emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
blob bc0d67f5b385509c73394125a0250a827b8529c6 8921 bytes (raw)
name: contrib/babel/lisp/langs/org-babel-R.el 	 # note: path name is non-authoritative(*)

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
 
;;; org-babel-R.el --- org-babel functions for R code evaluation

;; Copyright (C) 2009 Eric Schulte

;; Author: Eric Schulte
;; Keywords: literate programming, reproducible research, R, statistics
;; Homepage: http://orgmode.org
;; Version: 0.01

;;; License:

;; This program is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 3, or (at your option)
;; any later version.
;;
;; This program is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.
;;
;; You should have received a copy of the GNU General Public License
;; along with GNU Emacs; see the file COPYING.  If not, write to the
;; Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
;; Boston, MA 02110-1301, USA.

;;; Commentary:

;; Org-Babel support for evaluating R code

;;; Code:
(require 'org-babel)

(org-babel-add-interpreter "R")

(add-to-list 'org-babel-tangle-langs '("R" "R" "#!/usr/bin/env Rscript"))

(defun org-babel-execute:R (body params)
  "Execute a block of R code with org-babel.  This function is
called by `org-babel-execute-src-block'."
  (message "executing R source code block...")
  (save-excursion
    (let* ((processed-params (org-babel-process-params params))
           (result-type (fourth processed-params))
           (session (org-babel-R-initiate-session (first processed-params) params))
           (vars (second processed-params))
	   (column-names-p (and (cdr (assoc :colnames params))
				(string= "yes" (cdr (assoc :colnames params)))))
	   (row-names-p (and (cdr (assoc :rownames params))
				(string= "yes" (cdr (assoc :rownames params)))))
	   (out-file (cdr (assoc :file params)))
	   (augmented-body
	    (concat
	     (if out-file (concat (org-babel-R-construct-graphics-device-call out-file params) "\n") "")
	     (mapconcat ;; define any variables
	      (lambda (pair) (org-babel-R-assign-elisp (car pair) (cdr pair))) vars "\n")
	     "\n" body "\n" (if out-file "dev.off()\n" "")))
	   (result (org-babel-R-evaluate session augmented-body result-type column-names-p row-names-p)))
      (or out-file result))))

(defun org-babel-prep-session:R (session params)
  "Prepare SESSION according to the header arguments specified in PARAMS."
  (let* ((session (org-babel-R-initiate-session session params))
         (vars (org-babel-ref-variables params)))
    (mapc (lambda (pair) (org-babel-R-assign-elisp session (car pair) (cdr pair))) vars)
    session))

(defun org-babel-load-session:R (session body params)
  "Load BODY into SESSION."
  (save-window-excursion
    (let ((buffer (org-babel-prep-session:R session params)))
      (with-current-buffer buffer
        (goto-char (process-mark (get-buffer-process (current-buffer))))
        (insert (org-babel-chomp body)))
      buffer)))

;; helper functions

(defun org-babel-R-quote-tsv-field (s)
  "Quote field S for export to R."
  (if (stringp s)
      (concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
    (format "%S" s)))

(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 (org-babel-maybe-remote-file transition-file)
          (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
          (insert "\n"))
        (format "%s <- read.table(\"%s\", header=%s, sep=\"\\t\", as.is=TRUE)"
                name transition-file (if (eq (second value) 'hline) "TRUE" "FALSE")))
    (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))

(defun org-babel-R-initiate-session (session params)
  "If there is not a current R process then create one."
  (unless (string= session "none")
    (let ((session (or session "*R*"))
	  (ess-ask-for-ess-directory (not (cdr (assoc :dir params)))))
      (if (org-babel-comint-buffer-livep session)
	  session
	(save-window-excursion
	  (R)
	  (rename-buffer (if (bufferp session) (buffer-name session)
			   (if (stringp session) session (buffer-name)))) (current-buffer))))))

(defun org-babel-R-construct-graphics-device-call (out-file params)
  "Construct the call to the graphics device"
  (let ((devices
	 '((:bmp . "bmp")
	   (:jpg . "jpeg")
	   (:jpeg . "jpeg")
	   (:tiff . "tiff")
	   (:png . "png")
	   (:pdf . "pdf")
	   (:ps . "postscript")
	   (:postscript . "postscript")))
	(allowed-args '(:width :height :bg :units :pointsize
			       :antialias :quality :compression :res :type
			       :family :title :fonts :version :paper :encoding
			       :pagecentre :colormodel :useDingbats :horizontal))
	(device (and (string-match ".+\\.\\([^.]+\\)" out-file) (match-string 1 out-file)))
	(extra-args (cdr (assq :R-dev-args params))) filearg args)
    (setq device (or (and device (cdr (assq (intern (concat ":" device)) devices))) "png"))
    (setq filearg (if (member device '("pdf" "postscript")) "file" "filename"))
    (setq args (mapconcat (lambda (pair)
			    (if (member (car pair) allowed-args)
				(format ",%s=%s" (substring (symbol-name (car pair)) 1) (cdr pair)) ""))
			  params ""))
    (format "%s(%s=\"%s\"%s%s%s)\n" device filearg out-file args (if extra-args "," "") (or extra-args ""))))

(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)")

(defun org-babel-R-evaluate (session body result-type column-names-p row-names-p)
  "Pass BODY to the R process in SESSION.  If RESULT-TYPE equals
'output then return a list of the outputs of the statements in
BODY, if RESULT-TYPE equals 'value then return the value of the
last statement in BODY, as elisp."
  (if (not session)
      ;; external process evaluation
      (case result-type
	(output
	 (with-temp-buffer
	   (insert body)
	   (org-babel-shell-command-on-region (point-min) (point-max) "R --slave --no-save" 'current-buffer 'replace)
	   (buffer-string)))
	(value
	 (let* ((tmp-file (make-temp-file "R-out-functional-results")) exit-code
		(stderr
		 (with-temp-buffer
		   (insert (format org-babel-R-wrapper-method
				   body tmp-file (if row-names-p "TRUE" "FALSE") (if column-names-p (if row-names-p "NA" "TRUE") "FALSE")))
		   (setq exit-code (org-babel-shell-command-on-region
				    (point-min) (point-max) "R --no-save" nil 'replace (current-buffer)))
		   (buffer-string))))
	   (if (> exit-code 0) (org-babel-error-notify exit-code stderr))
	   (org-babel-R-process-value-result
	    (org-babel-import-elisp-from-file (org-babel-maybe-remote-file tmp-file))
	    column-names-p))))
    ;; comint session evaluation
    (org-babel-comint-in-buffer session
      (let* ((tmp-file (make-temp-file "org-babel-R"))
	     (full-body
	      (case result-type
		(value
		 (mapconcat #'org-babel-chomp (list body
						    (format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=%s, col.names=%s, quote=FALSE)" tmp-file (if row-names-p "TRUE" "FALSE") (if column-names-p  (if row-names-p "NA" "TRUE") "FALSE"))
						    org-babel-R-eoe-indicator) "\n"))
		(output
		 (mapconcat #'org-babel-chomp (list body org-babel-R-eoe-indicator) "\n"))))
	     (raw (org-babel-comint-with-output session org-babel-R-eoe-output nil
                    (insert full-body) (inferior-ess-send-input)))
	     (comint-prompt-regexp
	      (concat "^\\("
		      inferior-ess-primary-prompt
		      "\\|"
		      inferior-ess-secondary-prompt
		      "\\)*"))
	     broke results)
        (case result-type
          (value (org-babel-R-process-value-result
		  (org-babel-import-elisp-from-file
		   (org-babel-maybe-remote-file tmp-file))
		  column-names-p))
          (output
	   (flet ((extractor
		   (el)
		   (if (or broke
			   (and (string-match (regexp-quote org-babel-R-eoe-output) el)
				(setq broke t)))
		       nil
		     (if (= (length el) 0)
			 nil
		       (if (string-match comint-prompt-regexp el)
			   (substring el (match-end 0))
			 el)))))
	     (mapconcat
	      #'identity
	      (delete nil (mapcar #'extractor (mapcar #'org-babel-chomp raw))) "\n"))))))))

(defun org-babel-R-process-value-result (result column-names-p)
  "R-specific processing of return value prior to return to org-babel.

Currently, insert hline if column names in output have been requested."
  (if column-names-p
      (cons (car result) (cons 'hline (cdr result)))
    result))
  

(provide 'org-babel-R)
;;; org-babel-R.el ends here

debug log:

solving f0d79b9 ...
found f0d79b9 in https://list.orgmode.org/orgmode/87eij95n7m.fsf@z.nozav.org/
found a8071b2 in https://git.savannah.gnu.org/cgit/emacs/org-mode.git
preparing index
index prepared:
100644 a8071b246e6f977bcc193117db59d7cb11f76370	contrib/babel/lisp/langs/org-babel-R.el

applying [1/1] https://list.orgmode.org/orgmode/87eij95n7m.fsf@z.nozav.org/
diff --git a/contrib/babel/lisp/langs/org-babel-R.el b/contrib/babel/lisp/langs/org-babel-R.el
index a8071b2..f0d79b9 100644

Checking patch contrib/babel/lisp/langs/org-babel-R.el...
Applied patch contrib/babel/lisp/langs/org-babel-R.el cleanly.

index at:
100644 bc0d67f5b385509c73394125a0250a827b8529c6	contrib/babel/lisp/langs/org-babel-R.el

(*) Git path names are given by the tree(s) the blob belongs to.
    Blobs themselves have no identifier aside from the hash of its contents.^

Code repositories for project(s) associated with this public inbox

	https://git.savannah.gnu.org/cgit/emacs/org-mode.git

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).