Update Org to v9.0.9

Please see etc/ORG-NEWS for details.

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"))))