refactor: remove fs dependency - file_exists with file.exists

DESCRIPTION

@@ -21,7 +21,6 @@ LinkingTo:
 Imports:
     Rcpp,
     Matrix,
-    fs,
     data.table,
     parallelly
 Suggests:

NAMESPACE

@@ -10,6 +10,5 @@ export(region_map)
 export(set_log_level)
 export(set_threads)
 importFrom(Rcpp,sourceCpp)
-importFrom(fs,file_exists)
 importFrom(parallelly,availableCores)
 useDynLib(iscream, .registration = TRUE)

R/query_all.R

@@ -12,7 +12,6 @@
 #' ("dgCMatrix"). Set this `TRUE` only for scWGBS data
 #' @param nthreads Set number of threads to use overriding the
 #' `"iscream.threads"` option. See `?set_threads` for more information.
-#' @importFrom fs file_exists
 #' @return A named list of
 #' - M and coverage matrices
 #' - a character vector of chromosomes and numeric vector of corresponding CpG

R/region_map.R

@@ -23,7 +23,6 @@
 #' `mval =` FALSE and aggregated M values if `mval =` TRUE
 #' - `"average"` averages the values in the region with average beta values if
 #' `mval =` FALSE and average M values if `mval =` TRUE
-#' @importFrom fs file_exists
 #' @return A data.frame
 #'
 #' @export

R/verify_files.R

@@ -2,13 +2,12 @@
 #'
 #' @param files_vec A vector of file paths
 #' @param error_file_prefix Error message prefix for 'Bedfile' vs 'Tabix file'
-#' @importFrom fs file_exists
 #' @return TRUE if all input bedfiles have an associated tabix index file.
 #' FALSE if not
 #'
 #' @keywords internal
 check_files_exist <- function(files_vec, error_file_prefix = "Bedfile") {
-  valid_files <- file_exists(files_vec)
+  valid_files <- file.exists(files_vec)
   missing_files <- files_vec[!valid_files]
   if (length(missing_files != 0)) {
     stop(paste0(error_file_prefix, ": ", missing_files, " could not be found\n"))
@@ -19,7 +18,6 @@ check_files_exist <- function(files_vec, error_file_prefix = "Bedfile") {
 #'
 #' @param bedfiles A vector of bedfile paths
 #' @param verify_tabix Whether to verify the presence of tabix files
-#' @importFrom fs file_exists
 #' @return TRUE if all input bedfiles have an associated tabix index file.
 #' FALSE if not
 #'

tests/testthat/test-region_map.R

@@ -1,12 +1,11 @@
-library(fs)
 extdata <- system.file("extdata", package = "iscream")
 bedfiles <- list.files(extdata, pattern = "[a|b|c|d].bed.gz$", full.names = TRUE)
 regions <- c("chr1:1-6", "chr1:7-10", "chr1:11-14")
 
-m_agg <- read.csv(path(extdata, "region_map_m_agg.test"))
-m_ave <- read.csv(path(extdata, "region_map_m_ave.test"))
-beta_ave <- read.csv(path(extdata, "region_map_beta_ave.test"))
-beta_agg <- read.csv(path(extdata, "region_map_beta_agg.test"))
+m_agg <- read.csv(file.path(extdata, "region_map_m_agg.test"))
+m_ave <- read.csv(file.path(extdata, "region_map_m_ave.test"))
+beta_ave <- read.csv(file.path(extdata, "region_map_beta_ave.test"))
+beta_agg <- read.csv(file.path(extdata, "region_map_beta_agg.test"))
 
 test_that("region_map 1 thread", {
   expect_equal(