closes #228: do not hard-code globalenv() as the environment for knit…

…() any more; the default envir is parent.frame() for knit() now

R/block.R

@@ -61,7 +61,7 @@ block_exec = function(params) {
   options = params
 
   ## eval chunks (in an empty envir if cache)
-  env = if (options$cache) new.env(parent = globalenv()) else globalenv()
+  env = if (options$cache) new.env(parent = knit_global()) else knit_global()
   .knitEnv$knit_env = env # make a copy of the envir
   obj.before = ls(globalenv(), all.names = TRUE)  # global objects before chunk
 
@@ -172,15 +172,16 @@ block_exec = function(params) {
   output = str_c(unlist(wrap(res, options)), collapse = '') # wrap all results together
 
   res.after = run_hooks(before = FALSE, options, env) # run 'after' hooks
-  if (options$cache) copy_env(env, globalenv())
+  if (options$cache) copy_env(env, knit_global())
 
   output = str_c(c(res.before, output, res.after), collapse = '')  # insert hook results
   output = if (length(output) == 0L) '' else knit_hooks$get('chunk')(output, options)
   plot_counter(reset = TRUE)  # restore plot number
 
   if (options$cache) {
     obj.after = ls(globalenv(), all.names = TRUE)  # figure out new global objs
-    objs = c(ls(env, all.names = TRUE), setdiff(obj.after, obj.before))
+    copy_env(globalenv(), knit_global(), setdiff(obj.after, obj.before))
+    objs = ls(env, all.names = TRUE)
     block_cache(options, output, objs)
     if (options$autodep) cache$objects(objs, code, options$label, options$cache.path)
   }
@@ -191,7 +192,7 @@ block_exec = function(params) {
 block_cache = function(options, output, objects) {
   hash = options$hash
   outname = str_c('.', hash)
-  assign(outname, output, envir = globalenv())
+  assign(outname, output, envir = knit_global())
   ## purge my old cache and cache of chunks dependent on me
   cache$purge(str_c(valid_path(options$cache.path,
                                c(options$label, dep_list$get(options$label))), '_*'))
@@ -218,7 +219,7 @@ inline_exec = function(block) {
   owd = setwd(input_dir()); on.exit(setwd(owd))
   loc = block$location
   for (i in 1:n) {
-    res = try(eval(parse(text = code[i]), envir = globalenv()))
+    res = try(eval(parse(text = code[i]), envir = knit_global()))
     d = nchar(input)
     ## replace with evaluated results
     str_sub(input, loc[i, 1], loc[i, 2]) = if (length(res)) {

R/cache.R

@@ -17,10 +17,10 @@ new_cache = function() {
   cache_save = function(keys, outname, hash) {
     # keys are new variables created; outname is the text output of a chunk
     path = cache_path(hash)
-    save(list = outname, file = str_c(path, '.RData'), envir = globalenv())
+    save(list = outname, file = str_c(path, '.RData'), envir = knit_global())
     # FIXME: after R 2.15.0, this line can be removed
     keys = setdiff(keys, '.Random.seed')
-    tools:::makeLazyLoadDB(globalenv(), path, variables = keys)
+    tools:::makeLazyLoadDB(knit_global(), path, variables = keys)
   }
 
   save_objects = function(objs, label, path) {
@@ -43,10 +43,10 @@ new_cache = function() {
 
   cache_load = function(hash) {
     path = cache_path(hash)
-    lazyLoad(path, envir = globalenv())
+    lazyLoad(path, envir = knit_global())
     # load output from last run if exists
     if (file.exists(path2 <- str_c(path, '.RData'))) {
-      load(path2, envir = globalenv())
+      load(path2, envir = knit_global())
     }
   }
 
@@ -69,8 +69,8 @@ new_cache = function() {
 
   ## code output is stored in .[hash], so cache=TRUE won't lose output as cacheSweave does
   cache_output = function(hash) {
-    if (exists(str_c('.', hash), envir = globalenv(), mode = 'character')) {
-      get(str_c('.', hash), envir = globalenv(), mode = 'character')
+    if (exists(str_c('.', hash), envir = knit_global(), mode = 'character')) {
+      get(str_c('.', hash), envir = knit_global(), mode = 'character')
     } else ''
   }
 

R/output.R

@@ -53,6 +53,8 @@
 #'   \code{\link[utils]{Stangle}})
 #' @param text a character vector as an alternative way to provide the input
 #'   file
+#' @param envir the environment in which the code chunks are to be evaluated
+#'   (can use \code{\link{new.env}()} to guarantee an empty new environment)
 #' @return The compiled document is written into the output file, and the path
 #'   of the output file is returned, but if the \code{output} path is
 #'   \code{NULL}, the output is returned as a character vector.
@@ -90,7 +92,7 @@
 #' ## or setwd(dirname(f)); knit(basename(f))
 #'
 #' purl(f)  # extract R code only
-knit = function(input, output = NULL, tangle = FALSE, text = NULL) {
+knit = function(input, output = NULL, tangle = FALSE, text = NULL, envir = parent.frame()) {
 
   in.file = !missing(input) && is.character(input)  # is a file input
   optk = opts_knit$get(); on.exit(opts_knit$set(optk), add = TRUE)
@@ -167,6 +169,7 @@ knit = function(input, output = NULL, tangle = FALSE, text = NULL) {
 
   progress = opts_knit$get('progress')
   if (in.file) message(ifelse(progress, '\n\n', ''), 'processing file: ', input)
+  .knitEnv$knit_global = envir  # the envir to eval code
   res = process_file(text, output)
   cat(res, file = if (is.null(output)) '' else output)
   dep_list$restore()  # empty dependency list

R/utils.R

@@ -30,7 +30,7 @@ comment_out = function(x, options) {
 ## assign string in comments to a global variable
 comment_to_var = function(x, varname, pattern) {
   if (str_detect(x, pattern)) {
-    assign(varname, str_replace(x, pattern, ''), envir = globalenv())
+    assign(varname, str_replace(x, pattern, ''), envir = knit_global())
     return(TRUE)
   }
   FALSE
@@ -287,11 +287,11 @@ fix_options = function(options) {
 ## try eval an option (character) to its value
 eval_opt = function(x) {
   if (!is.character(x)) return(x)
-  eval(parse(text = x), envir = globalenv())
+  eval(parse(text = x), envir = knit_global())
 }
 
 ## eval options as symbol/language objects
-eval_lang = function(x, envir = globalenv()) {
+eval_lang = function(x, envir = knit_global()) {
   if (!is.symbol(x) && !is.language(x)) return(x)
   eval(x, envir = envir)
 }