close #1403: use a much more conservative strategy to find global var…

…iables in a chunk (basically consider all variables to be global)

NEWS.md

@@ -1,5 +1,9 @@
 # CHANGES IN knitr VERSION 1.17 (unreleased)
 
+## MAJOR CHANGES
+
+- the automatic detection of chunk dependencies (via the chunk option `autodep = TRUE`) is more conservative by default now; chunk B depends on chunk A if _any_ variables in B are created in A, no matter if these variables are local or global in B; you can use the chunk option `cache.globals` to manually provide a vector of variable names that should be considered "global" to avoid the dependency when local variables in B are also found in A (thanks, @knokknok, #1403)
+
 ## BUG FIXES
 
 - when a table only has one column, `kable()` does not work in R Markdown documents (thanks, @expersso, https://github.com/yihui/printr/issues/31)

R/block.R

@@ -259,7 +259,11 @@ block_exec = function(options) {
     # make sure all objects to be saved exist in env
     objs = intersect(c(objs, obj.new), ls(env, all.names = TRUE))
     if (options$autodep) {
-      cache$objects(objs, code, options$label, options$cache.path)
+      # you shall manually specify global object names if find_symbols() is not reliable
+      cache$objects(
+        objs, options$cache.globals %n% find_symbols(code), options$label,
+        options$cache.path
+      )
       dep_auto()
     }
     if (options$cache < 3) {

R/cache.R

@@ -48,10 +48,9 @@ new_cache = function() {
     } else lines = x
     writeLines(lines, con = path)
   }
-  cache_objects = function(keys, code, label, path) {
+  cache_objects = function(keys, globals, label, path) {
     save_objects(keys, label, valid_path(path, '__objects'))
-    # find globals in code; may not be reliable
-    save_objects(find_globals(code), label, valid_path(path, '__globals'))
+    save_objects(globals, label, valid_path(path, '__globals'))
   }
 
   cache_load = function(hash, lazy = TRUE) {
@@ -116,6 +115,14 @@ known_globals = c(
   '{', '[', '(', ':', '<-', '=', '+', '-', '*', '/', '%%', '%/%', '%*%', '%o%', '%in%'
 )
 
+# analyze code and find out all possible variables (not necessarily global variables)
+find_symbols = function(code) {
+  if (is.null(code) || length(p <- parse(text = code, keep.source = TRUE)) == 0) return()
+  p = getParseData(p)
+  p = p[p$terminal & p$token %in% c('SYMBOL', 'SYMBOL_FUNCTION_CALL', 'SPECIAL'), ]
+  unique(p$text)
+}
+
 # a variable name to store the metadata object from code chunks
 cache_meta_name = function(hash) sprintf('.%s_meta', hash)
 # a variable name to store the text output of code chunks

tests/testit/test-cache.R

@@ -13,6 +13,11 @@ assert(
   identical(find_globals(c('a=1%*%1%o%2 %in% d', 'b=d%%10+3%/%2-z[1:3]')), c('d', 'z'))
 )
 
+assert(
+  'find_symbols() identifies all symbols',
+  find_symbols('x = x + 1; rnorm(1, std = z)') %==% c('x', 'rnorm', 'z')
+)
+
 knit_lazy = function(lazy = TRUE) {
   in_dir(tempdir(), {
     txt = c(sprintf('```{r test, cache=TRUE, cache.lazy=%s}', lazy),