class = "std::domain_error")
       cs_swap_colnames(nc, "c1", "c2")
       expect_equal(colnames(nc), newColNames)
 

tests/testthat/test-moveNode.R

@@ -8,10 +8,10 @@ test_that("gh_pop_move", {
   old.parent <- gs_pop_get_parent(gh, "CD4")
 
   new.parent <- "CD4"
-  expect_error(gh_pop_move(gh, "CD4", new.parent), "itself")
+  expect_error(gh_pop_move(gh, "CD4", new.parent), "itself", class = "std::domain_error")
 
   new.parent <- "CD4/CCR7- 45RA+"
-  expect_error(gh_pop_move(gh, "CD4", new.parent), "descendants")
+  expect_error(gh_pop_move(gh, "CD4", new.parent), "descendants", class = "std::domain_error")
 
   new.parent <- "singlets"
   suppressMessages(gh_pop_move(gh, "CD4", new.parent))