[SPARK-29777][SPARKR] SparkR::cleanClosure aggressively removes a fun…

…ction required by user function

### What changes were proposed in this pull request?
The implementation for walking through the user function AST and picking referenced variables and functions, had an optimization to skip a branch if it had already seen it. This runs into an interesting problem in the following example

```
df <- createDataFrame(data.frame(x=1))
f1 <- function(x) x + 1
f2 <- function(x) f1(x) + 2
dapplyCollect(df, function(x) { f1(x); f2(x) })
```
Results in error:
```
org.apache.spark.SparkException: R computation failed with
 Error in f1(x) : could not find function "f1"
Calls: compute -> computeFunc -> f2
```

### Why are the changes needed?
Bug fix

### Does this PR introduce any user-facing change?
No

### How was this patch tested?
Unit tests in `test_utils.R`

Closes #26429 from falaki/SPARK-29777.

Authored-by: Hossein <hossein@databricks.com>
Signed-off-by: HyukjinKwon <gurwls223@apache.org>

R/pkg/R/utils.R

@@ -543,10 +543,14 @@ processClosure <- function(node, oldEnv, defVars, checkedFuncs, newEnv) {
               funcList <- mget(nodeChar, envir = checkedFuncs, inherits = F,
                                ifnotfound = list(list(NULL)))[[1]]
               found <- sapply(funcList, function(func) {
-                ifelse(identical(func, obj), TRUE, FALSE)
+                ifelse(
+                  identical(func, obj) &&
+                    # Also check if the parent environment is identical to current parent
+                    identical(parent.env(environment(func)), func.env),
+                  TRUE, FALSE)
               })
               if (sum(found) > 0) {
-                # If function has been examined, ignore.
+                # If function has been examined ignore
                 break
               }
               # Function has not been examined, record it and recursively clean its closure.

R/pkg/tests/fulltests/test_utils.R

@@ -110,6 +110,15 @@ test_that("cleanClosure on R functions", {
   actual <- get("y", envir = env, inherits = FALSE)
   expect_equal(actual, y)
 
+  # Test for combination for nested and sequenctial functions in a closure
+  f1 <- function(x) x + 1
+  f2 <- function(x) f1(x) + 2
+  userFunc <- function(x) { f1(x); f2(x) }
+  cUserFuncEnv <- environment(cleanClosure(userFunc))
+  expect_equal(length(cUserFuncEnv), 2)
+  innerCUserFuncEnv <- environment(cUserFuncEnv$f2)
+  expect_equal(length(innerCUserFuncEnv), 1)
+
   # Test for function (and variable) definitions.
   f <- function(x) {
     g <- function(y) { y * 2 }