Ensure that all system.file calls must work

Shians · Oct 10, 2024 · d06902a · d06902a
1 parent 5a411a6
commit d06902a
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Showing 15 changed files with 23 additions and 21 deletions.
diff --git a/R/NanoMethResults.R b/R/NanoMethResults.R
@@ -14,7 +14,7 @@
 #' @return a NanoMethResult object to be used with plotting functions
 #'
 #' @examples
-#' methy <- system.file(package = "NanoMethViz", "methy_subset.tsv.bgz")
+#' methy <- system.file(package = "NanoMethViz", "methy_subset.tsv.bgz", mustWork = FALSE)
 #' sample <- c(
 #'     "B6Cast_Prom_1_bl6",
 #'     "B6Cast_Prom_1_cast",

diff --git a/R/bsseq_to_edger.R b/R/bsseq_to_edger.R
@@ -8,7 +8,7 @@
 #' @export
 #'
 #' @examples
-#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz")
+#' methy <- system.file("methy_subset.tsv.bgz", package = "NanoMethViz", mustWork = FALSE)
 #' bsseq <- methy_to_bsseq(methy)
 #' edger_mat <- bsseq_to_edger(bsseq)
 bsseq_to_edger <- function(bsseq, regions = NULL) {

diff --git a/R/create_tabix_file.R b/R/create_tabix_file.R
@@ -11,7 +11,7 @@
 #' @export
 #' @examples
 #' methy_calls <- system.file(package = "NanoMethViz",
-#'     c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"))
+#'     c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"), mustWork = FALSE)
 #' temp_file <- paste0(tempfile(), ".tsv.bgz")
 #'
 #' create_tabix_file(methy_calls, temp_file)

diff --git a/R/get_cgi.R b/R/get_cgi.R
@@ -15,10 +15,10 @@ get_cgi <- function(genome) {
 
     rds_path <- switch(
         genome,
-        hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz"),
-        hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz"),
-        mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz"),
-        grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz")
+        hg19 = system.file("cgi_hg19.rds", package = "NanoMethViz", mustWork = FALSE),
+        hg38 = system.file("cgi_hg38.rds", package = "NanoMethViz", mustWork = FALSE),
+        mm10 = system.file("cgi_mm10.rds", package = "NanoMethViz", mustWork = FALSE),
+        grcm39 = system.file("cgi_GRCm39.rds", package = "NanoMethViz", mustWork = FALSE)
     )
 
     readRDS(rds_path)

diff --git a/R/modbam_to_tabix.R b/R/modbam_to_tabix.R
@@ -21,7 +21,8 @@
 #' mbr <- ModBamResult(
 #'     methy = ModBamFiles(
 #'         samples = "sample1",
-#'         paths = system.file("peg3.bam", package = "NanoMethViz")
+#'         paths = system.file("peg3.bam", package = "NanoMethViz",
+#'         mustWork = FALSE)
 #'     ),
 #'     samples = data.frame(
 #'         sample = "sample1",

diff --git a/R/utils.R b/R/utils.R
@@ -11,7 +11,7 @@
 #' @examples
 #' nmr <- load_example_nanomethresult()
 load_example_nanomethresult <- function() {
-    methy <- system.file(package = "NanoMethViz", "methy_subset.tsv.bgz")
+    methy <- system.file(package = "NanoMethViz", "methy_subset.tsv.bgz", mustWork = FALSE)
 
     sample <- c(
         "B6Cast_Prom_1_bl6",
@@ -51,7 +51,7 @@ load_example_nanomethresult <- function() {
 load_example_modbamresult <- function() {
     ModBamResult(
         methy = ModBamFiles(
-            paths = system.file(package = "NanoMethViz", "peg3.bam"),
+            paths = system.file(package = "NanoMethViz", "peg3.bam", mustWork = FALSE),
             samples = "sample1"
         ),
         samples = tibble::tibble(

diff --git a/man/NanoMethResult-class.Rd b/man/NanoMethResult-class.Rd
diff --git a/man/bsseq_to_edger.Rd b/man/bsseq_to_edger.Rd
diff --git a/man/create_tabix_file.Rd b/man/create_tabix_file.Rd
diff --git a/man/modbam_to_tabix.Rd b/man/modbam_to_tabix.Rd
diff --git a/tests/testthat/test-ModBamResults.R b/tests/testthat/test-ModBamResults.R
@@ -22,15 +22,15 @@ test_that("ModBamResults getters and setters work", {
 
     expect_error(
         ModBamFiles(
-            paths = system.file(package = "NanoMethViz", "missing.bam"),
+            paths = system.file(package = "NanoMethViz", "missing.bam", mustWork = FALSE),
             samples = "sample1"
         ),
         regex = "Path .+ does not exist"
     )
 
     expect_error(
         ModBamFiles(
-            paths = system.file(package = "NanoMethViz", "no_index.bam"),
+            paths = system.file(package = "NanoMethViz", "no_index.bam", mustWork = FALSE),
             samples = "sample1"
         ),
         regex = ".+ does not have bam index"

diff --git a/tests/testthat/test-modbam_to_tabix.R b/tests/testthat/test-modbam_to_tabix.R
@@ -3,7 +3,7 @@ test_that("Modbam to tabix conversion works", {
     mbr <- ModBamResult(
         methy = ModBamFiles(
             samples = "sample1",
-            paths = system.file("peg3.bam", package = "NanoMethViz")
+            paths = system.file("peg3.bam", package = "NanoMethViz", mustWork = FALSE)
         ),
         samples = data.frame(
             sample = "sample1",

diff --git a/tests/testthat/test-plot_basic.R b/tests/testthat/test-plot_basic.R
@@ -5,7 +5,7 @@ test_that("Plotting gene works", {
 
     mbr_lower <- load_example_modbamresult()
     methy(mbr_lower) <- ModBamFiles(
-        paths = system.file(package = "NanoMethViz", "peg3_lower_case.bam"),
+        paths = system.file(package = "NanoMethViz", "peg3_lower_case.bam", mustWork = FALSE),
         samples = "sample1"
     )
 

diff --git a/tests/testthat/test-query_methy.R b/tests/testthat/test-query_methy.R
@@ -61,7 +61,7 @@ test_that("Querying methylation works", {
     expect_true(length(methy_data_list) == 4)
 
     # test to make sure that reading from text connection works for methylation data
-    methy_data_with_inf <- readLines(system.file("methy_data_with_inf.tsv", package = "NanoMethViz"))
+    methy_data_with_inf <- readLines(system.file("methy_data_with_inf.tsv", package = "NanoMethViz", mustWork = FALSE))
     methy_data <- expect_no_warning(read_methy_lines(methy_data_with_inf))
     expect_equal(nrow(methy_data), length(methy_data_with_inf))
 

diff --git a/tests/testthat/test-tabix_utils.R b/tests/testthat/test-tabix_utils.R
@@ -1,7 +1,7 @@
 test_that("Importing nanopolish works", {
     # setup
     methy_calls <- system.file(package = "NanoMethViz",
-        c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"))
+        c("sample1_nanopolish.tsv.gz", "sample2_nanopolish.tsv.gz"), mustWork = FALSE)
     temp_file <- paste0(tempfile(), ".tsv.bgz")
     withr::defer(file.remove(temp_file))
 
@@ -13,7 +13,7 @@ test_that("Importing nanopolish works", {
 test_that("Importing megalodon works", {
     # setup
     methy_calls <- system.file(package = "NanoMethViz",
-       "megalodon_calls.txt.gz")
+       "megalodon_calls.txt.gz", mustWork = FALSE)
     temp_file <- paste0(tempfile(), ".tsv.bgz")
     withr::defer(file.remove(temp_file))