Use system.file() for reading files in tests

trias-project · Feb 7, 2023 · 35b3b0f · 35b3b0f
1 parent fb016e4
commit 35b3b0f
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Showing 3 changed files with 22 additions and 12 deletions.
diff --git a/tests/testthat/test-output_apply_gam.R b/tests/testthat/test-output_apply_gam.R
@@ -25,17 +25,23 @@ df_bad <- data.frame(
 )
 
 df_bad_p_values_occupancy <- read.delim(
-  paste0(
-    "./data_test_output_apply_gam/",
-    "example_gam_taxonKey2876049_p-values_error.tsv"
+  file = system.file(
+    "tests",
+    "testthat",
+    "data_test_output_apply_gam",
+    "example_gam_taxonKey2876049_p-values_error.tsv",
+    package = "trias"
   ),
   sep = "\t"
 )
 
 df_bad_gam_not_perf <- read.delim(
-  paste0(
-    "./data_test_output_apply_gam/",
-    "example_gam_taxonKey2927530_no_gam.tsv"
+  system.file(
+    "tests",
+    "testthat",
+    "data_test_output_apply_gam",
+    "example_gam_taxonKey2927530_no_gam.tsv",
+    package = "trias"
   ),
   sep = "\t"
 )

diff --git a/tests/testthat/test-visualize_pathways_level1.R b/tests/testthat/test-visualize_pathways_level1.R
@@ -2,9 +2,11 @@ context("test_visualize_pathways_level1")
 
 # input df
 input_test_df <- read.delim(
-  paste0(
-    "./data_test_pathways/",
-    "input_data_pathways.tsv"
+  system.file("tests", 
+              "testthat", 
+              "data_test_pathways", 
+              "input_data_pathways.tsv",
+              package = "trias"
   ),
   sep = "\t",
   stringsAsFactors = FALSE

diff --git a/tests/testthat/test-visualize_pathways_level2.R b/tests/testthat/test-visualize_pathways_level2.R
@@ -2,9 +2,11 @@ context("test_visualize_pathways_level2")
 
 # input df
 input_test_df <- read.delim(
-  paste0(
-    "./data_test_pathways/",
-    "input_data_pathways.tsv"
+  system.file("tests", 
+              "testthat", 
+              "data_test_pathways", 
+              "input_data_pathways.tsv",
+              package = "trias"
   ),
   sep = "\t",
   stringsAsFactors = FALSE