Fix example

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bedbaser
 Title: A BEDbase client
-Version: 0.99.15
+Version: 0.99.16
 Authors@R: c(
     person(
         given = "Jen",

R/bedbaser.R

@@ -41,7 +41,7 @@
 #' @examples
 #' api <- BEDbase(cache_path = tempdir())
 #' ex_bed <- bb_example(api, "bed")
-#' ex_bed_md <- bb_metadata(api, "bed")
+#' bb_metadata(api, ex_bed$id)
 #'
 #' @export
 BEDbase <- function(cache_path, quietly = FALSE) {
@@ -415,8 +415,7 @@ bb_to_granges <- function(
 #'
 #' @examples
 #' api <- BEDbase()
-#' id <- "lola_hg38_ucsc_features"
-#' bb_to_grangeslist(api, id)
+#' bb_to_grangeslist(api, "lola_hg38_ucsc_features")
 #'
 #' @export
 bb_to_grangeslist <- function(api, bedset_id, quietly = TRUE) {
@@ -444,8 +443,8 @@ bb_to_grangeslist <- function(api, bedset_id, quietly = TRUE) {
 #'
 #' @examples
 #' api <- BEDbase()
-#' ex <- bb_example(api, "bed")
-#' bb_save(api, ex$id, tempdir())
+#' ex_bed <- bb_example(api, "bed")
+#' bb_save(api, ex_bed$id, tempdir())
 #'
 #' @export
 bb_save <- function(

R/utils.R

@@ -36,15 +36,14 @@
 #' .get_file(md, tempdir(), "bed", "http")
 #'
 #' @noRd
-.get_file <- function(
-        metadata, cache_or_path, file_type = c("bed", "bigbed"),
-        access_type = c("s3", "http"), quietly = TRUE) {
+.get_file <- function(metadata, cache_or_path, file_type = c("bed", "bigbed"),
+    access_type = c("s3", "http"), quietly = TRUE) {
     file_details <- .format_metadata_files(metadata$files) |>
         dplyr::filter(
             name == paste(file_type, "file", sep = "_"),
             access_id == access_type
         )
-    if (is(cache_or_path, "BiocFileCache")) {
+    if (methods::is(cache_or_path, "BiocFileCache")) {
         cached_file <- .download_to_cache(
             metadata$id, file_details$url,
             cache_or_path, quietly
@@ -153,9 +152,8 @@
 #' .bed_file_to_granges(file_path, md)
 #'
 #' @noRd
-.bed_file_to_granges <- function(
-        file_path, metadata, extra_cols = NULL,
-        quietly = TRUE) {
+.bed_file_to_granges <- function(file_path, metadata, extra_cols = NULL,
+    quietly = TRUE) {
     args <- list(con = file_path)
     args["format"] <- gsub("peak", "Peak", metadata$bed_format)
     nums <- stringr::str_replace(metadata$bed_type, "bed", "") |>

tests/testthat/test-bedbaser.R

@@ -98,15 +98,15 @@ test_that("bb_to_granges returns a GRanges object given a 3+0 bed file", {
     md <- bb_metadata(api, id, TRUE)
     expect_equal("bed3+0", md$bed_type)
     gro <- bb_to_granges(api, id)
-    expect_true(is((gro)[1], "GRanges"))
+    expect_true(methods::is((gro)[1], "GRanges"))
 })
 
 test_that("bb_to_granges returns a GRanges object given a bigbed file", {
     api <- BEDbase(quietly = TRUE)
     id <- "ffc1e5ac45d923135500bdd825177356"
     if (.Platform$OS.type != "windows") {
         gro <- bb_to_granges(api, id, "bigbed")
-        expect_true(is((gro)[1], "GRanges"))
+        expect_true(methods::is((gro)[1], "GRanges"))
     } else {
         expect_warning(
             rlang::warn("This feature does not work on Windows."),
@@ -121,7 +121,7 @@ test_that("bb_to_granges returns a GRanges object given narrowpeak (6+4) file",
     md <- bb_metadata(api, id, TRUE)
     expect_equal("bed6+4", md$bed_type)
     gro <- bb_to_granges(api, id)
-    expect_true(is((gro)[1], "GRanges"))
+    expect_true(methods::is((gro)[1], "GRanges"))
     df <- as.data.frame(gro)
     expect_contains(
         c(
@@ -170,7 +170,7 @@ test_that("bb_to_granges allows passing extra_cols", {
 test_that("bb_to_grangeslist creates a GRangesList", {
     api <- BEDbase(quietly = TRUE)
     grl <- bb_to_grangeslist(api, "lola_hg38_ucsc_features")
-    expect_true(is((grl)[1], "CompressedGRangesList"))
+    expect_true(methods::is((grl)[1], "CompressedGRangesList"))
     expect_equal(11, length(grl))
 })
 

tests/testthat/test-utils.R

@@ -3,7 +3,7 @@ test_that(".format_metadata_files returns a tibble with a url column", {
     ex_bed <- bb_example(api, "bed")
     ex_md <- bb_metadata(api, ex_bed$id, TRUE)
     mdf <- .format_metadata_files(ex_md$files)
-    expect_true(is((mdf)[1], "tbl_df"))
+    expect_true(methods::is((mdf)[1], "tbl_df"))
     expect_true("url" %in% names(mdf))
 })