diff options
Diffstat (limited to 'lisp/org/ob-R.el')
| -rw-r--r-- | lisp/org/ob-R.el | 122 |
1 files changed, 111 insertions, 11 deletions
diff --git a/lisp/org/ob-R.el b/lisp/org/ob-R.el index 309a0acf7e7..169e1d6d6ce 100644 --- a/lisp/org/ob-R.el +++ b/lisp/org/ob-R.el @@ -4,6 +4,7 @@ ;; Author: Eric Schulte ;; Dan Davison +;; Maintainer: Jeremie Juste ;; Keywords: literate programming, reproducible research, R, statistics ;; Homepage: https://orgmode.org @@ -39,6 +40,13 @@ (declare-function ess-wait-for-process "ext:ess-inf" (&optional proc sec-prompt wait force-redisplay)) +;; FIXME: Temporary declaration to silence the byte-compiler +(defvar user-inject-src-param) +(defvar ess-eval-visibly-tmp) +(defvar ess-eval-visibly) +(defvar ess-inject-source) +(defvar user-inject-src-param) + (defconst org-babel-header-args:R '((width . :any) (height . :any) @@ -157,6 +165,7 @@ This function is called by `org-babel-execute-src-block'." (save-excursion (let* ((result-params (cdr (assq :result-params params))) (result-type (cdr (assq :result-type params))) + (async (org-babel-comint-use-async params)) (session (org-babel-R-initiate-session (cdr (assq :session params)) params)) (graphics-file (and (member "graphics" (assq :result-params params)) @@ -183,7 +192,8 @@ This function is called by `org-babel-execute-src-block'." (cdr (assq :colname-names params)) colnames-p)) (or (equal "yes" rownames-p) (org-babel-pick-name - (cdr (assq :rowname-names params)) rownames-p))))) + (cdr (assq :rowname-names params)) rownames-p)) + async))) (if graphics-file nil result)))) (defun org-babel-prep-session:R (session params) @@ -321,7 +331,7 @@ Each member of this list is a list with three members: (device-info (or (assq (intern (concat ":" device)) org-babel-R-graphics-devices) (assq :png org-babel-R-graphics-devices))) - (extra-args (cdr (assq :R-dev-args params))) filearg args) + (extra-args (cdr (assq :R-dev-args params))) filearg args) (setq device (nth 1 device-info)) (setq filearg (nth 2 device-info)) (setq args (mapconcat @@ -348,7 +358,7 @@ Each member of this list is a list with three members: { tfile<-tempfile() write.table(object, file=tfile, sep=\"\\t\", - na=\"nil\",row.names=%s,col.names=%s, + na=\"\",row.names=%s,col.names=%s, quote=FALSE) file.rename(tfile,transfer.file) }, @@ -370,11 +380,14 @@ Has four %s escapes to be filled in: 4. The name of the file to write to") (defun org-babel-R-evaluate - (session body result-type result-params column-names-p row-names-p) + (session body result-type result-params column-names-p row-names-p async) "Evaluate R code in BODY." (if session - (org-babel-R-evaluate-session - session body result-type result-params column-names-p row-names-p) + (if async + (ob-session-async-org-babel-R-evaluate-session + session body result-type result-params column-names-p row-names-p) + (org-babel-R-evaluate-session + session body result-type result-params column-names-p row-names-p)) (org-babel-R-evaluate-external-process body result-type result-params column-names-p row-names-p))) @@ -450,11 +463,13 @@ last statement in BODY, as elisp." (car (split-string line "\n"))) (substring line (match-end 1)) line)) - (org-babel-comint-with-output (session org-babel-R-eoe-output) - (insert (mapconcat 'org-babel-chomp - (list body org-babel-R-eoe-indicator) - "\n")) - (inferior-ess-send-input)))))) "\n")))) + (with-current-buffer session + (let ((comint-prompt-regexp (concat "^" comint-prompt-regexp))) + (org-babel-comint-with-output (session org-babel-R-eoe-output) + (insert (mapconcat 'org-babel-chomp + (list body org-babel-R-eoe-indicator) + "\n")) + (inferior-ess-send-input)))))))) "\n")))) (defun org-babel-R-process-value-result (result column-names-p) "R-specific processing of return value. @@ -465,6 +480,91 @@ Insert hline if column names in output have been requested." (error "Could not parse R result")) result)) + +;;; async evaluation + +(defconst ob-session-async-R-indicator "'ob_comint_async_R_%s_%s'") + +(defun ob-session-async-org-babel-R-evaluate-session + (session body result-type _ column-names-p row-names-p) + "Asynchronously evaluate BODY in SESSION. +Returns a placeholder string for insertion, to later be replaced +by `org-babel-comint-async-filter'." + (org-babel-comint-async-register + session (current-buffer) + "^\\(?:[>.+] \\)*\\[1\\] \"ob_comint_async_R_\\(.+?\\)_\\(.+\\)\"$" + 'org-babel-chomp + 'ob-session-async-R-value-callback) + (cl-case result-type + (value + (let ((tmp-file (org-babel-temp-file "R-"))) + (with-temp-buffer + (insert + (org-babel-chomp body)) + (let ((ess-local-process-name + (process-name (get-buffer-process session)))) + (ess-eval-buffer nil))) + (with-temp-buffer + (insert + (mapconcat + 'org-babel-chomp + (list (format org-babel-R-write-object-command + (if row-names-p "TRUE" "FALSE") + (if column-names-p + (if row-names-p "NA" "TRUE") + "FALSE") + ".Last.value" + (org-babel-process-file-name tmp-file 'noquote)) + (format ob-session-async-R-indicator + "file" tmp-file)) + "\n")) + (let ((ess-local-process-name + (process-name (get-buffer-process session)))) + (ess-eval-buffer nil))) + tmp-file)) + (output + (let ((uuid (md5 (number-to-string (random 100000000)))) + (ess-local-process-name + (process-name (get-buffer-process session)))) + (with-temp-buffer + (insert (format ob-session-async-R-indicator + "start" uuid)) + (insert "\n") + (insert body) + (insert "\n") + (insert (format ob-session-async-R-indicator + "end" uuid)) + (setq ess-eval-visibly-tmp ess-eval-visibly) + (setq user-inject-src-param ess-inject-source) + (setq ess-eval-visibly nil) + (setq ess-inject-source 'function-and-buffer) + (ess-eval-buffer nil)) + (setq ess-eval-visibly ess-eval-visibly-tmp) + (setq ess-inject-source user-inject-src-param) + uuid)))) + +(defun ob-session-async-R-value-callback (params tmp-file) + "Callback for async value results. +Assigned locally to `ob-session-async-file-callback' in R +comint buffers used for asynchronous Babel evaluation." + (let* ((graphics-file (and (member "graphics" (assq :result-params params)) + (org-babel-graphical-output-file params))) + (colnames-p (unless graphics-file (cdr (assq :colnames params))))) + (org-babel-R-process-value-result + (org-babel-result-cond (assq :result-params params) + (with-temp-buffer + (insert-file-contents tmp-file) + (org-babel-chomp (buffer-string) "\n")) + (org-babel-import-elisp-from-file tmp-file '(16))) + (or (equal "yes" colnames-p) + (org-babel-pick-name + (cdr (assq :colname-names params)) colnames-p))))) + + + +;;; ob-session-async-R.el ends here + + (provide 'ob-R) ;;; ob-R.el ends here |