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org-mode/testing/lisp/test-ob-R.el

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;;; 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
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