summaryrefslogtreecommitdiff
path: root/lisp/org/ob-R.el
diff options
context:
space:
mode:
Diffstat (limited to 'lisp/org/ob-R.el')
-rw-r--r--lisp/org/ob-R.el270
1 files changed, 175 insertions, 95 deletions
diff --git a/lisp/org/ob-R.el b/lisp/org/ob-R.el
index 51d342702ce..3accade49f5 100644
--- a/lisp/org/ob-R.el
+++ b/lisp/org/ob-R.el
@@ -1,4 +1,4 @@
-;;; ob-R.el --- org-babel functions for R code evaluation
+;;; ob-R.el --- Babel Functions for R -*- lexical-binding: t; -*-
;; Copyright (C) 2009-2017 Free Software Foundation, Inc.
@@ -27,16 +27,17 @@
;; Org-Babel support for evaluating R code
;;; Code:
+
+(require 'cl-lib)
(require 'ob)
-(eval-when-compile (require 'cl))
(declare-function orgtbl-to-tsv "org-table" (table params))
(declare-function R "ext:essd-r" (&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 org-number-sequence "org-compat" (from &optional to inc))
-(declare-function org-remove-if-not "org" (predicate seq))
+(declare-function ess-wait-for-process "ext:ess-inf"
+ (&optional proc sec-prompt wait force-redisplay))
(defconst org-babel-header-args:R
'((width . :any)
@@ -60,12 +61,25 @@
(useDingbats . :any)
(horizontal . :any)
(results . ((file list vector table scalar verbatim)
- (raw org html latex code pp wrap)
- (replace silent append prepend)
+ (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."
@@ -73,56 +87,103 @@
:version "24.1"
:type 'string)
-(defvar ess-local-process-name) ; dynamically scoped
+(defvar ess-current-process-name) ; dynamically scoped
+(defvar ess-local-process-name) ; dynamically scoped
(defun org-babel-edit-prep:R (info)
- (let ((session (cdr (assoc :session (nth 2 info)))))
- (when (and session (string-match "^\\*\\(.+?\\)\\*$" session))
- (save-match-data (org-babel-R-initiate-session session nil)))))
-
-(defun org-babel-expand-body:R (body params &optional graphics-file)
+ (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."
- (let ((graphics-file
- (or graphics-file (org-babel-R-graphical-output-file params))))
- (mapconcat
- #'identity
- (let ((inside
- (append
- (when (cdr (assoc :prologue params))
- (list (cdr (assoc :prologue params))))
- (org-babel-variable-assignments:R params)
- (list body)
- (when (cdr (assoc :epilogue params))
- (list (cdr (assoc :epilogue params)))))))
- (if graphics-file
- (append
- (list (org-babel-R-construct-graphics-device-call
- graphics-file params))
- inside
- (list "dev.off()"))
- inside))
- "\n")))
+ (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 (assoc :result-params params)))
- (result-type (cdr (assoc :result-type params)))
+ (let* ((result-params (cdr (assq :result-params params)))
+ (result-type (cdr (assq :result-type params)))
(session (org-babel-R-initiate-session
- (cdr (assoc :session params)) params))
- (colnames-p (cdr (assoc :colnames params)))
- (rownames-p (cdr (assoc :rownames params)))
- (graphics-file (org-babel-R-graphical-output-file params))
- (full-body (org-babel-expand-body:R body params graphics-file))
+ (cdr (assq :session params)) params))
+ (colnames-p (cdr (assq :colnames params)))
+ (rownames-p (cdr (assq :rownames params)))
+ (graphics-file (and (member "graphics" (assq :result-params params))
+ (org-babel-graphical-output-file 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 (assoc :colname-names params)) colnames-p))
+ (cdr (assq :colname-names params)) colnames-p))
(or (equal "yes" rownames-p)
(org-babel-pick-name
- (cdr (assoc :rowname-names params)) rownames-p)))))
+ (cdr (assq :rowname-names params)) rownames-p)))))
(if graphics-file nil result))))
(defun org-babel-prep-session:R (session params)
@@ -148,21 +209,21 @@ This function is called by `org-babel-execute-src-block'."
(defun org-babel-variable-assignments:R (params)
"Return list of R statements assigning the block's variables."
- (let ((vars (mapcar #'cdr (org-babel-get-header params :var))))
+ (let ((vars (org-babel--get-vars params)))
(mapcar
(lambda (pair)
(org-babel-R-assign-elisp
(car pair) (cdr pair)
- (equal "yes" (cdr (assoc :colnames params)))
- (equal "yes" (cdr (assoc :rownames params)))))
+ (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 (assoc :colname-names params))))
- (cdr (nth i (cdr (assoc :rowname-names params)))))))
- (org-number-sequence 0 (1- (length 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."
@@ -173,35 +234,25 @@ This function is called by `org-babel-execute-src-block'."
(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 (org-remove-if-not 'sequencep value)))
+ (let* ((lengths (mapcar 'length (cl-remove-if-not 'sequencep value)))
(max (if lengths (apply 'max lengths) 0))
- (min (if lengths (apply 'min lengths) 0))
- (transition-file (org-babel-temp-file "R-import-")))
+ (min (if lengths (apply 'min lengths) 0)))
;; Ensure VALUE has an orgtbl structure (depth of at least 2).
(unless (listp (car value)) (setq value (list value)))
- (with-temp-file transition-file
- (insert
- (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))
- "\n"))
- (let ((file (org-babel-process-file-name transition-file 'noquote))
+ (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 "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE)" name file header row-names)
- (format "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE,
- fill=TRUE,
- col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
+ (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))))
- (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
+ (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)
@@ -209,8 +260,9 @@ This function is called by `org-babel-execute-src-block'."
(unless (string= session "none")
(let ((session (or session "*R*"))
(ess-ask-for-ess-directory
- (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory)
- (not (cdr (assoc :dir params))))))
+ (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
@@ -218,6 +270,10 @@ This function is called by `org-babel-execute-src-block'."
;; Session buffer exists, but with dead process
(set-buffer session))
(require '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)
@@ -234,11 +290,6 @@ current code buffer."
(process-name (get-buffer-process session)))
(ess-make-buffer-current))
-(defun org-babel-R-graphical-output-file (params)
- "Name of file to which R should send graphical output."
- (and (member "graphics" (cdr (assq :result-params params)))
- (cdr (assq :file params))))
-
(defvar org-babel-R-graphics-devices
'((:bmp "bmp" "filename")
(:jpg "jpeg" "filename")
@@ -265,8 +316,7 @@ Each member of this list is a list with three members:
:type :family :title :fonts :version
:paper :encoding :pagecentre :colormodel
:useDingbats :horizontal))
- (device (and (string-match ".+\\.\\([^.]+\\)" out-file)
- (match-string 1 out-file)))
+ (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)))
@@ -280,14 +330,43 @@ Each member of this list is a list with three members:
(substring (symbol-name (car pair)) 1)
(cdr pair)) ""))
params ""))
- (format "%s(%s=\"%s\"%s%s%s)"
+ (format "%s(%s=\"%s\"%s%s%s); tryCatch({"
device filearg out-file args
(if extra-args "," "") (or extra-args ""))))
-(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
-(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
-
-(defvar 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=\"nil\",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\")")
+(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=\"nil\",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\")"
+ "A template for an R command to evaluate a block of code and write the result to a 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)
@@ -299,12 +378,12 @@ Each member of this list is a list with three members:
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)
+ (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
+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."
- (case result-type
+ (cl-case result-type
(value
(let ((tmp-file (org-babel-temp-file "R-")))
(org-babel-eval org-babel-R-command
@@ -319,7 +398,7 @@ last statement in BODY, as elisp."
(org-babel-result-cond result-params
(with-temp-buffer
(insert-file-contents tmp-file)
- (buffer-string))
+ (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))))
@@ -327,12 +406,12 @@ last statement in BODY, as elisp."
(defvar ess-eval-visibly-p)
(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
+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."
- (case result-type
+ (cl-case result-type
(value
(with-temp-buffer
(insert (org-babel-chomp body))
@@ -353,12 +432,12 @@ last statement in BODY, as elisp."
(org-babel-result-cond result-params
(with-temp-buffer
(insert-file-contents tmp-file)
- (buffer-string))
+ (org-babel-chomp (buffer-string) "\n"))
(org-babel-import-elisp-from-file tmp-file '(16)))
column-names-p)))
(output
(mapconcat
- #'org-babel-chomp
+ 'org-babel-chomp
(butlast
(delq nil
(mapcar
@@ -366,11 +445,12 @@ last statement in BODY, as elisp."
(mapcar
(lambda (line) ;; cleanup extra prompts left in output
(if (string-match
- "^\\([ ]*[>+\\.][ ]?\\)+\\([[0-9]+\\|[ ]\\)" line)
+ "^\\([>+.]\\([ ][>.+]\\)*[ ]\\)"
+ (car (split-string line "\n")))
(substring line (match-end 1))
line))
(org-babel-comint-with-output (session org-babel-R-eoe-output)
- (insert (mapconcat #'org-babel-chomp
+ (insert (mapconcat 'org-babel-chomp
(list body org-babel-R-eoe-indicator)
"\n"))
(inferior-ess-send-input)))))) "\n"))))
generated by cgit v1.2.3 (git 2.39.1) at 2025-04-07 05:21:21 +0000