emacs-orgmode@gnu.org archives
 help / color / mirror / code / Atom feed
blob 14e2c976ad9f15fcb1ecb9b803bdcb1dd785a4f2 16931 bytes (raw)
name: lisp/ob-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
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
 
;;; ob-R.el --- Babel Functions for R                -*- lexical-binding: t; -*-

;; Copyright (C) 2009-2020 Free Software Foundation, Inc.

;; Author: Eric Schulte
;;	Dan Davison
;; Keywords: literate programming, reproducible research, R, statistics
;; Homepage: https://orgmode.org

;; This file is part of GNU Emacs.

;; GNU Emacs 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 of the License, or
;; (at your option) any later version.

;; GNU Emacs 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.  If not, see <https://www.gnu.org/licenses/>.

;;; Commentary:

;; Org-Babel support for evaluating R code

;;; Code:

(require 'cl-lib)
(require 'ob)

(declare-function orgtbl-to-tsv "org-table" (table params))
(declare-function R "ext:essd-r" (&optional start-args))
(declare-function inferior-ess-send-input "ext:ess-inf" ())
(declare-function ess-make-buffer-current "ext:ess-inf" ())
(declare-function ess-eval-buffer "ext:ess-inf" (vis))
(declare-function ess-wait-for-process "ext:ess-inf"
		  (&optional proc sec-prompt wait force-redisplay))

(defconst org-babel-header-args:R
  '((width		 . :any)
    (height		 . :any)
    (bg			 . :any)
    (units		 . :any)
    (pointsize		 . :any)
    (antialias		 . :any)
    (quality		 . :any)
    (compression	 . :any)
    (res		 . :any)
    (type		 . :any)
    (family		 . :any)
    (title		 . :any)
    (fonts		 . :any)
    (version		 . :any)
    (paper		 . :any)
    (encoding		 . :any)
    (pagecentre		 . :any)
    (colormodel		 . :any)
    (useDingbats	 . :any)
    (horizontal		 . :any)
    (results             . ((file list vector table scalar verbatim)
			    (raw html latex org code pp drawer)
			    (replace silent none append prepend)
			    (output value graphics))))
  "R-specific header arguments.")

(defconst ob-R-safe-header-args
  (append org-babel-safe-header-args
	  '(:width :height :bg :units :pointsize :antialias :quality
		   :compression :res :type :family :title :fonts
		   :version :paper :encoding :pagecentre :colormodel
		   :useDingbats :horizontal))
  "Header args which are safe for R babel blocks.

See `org-babel-safe-header-args' for documentation of the format of
this variable.")

(defvar org-babel-default-header-args:R '())
(put 'org-babel-default-header-args:R 'safe-local-variable
     (org-babel-header-args-safe-fn ob-R-safe-header-args))

(defcustom org-babel-R-command "R --slave --no-save"
  "Name of command to use for executing R code."
  :group 'org-babel
  :version "24.1"
  :type 'string)

(defvar ess-current-process-name) ; dynamically scoped
(defvar ess-local-process-name)   ; dynamically scoped
(defun org-babel-edit-prep:R (info)
  (let ((session (cdr (assq :session (nth 2 info)))))
    (when (and session
	       (string-prefix-p "*"  session)
	       (string-suffix-p "*" session))
      (org-babel-R-initiate-session session nil))))

;; The usage of utils::read.table() ensures that the command
;; read.table() can be found even in circumstances when the utils
;; package is not in the search path from R.
(defconst ob-R-transfer-variable-table-with-header
  "%s <- local({
     con <- textConnection(
       %S
     )
     res <- utils::read.table(
       con,
       header    = %s,
       row.names = %s,
       sep       = \"\\t\",
       as.is     = TRUE
     )
     close(con)
     res
   })"
  "R code used to transfer a table defined as a variable from org to R.

This function is used when the table contains a header.")

(defconst ob-R-transfer-variable-table-without-header
  "%s <- local({
     con <- textConnection(
       %S
     )
     res <- utils::read.table(
       con,
       header    = %s,
       row.names = %s,
       sep       = \"\\t\",
       as.is     = TRUE,
       fill      = TRUE,
       col.names = paste(\"V\", seq_len(%d), sep =\"\")
     )
     close(con)
     res
   })"
  "R code used to transfer a table defined as a variable from org to R.

This function is used when the table does not contain a header.")

(defun org-babel-expand-body:R (body params &optional _graphics-file)
  "Expand BODY according to PARAMS, return the expanded body."
  (mapconcat 'identity
	     (append
	      (when (cdr (assq :prologue params))
		(list (cdr (assq :prologue params))))
	      (org-babel-variable-assignments:R params)
	      (list body)
	      (when (cdr (assq :epilogue params))
		(list (cdr (assq :epilogue params)))))
	     "\n"))

(defun org-babel-execute:R (body params)
  "Execute a block of R code.
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)))
           (session (org-babel-R-initiate-session
		     (cdr (assq :session params)) params))
	   (graphics-file (and (member "graphics" (assq :result-params params))
			       (org-babel-graphical-output-file params)))
	   (colnames-p (unless graphics-file (cdr (assq :colnames params))))
	   (rownames-p (unless graphics-file (cdr (assq :rownames params))))
	   (full-body
	    (let ((inside
		   (list (org-babel-expand-body:R body params graphics-file))))
	      (mapconcat 'identity
			 (if graphics-file
			     (append
			      (list (org-babel-R-construct-graphics-device-call
				     graphics-file params))
			      inside
			      (list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
			   inside)
			 "\n")))
	   (result
	    (org-babel-R-evaluate
	     session full-body result-type result-params
	     (or (equal "yes" colnames-p)
		 (org-babel-pick-name
		  (cdr (assq :colname-names params)) colnames-p))
	     (or (equal "yes" rownames-p)
		 (org-babel-pick-name
		  (cdr (assq :rowname-names params)) rownames-p)))))
      (if graphics-file nil 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))
	 (var-lines (org-babel-variable-assignments:R params)))
    (org-babel-comint-in-buffer session
      (mapc (lambda (var)
              (end-of-line 1) (insert var) (comint-send-input nil t)
              (org-babel-comint-wait-for-output session))
	    var-lines))
    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-variable-assignments:R (params)
  "Return list of R statements assigning the block's variables."
  (let ((vars (org-babel--get-vars params)))
    (mapcar
     (lambda (pair)
       (org-babel-R-assign-elisp
	(car pair) (cdr pair)
	(equal "yes" (cdr (assq :colnames params)))
	(equal "yes" (cdr (assq :rownames params)))))
     (mapcar
      (lambda (i)
	(cons (car (nth i vars))
	      (org-babel-reassemble-table
	       (cdr (nth i vars))
	       (cdr (nth i (cdr (assq :colname-names params))))
	       (cdr (nth i (cdr (assq :rowname-names params)))))))
      (number-sequence 0 (1- (length vars)))))))

(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 colnames-p rownames-p)
  "Construct R code assigning the elisp VALUE to a variable named NAME."
  (if (listp value)
      (let* ((lengths (mapcar 'length (cl-remove-if-not 'sequencep value)))
	     (max (if lengths (apply 'max lengths) 0))
	     (min (if lengths (apply 'min lengths) 0)))
        ;; Ensure VALUE has an orgtbl structure (depth of at least 2).
        (unless (listp (car value)) (setq value (list value)))
	(let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
	      (header (if (or (eq (nth 1 value) 'hline) colnames-p)
			  "TRUE" "FALSE"))
	      (row-names (if rownames-p "1" "NULL")))
	  (if (= max min)
	      (format ob-R-transfer-variable-table-with-header
		      name file header row-names)
	    (format ob-R-transfer-variable-table-without-header
		    name file header row-names max))))
    (cond ((integerp value) (format "%s <- %s" name (concat (number-to-string value) "L")))
	  ((floatp   value) (format "%s <- %s" name value))
	  ((stringp  value) (format "%s <- %S" name (org-no-properties value)))
	  (t                (format "%s <- %S" name (prin1-to-string value))))))


(defvar ess-ask-for-ess-directory) ; dynamically scoped
(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
	   (and (boundp 'ess-ask-for-ess-directory)
		ess-ask-for-ess-directory
		(not (cdr (assq :dir params))))))
      (if (org-babel-comint-buffer-livep session)
	  session
	(save-window-excursion
	  (when (get-buffer session)
	    ;; Session buffer exists, but with dead process
	    (set-buffer session))
	  (require 'ess) (R)
	  (let ((R-proc (get-process (or ess-local-process-name
					 ess-current-process-name))))
	    (while (process-get R-proc 'callbacks)
	      (ess-wait-for-process R-proc)))
	  (rename-buffer
	   (if (bufferp session)
	       (buffer-name session)
	     (if (stringp session)
		 session
	       (buffer-name))))
	  (current-buffer))))))

(defun org-babel-R-associate-session (session)
  "Associate R code buffer with an R session.
Make SESSION be the inferior ESS process associated with the
current code buffer."
  (setq ess-local-process-name
	(process-name (get-buffer-process session)))
  (ess-make-buffer-current))

(defvar org-babel-R-graphics-devices
  '((:bmp "bmp" "filename")
    (:jpg "jpeg" "filename")
    (:jpeg "jpeg" "filename")
    (:tikz "tikz" "file")
    (:tiff "tiff" "filename")
    (:png "png" "filename")
    (:svg "svg" "file")
    (:pdf "pdf" "file")
    (:ps "postscript" "file")
    (:postscript "postscript" "file"))
  "An alist mapping graphics file types to R functions.

Each member of this list is a list with three members:
1. the file extension of the graphics file, as an elisp :keyword
2. the R graphics device function to call to generate such a file
3. the name of the argument to this function which specifies the
   file to write to (typically \"file\" or \"filename\")")

(defun org-babel-R-construct-graphics-device-call (out-file params)
  "Construct the call to the graphics device."
  (let* ((allowed-args '(:width :height :bg :units :pointsize
				:antialias :quality :compression :res
				:type :family :title :fonts :version
				:paper :encoding :pagecentre :colormodel
				:useDingbats :horizontal))
	 (device (file-name-extension out-file))
	 (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)
    (setq device (nth 1 device-info))
    (setq filearg (nth 2 device-info))
    (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); tryCatch({"
	    device filearg out-file args
	    (if extra-args "," "") (or extra-args ""))))

(defconst org-babel-R-eoe-indicator "'org_babel_R_eoe'")
(defconst org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")

(defconst org-babel-R-write-object-command "{
    function(object,transfer.file) {
        object
        invisible(
            if (
                inherits(
                    try(
                        {
                            tfile<-tempfile()
                            write.table(object, file=tfile, sep=\"\\t\",
                                        na=\"nil\",row.names=%s,col.names=%s,
                                        quote=FALSE)
                            file.rename(tfile,transfer.file)
                        },
                        silent=TRUE),
                    \"try-error\"))
                {
                    if(!file.exists(transfer.file))
                        file.create(transfer.file)
                }
            )
    }
}(object=%s,transfer.file=\"%s\")"
  "A template for an R command to evaluate a block of code and write the result to a file.

Has four %s escapes to be filled in:
1. Row names, \"TRUE\" or \"FALSE\"
2. Column names, \"TRUE\" or \"FALSE\"
3. The code to be run (must be an expression, not a statement)
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)
  "Evaluate R code in BODY."
  (if session
      (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)))

(defun org-babel-R-evaluate-external-process
    (body result-type result-params column-names-p row-names-p)
  "Evaluate BODY in external R process.
If RESULT-TYPE equals `output' then return standard output as a
string.  If RESULT-TYPE equals `value' then return the value of the
last statement in BODY, as elisp."
  (cl-case result-type
    (value
     (let ((tmp-file (org-babel-temp-file "R-")))
       (org-babel-eval org-babel-R-command
		       (format org-babel-R-write-object-command
			       (if row-names-p "TRUE" "FALSE")
			       (if column-names-p
				   (if row-names-p "NA" "TRUE")
				 "FALSE")
			       (format "{function ()\n{\n%s\n}}()" body)
			       (org-babel-process-file-name tmp-file 'noquote)))
       (org-babel-R-process-value-result
	(org-babel-result-cond result-params
	  (with-temp-buffer
	    (insert-file-contents tmp-file)
	    (org-babel-chomp (buffer-string) "\n"))
	  (org-babel-import-elisp-from-file tmp-file '(16)))
	column-names-p)))
    (output (org-babel-eval org-babel-R-command body))))

(defvar ess-eval-visibly-p)

(defun org-babel-R-evaluate-session
    (session body result-type result-params column-names-p row-names-p)
  "Evaluate BODY in SESSION.
If RESULT-TYPE equals `output' then return standard output as a
string.  If RESULT-TYPE equals `value' then return the value of the
last statement in BODY, as elisp."
  (cl-case result-type
    (value
     (with-temp-buffer
       (insert (org-babel-chomp body))
       (let ((ess-local-process-name
	      (process-name (get-buffer-process session)))
	     (ess-eval-visibly-p nil))
	 (ess-eval-buffer nil)))
     (let ((tmp-file (org-babel-temp-file "R-")))
       (org-babel-comint-eval-invisibly-and-wait-for-file
	session tmp-file
	(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)))
       (org-babel-R-process-value-result
	(org-babel-result-cond result-params
	  (with-temp-buffer
	    (insert-file-contents tmp-file)
	    (org-babel-chomp (buffer-string) "\n"))
	  (org-babel-import-elisp-from-file tmp-file '(16)))
	column-names-p)))
    (output
     (let* ((tmp-file (org-babel-temp-file "R-")))
       (with-temp-file tmp-file
	 (insert body))
       (with-current-buffer session
	 (let* ((process (get-buffer-process (current-buffer)))
		(string-buffer "")
		(comint-output-filter-functions
		 (cons (lambda (text) (setq string-buffer
					    (concat string-buffer text)))
		       comint-output-filter-functions)))
	   (ess-send-string
	    process (format "tryCatch(source('%s', print.eval=TRUE), finally=print(%s))"
			    (org-babel-process-file-name tmp-file 'noquote)
			    org-babel-R-eoe-indicator))
	   (while (not (string-match (regexp-quote org-babel-R-eoe-output)
				     string-buffer))
	     (accept-process-output process))
	   (substring string-buffer 0 (match-beginning 0))))))))

(defun org-babel-R-process-value-result (result column-names-p)
  "R-specific processing of return value.
Insert hline if column names in output have been requested."
  (if column-names-p
      (condition-case nil
	  (cons (car result) (cons 'hline (cdr result)))
	(error "Could not parse R result"))
    result))

(provide 'ob-R)

;;; ob-R.el ends here

debug log:

solving 5ddf0ebd1 ...
found 5ddf0ebd1 in https://list.orgmode.org/orgmode/CA+M2ft_sg=CQd7W_HjLzwEFVuK9pG_NGR15xop3OU0i2G3ccvA@mail.gmail.com/ ||
	https://list.orgmode.org/orgmode/87pn6y9dqy.fsf@gmail.com/
found b37e3965a in https://list.orgmode.org/orgmode/CA+M2ft_sg=CQd7W_HjLzwEFVuK9pG_NGR15xop3OU0i2G3ccvA@mail.gmail.com/ ||
	https://list.orgmode.org/orgmode/87tuwa9ez4.fsf@gmail.com/
found 5e9d35f58 in https://git.savannah.gnu.org/cgit/emacs/org-mode.git
preparing index
index prepared:
100644 5e9d35f58e2d2677a4d81928f8ab80e4e9ade4d2	lisp/ob-R.el

applying [1/2] https://list.orgmode.org/orgmode/CA+M2ft_sg=CQd7W_HjLzwEFVuK9pG_NGR15xop3OU0i2G3ccvA@mail.gmail.com/
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 5e9d35f58..b37e3965a 100644

Checking patch lisp/ob-R.el...
Hunk #1 succeeded at 437 (offset -2 lines).
Applied patch lisp/ob-R.el cleanly.

skipping https://list.orgmode.org/orgmode/87tuwa9ez4.fsf@gmail.com/ for b37e3965a
index at:
100644 beb393a1a066dab4d59048e5004bb69c065b58a7	lisp/ob-R.el

applying [2/2] https://list.orgmode.org/orgmode/CA+M2ft_sg=CQd7W_HjLzwEFVuK9pG_NGR15xop3OU0i2G3ccvA@mail.gmail.com/
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index b37e3965a..5ddf0ebd1 100644

Checking patch lisp/ob-R.el...
Hunk #1 succeeded at 439 (offset -2 lines).
Hunk #2 succeeded at 448 (offset -2 lines).
Applied patch lisp/ob-R.el cleanly.

skipping https://list.orgmode.org/orgmode/87pn6y9dqy.fsf@gmail.com/ for 5ddf0ebd1
index at:
100644 14e2c976ad9f15fcb1ecb9b803bdcb1dd785a4f2	lisp/ob-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).