From: Aaron Ecay <aaronecay@gmail.com>
To: "Charles C. Berry" <ccberry@ucsd.edu>
Cc: emacs-orgmode@gnu.org
Subject: Re: R code block produces only partial output
Date: Mon, 01 Sep 2014 01:00:55 -0400 [thread overview]
Message-ID: <87k35orl2w.fsf@gmail.com> (raw)
In-Reply-To: <87lhq9tcdj.fsf@gmail.com>
[-- Attachment #1: Type: text/plain, Size: 1013 bytes --]
Hi Chuck,
Attached is a new version of the patch, including a few more tests. I
have one question:
2014ko abuztuak 28an, Aaron Ecay-ek idatzi zuen:
>> but the patch here uses on.exit(file.create(...)) to ensure that that
>> file is created. One hiccup (not sure if it exists in master,too) is
>> that starting a remote session and then trying to run src blocks from
>> a buffer for a local file will hang (because a local temp file is used
>> for sentinel). So there is still stuff to do.
>
> Hmm, OK.
Can you give a recipe to reproduce this? Everything seems to work for
me using the following test code, although there is an unexplained ~10s
delay while babel sits in the ‘(while (not (file-exists-p file)) ...)’
loop at the end of ‘org-babel-comint-eval-invisibly-and-wait-for-file’.
,----
| #+name: foo
| #+begin_src R :session *foo* :dir /ssh:aecay@foo:/home/aecay :results output
| 1+1
| #+end_src
|
| #+RESULTS: foo
| : [1] 2
`----
Thanks,
--
Aaron Ecay
[-- Attachment #2: 0001-ob-R-overhaul-handling-of-output-results-type-in-a-s.patch --]
[-- Type: text/x-diff, Size: 7157 bytes --]
From 65aa82b71e709250717896ab9bc85bf144a8ee30 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
* lisp/ob-R.el (org-babel-R-check-evaluate-package): New function.
(org-babel-R-initiate-session): Use it.
(org-babel-R-evaluate-session): Use the evaluate package to capture
session output.
This uses the “evaluate” R package[1] to capture the
output (incl. warnings, errors, and messages) from a babel R session.
This avoids the output showing up in the session buffer, and dodges
some previous issues with removing R prompts (>) when scraping the
output from the session buffer.
Thanks to Charles C. Berry for assistance with this code.
[1] <http://cran.r-project.org/web/packages/evaluate/index.html>
---
lisp/ob-R.el | 73 +++++++++++++++++++++++++++++++++++------------
testing/lisp/test-ob-R.el | 61 +++++++++++++++++++++++++++++++++++++++
2 files changed, 115 insertions(+), 19 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 41b943c..81b3290 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -245,6 +245,22 @@ This function is called by `org-babel-execute-src-block'."
((stringp value) (format "%s <- %S" name (org-no-properties value)))
(t (format "%s <- %S" name (prin1-to-string value))))))
+(defvar ess-execute-in-process-buffer)
+(defun org-babel-R-check-evaluate-package (&optional recursive)
+ (save-window-excursion
+ (let ((ess-execute-in-process-buffer nil)
+ (r-buff (current-buffer)))
+ (ess-execute "library(evaluate)" nil "org-babel-R-auto")
+ (when (with-current-buffer "*org-babel-R-auto*"
+ (goto-char (point-min))
+ (search-forward "Error" nil t))
+ (if (and (not recursive)
+ (y-or-n-p "Cannot load the evaluate package required for babel session support, would you like to install it from CRAN?"))
+ (progn
+ (message "Downloading and installing package (may take some time)")
+ (ess-execute "install.packages(\"evaluate\")" nil "org-babel-R-auto")
+ (org-babel-R-check-evaluate-package t))
+ (user-error "R package evaluate is required, but not available."))))))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
@@ -261,7 +277,9 @@ This function is called by `org-babel-execute-src-block'."
(when (get-buffer session)
;; Session buffer exists, but with dead process
(set-buffer session))
- (require 'ess) (R)
+ (require 'ess)
+ (R)
+ (org-babel-R-check-evaluate-package)
(rename-buffer
(if (bufferp session)
(buffer-name session)
@@ -365,8 +383,27 @@ last statement in BODY, as elisp."
(defvar ess-eval-visibly-p)
+(defconst org-babel-R-session-cmd
+ "local({
+ on.exit(file.create(%S))
+ sink(%S)
+ withCallingHandlers(
+ replay(
+ Filter(Negate(is.source),
+ evaluate(%S, envir=parent.frame(2), new_device = FALSE,
+ stop_on_error = 0L))),
+ message = function (x) {
+ cat(x$message);
+ invokeRestart(\"muffleMessage\")
+ },
+ error = function (e) {
+ cat(e$message)
+ })
+ sink()})"
+"format string for an `R :session :results output' regime.")
+
(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 +433,21 @@ 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* ((output-file (org-babel-temp-file "R-"))
+ (sentinel-file (concat output-file "-sentinel")))
+ (org-babel-comint-eval-invisibly-and-wait-for-file
+ session sentinel-file
+ (format
+ org-babel-R-session-cmd
+ (org-babel-local-file-name sentinel-file)
+ (org-babel-local-file-name output-file)
+ (org-babel-chomp body)))
+ (with-temp-buffer
+ (insert-file-contents output-file)
+ (goto-char (point-min))
+ (flush-lines "^$")
+ (delete-trailing-whitespace)
+ (buffer-string))))))
(defun org-babel-R-process-value-result (result column-names-p)
"R-specific processing of return value.
diff --git a/testing/lisp/test-ob-R.el b/testing/lisp/test-ob-R.el
index e3f13f1..3d7ebef 100644
--- a/testing/lisp/test-ob-R.el
+++ b/testing/lisp/test-ob-R.el
@@ -79,6 +79,67 @@ x
(should (equal '(("col") ("a") ("b"))
(org-babel-execute-src-block)))))
+(ert-deftest test-ob-R/session-output ()
+ (org-test-with-temp-text "#+begin_src R :results output :session *foo*
+ 1
+ message(\"hi\")
+ 2
+ warning(\"hi2\")
+ 3
+ stop(\"hi3\")
+ 4
+#+end_src
+"
+ (should (string= (org-babel-execute-src-block)
+ "[1] 1
+hi
+[1] 2
+Warning message:
+hi2
+[1] 3
+Error: hi3
+[1] 4"))))
+
+(ert-deftest test-ob-R/session-output-stray-open-paren ()
+ (org-test-with-temp-text "#+begin_src R :results output :session *foo*
+ (
+#+end_src
+"
+ (should (string= (org-babel-execute-src-block)
+ "<text>:2:0: unexpected end of input
+1: (
+ ^"))))
+
+(ert-deftest test-ob-R/session-output-stray-close-paren ()
+ (org-test-with-temp-text "#+begin_src R :results output :session *foo*
+ )
+#+end_src
+"
+ (should (string= (org-babel-execute-src-block)
+ "<text>:1:1: unexpected ')'
+1: )
+ ^"))))
+
+(ert-deftest test-ob-R/session-output-stray-single-quote ()
+ (org-test-with-temp-text "#+begin_src R :results output :session *foo*
+ '
+#+end_src
+"
+ (should (string= (org-babel-execute-src-block)
+ "<text>:1:1: unexpected INCOMPLETE_STRING
+1: '
+ ^"))))
+
+(ert-deftest test-ob-R/session-output-stray-dbl-quote ()
+ (org-test-with-temp-text "#+begin_src R :results output :session *foo*
+ \"
+#+end_src
+"
+ (should (string= (org-babel-execute-src-block)
+ "<text>:1:1: unexpected INCOMPLETE_STRING
+1: \"
+ ^"))))
+
(provide 'test-ob-R)
;;; test-ob-R.el ends here
--
2.1.0
next prev parent reply other threads:[~2014-09-01 5:01 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
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 [this message]
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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