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
| | ;;; test-ob-R.el --- tests for ob-R.el -*- lexical-binding: t; -*-
;; Copyright (c) 2011-2014, 2019 Eric Schulte
;; Authors: Eric Schulte
;; This file is not part of GNU Emacs.
;; 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 of the License, 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 this program. If not, see <https://www.gnu.org/licenses/>.
;;; Code:
(org-test-for-executable "R")
(require 'ob-core)
(unless (featurep 'ess)
(signal 'missing-test-dependency "ESS"))
(defvar ess-ask-for-ess-directory)
(defvar ess-history-file)
(defvar ess-r-post-run-hook)
(declare-function
ess-command "ext:ess-inf"
(cmd &optional out-buffer sleep no-prompt-check wait proc proc force-redisplay timeout))
(declare-function ess-calculate-width "ext:ess-inf" (opt))
(unless (featurep 'ob-R)
(signal 'missing-test-dependency "Support for R code blocks"))
(ert-deftest test-ob-R/simple-session ()
(let (ess-ask-for-ess-directory ess-history-file)
(org-test-with-temp-text
"#+begin_src R :session R\n paste(\"Yep!\")\n#+end_src\n"
(should (string= "Yep!" (org-babel-execute-src-block))))))
(ert-deftest test-ob-R/colnames-yes-header-argument ()
(org-test-with-temp-text "#+name: eg
| col |
|-----|
| a |
| b |
#+header: :colnames yes
#+header: :var x = eg
#+begin_src R
x
#+end_src"
(org-babel-next-src-block)
(should (equal '(("col") hline ("a") ("b"))
(org-babel-execute-src-block)))))
(ert-deftest test-ob-R/colnames-nil-header-argument ()
(org-test-with-temp-text "#+name: eg
| col |
|-----|
| a |
| b |
#+header: :colnames nil
#+header: :var x = eg
#+begin_src R
x
#+end_src"
(org-babel-next-src-block)
(should (equal '(("col") hline ("a") ("b"))
(org-babel-execute-src-block)))))
(ert-deftest test-ob-R/colnames-no-header-argument ()
(org-test-with-temp-text "#+name: eg
| col |
|-----|
| a |
| b |
#+header: :colnames no
#+header: :var x = eg
#+begin_src R
x
#+end_src"
(org-babel-next-src-block)
(should (equal '(("col") ("a") ("b"))
(org-babel-execute-src-block)))))
(ert-deftest test-ob-R/results-file ()
(let (ess-ask-for-ess-directory ess-history-file)
(org-test-with-temp-text
"#+NAME: TESTSRC
#+BEGIN_SRC R :results file
a <- file.path(\"junk\", \"test.org\")
a
#+END_SRC"
(goto-char (point-min)) (org-babel-execute-maybe)
(org-babel-goto-named-result "TESTSRC") (forward-line 1)
(should (string= "[[file:junk/test.org]]"
(buffer-substring-no-properties (point-at-bol) (point-at-eol))))
(goto-char (point-min)) (forward-line 1)
(insert "#+header: :session\n")
(goto-char (point-min)) (org-babel-execute-maybe)
(org-babel-goto-named-result "TESTSRC") (forward-line 1)
(should (string= "[[file:junk/test.org]]"
(buffer-substring-no-properties (point-at-bol) (point-at-eol)))))))
(ert-deftest test-ob-r/output-with-<> ()
"make sure angle brackets are well formatted"
(let (ess-ask-for-ess-directory ess-history-file)
(should (string="[1] \"<X> <Y> <!>\"
[1] \"one <two> three\"
[1] \"end35\"
"
(org-test-with-temp-text "#+begin_src R :results output
print(\"<X> <Y> <!>\")
print(\"one <two> three\")
print(\"end35\")
#+end_src
"
(org-babel-execute-src-block))
))))
;; (ert-deftest test-ob-r/output-with-error ()
;; "make sure angle brackets are well formatted"
;; (let (ess-ask-for-ess-directory ess-history-file)
;; (should (string="Error in print(1/a) : object 'a' not found"
;; (org-test-with-temp-text "#+begin_src R :results output
;; print(1/a)
;; #+end_src
;; "
;; (org-babel-execute-src-block))
;; ))))
(ert-deftest test-ob-R/output-nonprinted ()
(let (ess-ask-for-ess-directory ess-history-file)
(org-test-with-temp-text
"#+begin_src R :results output
4.0 * 3.5
log(10)
log10(10)
\(3 + 1) * 5
3^-1
1/0
#+end_src"
(should (string= "[1] 14\n[1] 2.302585\n[1] 1\n[1] 20\n[1] 0.3333333\n[1] Inf\n" (org-babel-execute-src-block))))))
(ert-deftest test-ob-r/NA-blank ()
"For :results value, NAs should be empty"
(let (ess-ask-for-ess-directory ess-history-file)
(should (equal '(("A" "B") hline ("" 1) (1 2) (1 "") (1 4) (1 4))
(org-test-with-temp-text "#+BEGIN_SRC R :results value :colnames yes
data.frame(A=c(NA,1,1,1,1),B=c(1,2,NA,4,4))
#+end_src"
(org-babel-execute-src-block))))))
(ert-deftest ob-session-async-R-simple-session-async-value ()
(let (ess-ask-for-ess-directory
ess-history-file
(org-babel-temporary-directory "/tmp")
(org-confirm-babel-evaluate nil))
(org-test-with-temp-text
"#+begin_src R :session R :async yes\n Sys.sleep(.1)\n paste(\"Yep!\")\n#+end_src\n"
(should (let ((expected "Yep!"))
(and (not (string= expected (org-babel-execute-src-block)))
(string= expected
(progn
(sleep-for 0.200)
(goto-char (org-babel-where-is-src-block-result))
(org-babel-read-result)))))))))
(ert-deftest ob-session-async-R-simple-session-async-output ()
(let (ess-ask-for-ess-directory
ess-history-file
(org-babel-temporary-directory "/tmp")
(org-confirm-babel-evaluate nil)
;; Workaround for Emacs 27. See https://orgmode.org/list/87ilduqrem.fsf@localhost
(ess-r-post-run-hook (lambda () (ess-command (ess-calculate-width 9999)))))
(org-test-with-temp-text
"#+begin_src R :session R :results output :async yes\n Sys.sleep(.1)\n 1:5\n#+end_src\n"
(should (let ((expected "[1] 1 2 3 4 5"))
(and (not (string= expected (org-babel-execute-src-block)))
(string= expected
(progn
(sleep-for 0.200)
(goto-char (org-babel-where-is-src-block-result))
(org-babel-read-result)))))))))
(ert-deftest ob-session-async-R-named-output ()
(let (ess-ask-for-ess-directory
ess-history-file
(org-babel-temporary-directory "/tmp")
org-confirm-babel-evaluate
(src-block "#+begin_src R :async :session R :results output\n 1:5\n#+end_src")
(results-before "\n\n#+NAME: foobar\n#+RESULTS:\n: [1] 1")
(results-after "\n\n#+NAME: foobar\n#+RESULTS:\n: [1] 1 2 3 4 5\n")
;; Workaround for Emacs 27. See https://orgmode.org/list/87ilduqrem.fsf@localhost
(ess-r-post-run-hook (lambda () (ess-command (ess-calculate-width 9999)))))
(org-test-with-temp-text
(concat src-block results-before)
(should (progn (org-babel-execute-src-block)
(sleep-for 0.200)
(string= (concat src-block results-after)
(buffer-string)))))))
(ert-deftest ob-session-async-R-named-value ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :async :session R :results value\n paste(\"Yep!\")\n#+end_src")
(results-before "\n\n#+NAME: foobar\n#+RESULTS:\n: [1] 1")
(results-after "\n\n#+NAME: foobar\n#+RESULTS:\n: Yep!\n"))
(org-test-with-temp-text
(concat src-block results-before)
(should (progn (org-babel-execute-src-block)
(sleep-for 0.200)
(string= (concat src-block results-after)
(buffer-string)))))))
(ert-deftest ob-session-async-R-output-drawer ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :async :session R :results output drawer\n 1:5\n#+end_src")
(result "\n\n#+RESULTS:\n:results:\n[1] 1 2 3 4 5\n:end:\n")
;; Workaround for Emacs 27. See https://orgmode.org/list/87ilduqrem.fsf@localhost
(ess-r-post-run-hook (lambda () (ess-command (ess-calculate-width 9999)))))
(org-test-with-temp-text
src-block
(should (progn (org-babel-execute-src-block)
(sleep-for 0.200)
(string= (concat src-block result)
(buffer-string)))))))
(ert-deftest ob-session-async-R-value-drawer ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :async :session R :results value drawer\n 1:3\n#+end_src")
(result "\n\n#+RESULTS:\n:results:\n1\n2\n3\n:end:\n"))
(org-test-with-temp-text
src-block
(should (progn (org-babel-execute-src-block)
(sleep-for 0.200)
(string= (concat src-block result)
(buffer-string)))))))
; add test for :result output
(ert-deftest ob-session-R-result-output ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(src-block "#+begin_src R :session R :results output \n 1:3\n#+end_src")
(result "\n\n#+RESULTS:\n: [1] 1 2 3\n" ))
(org-test-with-temp-text
src-block
(should (progn (org-babel-execute-src-block)
(sleep-for 0.200)
(string= (concat src-block result)
(buffer-string)))))))
(ert-deftest ob-session-R-result-value ()
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp"))
(org-test-with-temp-text
"#+begin_src R :session R :results value \n 1:50\n#+end_src"
(should
(equal (number-sequence 1 50)
(mapcar #'car (org-babel-execute-src-block)))))))
;; test for printing of (nested) list
(ert-deftest ob-R-nested-list ()
"List are printed as the first column of a table and nested lists are ignored"
(let (ess-ask-for-ess-directory
ess-history-file
org-confirm-babel-evaluate
(org-babel-temporary-directory "/tmp")
(text "
#+NAME: example-list
- simple
- not
- nested
- list
#+BEGIN_SRC R :var x=example-list
x
#+END_SRC
")
(result "
#+RESULTS:
| simple |
| list |
"))
(org-test-with-temp-text-in-file
text
(goto-char (point-min))
(org-babel-next-src-block)
(should (progn
(org-babel-execute-src-block)
(sleep-for 0.200)
(string= (concat text result)
(buffer-string)))))))
(provide 'test-ob-R)
;;; test-ob-R.el ends here
|