tests/testthat/test-genecovr.R

In NBISweden/genecovr: Gene body coverage analysis to evaluate genome assemblies

skip("Skip on github until resolve issue of testing package binary")
pkg_path <- getwd()
tmp <- tempdir(check = TRUE)
withr::local_dir(tmp)
withr::local_temp_libpaths()
withr::local_path(file.path(.libPaths()[1], "genecovr", "bin"))
devtools::install(pkg = pkg_path, quick = TRUE, upgrade = "never")

create_file <- function(fn) system.file("extdata", fn, package = "genecovr")

data <- as.data.frame(rbind(
  c(
    "nonpol", create_file("transcripts2nonpolished.psl"),
    create_file("nonpolished.fai"), create_file("transcripts.fai")
  ),
  c(
    "pol", create_file("transcripts2polished.psl"),
    create_file("polished.fai"), create_file("transcripts.fai")
  )
))
colnames(data) <- NULL
withr::local_file(write.csv(data, file = "assemblies.csv", row.names = FALSE))

test_that("genecovr runs as expected", {
  system(paste(
    paste0("R_LIBS_USER=", .libPaths()[1]),
    "genecovr", "assemblies.csv"
  ))
  expect_equal(length(list.files(pattern = "*.png")), 15)
  expect_equal(length(grep("Rplots", list.files(pattern = "*.pdf"),
    invert = TRUE
  )), 15)
  expect_equal(length(list.files(pattern = "*.csv.gz")), 4)
  expect_equal(length(list.files(pattern = "*.tsv.gz")), 1)
})

withr::defer(unlink(tmp, recursive = TRUE))