Error in `system2(cutadapt, args = "--version", stdout = TRUE, stderr = TRUE)`: '"/usr/bin/cutadapt"' not found

data_directory <- system.file("extdata", package = "demulticoder")
analysis_setup <- prepare_reads(data_directory, overwrite_existing = TRUE)
cut_trim(analysis_setup, cutadapt_path = "/usr/bin/cutadapt", overwrite_existing = TRUE)
final_asv_matrix <- list.files(analysis_setup$directory_paths$output_directory, pattern = "^final_asv_abundance_matrix_*\\.RData$", full.names = TRUE)
asvplots <- list.files(analysis_setup$directory_paths$output_directory, pattern = "^track_reads_*\\.RData$", full.names = TRUE)

test_that("make_asv_abund_matrix works correctly", {
data_directory <- system.file("extdata", package = "demulticoder")
analysis_setup <- prepare_reads(data_directory, overwrite_existing = TRUE)
cut_trim(analysis_setup, cutadapt_path = "/usr/bin/cutadapt", overwrite_existing = TRUE)
make_asv_abund_matrix(analysis_setup, overwrite_existing = TRUE)
rdata_files <- list.files(analysis_setup$directory_paths$temp_directory, pattern = "^asvabund_matrixDADA2_.*\\.RData$", full.names = TRUE)
asvplots <- list.files(analysis_setup$directory_paths$output_directory, pattern = "^asv_seqlength_plot_.*\\.RData$", full.names = TRUE)
expect_true(all(file.exists(rdata_files)))
expect_true(all(file.exists(asvplots)))
})