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org-babel-R can now run in 'script' mode
This commit is contained in:
Eric Schulte
parent
ccddf78dca
commit
d3f1d07066
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@ -33,17 +33,34 @@
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(org-babel-add-interpreter "R")
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(defvar org-babel-R-buffer "org-babel-R"
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"Holds the buffer for the current R process")
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(defun org-babel-R-initiate-R-buffer ()
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"If there is not a current R process then create one."
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(unless (org-babel-comint-buffer-livep org-babel-R-buffer)
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(save-window-excursion (R) (setf org-babel-R-buffer (current-buffer)))))
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(defun org-babel-execute:R (body params)
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"Execute a block of R code with org-babel. This function is
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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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(results-params (split-string (cdr (assoc :results params))))
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results)
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(org-babel-R-initiate-R-buffer)
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(mapc (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars)
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(org-babel-R-input-command body)
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(org-babel-R-last-value-as-elisp))))
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(cond
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((member "script" results-params) ;; collect all output
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(let ((tmp-file (make-temp-file "org-babel-R-script-output")))
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(org-babel-comint-input-command org-babel-R-buffer (format "sink(%S)" tmp-file))
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(org-babel-comint-input-command org-babel-R-buffer body)
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(org-babel-comint-input-command org-babel-R-buffer "sink()")
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(with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
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((member "last" results-params) ;; the value of the last statement
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(org-babel-comint-input-command org-babel-R-buffer body)
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(org-babel-R-last-value-as-elisp))))))
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(defun org-babel-R-quote-tsv-field (s)
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"Quote field S for export to R."
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@ -55,7 +72,8 @@ called by `org-babel-execute-src-block'."
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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 org-babel-R-buffer (error "No active R buffer"))
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(org-babel-R-input-command
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(org-babel-comint-input-command
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org-babel-R-buffer
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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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@ -70,9 +88,10 @@ R process in `org-babel-R-buffer'."
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(defun org-babel-R-last-value-as-elisp ()
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"Return the last value returned by R as Emacs lisp."
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(let ((tmp-file (make-temp-file "org-babel-R")) result)
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(org-babel-R-input-command
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(org-babel-comint-input-command
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org-babel-R-buffer
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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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tmp-file))
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(with-temp-buffer
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(condition-case nil
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(progn
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@ -81,7 +100,6 @@ R process in `org-babel-R-buffer'."
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(setq result (mapcar (lambda (row)
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(mapcar #'org-babel-R-read row))
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(org-table-to-lisp))))
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(error nil))
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(if (null (cdr result)) ;; if result is trivial vector, then scalarize it
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(if (consp (car result))
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@ -98,66 +116,5 @@ R process in `org-babel-R-buffer'."
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(match-string 1 cell))
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cell)))
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;; functions for evaluation of R code
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(defvar org-babel-R-buffer nil
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"Holds the buffer for the current R process")
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(defun org-babel-R-initiate-R-buffer ()
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"If there is not a current R process then create one."
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(unless (and (buffer-live-p org-babel-R-buffer) (get-buffer org-babel-R-buffer))
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(save-excursion
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(R)
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(setf org-babel-R-buffer (current-buffer))
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(org-babel-R-wait-for-output)
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(org-babel-R-input-command ""))))
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(defun org-babel-R-command-to-string (command)
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"Send a command to R, and return the results as a string."
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(org-babel-R-input-command command)
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(org-babel-R-last-output))
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(defun org-babel-R-input-command (command)
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"Pass COMMAND to the R process running in `org-babel-R-buffer'."
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(save-excursion
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(save-match-data
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(set-buffer org-babel-R-buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(insert command)
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(comint-send-input)
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(org-babel-R-wait-for-output))))
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(defun org-babel-R-wait-for-output ()
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"Wait until output arrives"
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(save-excursion
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(save-match-data
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(set-buffer org-babel-R-buffer)
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(while (progn
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(goto-char comint-last-input-end)
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(not (re-search-forward comint-prompt-regexp nil t)))
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(accept-process-output (get-buffer-process (current-buffer)))))))
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(defun org-babel-R-last-output ()
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"Return the last R output as a string"
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(save-excursion
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(save-match-data
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(set-buffer org-babel-R-buffer)
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(goto-char (process-mark (get-buffer-process (current-buffer))))
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(forward-line 0)
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(let ((raw (buffer-substring comint-last-input-end (- (point) 1)))
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output output-flag)
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(mapconcat
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(lambda (el)
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(if (stringp el)
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(format "%s" el)
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(format "%S" el)))
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(delq nil
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(mapcar
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(lambda (line)
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(unless (string-match "^>" line)
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(and (string-match "\\[[[:digit:]]+\\] *\\(.*\\)$" line)
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(match-string 1 line))))
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;; drop first, because it's the last line of input
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(cdr (split-string raw "[\n\r]")))) "\n")))))
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(provide 'org-babel-R)
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;;; org-babel-R.el ends here
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@ -36,14 +36,14 @@
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(require 'org-babel)
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(require 'comint)
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(defun org-babel-ensure-buffer-livep (buffer)
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(unless (and (buffer-live-p buffer) (get-buffer buffer) (get-buffer-process buffer))
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(error (format "buffer %s doesn't exist or has no process" buffer))))
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(defun org-babel-comint-buffer-livep (buffer)
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(and (buffer-live-p buffer) (get-buffer buffer) (get-buffer-process buffer)))
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(defmacro org-babel-comint-in-buffer (buffer &rest body)
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`(save-window-excursion
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(save-match-data
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(org-babel-ensure-buffer-livep buffer)
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(unless (org-babel-comint-buffer-livep buffer)
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(error (format "buffer %s doesn't exist or has no process" buffer)))
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(set-buffer buffer)
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,@body)))
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@ -468,19 +468,39 @@ for the execution of source-code blocks.
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*** TODO rework evaluation lang-by-lang [0/4]
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This should include...
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- STDOUT and functional results
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- functional results working with the comint buffer
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- results headers
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- script :: return the output of STDOUT
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- write a macro which runs the first redirection, executes the
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body, then runs the second redirection
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- last :: return the value of the last statement
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-
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- sessions in comint buffers
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**** TODO R
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- [X] functional results working with comint
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- [X] script results
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- [ ] implement echo
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To redirect output to a file, you can use the =sink()= command.
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#+srcname: task-R-with-inf-process-buffer
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#+begin_src R
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#+begin_src R :results replace script scalar
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a <- 8
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b <- 9
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c <- 10
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a + b
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21
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a + b + c
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#+end_src
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#+resname: task-R-with-inf-process-buffer
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: [1] 17
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: [1] 21
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: [1] 27
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**** TODO Ruby
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#+srcname: ruby-use-last-output
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