[rkward-cvs] SF.net SVN: rkward:[4228] branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted
tfry at users.sourceforge.net
tfry at users.sourceforge.net
Mon Apr 30 16:52:24 UTC 2012
Revision: 4228
http://rkward.svn.sourceforge.net/rkward/?rev=4228&view=rev
Author: tfry
Date: 2012-04-30 16:52:24 +0000 (Mon, 30 Apr 2012)
Log Message:
-----------
Inline former footnotes 4-10 and 20-23. Restore \url{}-markup.
Modified Paths:
--------------
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex
branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex 2012-04-30 16:08:31 UTC (rev 4227)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/GUI_elements.tex 2012-04-30 16:52:24 UTC (rev 4228)
@@ -473,9 +473,9 @@
\citep{Leisch2002, Kuhn2006}.
Images contained in the output are stored as
-portable network graphics (PNG)\footnote{http://www.libpng.org/pub/png/} by
-default, but JPEG\footnote{http://www.jpeg.org/jpeg/index.html} and
-scalable vector graphics (SVG)\footnote{http://www.w3.org/Graphics/SVG/}
+portable network graphics (PNG; \url{http://www.libpng.org/pub/png/}) by
+default, but JPEG (\url{http://www.jpeg.org/jpeg/index.html}) and
+scalable vector graphics (SVG; \url{http://www.w3.org/Graphics/SVG/})
can also be used. Similarly, the size of
images can be configured by the user. It is expected that SVG will
become the default output format eventually, but currently some SVG
@@ -491,7 +491,7 @@
\subsection{Package management}
\label{sec:package_management}
The number of \proglang{R} packages available from the comprehensive \proglang{R} archive
-network (CRAN), Omegahat\footnote{http://www.omegahat.org/} and Bioconductor \citep{Gentleman2004} has grown exponentially since \proglang{R}\, 1.3.0
+network (CRAN), Omegahat (\url{http://www.omegahat.org/}) and Bioconductor \citep{Gentleman2004} has grown exponentially since \proglang{R}\, 1.3.0
(2001) to \proglang{R}\, 2.7.0 (2008) \citep{Fox2008, Ligges2003, Visne2009}. \pkg{RKWard}
utilizes functionality from a growing number of these packages, but avoids
making the installation of all supported packages a pre-requirement to using
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex 2012-04-30 16:08:31 UTC (rev 4227)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/background.tex 2012-04-30 16:52:24 UTC (rev 4228)
@@ -45,7 +45,7 @@
\pkg{RKWard} provides a high level of transparency about the steps that are needed to
perform any supported task in \proglang{R}, in order to make it easy for the user to see
complete codes for all GUI actions\footnote{
- This distinguishes \pkg{RKWard} from \proglang{R} GUIs such as \pkg{Red-R} (http://www.red-r.org/), which
+ This distinguishes \pkg{RKWard} from \proglang{R} GUIs such as \pkg{Red-R} (\url{http://www.red-r.org/}), which
specifically aims to hide the complexities of the \proglang{R} programming language, following the concept of visual data-flow
programming \citep{Sutherland1966}. In contrast, \pkg{RKWard} limits itself to generate \proglang{R} code from GUI settings.
}. In doing so, \pkg{RKWard} deliberately generates
@@ -77,10 +77,13 @@
which are not included in the official \pkg{RKWard} releases. Details on the definition of plugins,
and a commented example can be found in the technical supplement to this article.
-\pkg{RKWard} is licensed under the terms of the GNU General Public License\footnote{http://www.gnu.org/licenses/gpl.html} Version 2
+\pkg{RKWard} is licensed under the terms of the GNU General Public License Version 2
or higher. However, due to its dependencies, \pkg{RKWard} binaries are effectively
distributable only under the terms of Version 2 of the license. Parts of the documentation are available under the
-GNU Free Documentation License\footnote{http://www.gnu.org/licenses/fdl.html}. While the project remains in constant development, a growing
+GNU Free Documentation License.
+Full terms and explanations of both licenses are available at \url{http://www.gnu.org/licenses/gpl.html}
+and \url{http://www.gnu.org/licenses/fdl.html}, respectively.
+While the project remains in constant development, a growing
number of users employs \pkg{RKWard} in productive scenarios. The source code,
selected binaries and documentation is hosted at SourceForge
(\url{http://rkward.sourceforge.net/}). Selected key milestones of the development of \pkg{RKWard} are
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex 2012-04-30 16:08:31 UTC (rev 4227)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/installing_starting_RKWard.tex 2012-04-30 16:52:24 UTC (rev 4228)
@@ -11,24 +11,18 @@
\subsection{Installation on the GNU/Linux platform}
Historically, \pkg{RKWard} originated on the GNU/Linux platform, and binary packages are available for many
-major GNU/Linux distributions, including Debian, Ubuntu, OpenSuse, Gentoo, Fedora, but also for other POSIX\footnote{
-http://standards.ieee.org/develop/wg/POSIX.html
-}
-compliant systems such as FreeBSD. The exact size of the installation is system dependent. On Debian x86, the
+major GNU/Linux distributions, including Debian, Ubuntu, OpenSuse, Gentoo, Fedora, but also for other POSIX
+compliant systems such as FreeBSD (\url{http://standards.ieee.org/develop/wg/POSIX.html}). The exact size of the installation is system dependent. On Debian x86, the
package is currently around 1.5 MB (megabyte) compressed, and 5.5 MB uncompressed. However, if the \pkg{KDE}
runtime environment is not yet installed, an installation of \pkg{RKWard} may need several hundred MB of disc
space.
On systems which provide up-to-date packages of \proglang{R} and \pkg{KDE}, compilation from source is
-generally unproblematic\footnote{
- See http://p.sf.net/rkward/compilling for details.
-}.
+generally unproblematic. Instructions are provided at \url{http://p.sf.net/rkward/compiling}.
\subsection{Installation on Microsoft Windows}
\pkg{RKWard} will run on Windows XP, Windows Server 2003, Vista, and Windows 7. 32-bit binaries are
-provided by the project\footnote{
- See http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows\#Installing
-}. Users can
+provided by the project (download links and instructions are provided at \url{http://p.sf.net/rkward/windows}). Users can
choose between a small installer (1.7 MB), which will add \pkg{RKWard} to pre-existing installations of
\proglang{R} and \pkg{KDE}, and an installation bundle, which provides \pkg{RKWard}, \proglang{R}, and
\pkg{KDE}. This bundle just needs to be unpacked to any user-writable folder, and can be run without any
@@ -38,9 +32,7 @@
current installation bundle is 132 MB compressed, and around 670 MB installed.
Source installation on the Microsoft Windows platform is comparatively difficult, since various tools need to
-be installed\footnote{
- See http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows/Packaging for details.
-}.
+be installed (see \url{http://sourceforge.net/apps/mediawiki/rkward/?title=RKWard\_on\_Windows/Packaging} for details).
\subsection{Installation on Mac OS X}
At the time of this writing, the developers lack the resources to support a Mac OS X port, and especially
Modified: branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex
===================================================================
--- branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex 2012-04-30 16:08:31 UTC (rev 4227)
+++ branches/jss_dec_10/FINAL_JSS_TEX/FINAL_splitted/technical.tex 2012-04-30 16:52:24 UTC (rev 4228)
@@ -6,6 +6,9 @@
plugin framework (Section~\ref{sec:technical_plugins}) used in \pkg{RKWard}, since this is central to the extensibility of
\pkg{RKWard}, and we will conclude with an example for extending \pkg{RKWard} by a plugin (Section~\ref{sec:example_plugin}).
+Note that this document refers to \pkg{RKWard} version 0.5.6. Several technical details, described here, have changed
+in \pkg{RKWard} version 0.5.7 and the current development version.
+
\section{Asynchronous command execution}
\label{sec:technical_asynchronous}
One central design decision in the implementation of \pkg{RKWard} is that the
@@ -151,8 +154,8 @@
\citep{Faure2000}. This is especially helpful in providing an integrated GUI across
the many different kinds of document windows and tool views supported in \pkg{RKWard}.
-Plugins in \pkg{RKWard} rely on XML\footnote{http://www.w3.org/XML/}
-and \proglang{ECMAScript}\footnote{http://www.ecmascript.org/} (see Section~\ref{sec:technical_plugins}). XML is not
+Plugins in \pkg{RKWard} rely on XML (\url{http://www.w3.org/XML/})
+and \proglang{ECMAScript} (\url{http://www.ecmascript.org/}; see Section~\ref{sec:technical_plugins}). XML is not
only well suited to describe the layout of the GUI of plugins, but simple
functional logic can also be represented \citep[see also][]{Visne2009}. \proglang{ECMAScript} was
chosen for the generation of \proglang{R} commands within plugins, in particular due to its
@@ -382,11 +385,10 @@
it becomes instantly available after the configuration dialog is closed. External plugin sets are
neither officially included nor supported by the \pkg{RKWard} developers. However, they allow plugin
developers to easily extend \pkg{RKWard} with state-of-the-art or highly specialized features. To
-achieve this, \pkg{RKWard} draws on \pkg{KNewStuff2}\footnote{
- http://websvn.kde.org/trunk/KDE/kdelibs/knewstuff/
-}, a \pkg{KDE} library providing support for \pkg{GHNS}\footnote{
+achieve this, \pkg{RKWard} draws on \pkg{KNewStuff2}, a \pkg{KDE} library providing support for \pkg{GHNS}\footnote{
\pkg{GHNS} (Get Hot New Stuff) is a technology platform (software and specifications) for desktop users to share their work. It is hosted
-under the umbrella of the freedesktop.org project (http://ghns.freedesktop.org).}.
+under the umbrella of the freedesktop.org project at \url{http://ghns.freedesktop.org}.
+}.
\subsubsection{Automated testing}
\label{sec:technical_processes_automatedtesting}
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