[rkward] /: Update various external links in the sources.

Thomas Friedrichsmeier thomas.friedrichsmeier at ruhr-uni-bochum.de
Mon Jun 8 12:56:43 UTC 2015 

Git commit 7b1b8d2bff92a44ca54a6a25e5a7cf2a8275aeba by Thomas Friedrichsmeier.
Committed on 08/06/2015 at 12:56.
Pushed by tfry into branch 'master'.

Update various external links in the sources.
Clean some(!) cruft from the TODO file.

M  +1    -1    INSTALL
M  +1    -93   TODO
M  +1    -1    rkward/core/rkmodificationtracker.cpp
M  +1    -1    rkward/plugin/rkstandardcomponentgui.cpp
M  +1    -1    rkward/rbackend/rklocalesupport.cpp
M  +1    -1    rkward/rbackend/rkstructuregetter.cpp
M  +1    -1    rkward/rkconsole.cpp
M  +1    -1    rkward/rkward.cpp
M  +1    -1    rkward/robjectviewer.cpp
M  +1    -1    rkward/windows/rkcommandeditorwindow.cpp
M  +1    -1    rkward/windows/rkfilebrowser.cpp
M  +1    -1    rkward/windows/rkmdiwindow.cpp
M  +1    -1    rkward/windows/rktoolwindowlist.cpp

http://commits.kde.org/rkward/7b1b8d2bff92a44ca54a6a25e5a7cf2a8275aeba

diff --git a/INSTALL b/INSTALL
index 546b823..090dc51 100644
--- a/INSTALL
+++ b/INSTALL
@@ -75,4 +75,4 @@ Automated tests
 
 A series of automated functionality tests can be run unsing 'make plugintests' *after* completing the installation. Unfortunately, these tests are rather prone to false alarms, and thus end users are not currently encouraged to run the tests. However, esp. developers, and packagers patching the sources should run 'make plugintests' after doing their changes. For failed tests, please take some time trying to understand, exactly how the test failed. Often it's just a harmless difference in rounding or formatting of output.
 
-If you see a genuine test failure, unrelated to your patches, please report this to rkward-devel AT lists DOT sourceforge DOT net, including details on your installed versions of KDE, R, and RKWard.
+If you see a genuine test failure, unrelated to your patches, please report this to rkward-devel AT kde DOT org, including details on your installed versions of KDE, R, and RKWard.
diff --git a/TODO b/TODO
index 9d27b50..cdc9263 100644
--- a/TODO
+++ b/TODO
@@ -39,7 +39,6 @@ Bugs:
 		- Produce lots and lots of output -> watch mem usage grow
 		- Probably the RKConsole is to blame (run outside console -> no significant increase)
 			- Maybe the kate-part needs to be reset (syntax parse tree) every once in a while?
-	- rnorm () and friends auto-print value only once. R_Visible is 0 on subsequent calls (what in the world is going on, here?)
 	- RKEditorDataFrame:
 		- sometimes the current cell indicator (the box around the current cell) gets lost.
 			- Navigation and editing is still fine
@@ -51,12 +50,10 @@ Bugs:
 			- 2. before the edit has been synced to the backend, a different command touches the data
 			- The editor should keep track of which / how many synchronisation commands are still outstanding.
 			- If an edited object was touched while sync commands are still outstanding, complain and let the user handle the situation
-	- Quitting via q() in the R console will often lead to a segfault during shutdown
 	- options ("pager") is currently broken in RKWard. May not be a problem, but we offer a GUI to configure it in Settings->Configure RKWard...
 
 Compilation / technical
 	- Incorporate FreeBSD patches http://www.freshports.org/math/rkward/files.php?message_id=200609172111.k8HLBiob081349@repoman.freebsd.org
-	- cleanup DISABLE_RKWINDOWCATCHER (either get rid of it, or do it right)
 	- eventually the whole RData-structure should be made to use QList-types
 
 R backend:
@@ -116,16 +113,8 @@ UI-stuff
 		- optionally keep a file log!
 	- find out how to save toolbar states properly in parts-GUI
 		- also setting the toolbar state for all windows with that toolbar
-	- David's usability items
 	- from Ralf:
 		- show first few values of vectors/scalars in tool-tip in workspace browser
-	- Debugging functionality
-		- ideally the whole thing: setting breakpoints, etc.
-		- realistically, maybe we can override browser () or do_browser with something nicer
-	- Preview of plots
-		- Maybe use a button (along the submit / close / etc. buttons instead)?
-		- The preview window should be a specialized RKCaughtWindow
-			- It should show info on state (up to date / updating / error / etc).
 	- Graphics Device List window
 		- (see http://sourceforge.net/mailarchive/message.php?msg_id=37825223)
 		- par (no.readonly=TRUE) and par () to fetch available parameters and determine read-only state
@@ -133,18 +122,13 @@ UI-stuff
 		- access to graphics device plugins
 	- Help system
 		- find a good way to open R help pages in the same window
-		- open link in new tab, etc.
 	- Working directory
 		- show current wd in <browser>, somewhere
 	- Settings UI:
-		- see http://sourceforge.net/mailarchive/forum.php?thread_name=200703230304.43023.kapatp%40gmail.com&forum_name=rkward-devel
+		- see https://mail.kde.org/pipermail/rkward-devel/2007-March/001139.html
 		- R-Backend-Settings:
 			- the options should gain a "use default" checkbox to cope with changing R option defaults
 			- tooltips for the options on "R-Backend" tab about the internal R-function call
-	- UI geometry:
-		- see https://sourceforge.net/mailarchive/forum.php?thread_name=200704181922.07780.michellang%40gmail.com&forum_name=rkward-devel
-		- save size/proportions of R script file, R console, Workspace browser...
-		- save attach/detach status of the windows
 	- project/session handling: files, workspace, current working directory.
 	- file system browser tab
 		- a way to inline pdf/ps/jpg/png files like in KDevelop?
@@ -163,13 +147,9 @@ Internal stuff:
 		- does locale switching / detection work? Does Qt have something, yet?
 	- Handling fonts:
 		- http://sourceforge.net/mailarchive/forum.php?thread_id=31631211&forum_id=12970
-	- Look at package odfWeave, and find out, how to use this
-		- replace remaining direct HTML fragments in plugins with wrapper calls
-	- should we override bindingIsActive()?
 	RKVariable:
 		- True Support for Logicals
 		- In the current design, RKVariable would not handle storage mode changes from outside well at all
-		- use QIntDict instead of string-map for value-labels / factor levels? Qt4: QHash
 	RCommandReceiver:
 		- add virtual rCommandStarted () function, so receivers can find out, when their command becomes active
 	REmbedInternal:
@@ -189,14 +169,12 @@ Internal stuff:
 	- RThread:
 		- Detection of commands that run for a suspiciously long time
 			- Show "do you want to cancel ..." option after configurable amount of time
-	- use R_DirtyImage to determine, whether workspace needs to be saved
 	- Object editing / modification tracking:
 		- functions to set double/int/string-vectors directly. Use in paste-operations
 	- error-handling/raising in .rk.do.call
 	- I've changed the simple RInterface::issueCommand (QString, ...) command to return a pointer to the RCommand created. This will allow for lots of small cleanups. Do them.
 		- well, on second thought, it might be better to rely more on RCommand::id () instead of pointers. Why? The id is unique (until integer overflow). The pointer may be reused after a delete -> potential problem when trying to cancel command which is actually already deleted (and potentially other cases)
 		- let's set this back for a while
-	- give informative feedback on syntax errors (line numbers, etc.)!
 	- .rk.get.available.packages ()
 		- use external (file) storage for cache to save mem
 	- Always save workplace layout to a file, never to config. Even for the "global" option.
@@ -204,7 +182,6 @@ Internal stuff:
 		- in the documentation we call the return value of value() the "default property". Why not simply define a "default property" for each component, instead of reimplementing value()?
 
 General code:
-	- use constBegin (), constEnd ()
 	- get rid of all the superflous dependencies: http://lists.debian.org/debian-devel/2005/12/msg00439.html
 	- remove classes/files:
 		- RKGlobals
@@ -215,10 +192,6 @@ General code:
 R plugins:
 	- distribution plugins (probabilities and quantiles)
 		- probably all these could use an option "Store result (to name) / Print result / print and store"
-		- when changing this, they should first be changed to use common base functionality:
-			- the tail, log, and print options would be in a single embedded plugin
-			- a common PHP file would be included that generates uniform code (a small set of options would be needed to define the parts that are different across distributions)
-			- something similar should be done for the plots
 	- plugin help files:
 		- It would be nice to add the <id="..."> fetaure like <settings id=".."> in the technical section too. Also may be add something like <tag=".."> for the tags or variable which can be in italics, grey color.
 		- Find a way to make help searchable, preferentially within the R help search window
@@ -241,10 +214,6 @@ R plugins:
 		- use smart sorting, esp. of generated string
 		- add labels, add "up to level" option
 		- add constant term option
-	- multi-object option group:
-		- provide the set of enclosed options for each of the selected variables
-		- will provide dynamic properties based on which variables are selected in the source
-		- how to determine default values?
 
 API documentation:
 	- add page containing a rough overview of general architecture
@@ -258,64 +227,3 @@ Configuration:
 		- disable html help
 	- new dataeditor options:
 		- see comments on RKEditorDataFrame
-
-
-################## Some internal notes below ##############
-
-################## menu structure file/workspace ###########
-File
-	New
-		Dataset
-		Script File
-	Open R Script File
-	Open Recent (Script File)
-	Save/Load R Objects
-		Save
-			...
-		Load
-			...
-	Save
-	Save As
-	Reload
-	Print
-	Quit
-
-Workspace
-	Open Workspace
-	Open Recent (Workspace)
-	Save Workspace
-	Save Workspace As
-	Configure Packages (redundant)
-
-How should this be changed? Maybe:
-
-File
-	New
-		Dataset
-		Script File
-	Open R Script File
-	Open Recent (Script File)
-	Open Workspace
-	Open Recent (Workspace)
-	Import (previously Load R Objects)
-	Export (previously Save R Objects)
-	Save
-	Save As
-	Save Workspace
-	Save Workspace As
-	Reload
-	Print
-	Quit
-
-
-################## cryptic notes ######################
-
-translation of plugins and help files (no, this is not good, yet. Not modular, order gets messed up, context information is lacking. We need a dedicated simple parser that will understand the files it deals with, and extracts the strings with relevant context info).
-in Makefil.am:
-# experimental: extract all messages. Probably it would make sense to split this up, however, perhaps per .pluginmap, or per directory!
-messages:
-	extractrc `find . -name \*.rkh` --tag=title --tag=summary --tag=usage --tag=section --tag=related --tag=technical > messages.cpp
-	extractattr `find . -name \*.rkh` --attr=section,title --attr=section,shorttitle >> messages.cpp
-	extractattr `find . -name \*.pluginmap` --attr=component,label --attr=menu,label --attr=entry,label >> messages.cpp
-	extractrc `find . -name \*.xml` --tag=text >> messages.cpp
-	extractattr `find . -name \*.xml` --attr=dialog,label --attr=wizard,label --attr=tab,label --attr=page,label --attr=frame,label --attr=varselector,label --attr=varslot,label --attr=radio,label --attr=dropdown,label --attr=option,label --attr=checkbox,label --attr=spinbox,label --attr=browser,label --attr=saveobject,label --attr=formula,label >> messages.cpp
diff --git a/rkward/core/rkmodificationtracker.cpp b/rkward/core/rkmodificationtracker.cpp
index ba0f30d..72c68eb 100644
--- a/rkward/core/rkmodificationtracker.cpp
+++ b/rkward/core/rkmodificationtracker.cpp
@@ -63,7 +63,7 @@ bool RKModificationTracker::removeObject (RObject *object, RKEditor *editor, boo
 
 	if (!object->isPseudoObject ()) {
 		if (removed_in_workspace) {
-			if (ed && (ed->getObject () == object)) {	// NOTE: do not allow restoring of columns in a data.frame this way. See http://www.mail-archive.com/rkward-devel@lists.sourceforge.net/msg01731.html and replies.
+			if (ed && (ed->getObject () == object)) {	// NOTE: do not allow restoring of columns in a data.frame this way. See https://mail.kde.org/pipermail/rkward-devel/2012-March/003225.html and replies.
 				if (KMessageBox::questionYesNo (0, i18n ("The object '%1' was removed from workspace or changed to a different type of object, but is currently opened for editing. Do you want to restore it?", object->getFullName ()), i18n ("Restore object?")) == KMessageBox::Yes) {
 					ed->restoreObject (object);
 					/* TODO: It would make a lot of sense to allow restoring to a different name, and possibly different location. This may need some thinking. Probably something like:
diff --git a/rkward/plugin/rkstandardcomponentgui.cpp b/rkward/plugin/rkstandardcomponentgui.cpp
index d4753bb..a8cb34a 100644
--- a/rkward/plugin/rkstandardcomponentgui.cpp
+++ b/rkward/plugin/rkstandardcomponentgui.cpp
@@ -145,7 +145,7 @@ void RKStandardComponentGUI::showEvent (QShowEvent *e) {
 
 	QWidget::showEvent (e);
 
-	// HACK: Workaround for this issue (caused by a mysterious Qt bug, apparently): http://www.mail-archive.com/rkward-devel@lists.sourceforge.net/msg01340.html
+	// HACK: Workaround for this issue (caused by a mysterious Qt bug, apparently): https://mail.kde.org/pipermail/rkward-devel/2011-June/002831.html
 	QSize min = minimumSize ();
 	if ((min.width () < 50) || (min.height () < 50)) min = sizeHint ();
 	setMinimumSize (min.expandedTo (QSize (50, 50)));
diff --git a/rkward/rbackend/rklocalesupport.cpp b/rkward/rbackend/rklocalesupport.cpp
index 690dd72..16b843e 100644
--- a/rkward/rbackend/rklocalesupport.cpp
+++ b/rkward/rbackend/rklocalesupport.cpp
@@ -21,7 +21,7 @@
 #include <QByteArray>
 
 #ifndef Q_WS_WIN
-	// see https://sourceforge.net/tracker/?func=detail&atid=459009&aid=1698809&group_id=50231
+	// see http://sourceforge.net/p/rkward/patches/4/
 	// seems to be needed for GCC 4.3 as well.
 #	include <langinfo.h>
 #endif
diff --git a/rkward/rbackend/rkstructuregetter.cpp b/rkward/rbackend/rkstructuregetter.cpp
index 43a8d60..d50aaca 100644
--- a/rkward/rbackend/rkstructuregetter.cpp
+++ b/rkward/rbackend/rkstructuregetter.cpp
@@ -394,7 +394,7 @@ void RKStructureGetter::getStructureWorker (SEXP val, const QString &name, int a
 		} else if (do_cont) {
 			RK_DEBUG (RBACKEND, DL_DEBUG, "recurse into list %s", name.toLatin1().data ());
 			// fewer elements than names() can happen, although I doubt it is supposed to happen.
-			// see http://sourceforge.net/tracker/?func=detail&aid=3002439&group_id=50231&atid=459007
+			// see http://sourceforge.net/p/rkward/bugs/67/
 			bool may_be_special = Rf_length (value) < childcount;
 			if (Rf_isList (value) && (!may_be_special)) {		// old style list
 				for (int i = 0; i < childcount; ++i) {
diff --git a/rkward/rkconsole.cpp b/rkward/rkconsole.cpp
index ff49737..cda708e 100644
--- a/rkward/rkconsole.cpp
+++ b/rkward/rkconsole.cpp
@@ -981,7 +981,7 @@ void RKConsole::contextMenuEvent (QContextMenuEvent * event) {
 void RKConsole::activate (bool with_focus) {
 	RK_TRACE (APP);
 
-	// see http://www.mail-archive.com/rkward-devel@lists.sourceforge.net/msg00933.html
+	// see https://mail.kde.org/pipermail/rkward-devel/2010-September/002422.html
 	if (with_focus) view->removeSelection ();
 	RKMDIWindow::activate (with_focus);
 }
diff --git a/rkward/rkward.cpp b/rkward/rkward.cpp
index a8816a1..39c1c94 100644
--- a/rkward/rkward.cpp
+++ b/rkward/rkward.cpp
@@ -438,7 +438,7 @@ void RKWardMainWindow::initActions() {
 #if 0
 	// TODO: Fix import dialog and re-enable it: https://mail.kde.org/pipermail/rkward-devel/2015-June/004156.html
 #ifdef Q_WS_WIN
-	// TODO: find the cause and fix it! http://sourceforge.net/tracker/?func=detail&aid=2848341&group_id=50231&atid=459007
+	// TODO: find the cause and fix it! http://sourceforge.net/p/rkward/bugs/54/
 #	ifdef __GNUC__
 #		warning TODO: import data dialog is disabled on windows due to bug in kdelibs
 #	endif
diff --git a/rkward/robjectviewer.cpp b/rkward/robjectviewer.cpp
index f35bb0c..83c975f 100644
--- a/rkward/robjectviewer.cpp
+++ b/rkward/robjectviewer.cpp
@@ -129,7 +129,7 @@ void RObjectViewer::initDescription (bool notify) {
 	if (!_object) return;
 
 	setCaption (i18n("Object Viewer: %1", _object->getShortName ()));
-	// make the description use less height. Trying to specify <nobr>s, here, is no good idea (see https://sourceforge.net/tracker/?func=detail&atid=459007&aid=2859182&group_id=50231)
+	// make the description use less height. Trying to specify <nobr>s, here, is no good idea (see http://sourceforge.net/p/rkward/bugs/55/)
 	description_label->setText (_object->getObjectDescription ().replace ("<br>", "    "));
 	if (notify) {
 		QString reason = i18n ("The object was changed. You may want to click \"Update\"");
diff --git a/rkward/windows/rkcommandeditorwindow.cpp b/rkward/windows/rkcommandeditorwindow.cpp
index c734766..182a073 100644
--- a/rkward/windows/rkcommandeditorwindow.cpp
+++ b/rkward/windows/rkcommandeditorwindow.cpp
@@ -378,7 +378,7 @@ bool RKCommandEditorWindow::openURL (const KUrl url, const QString& encoding, bo
 				if (!encoding.isEmpty () && (conf.readEntry ("Encoding", encoding) != encoding)) conf.writeEntry ("Encoding", encoding);
 				if (conf.readEntry ("URL", url) != url) conf.writeEntry ("URL", url);
 				/* HACK: What the...?! Somehow, at least on longer R scripts, stored Mode="Normal" in combination with R Highlighting
-				 * causes code folding to fail (KDE 4.8.4, https://sourceforge.net/tracker/?func=detail&atid=459007&aid=3564769&group_id=50231).
+				 * causes code folding to fail (KDE 4.8.4, http://sourceforge.net/p/rkward/bugs/122/).
 				 * Forcing Mode == Highlighting appears to help. */
 				if (use_r_highlighting) conf.writeEntry ("Mode", conf.readEntry ("Highlighting", "Normal"));
 				iface->readSessionConfig (conf);
diff --git a/rkward/windows/rkfilebrowser.cpp b/rkward/windows/rkfilebrowser.cpp
index 3c15c5a..3ecd3a9 100644
--- a/rkward/windows/rkfilebrowser.cpp
+++ b/rkward/windows/rkfilebrowser.cpp
@@ -143,7 +143,7 @@ void RKFileBrowserWidget::contextMenuHook(const KFileItem& item, QMenu* menu) {
 	dummy.append (item);
 	fi_actions->setItemListProperties (KFileItemListProperties (dummy));
 
-	// some versions of KDE appear to re-use the actions, others don't, and yet other are just plain broken (see this thread: http://www.mail-archive.com/rkward-devel@lists.sourceforge.net/msg01279.html)
+	// some versions of KDE appear to re-use the actions, others don't, and yet other are just plain broken (see this thread: https://mail.kde.org/pipermail/rkward-devel/2011-March/002770.html)
 	// Therefore, we remove all actions, explicitly, each time the menu is shown, then add them again.
 	QList<QAction*> menu_actions = menu->actions ();
 	foreach (QAction* act, menu_actions) if (added_service_actions.contains (act)) menu->removeAction (act);
diff --git a/rkward/windows/rkmdiwindow.cpp b/rkward/windows/rkmdiwindow.cpp
index 567ee60..cf8be2f 100644
--- a/rkward/windows/rkmdiwindow.cpp
+++ b/rkward/windows/rkmdiwindow.cpp
@@ -273,7 +273,7 @@ void RKMDIWindow::enterEvent (QEvent *event) {
 	if (!isActive ()) {
 		if (RKSettingsModuleGeneral::mdiFocusPolicy () == RKSettingsModuleGeneral::RKMDIFocusFollowsMouse) {
 			if (!QApplication::activePopupWidget ()) {
-				// see https://sourceforge.net/tracker/?func=detail&atid=459007&aid=3327985&group_id=50231
+				// see http://sourceforge.net/p/rkward/bugs/90/
 				// enter events may be delivered while a popup-menu (in a different window) is executing. If we activate in this case, the popup-menu might get deleted
 				// while still handling events. Similar problems seem to occur, when the popup menu has just finished (by the user selecting an action) and this results
 				// in the mouse entering this widget. To prevent crashes in this second case, we delay the activation until the next iteration of the event loop.
diff --git a/rkward/windows/rktoolwindowlist.cpp b/rkward/windows/rktoolwindowlist.cpp
index cdcfd9f..5a9da8b 100644
--- a/rkward/windows/rktoolwindowlist.cpp
+++ b/rkward/windows/rktoolwindowlist.cpp
@@ -36,7 +36,7 @@ void RKToolWindowList::registerToolWindow (RKMDIWindow *window, const QString &i
 	tr.id = id;
 	tr.default_placement = default_placement;
 #ifdef Q_WS_MAC
-	// HACK: Workaround for shortcut conflict issue: http://www.mail-archive.com/rkward-devel@lists.sourceforge.net/msg01659.html
+	// HACK: Workaround for shortcut conflict issue: https://mail.kde.org/pipermail/rkward-devel/2011-December/003153.html
 	if (default_shortcut & Qt::AltModifier) default_shortcut |= Qt::ControlModifier;
 #endif
 	tr.default_shortcut = default_shortcut;

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