;;; 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 ;; 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 . ;;; 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 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 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 "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