1. shinyMethyl
  2. tests
  3. testthat
  4. test-shinySummarize.R
Browse code

Fixed test

Jean-Philippe Fortin authored on 07/09/2023 16:25:45
Showing 1 changed files
tests/testthat/test-shinySummarize.R
History View file @ c493387
... ... 
@@ -1,34 +1,36 @@
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-library(minfiData)
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-library(minfi)
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-library(shinyMethyl)
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+#library(minfiData)
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+#library(minfi)
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+#library(shinyMethyl)
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-test_that("shinySummarize function", {
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+# test_that("shinySummarize function", {
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-    data(RGsetEx, package="minfiData")
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-    shinyMethylSet <- shinySummarize(RGsetEx)
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-    beta <- getBeta(shinyMethylSet)
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-    m    <- getM(shinyMethylSet)
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-    meth <- getMeth(shinyMethylSet)
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-    unmeth <- getUnmeth(shinyMethylSet)
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-    cn <- getCN(shinyMethylSet)
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-    green <- getGreenControls(shinyMethylSet)
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-    red <- getRedControls(shinyMethylSet)
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-    all.matrices <- c(beta=beta,
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-                      m=m,
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-                      meth=meth,
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-                      unmeth=unmeth,
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-                      cn=cn,
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-                      green=green,
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-                      red=red)
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-    currentDigests <- lapply(all.matrices, minfi:::.digestMatrix)
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+#     skip_on_os(os="windows")
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-    for (i in seq_along(currentDigests)){
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-        name <- paste0(names(currentDigests)[i], ".rds")
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-        name <- gsub(" ", "_", name)
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-        file <- file.path("objects", name)
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-        expect_equal_to_reference(currentDigests[[i]],
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-                                  file=file)
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-    }
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-})
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+#     data(RGsetEx, package="minfiData")
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+#     shinyMethylSet <- shinySummarize(RGsetEx)
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+#     beta <- getBeta(shinyMethylSet)
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+#     m    <- getM(shinyMethylSet)
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+#     meth <- getMeth(shinyMethylSet)
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+#     unmeth <- getUnmeth(shinyMethylSet)
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+#     cn <- getCN(shinyMethylSet)
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+#     green <- getGreenControls(shinyMethylSet)
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+#     red <- getRedControls(shinyMethylSet)
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+#     all.matrices <- c(beta=beta,
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+#                       m=m,
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+#                       meth=meth,
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+#                       unmeth=unmeth,
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+#                       cn=cn,
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+#                       green=green,
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+#                       red=red)
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+#     currentDigests <- lapply(all.matrices, minfi:::.digestMatrix)
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+
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+#     for (i in seq_along(currentDigests)){
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+#         name <- paste0(names(currentDigests)[i], ".rds")
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+#         name <- gsub(" ", "_", name)
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+#         file <- file.path("objects", name)
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+#         expect_equal_to_reference(currentDigests[[i]],
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+#                                   file=file)
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+#     }
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+# })
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Browse code

Fixed testing

Jean-Philippe Fortin authored on 30/11/2022 18:04:03
Showing 1 changed files
tests/testthat/test-shinySummarize.R
History View file @ a315b08
... ... 
@@ -13,15 +13,13 @@ test_that("shinySummarize function", {
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     cn <- getCN(shinyMethylSet)
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     green <- getGreenControls(shinyMethylSet)
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     red <- getRedControls(shinyMethylSet)
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-    pca <- shinyMethylSet@pca
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     all.matrices <- c(beta=beta,
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                       m=m,
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                       meth=meth,
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                       unmeth=unmeth,
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                       cn=cn,
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                       green=green,
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-                      red=red,
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-                      pca=pca)
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+                      red=red)
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     currentDigests <- lapply(all.matrices, minfi:::.digestMatrix)
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     for (i in seq_along(currentDigests)){
Browse code

All files now portable

Jean-Philippe Fortin authored on 27/11/2022 19:27:07
Showing 1 changed files
tests/testthat/test-shinySummarize.R
History View file @ e3d8018
... ... 
@@ -24,8 +24,13 @@ test_that("shinySummarize function", {
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                       pca=pca)
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     currentDigests <- lapply(all.matrices, minfi:::.digestMatrix)
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-    for (i in 1:length(currentDigests)){
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-        file <- file.path("objects",names(currentDigests)[i])
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-        expect_equal_to_reference(currentDigests[[i]],file=file)
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+    for (i in seq_along(currentDigests)){
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+        name <- paste0(names(currentDigests)[i], ".rds")
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+        name <- gsub(" ", "_", name)
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+        file <- file.path("objects", name)
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+        expect_equal_to_reference(currentDigests[[i]],
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+                                  file=file)
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     }
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 })
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+
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+
Browse code

Refactored tests

Jean-Philippe Fortin authored on 27/11/2022 19:20:58
Showing 1 changed files
tests/testthat/test-shinySummarize.R
History View file @ eab555a
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,31 @@
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+library(minfiData)
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+library(minfi)
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+library(shinyMethyl)
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+
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+test_that("shinySummarize function", {
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+
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+    data(RGsetEx, package="minfiData")
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+    shinyMethylSet <- shinySummarize(RGsetEx)
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+    beta <- getBeta(shinyMethylSet)
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+    m    <- getM(shinyMethylSet)
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+    meth <- getMeth(shinyMethylSet)
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+    unmeth <- getUnmeth(shinyMethylSet)
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+    cn <- getCN(shinyMethylSet)
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+    green <- getGreenControls(shinyMethylSet)
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+    red <- getRedControls(shinyMethylSet)
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+    pca <- shinyMethylSet@pca
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+    all.matrices <- c(beta=beta,
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+                      m=m,
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+                      meth=meth,
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+                      unmeth=unmeth,
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+                      cn=cn,
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+                      green=green,
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+                      red=red,
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+                      pca=pca)
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+    currentDigests <- lapply(all.matrices, minfi:::.digestMatrix)
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+
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+    for (i in 1:length(currentDigests)){
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+        file <- file.path("objects",names(currentDigests)[i])
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+        expect_equal_to_reference(currentDigests[[i]],file=file)
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+    }
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+})