[O] [PATCH] Write org variables into own R environment

[Rainer M Krug]

* lisp/ob-R.el (org-babel-expand-body:R): Create empty environment
  called `org' in R before adding variables and afterwards lock it and
  add it to the R search path.
  (org-babel-variable-assignments:R): Assign variables into own
  `org' environment in R instead of .GlobalEnv

These patch implements the writing of org variables into a separate R
environment and attaches it to the search path.  For the usage of these
variables, nothing changes in R, but:

1) The org variables are now grouped and can be seen via `ls(org)' in
R and are not shown anymore in the .GlobalEnv when using `ls()'
2) As the environment `org' and all bindings are locked, the variables
can not be accidentally deleted. They can be overwritten, but they can
be restored by simply deleting the variable in R or by using
`org$VARIABLE' instead of `VARIABLE'
3) All variables can be saved by simply calling `save(org, FILENAME'
in R which makes it possible to store all variable definitions for
tangling in one file.
---
 lisp/ob-R.el | 25 +++++++++----------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 62aa7f2..82971de 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -103,8 +103,12 @@ this variable.")
             (append
              (when (cdr (assoc :prologue params))
                (list (cdr (assoc :prologue params))))
-             (org-babel-variable-assignments:R params)
-             (list body)
+            '("try(detach(org), silent=TRUE)")
+             '("org <- new.env()")
+            (org-babel-variable-assignments:R params)
+            '("lockEnvironment(org)")
+            '("attach(org)")
+            (list body)
              (when (cdr (assoc :epilogue params))
                (list (cdr (assoc :epilogue params)))))))
        (if graphics-file
@@ -203,20 +207,9 @@ This function is called by `org-babel-execute-src-block'."
                          "TRUE" "FALSE"))
              (row-names (if rownames-p "1" "NULL")))
          (if (= max min)
-             (format "%s <- read.table(\"%s\",
-                      header=%s,
-                      row.names=%s,
-                      sep=\"\\t\",
-                      as.is=TRUE)" name file header row-names)
-           (format "%s <- read.table(\"%s\",
-                   header=%s,
-                   row.names=%s,
-                   sep=\"\\t\",
-                   as.is=TRUE,
-                   fill=TRUE,
-                   col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
-                   name file header row-names max))))
-    (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
+             (format "assign( '%s', read.table(\"%s\", header=%s, 
row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = org ); lockBinding('%s', org)" 
name file header row-names name)
+           (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, 
sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep 
=\"\") ), envir = org ); lockBinding('%s', org)" name file header row-names max 
name))))
+    (format "assign('%s', %s, envir = org); lockBinding('%s', org)" name 
(org-babel-R-quote-tsv-field value) name)))
 
 (defvar ess-ask-for-ess-directory) ; dynamically scoped
 (defun org-babel-R-initiate-session (session params)
-- 
1.8.5.2 (Apple Git-48)

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