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@@ -39,21 +39,24 @@ called by `org-babel-execute-src-block'."
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(message "executing R source code block...")
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(save-window-excursion
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(let* ((vars (org-babel-ref-variables params))
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+ (full-body (concat
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+ (mapconcat ;; define any variables
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+ (lambda (pair)
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+ (org-babel-R-assign-elisp (car pair) (cdr pair)))
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+ vars "\n") "\n" body "\n"))
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(result-params (split-string (or (cdr (assoc :results params)) "")))
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(result-type (cond ((member "output" result-params) 'output)
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((member "value" result-params) 'value)
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(t 'value)))
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(session (org-babel-R-initiate-session (cdr (assoc :session params))))
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results)
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- ;; assign variables
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- (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)
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;; ;;; debugging statements
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;; (message (format "result-type=%S" result-type))
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;; (message (format "body=%S" body))
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;; (message (format "session=%S" session))
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;; (message (format "result-params=%S" result-params))
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;; evaluate body and convert the results to ruby
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- (setq results (org-babel-R-evaluate session body result-type))
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+ (setq results (org-babel-R-evaluate session full-body result-type))
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(setq results (if (member "scalar" result-params)
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results
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(let ((tmp-file (make-temp-file "org-babel-R")))
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@@ -77,62 +80,77 @@ called by `org-babel-execute-src-block'."
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(concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
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(format "%S" s)))
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-(defun org-babel-R-assign-elisp (session name value)
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- "Read the elisp VALUE into a variable named NAME in the current
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-R process in `org-babel-R-buffer'."
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- (unless session (error "No active R buffer"))
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- (org-babel-comint-input-command
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- session
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- (if (listp value)
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- (let ((transition-file (make-temp-file "org-babel-R-import")))
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- ;; ensure VALUE has an orgtbl structure (depth of at least 2)
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- (unless (listp (car value)) (setq value (list value)))
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- (with-temp-file transition-file
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- (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
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- (insert "\n"))
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- (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
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- name transition-file))
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- (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))))
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+(defun org-babel-R-assign-elisp (name value)
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+ "Read the elisp VALUE into a variable named NAME."
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+ (if (listp value)
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+ (let ((transition-file (make-temp-file "org-babel-R-import")))
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+ ;; ensure VALUE has an orgtbl structure (depth of at least 2)
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+ (unless (listp (car value)) (setq value (list value)))
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+ (with-temp-file transition-file
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+ (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
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+ (insert "\n"))
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+ (format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
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+ name transition-file))
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+ (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
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(defun org-babel-R-initiate-session (session)
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"If there is not a current R process then create one."
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- (setq session (or session "*R*"))
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- (if (org-babel-comint-buffer-livep session)
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- session
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- (save-window-excursion (R) (rename-buffer (if (bufferp session) (buffer-name session)
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- (if (stringp session) session (buffer-name)))) (current-buffer))))
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+ (unless (string= session "none")
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+ (setq session (or session "*R*"))
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+ (if (org-babel-comint-buffer-livep session)
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+ session
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+ (save-window-excursion (R) (rename-buffer (if (bufferp session) (buffer-name session)
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+ (if (stringp session) session (buffer-name)))) (current-buffer)))))
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(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
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(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
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+(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
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+write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)")
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(defun org-babel-R-evaluate (buffer body result-type)
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"Pass BODY to the R process in BUFFER. If RESULT-TYPE equals
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'output then return a list of the outputs of the statements in
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BODY, if RESULT-TYPE equals 'value then return the value of the
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last statement in BODY."
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- (org-babel-comint-in-buffer buffer
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- (let* ((tmp-file (make-temp-file "org-babel-R"))
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- (last-value-eval
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- (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
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- tmp-file))
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- (full-body (mapconcat #'org-babel-chomp (list body last-value-eval org-babel-R-eoe-indicator) "\n"))
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- (raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
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- (insert full-body) (inferior-ess-send-input)))
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- (results (let ((broke nil))
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- (delete nil (mapcar (lambda (el)
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- (if (or broke
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- (and (string-match (regexp-quote org-babel-R-eoe-output) el) (setq broke t)))
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- nil
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- (if (= (length el) 0)
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+ (if (not session)
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+ ;; external process evaluation
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+ (let ((in-tmp-file (make-temp-file "R-in-functional-results"))
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+ (out-tmp-file (make-temp-file "R-out-functional-results")))
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+ (case result-type
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+ (output
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+ (with-temp-file in-tmp-file (insert body))
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+ ;; (message "R --slave --no-save < '%s' > '%s'" in-tmp-file out-tmp-file)
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+ (shell-command-to-string (format "R --slave --no-save < '%s' > '%s'" in-tmp-file out-tmp-file)))
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+ (value
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+ (with-temp-file in-tmp-file
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+ (insert (format org-babel-R-wrapper-method body out-tmp-file)))
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+ ;; (message "R --no-save < '%s'" in-tmp-file)
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+ (shell-command (format "R --no-save < '%s'" in-tmp-file))))
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+ (with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
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+ ;; comint session evaluation
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+ (org-babel-comint-in-buffer buffer
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+ (let* ((tmp-file (make-temp-file "org-babel-R"))
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+ (last-value-eval
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+ (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
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+ tmp-file))
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+ (full-body (mapconcat #'org-babel-chomp (list body last-value-eval org-babel-R-eoe-indicator) "\n"))
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+ (raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
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+ (insert full-body) (inferior-ess-send-input)))
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+ (results (let ((broke nil))
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+ (delete nil (mapcar (lambda (el)
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+ (if (or broke
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+ (and (string-match (regexp-quote org-babel-R-eoe-output) el) (setq broke t)))
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nil
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- (if (string-match comint-prompt-regexp el)
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- (substring el (match-end 0))
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- el))))
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- (mapcar #'org-babel-trim raw))))))
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- (case result-type
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- (output (org-babel-trim (mapconcat #'identity results "\n")))
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- (value (org-babel-trim (with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
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- (t (reverse results))))))
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+ (if (= (length el) 0)
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+ nil
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+ (if (string-match comint-prompt-regexp el)
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+ (substring el (match-end 0))
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+ el))))
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+ (mapcar #'org-babel-trim raw))))))
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+ (case result-type
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+ (output (org-babel-trim (mapconcat #'identity results "\n")))
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+ (value (org-babel-trim (with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
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+ (t (reverse results)))))))
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(provide 'org-babel-R)
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;;; org-babel-R.el ends here
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