From: Aaron Ecay <aaronecay@gmail.com>
To: emacs-orgmode@gnu.org
Subject: Re: R code block produces only partial output
Date: Sat, 23 Aug 2014 13:10:36 -0400 [thread overview]
Message-ID: <87tx53p1wz.fsf@gmail.com> (raw)
In-Reply-To: <871ts7r4ho.fsf@gmail.com>
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Here’s another version of the previous patch which fixes a couple bugs
related to
1) changing the window configuration unwarrantedly
2) syntactically invalid R code (mismatched parens or quotes) could hang
emacs
It’s easy to get R to throw an error in the mismatched-parens case, but
more difficult to recover from the mismatched-quotes one. Thus, when
babel detects such a case it bails and signals a user-error in emacs.
(Under the present code in master, both the mismatched-parens and
mismatched-quotes cases hang emacs pending a manual C-g.)
The patch is now firmly into the territory of gross hacks, so I’d much
prefer the evaluate-based approach if it can be made palatable.
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From afa24835f2a170c59a044dcf3bcf0ee765e8b568 Mon Sep 17 00:00:00 2001
From: Aaron Ecay <aaronecay@gmail.com>
Date: Sat, 16 Aug 2014 00:49:05 -0400
Subject: [PATCH] ob-R: overhaul handling of :output results type in a session
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
* (org-babel-R-evaluate-session): Capture output using ‘ess-execute’.
This function dumps the output from R into a buffer; we then use some
tricks to clean it of spurious text.
---
lisp/ob-R.el | 69 ++++++++++++++++++++++++++++++++++++++++++++----------------
1 file changed, 51 insertions(+), 18 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 41b943c..fbd4af4 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -364,9 +364,10 @@ last statement in BODY, as elisp."
(output (org-babel-eval org-babel-R-command body))))
(defvar ess-eval-visibly-p)
+(defvar ess-execute-in-process-buffer)
(defun org-babel-R-evaluate-session
- (session body result-type result-params column-names-p row-names-p)
+ (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
@@ -396,23 +397,55 @@ last statement in BODY, as elisp."
(org-babel-import-elisp-from-file tmp-file '(16)))
column-names-p)))
(output
- (mapconcat
- 'org-babel-chomp
- (butlast
- (delq nil
- (mapcar
- (lambda (line) (when (> (length line) 0) line))
- (mapcar
- (lambda (line) ;; cleanup extra prompts left in output
- (if (string-match
- "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
- (substring line (match-end 1))
- line))
- (org-babel-comint-with-output (session org-babel-R-eoe-output)
- (insert (mapconcat 'org-babel-chomp
- (list body org-babel-R-eoe-indicator)
- "\n"))
- (inferior-ess-send-input)))))) "\n"))))
+ (let* ((sentinel-file (org-babel-temp-file "R-")))
+ ;; This code borrowed from
+ ;; `org-babel-comint-eval-invisibly-and-wait-for-file'
+ (unless (org-babel-comint-buffer-livep session)
+ (error "Buffer %s does not exist or has no process" session))
+ (if (file-exists-p sentinel-file) (delete-file sentinel-file))
+ (with-current-buffer session
+ (let ((ess-execute-in-process-buffer nil)
+ (temp-buffer-show-function #'ignore))
+ (ess-execute (format
+ "
+.org.old.opts <- options(prompt = \"# Org babel prompt\\n\", continue = \"# Org babel prompt\\n\")
+cat(\"# Org babel begin output\n\")
+{
+%s
+#ORG-BABEL-OOPS\"#'
+}
+cat(\"# Org babel end output\n\")
+options(.org.old.opts)
+rm(.org.old.opts)
+file.create(%S)
+"
+ (org-babel-chomp body)
+ (if (tramp-tramp-file-p sentinel-file)
+ (tramp-file-name-localname
+ (tramp-dissect-file-name sentinel-file))
+ sentinel-file))
+ nil "org-babel-R-output"))
+ ;; From Tramp 2.1.19 the following cache flush is not necessary
+ (if (file-remote-p default-directory)
+ (let (v)
+ (with-parsed-tramp-file-name default-directory nil
+ (tramp-flush-directory-property v "")))))
+ (while (not (file-exists-p sentinel-file)) (sit-for 0.25))
+ ;; End borrowed code.
+ (with-current-buffer "*org-babel-R-output*"
+ (goto-char (point-min))
+ (when (search-forward "ORG-BABEL-OOPS")
+ (user-error "Mismatched quotation marks in babel code; could not parse output."))
+ (search-forward "# Org babel begin output")
+ (delete-region (point-min) (1+ (point)))
+ (goto-char (point-max))
+ (search-backward "# Org babel end output")
+ (delete-region (point) (point-max))
+ (goto-char (point-min))
+ (flush-lines "^$")
+ (flush-lines "^# Org babel prompt$")
+ (delete-trailing-whitespace)
+ (buffer-string))))))
(defun org-babel-R-process-value-result (result column-names-p)
"R-specific processing of return value.
--
2.0.4
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--
Aaron Ecay
next prev parent reply other threads:[~2014-08-23 17:10 UTC|newest]
Thread overview: 41+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-08-04 11:18 R code block produces only partial output Andreas Kiermeier
2014-08-04 11:53 ` Eric Schulte
2014-08-04 12:23 ` Andreas Kiermeier
2014-08-04 13:10 ` Eric Schulte
2014-08-05 0:46 ` Andreas Kiermeier
2014-08-05 4:00 ` John Hendy
2014-08-05 4:31 ` Andreas Kiermeier
2014-08-05 18:05 ` Charles Berry
2014-08-05 19:02 ` Eric Schulte
2014-08-05 19:11 ` John Hendy
2014-08-05 19:57 ` Nick Dokos
2014-08-05 20:10 ` Nick Dokos
2014-08-05 22:21 ` Charles C. Berry
2014-08-06 3:32 ` Aaron Ecay
2014-08-06 11:30 ` Eric Schulte
2014-08-07 6:00 ` Aaron Ecay
2014-08-07 17:42 ` Charles C. Berry
2014-08-07 18:06 ` Aaron Ecay
2014-08-07 18:42 ` Charles C. Berry
2014-08-07 19:06 ` Thomas S. Dye
2014-08-09 8:54 ` Rainer M Krug
2014-08-16 5:05 ` Aaron Ecay
2014-08-16 18:50 ` Charles C. Berry
2014-08-16 20:58 ` Aaron Ecay
2014-08-17 6:03 ` Achim Gratz
2014-08-19 0:13 ` Aaron Ecay
2014-08-19 5:36 ` Achim Gratz
2014-08-23 8:32 ` Aaron Ecay
2014-08-23 9:24 ` Andreas Kiermeier
2014-08-23 17:10 ` Aaron Ecay [this message]
2014-08-23 18:35 ` Thomas S. Dye
2014-08-23 19:37 ` Ista Zahn
2014-08-24 0:10 ` Charles C. Berry
2014-08-28 5:24 ` Aaron Ecay
2014-09-01 5:00 ` Aaron Ecay
2014-09-01 16:08 ` Charles C. Berry
2014-08-09 8:48 ` Rainer M Krug
2014-08-06 1:11 ` Andreas Kiermeier
2014-08-06 2:21 ` Charles C. Berry
2014-08-06 3:24 ` Aaron Ecay
2014-08-06 15:59 ` Charles C. Berry
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