From b1199e03758f42fde2f75f02a4c18cd71fac5a03 Mon Sep 17 00:00:00 2001 From: "Rainer M. Krug" Date: Thu, 20 Mar 2014 11:35:44 +0100 Subject: [PATCH 1/8] ob-R.el: Write org variables into own R environment * 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)