Move vis and hpc packages to "Suggests:"

ropensci · Jul 16, 2018 · a999522 · a999522
1 parent f2efdf4
commit a999522
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -65,13 +65,10 @@ Imports:
   digest,
   dplyr,
   formatR,
-  future,
-  future.apply,
   fs,
   grDevices,
   igraph,
   knitr,
-  lubridate,
   magrittr,
   parallel,
   pkgconfig,
@@ -86,20 +83,23 @@ Imports:
   testthat,
   tibble,
   tidyselect (>= 0.2.4),
-  txtq,
   utils,
   withr
 Suggests: 
   abind,
   callr,
   clustermq,
   DBI,
+  future,
+  future.apply,
   ggplot2,
   ggraph,
+  lubridate,
   MASS,
   methods,
   networkD3,
   RSQLite,
+  txtq,
   rmarkdown,
   visNetwork
 VignetteBuilder: knitr

diff --git a/NAMESPACE b/NAMESPACE
@@ -183,11 +183,6 @@ importFrom(evaluate,try_capture_stack)
 importFrom(formatR,tidy_source)
 importFrom(fs,dir_create)
 importFrom(fs,file_create)
-importFrom(future,future)
-importFrom(future,plan)
-importFrom(future,resolved)
-importFrom(future,value)
-importFrom(future.apply,future_lapply)
 importFrom(grDevices,col2rgb)
 importFrom(grDevices,rgb)
 importFrom(igraph,V)
@@ -210,8 +205,6 @@ importFrom(igraph,topo_sort)
 importFrom(igraph,vertex)
 importFrom(igraph,vertex_attr)
 importFrom(knitr,knit)
-importFrom(lubridate,dseconds)
-importFrom(lubridate,duration)
 importFrom(magrittr,"%>%")
 importFrom(parallel,clusterCall)
 importFrom(parallel,clusterExport)
@@ -253,7 +246,6 @@ importFrom(tidyselect,num_range)
 importFrom(tidyselect,one_of)
 importFrom(tidyselect,starts_with)
 importFrom(tidyselect,vars_select)
-importFrom(txtq,txtq)
 importFrom(utils,capture.output)
 importFrom(utils,compareVersion)
 importFrom(utils,head)

diff --git a/NEWS.md b/NEWS.md
@@ -19,6 +19,7 @@
 - Add a `garbage_collection` argument to `make()`. If `TRUE`, `gc()` is called after every new build of a target.
 - Remove redundant calls to `sanitize_plan()` in `make()`.
 - Change `tracked()` to accept only a `drake_config()` object as an argument. Yes, it is technically a breaking change, but it is only a small break, and it is the correct API choice.
+- Move visualization and hpc package dependencies to "Suggests:" rather than "Imports:" in the `DESCRIPTION` file.
 
 # Version 5.2.1
 

diff --git a/R/build_times.R b/R/build_times.R
@@ -128,9 +128,10 @@ to_build_duration_df <- function(times){
 # we need to round to the nearest second
 # for times longer than a minute.
 to_build_duration <- function(x){
+  assert_pkgs("lubridate")
   round_these <- x >= 60
   x[round_these] <- round(x[round_these], digits = 0)
-  dseconds(x)
+  lubridate::dseconds(x)
 }
 
 time_columns <- c("elapsed", "user", "system")

diff --git a/R/future.R b/R/future.R
@@ -1,4 +1,5 @@
 run_future <- function(config){
+  assert_pkgs("future")
   queue <- new_priority_queue(config = config)
   workers <- initialize_workers(config)
   # While any targets are queued or running...

diff --git a/R/future_lapply.R b/R/future_lapply.R
@@ -1,4 +1,5 @@
 run_future_lapply <- function(config){
+  assert_pkgs(c("future", "future.apply"))
   prepare_distributed(config = config)
   mc_init_worker_cache(config)
   console_persistent_workers(config)

diff --git a/R/mclapply.R b/R/mclapply.R
@@ -1,4 +1,5 @@
 run_mclapply <- function(config){
+  assert_pkgs("txtq")
   if (config$jobs < 2 && !length(config$debug)) {
     return(run_loop(config = config))
   }
@@ -52,6 +53,7 @@ mc_process <- function(id, config){
 #' @param config `drake_config()` list
 #' @return nothing important
 mc_master <- function(config){
+  assert_pkgs("txtq")
   on.exit(mc_conclude_workers(config))
   config$queue <- new_priority_queue(config = config)
   if (!identical(config$ensure_workers, FALSE)){
@@ -69,6 +71,7 @@ mc_master <- function(config){
 }
 
 mc_worker <- function(worker, config){
+  assert_pkgs("txtq")
   ready_queue <- mc_get_ready_queue(worker, config)
   done_queue <- mc_get_done_queue(worker, config)
   while (TRUE){

diff --git a/R/package.R b/R/package.R
@@ -44,16 +44,13 @@
 #' @importFrom dplyr bind_rows do group_by mutate n select ungroup
 #' @importFrom evaluate try_capture_stack
 #' @importFrom formatR tidy_source
-#' @importFrom future future plan resolved value
-#' @importFrom future.apply future_lapply
 #' @importFrom fs dir_create file_create
 #' @importFrom grDevices col2rgb rgb
 #' @importFrom igraph adjacent_vertices components delete_vertices
 #'   degree edge edges igraph_opt igraph_options induced_subgraph is_dag
 #'   make_empty_graph plot.igraph set_vertex_attr simplify subcomponent
 #'   topo_sort V vertex vertex_attr
 #' @importFrom knitr knit
-#' @importFrom lubridate dseconds duration
 #' @importFrom magrittr %>%
 #' @importFrom parallel clusterCall clusterExport makePSOCKcluster
 #'   mclapply parLapply stopCluster
@@ -70,7 +67,6 @@
 #' @importFrom testthat context expect_false expect_true test_dir test_that
 #' @importFrom tibble as_tibble tibble
 #' @importFrom tidyselect vars_select
-#' @importFrom txtq txtq
 #' @importFrom utils capture.output compareVersion head installed.packages
 #'   packageVersion read.csv sessionInfo stack type.convert unzip write.table
 #' @importFrom withr local_dir with_dir with_options with_output_sink

diff --git a/R/predict_runtime.R b/R/predict_runtime.R
@@ -203,6 +203,7 @@ predict_load_balancing <- function(
   default_time = 0,
   warn = TRUE
 ){
+  assert_pkgs("lubridate")
   if (!is.null(future_jobs) || !is.null(digits)){
     warning(
       "The `future_jobs` and `digits` arguments ",

diff --git a/R/staged.R b/R/staged.R
@@ -141,6 +141,7 @@ run_parLapply_staged <- function(config) { # nolint
 }
 
 run_future_lapply_staged <- function(config){
+  assert_pkgs(c("future", "future.apply"))
   prepare_distributed(config = config)
   schedule <- config$schedule
   while (length(V(schedule)$name)){
@@ -163,16 +164,7 @@ run_future_lapply_staged <- function(config){
 }
 
 run_clustermq_staged <- function(config){
-  if (!requireNamespace("clustermq")){
-    # nocov start
-    drake_error(
-      "to use make(parallelism = \"clustermq_staged\"), ",
-      "you must install the clustermq package: ",
-      "https://github.com/mschubert/clustermq.",
-      config = config
-    )
-    # nocov end
-  }
+  assert_pkgs("clustermq")
   schedule <- config$schedule
   workers <- clustermq::workers(n_jobs = config$jobs)
   on.exit(workers$finalize())

diff --git a/codemeta.json b/codemeta.json
@@ -115,6 +115,30 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=DBI"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "future",
+      "name": "future",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=future"
+    },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "future.apply",
+      "name": "future.apply",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=future.apply"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "ggplot2",
@@ -139,6 +163,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=ggraph"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "lubridate",
+      "name": "lubridate",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=lubridate"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "MASS",
@@ -180,6 +216,18 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=RSQLite"
     },
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "txtq",
+      "name": "txtq",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=txtq"
+    },
     {
       "@type": "SoftwareApplication",
       "identifier": "rmarkdown",
@@ -296,30 +344,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=formatR"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "future",
-      "name": "future",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=future"
-    },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "future.apply",
-      "name": "future.apply",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=future.apply"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "fs",
@@ -361,18 +385,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=knitr"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "lubridate",
-      "name": "lubridate",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=lubridate"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "magrittr",
@@ -530,18 +542,6 @@
       },
       "sameAs": "https://CRAN.R-project.org/package=tidyselect"
     },
-    {
-      "@type": "SoftwareApplication",
-      "identifier": "txtq",
-      "name": "txtq",
-      "provider": {
-        "@id": "https://cran.r-project.org",
-        "@type": "Organization",
-        "name": "Comprehensive R Archive Network (CRAN)",
-        "url": "https://cran.r-project.org"
-      },
-      "sameAs": "https://CRAN.R-project.org/package=txtq"
-    },
     {
       "@type": "SoftwareApplication",
       "identifier": "utils",
@@ -562,7 +562,7 @@
   ],
   "releaseNotes": "https://github.com/ropensci/drake/blob/master/NEWS.md",
   "readme": "https://github.com/ropensci/drake/blob/master/README.md",
-  "fileSize": "382.335KB",
+  "fileSize": "379.308KB",
   "contIntegration": [
     "https://ci.appveyor.com/project/ropensci/drake",
     "https://travis-ci.org/ropensci/drake",

diff --git a/tests/testthat/test-cache.R b/tests/testthat/test-cache.R
@@ -129,6 +129,7 @@ test_with_dir("subspaces", {
 })
 
 test_with_dir("cache functions work", {
+  skip_if_not_installed("lubridate")
   # May have been loaded in a globalenv() testing scenario # nolint
   remove_these <- intersect(ls(envir = globalenv()), c("h", "j"))
   rm(list = remove_these, envir = globalenv())

diff --git a/tests/testthat/test-future.R b/tests/testthat/test-future.R
@@ -2,6 +2,8 @@ drake_context("future")
 
 test_with_dir("future package functionality", {
   skip_on_cran() # CRAN gets whitelist tests only (check time limits).
+  skip_if_not_installed("future")
+  skip_if_not_installed("future.apply")
   future::plan(future::sequential)
   scenario <- get_testing_scenario()
   e <- eval(parse(text = scenario$envir))
@@ -64,6 +66,8 @@ test_with_dir("prepare_distributed() writes cache folder if nonexistent", {
 
 test_with_dir("can gracefully conclude a crashed worker", {
   skip_on_cran() # CRAN gets whitelist tests only (check time limits).
+  skip_if_not_installed("future")
+  skip_if_not_installed("future.apply")
   for (caching in c("master", "worker")){
     con <- dbug()
     con$caching <- caching

diff --git a/tests/testthat/test-graph.R b/tests/testthat/test-graph.R
@@ -80,6 +80,7 @@ test_with_dir("Supplied graph is pruned.", {
 
 test_with_dir("we can generate different visNetwork dependency graphs", {
   skip_on_cran() # CRAN gets whitelist tests only (check time limits).
+  skip_if_not_installed("lubridate")
   load_mtcars_example()
   config <- drake_config(my_plan)
 

diff --git a/tests/testthat/test-memory-cache.R b/tests/testthat/test-memory-cache.R
@@ -21,6 +21,7 @@ test_with_dir("storr_environment is usable", {
 
 test_with_dir("arbitrary storr in-memory cache", {
   skip_on_cran() # CRAN gets whitelist tests only (check time limits).
+  skip_if_not_installed("lubridate")
   expect_false(file.exists(default_cache_path()))
   parallelism <- default_parallelism()
   jobs <- 1

diff --git a/tests/testthat/test-mtcars-example.R b/tests/testthat/test-mtcars-example.R
@@ -67,6 +67,7 @@ test_with_dir("mtcars example works", {
   expect_equal(sort(ls(envir = e)), coefs)
 
   # build_times() # nolint
+  skip_if_not_installed("lubridate")
   all_times <- build_times()
   expect_true(nrow(all_times) >= nrow(config$plan))
   some_times <- build_times(starts_with("coef"))

diff --git a/tests/testthat/test-parallel.R b/tests/testthat/test-parallel.R
@@ -186,6 +186,8 @@ test_with_dir("null cases for message queues", {
 
 test_with_dir("ensure_workers can be disabled", {
   skip_on_cran() # CRAN gets whitelist tests only (check time limits).
+  skip_if_not_installed("future")
+  skip_if_not_installed("future.apply")
   load_mtcars_example()
   future::plan(future::sequential)
   config <- drake_config(my_plan)