From 112c7d9236ea7f357ffea891c8a532304f626941 Mon Sep 17 00:00:00 2001 From: Eric Schulte Date: Mon, 15 Jun 2009 12:17:58 -0700 Subject: [PATCH] fixed non-session variable assignment in R --- lisp/langs/org-babel-R.el | 37 ++++++++-------- org-babel.org | 92 +++++++++++++++++++-------------------- 2 files changed, 64 insertions(+), 65 deletions(-) diff --git a/lisp/langs/org-babel-R.el b/lisp/langs/org-babel-R.el index a62531167..c80d6e34c 100644 --- a/lisp/langs/org-babel-R.el +++ b/lisp/langs/org-babel-R.el @@ -39,21 +39,24 @@ called by `org-babel-execute-src-block'." (message "executing R source code block...") (save-window-excursion (let* ((vars (org-babel-ref-variables params)) + (full-body (concat + (mapconcat ;; define any variables + (lambda (pair) + (org-babel-R-assign-elisp (car pair) (cdr pair))) + vars "\n") "\n" body "\n")) (result-params (split-string (or (cdr (assoc :results params)) ""))) (result-type (cond ((member "output" result-params) 'output) ((member "value" result-params) 'value) (t 'value))) (session (org-babel-R-initiate-session (cdr (assoc :session params)))) results) - ;; assign variables - (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars) ;; ;;; debugging statements ;; (message (format "result-type=%S" result-type)) ;; (message (format "body=%S" body)) ;; (message (format "session=%S" session)) ;; (message (format "result-params=%S" result-params)) ;; evaluate body and convert the results to ruby - (setq results (org-babel-R-evaluate session body result-type)) + (setq results (org-babel-R-evaluate session full-body result-type)) (setq results (if (member "scalar" result-params) results (let ((tmp-file (make-temp-file "org-babel-R"))) @@ -77,22 +80,18 @@ called by `org-babel-execute-src-block'." (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"") (format "%S" s))) -(defun org-babel-R-assign-elisp (session name value) - "Read the elisp VALUE into a variable named NAME in the current -R process in `org-babel-R-buffer'." - (unless session (error "No active R buffer")) - (org-babel-comint-input-command - session - (if (listp value) - (let ((transition-file (make-temp-file "org-babel-R-import"))) - ;; ensure VALUE has an orgtbl structure (depth of at least 2) - (unless (listp (car value)) (setq value (list value))) - (with-temp-file transition-file - (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) - (insert "\n")) - (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)" - name transition-file)) - (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))) +(defun org-babel-R-assign-elisp (name value) + "Read the elisp VALUE into a variable named NAME." + (if (listp value) + (let ((transition-file (make-temp-file "org-babel-R-import"))) + ;; ensure VALUE has an orgtbl structure (depth of at least 2) + (unless (listp (car value)) (setq value (list value))) + (with-temp-file transition-file + (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) + (insert "\n")) + (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)" + name transition-file)) + (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))) (defun org-babel-R-initiate-session (session) "If there is not a current R process then create one." diff --git a/org-babel.org b/org-babel.org index ea82f8a88..f53f5ecc2 100644 --- a/org-babel.org +++ b/org-babel.org @@ -2218,52 +2218,52 @@ org-babel functionality. of these tests may fail. #+TBLNAME: org-babel-tests -| functionality | block | arg | expected | results | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| basic evaluation | | | | | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| emacs lisp | basic-elisp | | 5 | 5 | pass | -| shell | basic-shell | | 6 | 6 | pass | -| ruby | basic-ruby | | org-babel | org-babel | pass | -| python | basic-python | | hello world | hello world | pass | -| R | basic-R | | 13 | 13 | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| tables | | | | | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| emacs lisp | table-elisp | | 3 | 3 | pass | -| ruby | table-ruby | | 1-2-3 | 1-2-3 | pass | -| python | table-python | | 5 | 5 | pass | -| R | table-R | | 3.5 | #ERROR | expected "3.5" but was "#ERROR" | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| source block references | | | | | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| all languages | chained-ref-last | | Array | Array | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| source block functions | | | | | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| emacs lisp | defun-fibb | | fibbd | fibbd | pass | -| run over | Fibonacci | 0 | 1 | 1 | pass | -| a | Fibonacci | 1 | 1 | 1 | pass | -| variety | Fibonacci | 2 | 2 | 2 | pass | -| of | Fibonacci | 3 | 3 | 3 | pass | -| different | Fibonacci | 4 | 5 | 5 | pass | -| arguments | Fibonacci | 5 | 8 | 8 | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| bugs and tasks | | | | | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| simple ruby arrays | ruby-array-test | | 3 | 3 | pass | -| R number evaluation | bug-R-number-evaluation | | 2 | #ERROR | expected "2" but was "#ERROR" | -| multi-line ruby blocks | multi-line-ruby-test | | 2 | 2 | pass | -| forcing vector results | test-forced-vector-results | | Array | Array | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| sessions | | | | | pass | -|-------------------------+----------------------------+-----+-------------+-------------+---------------------------------| -| set ruby session | set-ruby-session-var | | :set | :set | pass | -| get from ruby session | get-ruby-session-var | | 3 | | expected "3" but was "" | -| set python session | set-python-session-var | | set | set | pass | -| get from python session | get-python-session-var | | 4 | | expected "4" but was "" | -| set R session | set-R-session-var | | set | set | pass | -| get from R session | get-R-session-var | | 5 | nil | expected "5" but was "nil" | +| functionality | block | arg | expected | results | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| basic evaluation | | | | | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| emacs lisp | basic-elisp | | 5 | 5 | pass | +| shell | basic-shell | | 6 | 6 | pass | +| ruby | basic-ruby | | org-babel | org-babel | pass | +| python | basic-python | | hello world | hello world | pass | +| R | basic-R | | 13 | 13 | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| tables | | | | | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| emacs lisp | table-elisp | | 3 | 3 | pass | +| ruby | table-ruby | | 1-2-3 | 1-2-3 | pass | +| python | table-python | | 5 | 5 | pass | +| R | table-R | | 3.5 | 3.5 | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| source block references | | | | | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| all languages | chained-ref-last | | Array | Array | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| source block functions | | | | | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| emacs lisp | defun-fibb | | fibbd | fibbd | pass | +| run over | Fibonacci | 0 | 1 | 1 | pass | +| a | Fibonacci | 1 | 1 | 1 | pass | +| variety | Fibonacci | 2 | 2 | 2 | pass | +| of | Fibonacci | 3 | 3 | 3 | pass | +| different | Fibonacci | 4 | 5 | 5 | pass | +| arguments | Fibonacci | 5 | 8 | 8 | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| bugs and tasks | | | | | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| simple ruby arrays | ruby-array-test | | 3 | 3 | pass | +| R number evaluation | bug-R-number-evaluation | | 2 | 2 | pass | +| multi-line ruby blocks | multi-line-ruby-test | | 2 | 2 | pass | +| forcing vector results | test-forced-vector-results | | Array | Array | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| sessions | | | | | pass | +|-------------------------+----------------------------+-----+-------------+-------------+----------------------------| +| set ruby session | set-ruby-session-var | | :set | :set | pass | +| get from ruby session | get-ruby-session-var | | 3 | | expected "3" but was "" | +| set python session | set-python-session-var | | set | set | pass | +| get from python session | get-python-session-var | | 4 | | expected "4" but was "" | +| set R session | set-R-session-var | | set | set | pass | +| get from R session | get-R-session-var | | 5 | nil | expected "5" but was "nil" | #+TBLFM: $5='(if (= (length $3) 1) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5)) ** basic tests