mirror of
https://git.savannah.gnu.org/git/emacs/org-mode.git
synced 2024-11-23 07:18:53 +00:00
3ff21c7138
This patch adds options to org-babel-comint-with-output to skip prompt removal. Allowing individual languages to handle this cleanup can be more robust than relying on the generic ob-comint implementation. This allows ob-python to switch back to using `org-babel-comint-with-output' rather than its own bespoke reimplementation, reducing code duplication. Furthermore, this adds a new implementation of ob-R non-async session output evaluation, that is similar to the ob-python approach in that it avoids leaking prompts, rather than relying on the cleanup from `org-babel-comint-with-output'. A test is added to test-ob-R.el to demonstrate the improved robustness of the new approach; previously, this test would fail due to a false positive prompt, but now passes. * lisp/ob-comint.el (org-babel-comint--remove-prompts-p): New helper function to parse the prompt-handling argument in `org-babel-comint-with-output' and `org-babel-comint-async-register'. (org-babel-comint-with-output): Add a new argument to prevent extra processing for prompt cleanup. Also, search for the end-of-execution sentinel within the collected output rather than the comint buffer, which doesn't depend on the position of point during evaluation. (org-babel-comint-async-register): Move parsing of prompt-handling argument to `org-babel-comint--remove-prompts-p'. * lisp/ob-python.el: Require subr-x for Emacs 27 compatibility. (org-babel-python-send-string): Switch to using `org-babel-comint-with-output', rather than bespoke reimplementation. * lisp/ob-R.el: Require subr-x for Emacs 27 compatibility. (ess-send-string): Declare external function. (org-babel-R-evaluate-session): New implementation of output evaluation that avoids leaking prompts, by writing the code block to a tmp file and then sourcing it. * testing/lisp/test-ob-R.el (test-ob-r/session-output-with->-bol): New test for robustness against false positive prompts at the beginning of a line.
563 lines
20 KiB
EmacsLisp
563 lines
20 KiB
EmacsLisp
;;; ob-R.el --- Babel Functions for R -*- lexical-binding: t; -*-
|
|
|
|
;; Copyright (C) 2009-2024 Free Software Foundation, Inc.
|
|
|
|
;; Author: Eric Schulte
|
|
;; Dan Davison
|
|
;; Maintainer: Jeremie Juste <jeremiejuste@gmail.com>
|
|
;; Keywords: literate programming, reproducible research, R, statistics
|
|
;; URL: https://orgmode.org
|
|
|
|
;; This file is part of GNU Emacs.
|
|
|
|
;; GNU Emacs 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.
|
|
|
|
;; GNU Emacs 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 GNU Emacs. If not, see <https://www.gnu.org/licenses/>.
|
|
|
|
;;; Commentary:
|
|
|
|
;; Org-Babel support for evaluating R code
|
|
|
|
;;; Code:
|
|
|
|
(require 'org-macs)
|
|
(org-assert-version)
|
|
|
|
(require 'cl-lib)
|
|
(require 'ob)
|
|
|
|
(require 'subr-x) ; For `string-trim-right', Emacs < 28
|
|
|
|
(declare-function orgtbl-to-tsv "org-table" (table params))
|
|
(declare-function run-ess-r "ext:ess-r-mode" (&optional start-args))
|
|
(declare-function inferior-ess-send-input "ext:ess-inf" ())
|
|
(declare-function ess-make-buffer-current "ext:ess-inf" ())
|
|
(declare-function ess-eval-buffer "ext:ess-inf" (vis))
|
|
(declare-function ess-wait-for-process "ext:ess-inf"
|
|
(&optional proc sec-prompt wait force-redisplay))
|
|
(declare-function ess-send-string "ext:ess-inf"
|
|
(process string &optional visibly message type))
|
|
|
|
(defvar ess-current-process-name) ; ess-custom.el
|
|
(defvar ess-local-process-name) ; ess-custom.el
|
|
(defvar ess-ask-for-ess-directory) ; ess-custom.el
|
|
(defvar ess-directory-function) ; ess-custom.el
|
|
(defvar ess-directory) ; ess-custom.el
|
|
(defvar ess-gen-proc-buffer-name-function) ; ess-custom.el
|
|
(defvar ess-eval-visibly) ; ess-custom.el
|
|
|
|
(defconst org-babel-header-args:R
|
|
'((width . :any)
|
|
(height . :any)
|
|
(bg . :any)
|
|
(units . :any)
|
|
(pointsize . :any)
|
|
(antialias . :any)
|
|
(quality . :any)
|
|
(compression . :any)
|
|
(res . :any)
|
|
(type . :any)
|
|
(family . :any)
|
|
(title . :any)
|
|
(fonts . :any)
|
|
(version . :any)
|
|
(paper . :any)
|
|
(encoding . :any)
|
|
(pagecentre . :any)
|
|
(colormodel . :any)
|
|
(useDingbats . :any)
|
|
(horizontal . :any)
|
|
(async . ((yes no)))
|
|
(results . ((file list vector table scalar verbatim)
|
|
(raw html latex org code pp drawer)
|
|
(replace silent none append prepend)
|
|
(output value graphics))))
|
|
"R-specific header arguments.")
|
|
|
|
(defconst ob-R-safe-header-args
|
|
(append org-babel-safe-header-args
|
|
'(:width :height :bg :units :pointsize :antialias :quality
|
|
:compression :res :type :family :title :fonts
|
|
:version :paper :encoding :pagecentre :colormodel
|
|
:useDingbats :horizontal))
|
|
"Header args which are safe for R babel blocks.
|
|
|
|
See `org-babel-safe-header-args' for documentation of the format of
|
|
this variable.")
|
|
|
|
(defvar org-babel-default-header-args:R '())
|
|
(put 'org-babel-default-header-args:R 'safe-local-variable
|
|
(org-babel-header-args-safe-fn ob-R-safe-header-args))
|
|
|
|
(defcustom org-babel-R-command "R --slave --no-save"
|
|
"Name of command to use for executing R code."
|
|
:group 'org-babel
|
|
:version "24.1"
|
|
:type 'string)
|
|
|
|
;; The usage of utils::read.table() ensures that the command
|
|
;; read.table() can be found even in circumstances when the utils
|
|
;; package is not in the search path from R.
|
|
(defconst ob-R-transfer-variable-table-with-header
|
|
"%s <- local({
|
|
con <- textConnection(
|
|
%S
|
|
)
|
|
res <- utils::read.table(
|
|
con,
|
|
header = %s,
|
|
row.names = %s,
|
|
sep = \"\\t\",
|
|
as.is = TRUE
|
|
)
|
|
close(con)
|
|
res
|
|
})"
|
|
"R code used to transfer a table defined as a variable from org to R.
|
|
|
|
This function is used when the table contains a header.")
|
|
|
|
(defconst ob-R-transfer-variable-table-without-header
|
|
"%s <- local({
|
|
con <- textConnection(
|
|
%S
|
|
)
|
|
res <- utils::read.table(
|
|
con,
|
|
header = %s,
|
|
row.names = %s,
|
|
sep = \"\\t\",
|
|
as.is = TRUE,
|
|
fill = TRUE,
|
|
col.names = paste(\"V\", seq_len(%d), sep =\"\")
|
|
)
|
|
close(con)
|
|
res
|
|
})"
|
|
"R code used to transfer a table defined as a variable from org to R.
|
|
|
|
This function is used when the table does not contain a header.")
|
|
|
|
(defun org-babel-expand-body:R (body params &optional _graphics-file)
|
|
"Expand BODY according to PARAMS, return the expanded body."
|
|
(mapconcat 'identity
|
|
(append
|
|
(when (cdr (assq :prologue params))
|
|
(list (cdr (assq :prologue params))))
|
|
(org-babel-variable-assignments:R params)
|
|
(list body)
|
|
(when (cdr (assq :epilogue params))
|
|
(list (cdr (assq :epilogue params)))))
|
|
"\n"))
|
|
|
|
(defun org-babel-execute:R (body params)
|
|
"Execute a block of R code BODY according to PARAMS.
|
|
This function is called by `org-babel-execute-src-block'."
|
|
(save-excursion
|
|
(let* ((result-params (cdr (assq :result-params params)))
|
|
(result-type (cdr (assq :result-type params)))
|
|
(async (org-babel-comint-use-async params))
|
|
(session (org-babel-R-initiate-session
|
|
(cdr (assq :session params)) params))
|
|
(graphics-file (and (member "graphics" (assq :result-params params))
|
|
(org-babel-graphical-output-file params)))
|
|
(colnames-p (unless graphics-file (cdr (assq :colnames params))))
|
|
(rownames-p (unless graphics-file (cdr (assq :rownames params))))
|
|
(full-body
|
|
(let ((inside
|
|
(list (org-babel-expand-body:R body params graphics-file))))
|
|
(mapconcat 'identity
|
|
(if graphics-file
|
|
(append
|
|
(list (org-babel-R-construct-graphics-device-call
|
|
graphics-file params))
|
|
inside
|
|
(list "},error=function(e){plot(x=-1:1, y=-1:1, type='n', xlab='', ylab='', axes=FALSE); text(x=0, y=0, labels=e$message, col='red'); paste('ERROR', e$message, sep=' : ')}); dev.off()"))
|
|
inside)
|
|
"\n")))
|
|
(result
|
|
(org-babel-R-evaluate
|
|
session full-body result-type result-params
|
|
(or (equal "yes" colnames-p)
|
|
(org-babel-pick-name
|
|
(cdr (assq :colname-names params)) colnames-p))
|
|
(or (equal "yes" rownames-p)
|
|
(org-babel-pick-name
|
|
(cdr (assq :rowname-names params)) rownames-p))
|
|
async)))
|
|
(if graphics-file nil result))))
|
|
|
|
(defun org-babel-prep-session:R (session params)
|
|
"Prepare SESSION according to the header arguments specified in PARAMS."
|
|
(let* ((session (org-babel-R-initiate-session session params))
|
|
(var-lines (org-babel-variable-assignments:R params)))
|
|
(org-babel-comint-in-buffer session
|
|
(mapc (lambda (var)
|
|
(end-of-line 1) (insert var) (comint-send-input nil t)
|
|
(org-babel-comint-wait-for-output session))
|
|
var-lines))
|
|
session))
|
|
|
|
(defun org-babel-load-session:R (session body params)
|
|
"Load BODY into SESSION."
|
|
(save-window-excursion
|
|
(let ((buffer (org-babel-prep-session:R session params)))
|
|
(with-current-buffer buffer
|
|
(goto-char (process-mark (get-buffer-process (current-buffer))))
|
|
(insert (org-babel-chomp body)))
|
|
buffer)))
|
|
|
|
;; helper functions
|
|
|
|
(defun org-babel-variable-assignments:R (params)
|
|
"Return list of R statements assigning the block's variables.
|
|
Retrieve variables from PARAMS."
|
|
(let ((vars (org-babel--get-vars params)))
|
|
(mapcar
|
|
(lambda (pair)
|
|
(org-babel-R-assign-elisp
|
|
(car pair) (cdr pair)
|
|
(equal "yes" (cdr (assq :colnames params)))
|
|
(equal "yes" (cdr (assq :rownames params)))))
|
|
(mapcar
|
|
(lambda (i)
|
|
(cons (car (nth i vars))
|
|
(org-babel-reassemble-table
|
|
(cdr (nth i vars))
|
|
(cdr (nth i (cdr (assq :colname-names params))))
|
|
(cdr (nth i (cdr (assq :rowname-names params)))))))
|
|
(number-sequence 0 (1- (length vars)))))))
|
|
|
|
(defun org-babel-R-quote-tsv-field (s)
|
|
"Quote field S for export to R."
|
|
(if (stringp s)
|
|
(concat "\"" (mapconcat 'identity (split-string s "\"") "\"\"") "\"")
|
|
(format "%S" s)))
|
|
|
|
(defun org-babel-R-assign-elisp (name value colnames-p rownames-p)
|
|
"Construct R code assigning the elisp VALUE to a variable named NAME."
|
|
(if (listp value)
|
|
(let* ((lengths (mapcar 'length (cl-remove-if-not 'listp value)))
|
|
(max (if lengths (apply 'max lengths) 0))
|
|
(min (if lengths (apply 'min lengths) 0)))
|
|
;; Ensure VALUE has an orgtbl structure (depth of at least 2).
|
|
(unless (listp (car value)) (setq value (mapcar 'list value)))
|
|
(let ((file (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
|
|
(header (if (or (eq (nth 1 value) 'hline) colnames-p)
|
|
"TRUE" "FALSE"))
|
|
(row-names (if rownames-p "1" "NULL")))
|
|
(if (= max min)
|
|
(format ob-R-transfer-variable-table-with-header
|
|
name file header row-names)
|
|
(format ob-R-transfer-variable-table-without-header
|
|
name file header row-names max))))
|
|
(cond ((integerp value) (format "%s <- %s" name (concat (number-to-string value) "L")))
|
|
((floatp value) (format "%s <- %s" name value))
|
|
((stringp value) (format "%s <- %S" name (org-no-properties value)))
|
|
(t (format "%s <- %S" name (prin1-to-string value))))))
|
|
|
|
|
|
(defun org-babel-R-initiate-session (session _params)
|
|
"Create or return the current R SESSION buffer."
|
|
(unless (string= session "none")
|
|
(let* ((session (or session "*R*"))
|
|
;; Force using `default-directory', as we promise in the
|
|
;; manual. The caller should have taken care about setting
|
|
;; it according to :dir if necessary.
|
|
;; https://ess.r-project.org/Manual/ess.html#Changing-the-startup-actions
|
|
(ess-ask-for-ess-directory nil)
|
|
(ess-directory-function nil)
|
|
(ess-directory nil)
|
|
;; Make ESS name the process buffer as SESSION.
|
|
(ess-gen-proc-buffer-name-function
|
|
(lambda (_) session)))
|
|
(if (org-babel-comint-buffer-livep session)
|
|
session
|
|
(save-window-excursion
|
|
(when (get-buffer session)
|
|
;; Session buffer exists, but with dead process
|
|
(set-buffer session))
|
|
(org-require-package 'ess-r-mode "ESS")
|
|
(set-buffer (run-ess-r))
|
|
(let ((R-proc (get-process (or ess-local-process-name
|
|
ess-current-process-name))))
|
|
(while (process-get R-proc 'callbacks)
|
|
(ess-wait-for-process R-proc)))
|
|
(current-buffer))))))
|
|
|
|
(defun org-babel-R-associate-session (session)
|
|
"Associate R code buffer with an R session.
|
|
Make SESSION be the inferior ESS process associated with the
|
|
current code buffer."
|
|
(when-let* ((process (get-buffer-process session)))
|
|
(setq ess-local-process-name (process-name process))
|
|
(ess-make-buffer-current))
|
|
(setq-local ess-gen-proc-buffer-name-function (lambda (_) session)))
|
|
|
|
(defvar org-babel-R-graphics-devices
|
|
'((:bmp "bmp" "filename")
|
|
(:jpg "jpeg" "filename")
|
|
(:jpeg "jpeg" "filename")
|
|
(:tikz "tikz" "file")
|
|
(:tiff "tiff" "filename")
|
|
(:png "png" "filename")
|
|
(:svg "svg" "file")
|
|
(:pdf "pdf" "file")
|
|
(:ps "postscript" "file")
|
|
(:postscript "postscript" "file"))
|
|
"An alist mapping graphics file types to R functions.
|
|
|
|
Each member of this list is a list with three members:
|
|
1. the file extension of the graphics file, as an elisp :keyword
|
|
2. the R graphics device function to call to generate such a file
|
|
3. the name of the argument to this function which specifies the
|
|
file to write to (typically \"file\" or \"filename\")")
|
|
|
|
(defun org-babel-R-construct-graphics-device-call (out-file params)
|
|
"Construct the call to the graphics device."
|
|
(let* ((allowed-args '(:width :height :bg :units :pointsize
|
|
:antialias :quality :compression :res
|
|
:type :family :title :fonts :version
|
|
:paper :encoding :pagecentre :colormodel
|
|
:useDingbats :horizontal))
|
|
(device (file-name-extension out-file))
|
|
(device-info (or (assq (intern (concat ":" device))
|
|
org-babel-R-graphics-devices)
|
|
(assq :png org-babel-R-graphics-devices)))
|
|
(extra-args (cdr (assq :R-dev-args params))) filearg args)
|
|
(setq device (nth 1 device-info))
|
|
(setq filearg (nth 2 device-info))
|
|
(setq args (mapconcat
|
|
(lambda (pair)
|
|
(if (member (car pair) allowed-args)
|
|
(format ",%s=%S"
|
|
(substring (symbol-name (car pair)) 1)
|
|
(cdr pair)) ""))
|
|
params ""))
|
|
(format "%s(%s=\"%s\"%s%s%s); tryCatch({"
|
|
device filearg out-file args
|
|
(if extra-args "," "") (or extra-args ""))))
|
|
|
|
(defconst org-babel-R-eoe-indicator "'org_babel_R_eoe'")
|
|
(defconst org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
|
|
|
|
(defconst org-babel-R-write-object-command "{
|
|
function(object,transfer.file) {
|
|
object
|
|
invisible(
|
|
if (
|
|
inherits(
|
|
try(
|
|
{
|
|
tfile<-tempfile()
|
|
write.table(object, file=tfile, sep=\"\\t\",
|
|
na=\"\",row.names=%s,col.names=%s,
|
|
quote=FALSE)
|
|
file.rename(tfile,transfer.file)
|
|
},
|
|
silent=TRUE),
|
|
\"try-error\"))
|
|
{
|
|
if(!file.exists(transfer.file))
|
|
file.create(transfer.file)
|
|
}
|
|
)
|
|
}
|
|
}(object=%s,transfer.file=\"%s\")"
|
|
"Template for an R command to evaluate a block of code and write result to file.
|
|
|
|
Has four %s escapes to be filled in:
|
|
1. Row names, \"TRUE\" or \"FALSE\"
|
|
2. Column names, \"TRUE\" or \"FALSE\"
|
|
3. The code to be run (must be an expression, not a statement)
|
|
4. The name of the file to write to")
|
|
|
|
(defun org-babel-R-evaluate
|
|
(session body result-type result-params column-names-p row-names-p async)
|
|
"Evaluate R code in BODY."
|
|
(if session
|
|
(if async
|
|
(ob-session-async-org-babel-R-evaluate-session
|
|
session body result-type column-names-p row-names-p)
|
|
(org-babel-R-evaluate-session
|
|
session body result-type result-params column-names-p row-names-p))
|
|
(org-babel-R-evaluate-external-process
|
|
body result-type result-params column-names-p row-names-p)))
|
|
|
|
(defun org-babel-R-evaluate-external-process
|
|
(body result-type result-params column-names-p row-names-p)
|
|
"Evaluate BODY in external R process.
|
|
If RESULT-TYPE equals `output' then return standard output as a
|
|
string. If RESULT-TYPE equals `value' then return the value of the
|
|
last statement in BODY, as elisp."
|
|
(cl-case result-type
|
|
(value
|
|
(let ((tmp-file (org-babel-temp-file "R-")))
|
|
(org-babel-eval org-babel-R-command
|
|
(format org-babel-R-write-object-command
|
|
(if row-names-p "TRUE" "FALSE")
|
|
(if column-names-p
|
|
(if row-names-p "NA" "TRUE")
|
|
"FALSE")
|
|
(format "{function ()\n{\n%s\n}}()" body)
|
|
(org-babel-process-file-name tmp-file 'noquote)))
|
|
(org-babel-R-process-value-result
|
|
(org-babel-result-cond result-params
|
|
(with-temp-buffer
|
|
(insert-file-contents tmp-file)
|
|
(org-babel-chomp (buffer-string) "\n"))
|
|
(org-babel-import-elisp-from-file tmp-file '(16)))
|
|
column-names-p)))
|
|
(output (org-babel-eval org-babel-R-command body))))
|
|
|
|
(defvar ess-eval-visibly-p)
|
|
|
|
(defun org-babel-R-evaluate-session
|
|
(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
|
|
last statement in BODY, as elisp."
|
|
(cl-case result-type
|
|
(value
|
|
(with-temp-buffer
|
|
(insert (org-babel-chomp body))
|
|
(let ((ess-local-process-name
|
|
(process-name (get-buffer-process session)))
|
|
(ess-eval-visibly-p nil))
|
|
(ess-eval-buffer nil)))
|
|
(let ((tmp-file (org-babel-temp-file "R-")))
|
|
(org-babel-comint-eval-invisibly-and-wait-for-file
|
|
session tmp-file
|
|
(format org-babel-R-write-object-command
|
|
(if row-names-p "TRUE" "FALSE")
|
|
(if column-names-p
|
|
(if row-names-p "NA" "TRUE")
|
|
"FALSE")
|
|
".Last.value" (org-babel-process-file-name tmp-file 'noquote)))
|
|
(org-babel-R-process-value-result
|
|
(org-babel-result-cond result-params
|
|
(with-temp-buffer
|
|
(insert-file-contents tmp-file)
|
|
(org-babel-chomp (buffer-string) "\n"))
|
|
(org-babel-import-elisp-from-file tmp-file '(16)))
|
|
column-names-p)))
|
|
(output
|
|
(let ((tmp-src-file (org-babel-temp-file "R-")))
|
|
(with-temp-file tmp-src-file
|
|
(insert (concat
|
|
(org-babel-chomp body) "\n" org-babel-R-eoe-indicator)))
|
|
(with-current-buffer session
|
|
(org-babel-chomp
|
|
(string-trim-right
|
|
(org-babel-comint-with-output
|
|
(session org-babel-R-eoe-output nil nil 'disable-prompt-filtering)
|
|
(ess-send-string (get-buffer-process (current-buffer))
|
|
(format "source('%s', echo=F, print.eval=T)"
|
|
(org-babel-process-file-name
|
|
tmp-src-file 'noquote))))
|
|
(rx (literal org-babel-R-eoe-output) (zero-or-more anychar)))))))))
|
|
|
|
(defun org-babel-R-process-value-result (result column-names-p)
|
|
"R-specific processing of return value.
|
|
Insert hline if column names in output have been requested."
|
|
(if column-names-p
|
|
(condition-case nil
|
|
(cons (car result) (cons 'hline (cdr result)))
|
|
(error "Could not parse R result"))
|
|
result))
|
|
|
|
|
|
;;; async evaluation
|
|
|
|
(defconst ob-session-async-R-indicator "'ob_comint_async_R_%s_%s'")
|
|
|
|
(defun ob-session-async-org-babel-R-evaluate-session
|
|
(session body result-type column-names-p row-names-p)
|
|
"Asynchronously evaluate BODY in SESSION.
|
|
Returns a placeholder string for insertion, to later be replaced
|
|
by `org-babel-comint-async-filter'."
|
|
(org-babel-comint-async-register
|
|
session (current-buffer)
|
|
"^\\(?:[>.+] \\)*\\[1\\] \"ob_comint_async_R_\\(start\\|end\\|file\\)_\\(.+\\)\"$"
|
|
'org-babel-chomp
|
|
'ob-session-async-R-value-callback
|
|
'disable-prompt-filtering)
|
|
(cl-case result-type
|
|
(value
|
|
(let ((tmp-file (org-babel-temp-file "R-")))
|
|
(with-temp-buffer
|
|
(insert
|
|
(org-babel-chomp body))
|
|
(let ((ess-local-process-name
|
|
(process-name (get-buffer-process session))))
|
|
(ess-eval-buffer nil)))
|
|
(with-temp-buffer
|
|
(insert
|
|
(mapconcat
|
|
'org-babel-chomp
|
|
(list (format org-babel-R-write-object-command
|
|
(if row-names-p "TRUE" "FALSE")
|
|
(if column-names-p
|
|
(if row-names-p "NA" "TRUE")
|
|
"FALSE")
|
|
".Last.value"
|
|
(org-babel-process-file-name tmp-file 'noquote))
|
|
(format ob-session-async-R-indicator
|
|
"file" tmp-file))
|
|
"\n"))
|
|
(let ((ess-local-process-name
|
|
(process-name (get-buffer-process session))))
|
|
(ess-eval-buffer nil)))
|
|
tmp-file))
|
|
(output
|
|
(let ((uuid (org-id-uuid))
|
|
(ess-local-process-name
|
|
(process-name (get-buffer-process session)))
|
|
(ess-eval-visibly-p nil))
|
|
(with-temp-buffer
|
|
(insert (format ob-session-async-R-indicator
|
|
"start" uuid))
|
|
(insert "\n")
|
|
(insert body)
|
|
(insert "\n")
|
|
(insert (format ob-session-async-R-indicator
|
|
"end" uuid))
|
|
(ess-eval-buffer nil ))
|
|
uuid))))
|
|
|
|
(defun ob-session-async-R-value-callback (params tmp-file)
|
|
"Callback for async value results.
|
|
Assigned locally to `org-babel-comint-async-file-callback' in R
|
|
comint buffers used for asynchronous Babel evaluation."
|
|
(let* ((graphics-file (and (member "graphics" (assq :result-params params))
|
|
(org-babel-graphical-output-file params)))
|
|
(colnames-p (unless graphics-file (cdr (assq :colnames params)))))
|
|
(org-babel-R-process-value-result
|
|
(org-babel-result-cond (assq :result-params params)
|
|
(with-temp-buffer
|
|
(insert-file-contents tmp-file)
|
|
(org-babel-chomp (buffer-string) "\n"))
|
|
(org-babel-import-elisp-from-file tmp-file '(16)))
|
|
(or (equal "yes" colnames-p)
|
|
(org-babel-pick-name
|
|
(cdr (assq :colname-names params)) colnames-p)))))
|
|
|
|
|
|
|
|
;;; ob-session-async-R.el ends here
|
|
|
|
|
|
(provide 'ob-R)
|
|
|
|
;;; ob-R.el ends here
|