diff options
Diffstat (limited to 'lisp/ob-R.el')
| -rw-r--r-- | lisp/ob-R.el | 76 |
1 files changed, 38 insertions, 38 deletions
diff --git a/lisp/ob-R.el b/lisp/ob-R.el index 4b37c18..2993b09 100644 --- a/lisp/ob-R.el +++ b/lisp/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) 2009-2016 Free Software Foundation, Inc. @@ -27,8 +27,9 @@ ;; 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)) @@ -36,10 +37,7 @@ (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" - (proc &optional sec-prompt wait force-redisplay)) -(declare-function org-number-sequence "org-compat" (from &optional to inc)) -(declare-function org-remove-if-not "org" (predicate seq)) -(declare-function org-every "org" (pred seq)) + (&optional proc sec-prompt wait force-redisplay)) (defconst org-babel-header-args:R '((width . :any) @@ -92,9 +90,11 @@ this variable.") (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))))) + (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 @@ -139,28 +139,28 @@ This function is used when the table contains a header.") This function is used when the table does not contain a header.") -(defun org-babel-expand-body:R (body params &optional graphics-file) +(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 (assoc :prologue params)) - (list (cdr (assoc :prologue params)))) + (when (cdr (assq :prologue params)) + (list (cdr (assq :prologue params)))) (org-babel-variable-assignments:R params) (list body) - (when (cdr (assoc :epilogue params)) - (list (cdr (assoc :epilogue params))))) + (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))) + (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 @@ -180,10 +180,10 @@ This function is called by `org-babel-execute-src-block'." 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) @@ -209,21 +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." @@ -234,7 +234,7 @@ 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))) ;; Ensure VALUE has an orgtbl structure (depth of at least 2). @@ -262,7 +262,7 @@ This function is called by `org-babel-execute-src-block'." (ess-ask-for-ess-directory (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory - (not (cdr (assoc :dir params)))))) + (not (cdr (assq :dir params)))))) (if (org-babel-comint-buffer-livep session) session (save-window-excursion @@ -316,8 +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))) @@ -379,12 +378,12 @@ Has four %s escapes to be filled in: 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 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 @@ -399,7 +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)))) @@ -407,12 +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 last statement in BODY, as elisp." - (case result-type + (cl-case result-type (value (with-temp-buffer (insert (org-babel-chomp body)) @@ -433,7 +432,7 @@ 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 @@ -446,7 +445,8 @@ 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) |