pkg update and first config fix

org-brain not working, add org-roam

lisp/org/org-plot.el

@@ -1,11 +1,11 @@
 ;;; org-plot.el --- Support for Plotting from Org -*- lexical-binding: t; -*-
 
-;; Copyright (C) 2008-2021 Free Software Foundation, Inc.
+;; Copyright (C) 2008-2022 Free Software Foundation, Inc.
 ;;
 ;; Author: Eric Schulte <schulte dot eric at gmail dot com>
-;; Maintainer: TEC <tecosaur@gmail.com>
+;; Maintainer: TEC <orgmode@tec.tecosaur.net>
 ;; Keywords: tables, plotting
-;; Homepage: https://orgmode.org
+;; URL: https://orgmode.org
 ;;
 ;; This file is part of GNU Emacs.
 ;;
@@ -31,6 +31,9 @@
 
 ;;; Code:
 
+(require 'org-macs)
+(org-assert-version)
+
 (require 'cl-lib)
 (require 'org)
 (require 'org-table)
@@ -272,15 +275,15 @@ argument for the FUNCTION."
 	     for k in keys collect
 	     (cons k (funcall function (lookup k alist1) (lookup k alist2))))))
 
-(defun org--plot/item-frequencies (values &optional normalise)
+(defun org--plot/item-frequencies (values &optional normalize)
   "Return an alist indicating the frequency of values in VALUES list.
-When NORMALISE is non-nil, the count is divided by the number of values."
-  (let ((normaliser (if normalise (float (length values)) 1)))
+When NORMALIZE is non-nil, the count is divided by the number of values."
+  (let ((normaliser (if normalize (float (length values)) 1)))
     (cl-loop for (n . m) in (seq-group-by #'identity values)
 	     collect (cons n (/ (length m) normaliser)))))
 
 (defun org--plot/prime-factors (value)
-  "Return the prime decomposition of VALUE, e.g. for 12, '(3 2 2)."
+  "Return the prime decomposition of VALUE, e.g. for 12, (3 2 2)."
   (let ((factors '(1)) (i 1))
     (while (/= 1 value)
       (setq i (1+ i))
@@ -291,6 +294,11 @@ When NORMALISE is non-nil, the count is divided by the number of values."
 	))
     (cl-subseq factors 0 -1)))
 
+(defgroup org-plot nil
+  "Options for plotting in Org mode."
+  :tag "Org Plot"
+  :group 'org)
+
 (defcustom org-plot/gnuplot-script-preamble ""
   "String of function to be inserted before the gnuplot plot command is run.
 
@@ -621,8 +629,9 @@ manner suitable for prepending to a user-specified script."
   "Find any overlays for IMG-FILE in the current Org buffer, and refresh them."
   (dolist (img-overlay org-inline-image-overlays)
     (when (string= img-file (plist-get (cdr (overlay-get img-overlay 'display)) :file))
-      (when (file-exists-p img-file)
-        (image-refresh (overlay-get img-overlay 'display))))))
+      (when (and (file-exists-p img-file)
+                 (fboundp 'image-flush))
+        (image-flush (overlay-get img-overlay 'display))))))
 
 ;;-----------------------------------------------------------------------------
 ;; facade functions
@@ -667,7 +676,8 @@ line directly before or after the table."
 	   (num-cols (length (if (eq (nth 0 table) 'hline) (nth 1 table)
 			       (nth 0 table))))
 	   (type (assoc (plist-get params :plot-type)
-			org-plot/preset-plot-types)))
+			org-plot/preset-plot-types))
+           gnuplot-script)
 
       (unless type
 	(user-error "Org-plot type `%s' is undefined" (plist-get params :plot-type)))
@@ -682,9 +692,10 @@ line directly before or after the table."
 				  (looking-at "[[:space:]]*#\\+"))
 			(setf params (org-plot/collect-options params))))
       ;; Dump table to datafile
-      (if-let ((dump-func (plist-get type :data-dump)))
-	  (funcall dump-func table data-file num-cols params)
-	(org-plot/gnuplot-to-data table data-file params))
+      (let ((dump-func (plist-get type :data-dump)))
+        (if dump-func
+	    (funcall dump-func table data-file num-cols params)
+	  (org-plot/gnuplot-to-data table data-file params)))
       ;; Check type of ind column (timestamp? text?)
       (when (plist-get params :check-ind-type)
 	(let* ((ind (1- (plist-get params :ind)))
@@ -700,16 +711,17 @@ line directly before or after the table."
 				  ind-column))
 		 (plist-put params :textind t))))) ; ind holds text
       ;; Write script.
+      (setq gnuplot-script
+            (org-plot/gnuplot-script
+             table data-file num-cols params (plist-get params :script)))
       (with-temp-buffer
 	(if (plist-get params :script)	; user script
-	    (progn (insert
-		    (org-plot/gnuplot-script table data-file num-cols params t))
-		   (insert "\n")
+	    (progn (insert gnuplot-script "\n")
 		   (insert-file-contents (plist-get params :script))
 		   (goto-char (point-min))
 		   (while (re-search-forward "\\$datafile" nil t)
 		     (replace-match data-file nil nil)))
-	  (insert (org-plot/gnuplot-script table data-file num-cols params)))
+	  (insert gnuplot-script))
 	;; Graph table.
 	(gnuplot-mode)
         (condition-case nil