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Diffstat (limited to 'elpa/org-9.5.2/ob-R.el')
| -rw-r--r-- | elpa/org-9.5.2/ob-R.el | 570 |
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diff --git a/elpa/org-9.5.2/ob-R.el b/elpa/org-9.5.2/ob-R.el deleted file mode 100644 index 169e1d6..0000000 --- a/elpa/org-9.5.2/ob-R.el +++ /dev/null @@ -1,570 +0,0 @@ -;;; ob-R.el --- Babel Functions for R -*- lexical-binding: t; -*- - -;; Copyright (C) 2009-2021 Free Software Foundation, Inc. - -;; Author: Eric Schulte -;; Dan Davison -;; Maintainer: Jeremie Juste -;; Keywords: literate programming, reproducible research, R, statistics -;; Homepage: 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 '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)) - -;; FIXME: Temporary declaration to silence the byte-compiler -(defvar user-inject-src-param) -(defvar ess-eval-visibly-tmp) -(defvar ess-eval-visibly) -(defvar ess-inject-source) -(defvar user-inject-src-param) - -(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 'sequencep 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 (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)) - (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) - (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 result-params 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 (md5 (number-to-string (random 100000000)))) - (ess-local-process-name - (process-name (get-buffer-process session)))) - (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)) - (setq ess-eval-visibly-tmp ess-eval-visibly) - (setq user-inject-src-param ess-inject-source) - (setq ess-eval-visibly nil) - (setq ess-inject-source 'function-and-buffer) - (ess-eval-buffer nil)) - (setq ess-eval-visibly ess-eval-visibly-tmp) - (setq ess-inject-source user-inject-src-param) - uuid)))) - -(defun ob-session-async-R-value-callback (params tmp-file) - "Callback for async value results. -Assigned locally to `ob-session-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 |