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org-mode/lisp/ob-R.el
Ihor Radchenko 4929f0c55f
* lisp/ob-R.el: Fix ESS compatibility 
(org-babel-R-initiate-session): Fix `require'.  Do not use obsolete
`R' function.
2023-04-17 20:20:58 +02:00

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;;; ob-R.el --- Babel Functions for R -*- lexical-binding: t; -*-
;; Copyright (C) 2009-2023 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)
(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))
(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)
(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)
(defvar ess-current-process-name) ; dynamically scoped
(defvar ess-local-process-name) ; dynamically scoped
(defun org-babel-edit-prep:R (info)
(let ((session (cdr (assq :session (nth 2 info)))))
(when (and session
(string-prefix-p "*" session)
(string-suffix-p "*" session))
(org-babel-R-initiate-session session nil))))
;; 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.
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."
(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))))))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
"If there is not a current R process then create one."
(unless (string= session "none")
(let ((session (or session "*R*"))
(ess-ask-for-ess-directory
(and (boundp 'ess-ask-for-ess-directory)
ess-ask-for-ess-directory
(not (cdr (assq :dir params))))))
(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)))
(rename-buffer
(if (bufferp session)
(buffer-name session)
(if (stringp session)
session
(buffer-name))))
(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."
(setq ess-local-process-name
(process-name (get-buffer-process session)))
(ess-make-buffer-current))
(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
(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
"^\\([>+.]\\([ ][>.+]\\)*[ ]\\)"
(car (split-string line "\n")))
(substring line (match-end 1))
line))
(with-current-buffer session
(let ((comint-prompt-regexp (concat "^" comint-prompt-regexp)))
(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"))))
(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_\\(.+?\\)_\\(.+\\)\"$"
'org-babel-chomp
'ob-session-async-R-value-callback)
(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
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