tests/testthat/test_package_markdown.R

In o2r-project/containerit: Package R in Docker Containers

# Copyright 2018 Opening Reproducible Research (https://o2r.info)

context("Package R markdown files")

test_that("A markdown file can be packaged (using units example)", {
  output <- capture_output({
    the_dockerfile <- dockerfile(from = "package_markdown/units/",
                   maintainer = "Ted Tester",
                   image = "rocker/verse:3.5.2",
                   copy = "script_dir",
                   cmd = CMD_Render("package_markdown/units/2016-09-29-plot_units.Rmd"))
  })
  #write(the_dockerfile,"package_markdown/units/Dockerfile")
  expected_file <- readLines("package_markdown/units/Dockerfile")
  generated_file <- capture.output(print(the_dockerfile))
  expect_equal(generated_file, expected_file)
})

test_that("The render command supports output directory", {
  cmd = CMD_Render(path = tempdir(), output_dir = "/the_directory")
  expect_equal(stringr::str_count(toString(cmd), 'output_dir = \\\\\\"/the_directory\\\\\\"'), 1)
  expect_equal(stringr::str_count(toString(cmd), 'output_file'), 0)
})

test_that("The render command supports output file", {
  cmd = CMD_Render(path = tempdir(), output_file = "myfile.html")
  expect_equal(stringr::str_count(toString(cmd), 'output_file = \\\\\\"myfile.html\\\\\\"'), 1)
  expect_equal(stringr::str_count(toString(cmd), 'output_dir'), 0)
})

test_that("The render command supports output directory and output file at the same time", {
  cmd = CMD_Render(path = tempdir(), output_dir = "/the_directory", output_file = "myfile.html")
  expect_equal(stringr::str_count(toString(cmd), 'output_dir = \\\\\\"/the_directory\\\\\\"'), 1)
  expect_equal(stringr::str_count(toString(cmd), 'output_file = \\\\\\"myfile.html\\\\\\"'), 1)
})

test_that("The file is copied", {
  skip_on_ci()

  output <- capture_output(df_copy <- dockerfile(from = "package_markdown/units/", copy = "script"))
  expect_true(object = any(sapply(df_copy@instructions, function(x) { inherits(x, "Copy") })), info = "at least one Copy instruction")
})

test_that("File copying is disabled by default", {
  skip_on_ci()

  output <- capture_output(df_copy <- dockerfile(from = "package_markdown/units/"))
  expect_false(object = any(sapply(df_copy@instructions, function(x) { inherits(x, "Copy") })), info = "no Copy instruction")
})

test_that("File copying can be disabled with NA/NA_character", {
  skip_on_ci()

  output <- capture_output(df_copy <- dockerfile(from = "package_markdown/units/", copy = NA_character_))
  expect_false(object = any(sapply(df_copy@instructions, function(x) { inherits(x, "Copy") })), info = "no Copy instruction if NA_charachter_")

  output <- capture_output(df_copy2 <- dockerfile(from = "package_markdown/units/", copy = NA))
  expect_false(object = any(sapply(df_copy2@instructions, function(x) { inherits(x, "Copy") })), info = "no Copy instruction if NA")
})

test_that("File copying can be disabled with NULL", {
  skip_on_ci()

  output <- capture_output(df_copy <- dockerfile(from = "package_markdown/units/", copy = NULL))
  expect_false(object = any(sapply(df_copy@instructions, function(x) { inherits(x, "Copy") })), info = "no Copy instruction")
})

test_that("Packaging fails if dependency is missing and predetection is disabled", {
  skip_on_cran() # CRAN knows all packages
  skip_on_ci()

  output <- capture_output(
    expect_warning( # Gets a warning: "generated a condition with class packageNotFoundError/error/condition. It is less fragile to test custom conditions with `class`"
      expect_error(dockerfile(from = "package_markdown/missing_dependency/", predetect = FALSE), "there is no package")
    )
  )
})

test_that("Packaging works if dependency is missing in the base image and predetection is enabled", {
  skip_on_cran() # no missing packages on on CRAN
  skip_on_ci()

  output <- capture_output({
    predetected_df <- dockerfile(from = "package_markdown/missing_dependency/",
                                 maintainer = "o2r",
                                 image = getImageForVersion("3.4.4"),
                                 predetect = TRUE)
  })
  # write(predetected_df, "package_markdown/missing_dependency/Dockerfile")

  expect_s4_class(predetected_df, "Dockerfile")
  # package should still not be in this session library
  expect_error(library("coxrobust"))

  generated_file <- toString(predetected_df)
  expect_true(object = any(grepl("^RUN.*install2.*\"coxrobust\"", x = generated_file)), info = "Packages missing are detected")
  expect_true(object = any(grepl("^RUN.*install2.*\"rprojroot\"", x = generated_file)), info = "Packages missing are detected")

  expected_file <- readLines("package_markdown/missing_dependency/Dockerfile")
  expect_equal(capture.output(print(predetected_df)), expected_file)

  unlink("package_markdown/missing_dependency/*.md")
})