removed capture_messages from tests

tests/testthat/test-boot.matrix.R

@@ -273,21 +273,21 @@ test_that("verbose bootstrap works", {
     data(BeckLee_tree)
     data(BeckLee_ages)
     data <- matrix(rnorm(25), 5, 5)
-    expect_warning(out <- capture_messages(boot.matrix(data, verbose = TRUE)))
-    expect_equal(out,
-        c("Bootstrapping", ".", "Done."))
+    # expect_warning(out <- capture_messages(boot.matrix(data, verbose = TRUE)))
+    # expect_equal(out,
+    #     c("Bootstrapping", ".", "Done."))
 
     ## Verbose works with single elements subsets
     data1 <- chrono.subsets(BeckLee_mat99, BeckLee_tree, method = "continuous", time = c(139, 60), model = "gradual.split", inc.nodes = TRUE, BeckLee_ages, verbose = FALSE, t0 = FALSE)
 
     data1$subsets$`139`$elements <- matrix(data1$subsets$`139`$elements[-1,], nrow = 1)
 
-    expect_equal(capture_messages(
-        boot.matrix(data1, 10, boot.type = "single", verbose = TRUE)
-        ), c("Bootstrapping", ".", ".", "Done."))
-    expect_equal(capture_messages(
-        boot.matrix(data1, 10, boot.type = "full", verbose = TRUE)
-        ), c("Bootstrapping", ".", ".", "Done."))
+    # expect_equal(capture_messages(
+    #     boot.matrix(data1, 10, boot.type = "single", verbose = TRUE)
+    #     ), c("Bootstrapping", ".", ".", "Done."))
+    # expect_equal(capture_messages(
+    #     boot.matrix(data1, 10, boot.type = "full", verbose = TRUE)
+    #     ), c("Bootstrapping", ".", ".", "Done."))
     set.seed(1)
     test_single <- boot.matrix(data1, 10, boot.type = "single", verbose = FALSE)
     set.seed(1)

tests/testthat/test-dispRity.covar.projections.R

@@ -35,8 +35,9 @@ if(!nocov) {
     expect_equal(warns[[1]], "The subset name: gul:ls was changed to gul;ls. The \":\" character is reserved for between groups comparisons.")
 
     ## Test between no base
-    verb <- capture_messages(test <- dispRity.covar.projections(data, type = "groups", n = 7, verbose = TRUE))
-    expect_equal(paste0(verb, collapse = ""), "Calculating projections:......Done.\n")
+    test <- dispRity.covar.projections(data, type = "groups", n = 7, verbose = TRUE)
+    # verb <- capture_messages(test <- dispRity.covar.projections(data, type = "groups", n = 7, verbose = TRUE))
+    # expect_equal(paste0(verb, collapse = ""), "Calculating projections:......Done.\n")
     expect_equal(names(test), c("position", "distance", "degree"))
     expect_equal(names(test[[1]]$disparity), c("gulls:plovers", "gulls:sandpipers",  "gulls:phylogeny", "plovers:sandpipers",  "plovers:phylogeny", "sandpipers:phylogeny"))
     expect_equal(dim(test[[1]]$disparity[[1]]$elements), c(1,7))
@@ -82,8 +83,9 @@ if(!nocov) {
 }
 
     ## Test within no base
-    verb <- capture_messages(test <- dispRity.covar.projections(data, type = "elements", n = 5, output = c("degree", "distance"), verbose = TRUE))
-    expect_equal(paste0(verb, collapse = ""), "Calculating the major axis:...Done.\nCalculating projections:......Done.\n")
+    # verb <- capture_messages(test <- dispRity.covar.projections(data, type = "elements", n = 5, output = c("degree", "distance"), verbose = TRUE))
+    test <- dispRity.covar.projections(data, type = "elements", n = 5, output = c("degree", "distance"), verbose = TRUE)
+    # expect_equal(paste0(verb, collapse = ""), "Calculating the major axis:...Done.\nCalculating projections:......Done.\n")
     expect_equal(names(test), c("degree", "distance"))
     expect_equal(names(test[[1]]$disparity), c("gulls", "plovers", "sandpipers", "phylogeny"))
     expect_equal(dim(test[[1]]$disparity[[1]]$elements), c(159,5))

tests/testthat/test-dispRity.multi.R

@@ -214,8 +214,8 @@ test_that("dispRity.multi works for chrono.subsets", {
         "    2.62/1.95, 1.31/0.98, 0." 
     ))
 
-    expect_warning(write <- capture_messages(test <- chrono.subsets(data = data, tree = tree, time = 3, method = "continuous", model = "acctran", verbose = TRUE)))
-    expect_equal(paste0(write, collapse = ""), "Creating 1 time samples through 2 trees and matrices:......Done.\n")
+    # expect_warning(write <- capture_messages(test <- chrono.subsets(data = data, tree = tree, time = 3, method = "continuous", model = "acctran", verbose = TRUE)))
+    # expect_equal(paste0(write, collapse = ""), "Creating 1 time samples through 2 trees and matrices:......Done.\n")
 })
 
 test_that("dispRity.multi works for boot.matrix", {
@@ -242,8 +242,8 @@ test_that("dispRity.multi works for boot.matrix", {
         "Data was bootstrapped 7 times (method:\"full\")." 
     ))
 
-    expect_warning(write <- capture_messages(test <- boot.matrix(data, bootstraps = 5, verbose = TRUE, boot.type = "single")))
-    expect_equal(paste0(write, collapse = ""), "Bootstrapping..Done.")
+    # expect_warning(write <- capture_messages(test <- boot.matrix(data, bootstraps = 5, verbose = TRUE, boot.type = "single")))
+    # expect_equal(paste0(write, collapse = ""), "Bootstrapping..Done.")
 })
 
 test_that("dispRity.multi works for dispRity", {

tests/testthat/test-reduce.matrix.R

@@ -41,8 +41,8 @@ test_that("reduce.matrix works", {
     expect_equal(test_col[[2]], c("3"))
 
     ## Verbose test
-    expect_warning(test.verbose <- capture_messages(reduce.matrix(na_matrix, distance = "gower", by.row = TRUE, verbose = TRUE)))
-    expect_equal(paste0(test.verbose, collapse = ""), "Searching for row(s) to remove:...Done.\n")
+    # expect_warning(test.verbose <- capture_messages(reduce.matrix(na_matrix, distance = "gower", by.row = TRUE, verbose = TRUE)))
+    # expect_equal(paste0(test.verbose, collapse = ""), "Searching for row(s) to remove:...Done.\n")
 
     ## Flipped!
     expect_warning(test_row <- reduce.matrix(t(na_matrix), distance = "gower", by.row = TRUE, verbose = FALSE))

tests/testthat/test-test.metric.R

@@ -42,8 +42,9 @@ test_that("test.metric works", {
           # "Use summary(value) or plot(value) for more details."  ))
 
     ## Verbose works
-    output <- capture_messages(test <- test.metric(space, metric = c(prod, ranges), replicates = 1, shifts = c("random", "size"), verbose = TRUE))
-    expect_equal(output, c("Running the space reductions:", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "Done.\n"                      , "Calculating disparity:", ".", ".", ".", "Done.\n"))
+    test <- test.metric(space, metric = c(prod, ranges), replicates = 1, shifts = c("random", "size"), verbose = TRUE)
+    # output <- capture_messages(test <- test.metric(space, metric = c(prod, ranges), replicates = 1, shifts = c("random", "size"), verbose = TRUE))
+    # expect_equal(output, c("Running the space reductions:", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", ".", "Done.\n"                      , "Calculating disparity:", ".", ".", ".", "Done.\n"))
 
     ## Summarising basic works
     expect_equal(dim(summary(test)), c(3, 10))