R is working with no session
This commit is contained in:
Eric Schulte
parent
e2d3cc7830
commit
82ecab19fb
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@ -96,43 +96,62 @@ R process in `org-babel-R-buffer'."
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(defun org-babel-R-initiate-session (session)
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"If there is not a current R process then create one."
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(setq session (or session "*R*"))
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(if (org-babel-comint-buffer-livep session)
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session
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(save-window-excursion (R) (rename-buffer (if (bufferp session) (buffer-name session)
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(if (stringp session) session (buffer-name)))) (current-buffer))))
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(unless (string= session "none")
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(setq session (or session "*R*"))
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(if (org-babel-comint-buffer-livep session)
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session
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(save-window-excursion (R) (rename-buffer (if (bufferp session) (buffer-name session)
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(if (stringp session) session (buffer-name)))) (current-buffer)))))
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(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
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(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
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(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
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write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)")
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(defun org-babel-R-evaluate (buffer body result-type)
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"Pass BODY to the R process in BUFFER. If RESULT-TYPE equals
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'output then return a list of the outputs of the statements in
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BODY, if RESULT-TYPE equals 'value then return the value of the
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last statement in BODY."
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(org-babel-comint-in-buffer buffer
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(let* ((tmp-file (make-temp-file "org-babel-R"))
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(last-value-eval
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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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(full-body (mapconcat #'org-babel-chomp (list body last-value-eval org-babel-R-eoe-indicator) "\n"))
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(raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
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(insert full-body) (inferior-ess-send-input)))
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(results (let ((broke nil))
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(delete nil (mapcar (lambda (el)
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(if (or broke
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(and (string-match (regexp-quote org-babel-R-eoe-output) el) (setq broke t)))
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nil
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(if (= (length el) 0)
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(if (not session)
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;; external process evaluation
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(let ((in-tmp-file (make-temp-file "R-in-functional-results"))
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(out-tmp-file (make-temp-file "R-out-functional-results")))
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(case result-type
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(output
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(with-temp-file in-tmp-file (insert body))
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(message "R --slave --no-save < '%s' > '%s'" in-tmp-file out-tmp-file)
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(shell-command-to-string (format "R --slave --no-save < '%s' > '%s'" in-tmp-file out-tmp-file)))
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(value
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(with-temp-file in-tmp-file
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(insert (format org-babel-R-wrapper-method body out-tmp-file)))
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(message "R --no-save < '%s'" in-tmp-file)
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(shell-command (format "R --no-save < '%s'" in-tmp-file))))
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(with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
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;; comint session evaluation
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(org-babel-comint-in-buffer buffer
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(let* ((tmp-file (make-temp-file "org-babel-R"))
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(last-value-eval
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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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(full-body (mapconcat #'org-babel-chomp (list body last-value-eval org-babel-R-eoe-indicator) "\n"))
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(raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
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(insert full-body) (inferior-ess-send-input)))
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(results (let ((broke nil))
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(delete nil (mapcar (lambda (el)
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(if (or broke
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(and (string-match (regexp-quote org-babel-R-eoe-output) el) (setq broke t)))
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nil
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(if (string-match comint-prompt-regexp el)
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(substring el (match-end 0))
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el))))
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(mapcar #'org-babel-trim raw))))))
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(case result-type
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(output (org-babel-trim (mapconcat #'identity results "\n")))
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(value (org-babel-trim (with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
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(t (reverse results))))))
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(if (= (length el) 0)
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nil
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(if (string-match comint-prompt-regexp el)
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(substring el (match-end 0))
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el))))
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(mapcar #'org-babel-trim raw))))))
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(case result-type
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(output (org-babel-trim (mapconcat #'identity results "\n")))
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(value (org-babel-trim (with-temp-buffer (insert-file-contents tmp-file) (buffer-string))))
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(t (reverse results)))))))
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(provide 'org-babel-R)
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;;; org-babel-R.el ends here
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133
org-babel.org
133
org-babel.org
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@ -114,7 +114,7 @@ table, allowing the test suite to be run be evaluation of the table
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and the results to be collected in the same table.
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* Tasks [25/42]
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* Tasks [26/42]
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** TODO add a function to jump to a source-block by name
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I've had an initial stab at that in org-babel-find-named-block
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(library-of-babel branch).
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@ -497,65 +497,6 @@ tabel
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Another example is in the [[*operations%20in%20on%20tables][grades example]].
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** PROPOSED add =:none= session argument (for purely functional execution) [3/4]
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This would allow source blocks to be run in their own new process
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- These blocks could then also be run in the background (since we can
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detach and just wait for the process to signal that it has terminated)
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- We wouldn't be drowning in session buffers after running the tests
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- we can re-use much of the session code to run in a more /functional/
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mode
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While session provide a lot of cool features, like persistent
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environments, [[* DONE function to bring up inferior-process buffer][pop-to-session]], and hints at exportation for
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org-babel-tangle, they also have some down sides and I'm thinking that
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session-based execution maybe shouldn't be the default behavior.
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Down-sides to sessions
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- *much* more complicated than functional evaluation
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- maintaining the state of the session has weird issues
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- waiting for evaluation to finish
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- prompt issues like [[* TODO weird escaped characters in shell prompt break shell evaluation][shell-prompt-escapes-bug]]
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- can't run in background
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- litter emacs with session buffers
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*** DONE ruby
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#+srcname: ruby-task-no-session
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#+begin_src ruby :results replace output
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puts :eric
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puts :schulte
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[1, 2, 3]
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#+end_src
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#+resname: ruby-task-no-session
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| "eric" |
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| "schulte" |
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*** DONE python
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#+srcname: task-python-none-session
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#+begin_src python :session none :results replace value
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print 'something'
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print 'output'
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[1, 2, 3]
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#+end_src
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#+resname: task-python-none-session
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| 1 | 2 | 3 |
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*** DONE sh
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#+srcname: task-session-none-sh
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#+begin_src sh :results replace
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echo "first"
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echo "second"
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#+end_src
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#+resname: task-session-none-sh
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| "first" |
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| "second" |
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*** TODO R
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** PROPOSED Are we happy with current behaviour regarding vector/scalar output?
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This simple example of multilingual chaining produces vector output if
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there are spaces in the message and scalar otherwise.
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@ -806,6 +747,78 @@ $0
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waiting for guidance from those more familiar with yasnippets
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** DONE add =:none= session argument (for purely functional execution) [4/4]
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This would allow source blocks to be run in their own new process
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- These blocks could then also be run in the background (since we can
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detach and just wait for the process to signal that it has terminated)
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- We wouldn't be drowning in session buffers after running the tests
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- we can re-use much of the session code to run in a more /functional/
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mode
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While session provide a lot of cool features, like persistent
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environments, [[* DONE function to bring up inferior-process buffer][pop-to-session]], and hints at exportation for
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org-babel-tangle, they also have some down sides and I'm thinking that
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session-based execution maybe shouldn't be the default behavior.
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Down-sides to sessions
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- *much* more complicated than functional evaluation
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- maintaining the state of the session has weird issues
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- waiting for evaluation to finish
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- prompt issues like [[* TODO weird escaped characters in shell prompt break shell evaluation][shell-prompt-escapes-bug]]
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- can't run in background
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- litter emacs with session buffers
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*** DONE ruby
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#+srcname: ruby-task-no-session
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#+begin_src ruby :results replace output
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puts :eric
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puts :schulte
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[1, 2, 3]
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#+end_src
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#+resname: ruby-task-no-session
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| "eric" |
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| "schulte" |
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*** DONE python
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#+srcname: task-python-none-session
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#+begin_src python :session none :results replace value
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print 'something'
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print 'output'
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[1, 2, 3]
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#+end_src
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#+resname: task-python-none-session
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| 1 | 2 | 3 |
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*** DONE sh
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#+srcname: task-session-none-sh
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#+begin_src sh :results replace
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echo "first"
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echo "second"
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#+end_src
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#+resname: task-session-none-sh
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| "first" |
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| "second" |
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*** DONE R
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#+srcname: task-no-session-R
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#+begin_src R :results replace output
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a <- 8
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b <- 9
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a + b
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b - a
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#+end_src
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#+resname: task-no-session-R
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| "[1]" | 17 |
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| "[1]" | 1 |
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** DONE fully purge org-babel-R of direct comint interaction
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try to remove all code under the [[file:lisp/org-babel-R.el::functions%20for%20evaluation%20of%20R%20code][;; functions for evaluation of R code]] line
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