Bug/isolated object name replacement (#113)

* collate isolated objects using list name set method

* update tests

* correct test to trigger bug in previous implementation

Author: jmtaylor-fhcrc

R/build.R

@@ -117,7 +117,7 @@ callr_render <- function(files_to_process, render_args, render_mode, r_session_w
 
     if (render_mode == "isolate"){
       # Earlier object(s) with same name are overwritten here
-      objs <- utils::modifyList(objs, get_callr_globals(rs), keep.null = TRUE)
+      objs[names(get_callr_globals(rs))] <- get_callr_globals(rs)
       if ( file_to_process != files_to_process[ length(files_to_process) ] ){
         rs$close()
         rs <- callr::r_session$new(wait=TRUE, wait_timeout=r_session_wait_timeout)

tests/testthat/setup.R

@@ -74,6 +74,7 @@ createPkg <- function(temp_dir, package_name, more_args = list()){
     c(
       "library(DPR2)",
       "mymatrix <- matrix(1:16, nrow=4)",
+      "mydataframe <- data.frame(x=1:3, y=LETTERS[1:3])",
       "dpr_save('mymatrix')"
     ),
     file.path(path, "processing/02.R")

tests/testthat/test-build.R

@@ -41,11 +41,12 @@ testthat::test_that("checking package build", {
   )
   dpr_yaml_set(path, r_session_wait_timeout = 3000)
 
-  dpr_build(path, process_on_build = "02.R")
+  ## test tabular objects made in isolate can be overwritten, count vignettes, check data save 
+  dpr_build(path, process_on_build = c("01.R", "02.R"))
   vign <- list.files(file.path(path, "vignettes"))
   expect_true(length(vign) == 2)
   datn <- list.files(file.path(path, "data"))
-  expect_true(datn == "mymatrix.rda")
+  expect_true(all(datn == c("mydataframe.rda", "mymatrix.rda", "myyaml.rda")))
 
   dpr_build(path, process_on_build = "A1.R", build_tarball = TRUE)
   vign <- list.files(file.path(path, "vignettes"))