Fix issue where dependencies were not being tracked when checking produced files

.Rbuildignore

@@ -22,3 +22,5 @@
 ^\.github$
 \.*gcov$
 ^TODO\.md$
+^.*\.Rproj$
+^\.Rproj\.user$

R/orderly.R

@@ -121,6 +121,10 @@ orderly_run <- function(name, parameters = NULL, envir = NULL,
       outpack::outpack_packet_use_dependency(dat$depends$id[[i]],
                                              dat$depends$files[[i]])
     }
+    packet <- outpack::outpack_packet_current()
+    lapply(packet$depends, function(dependency) {
+      expected <- c(expected, dependency$files$here)
+    })
 
     ## TODO: if run fails we might not close out the device stack
     ## here, we do need to do that to make things easy for the user.

orderly2.Rproj

@@ -0,0 +1,20 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source

tests/testthat/helper-orderly.R

@@ -14,7 +14,8 @@ test_prepare_orderly_example <- function(examples, ...) {
     config <- c(config,
                 "global_resources: global")
     fs::dir_create(file.path(tmp, "global"))
-    fs::file_copy("examples/minimal/data.csv", file.path(tmp, "global"))
+    fs::file_copy(test_path("examples/minimal/data.csv"),
+                  file.path(tmp, "global"))
   }
 
   if ("plugin" %in% examples) {
@@ -29,7 +30,7 @@ test_prepare_orderly_example <- function(examples, ...) {
   writeLines(config, file.path(tmp, "orderly_config.yml"))
   fs::dir_create(file.path(tmp, "src"))
   for (i in examples) {
-    fs::dir_copy(file.path("examples", i), file.path(tmp, "src"))
+    fs::dir_copy(test_path("examples", i), file.path(tmp, "src"))
   }
   tmp
 }
@@ -54,3 +55,51 @@ json_to_df <- function(x) {
 hash_file <- function(...) {
   outpack:::hash_file(...)
 }
+
+
+test_path <- function(...) {
+  if (basename(getwd()) == "testthat") {
+    file.path(...)
+  } else {
+    testthat::test_path(...)
+  }
+}
+
+
+## Expects dependencies to be a list of name and id (or search query)
+## e.g.
+## list(a = "latest", b = "latest(parameter:x == 2)") # nolint
+## By convention will expect report artefact to be "data.rds" and will
+## map this to "input.rds" in the script.R
+create_random_report <- function(root, name = "data", dependencies = NULL) {
+  report_dir <- fs::dir_create(file.path(root, "src", name))
+  withr::defer_parent(unlink(report_dir, recursive = TRUE))
+
+  yml <- c(
+    "script: script.R",
+    "artefacts:",
+    "  data:",
+    "    description: Random data",
+    "    filenames: data.rds"
+  )
+
+  if (!is.null(dependencies)) {
+    assert_named(dependencies)
+    formatted_depends <- do.call(c, lapply(names(dependencies), function(name) {
+      id <- dependencies[[name]]
+      c(sprintf("  - %s:", name),
+        sprintf("      id: %s", id),
+                "      use:",
+                "        input.rds: data.rds")
+    }))
+    yml <- c(yml, "depends:", formatted_depends)
+    script <- c("x <- readRDS(\"input.rds\")",
+                "saveRDS(x + runif(10), \"data.rds\")")
+  } else {
+    script <- "saveRDS(runif(10), \"data.rds\")"
+  }
+
+  writeLines(yml, file.path(report_dir, "orderly.yml"))
+  writeLines(script, file.path(report_dir, "script.R"))
+  invisible(report_dir)
+}

tests/testthat/test-run.R

@@ -61,7 +61,7 @@ test_that("Check that required files are produced", {
   ## TODO: we might add something nice to expose the status of a
   ## currently running packet.
   expect_error(outpack::outpack_packet_end(),
-               "No current packet")
+               "No currently active packet")
 
   ## TODO: Still need something much nicer in outpack for this:
   root <- orderly_root(path, FALSE)
@@ -207,3 +207,23 @@ test_that("can use global resources", {
                list(list(here = "global_data.csv",
                          there = "data.csv")))
 })
+
+
+test_that("dependencies left in archive do not print extra files message", {
+  path <- test_prepare_orderly_example(NULL)
+  create_random_report(path, "a")
+  create_random_report(path, "b", list(a = "latest"))
+
+  id_a <- orderly_run("a", root = path)
+  expect_message(id_b <- orderly_run("b", root = path), NULL)
+
+  root <- orderly_root(path, FALSE)
+  meta <- root$outpack$metadata(id_b, full = TRUE)
+  expect_equal(meta$depends$packet, id_a)
+  expect_equal(meta$depends$files[[1]],
+               data_frame(here = "input.rds", there = "data.rds"))
+  expect_true(file.exists(
+    file.path(path, "archive", "b", id_b, "input.rds")))
+  expect_true(file.exists(
+    file.path(path, "archive", "b", id_b, "data.rds")))
+})