[PATCH] Write org variables into own R environment instead of .GlobalEnv

[Rainer M Krug <Rainer@krugs.de>]

[-- Attachment #1: Type: text/plain, Size: 4119 bytes --]


* (org-babel-R-assign-elisp): replaced simple assignments of variables
to variables in R with assignments into an environment called 'org'
and lock these so that they can not be modified anymore.

* (org-babel-expand-body:R): wrap the call
  of `org-babel-variable-assignments:R' into
  - detachment of org environment
  - creation of new environment org to delete the old environment
  - locking of the org environment to prevent adding of bindings
  - appending of environment to search path of R

These patch implements the writing of org variables into a separate R
environment and attaches it to the search path. This solves several
not so nice issues:

1) The org variables are now grouped and can be seen via 'ls(org)' in
R
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 | 47 +++++++++++++++++++++++++++++++----------------
 1 file changed, 31 insertions(+), 16 deletions(-)

diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 62aa7f2..da2aea2 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 +207,31 @@ 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)


-- 
Rainer M. Krug

email: RMKrug<at>gmail<dot>com

PGP: 0x0F52F982

[-- Attachment #2: Type: application/pgp-signature, Size: 494 bytes --]