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<div>
(This article was first published on <strong><a href="http://bio7.org/?p=2862"> R</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<h1><span><b>07.04.2017</b></span></h1>
<p><span>A new release of <a target="_blank" rel="nofollow" href="http://bio7.org/">Bio7</a> is available for Windows (64-bit) and Linux (64-bit).<br>
The MacOSX version will be released soon, too. This release comes with a plethora of new functions for R.</span></p>
<h2>General</h2>
<ul>
<li><span>Bio7 is now based on Eclipse 4.6.3</span></li>
<li><span>Redesigned all Bio7 icons and created new icons, too</span></li>
<li><span>Nearly all icons are now available for high dpi displays</span></li>
<li><span>A</span><span>dded a dark Theme for Bio7</span></li>
</ul>
<p><img sizes="(max-width: 1916px) 100vw, 1916px" alt="" class="wp-image-2829" src="https://i0.wp.com/bio7.org/wp-content/uploads/2017/03/blackskin3.jpg?w=450" data-recalc-dims="1"></p>
<ul>
<li><span>Added the default Eclipse theme as optional to Bio7</span></li>
<li><span>Added a new action for Linux and MacOSX to download and install Rserve (see Video in R section)<br>
</span></li>
<li><span>Added JavaScript editor support (default opened in text editor but if Eclipse JavaScript editor installed it can be opened and executed in the advanced editor)</span></li>
<li><span>Added a new action for the execution of JavaScript (and ImageJ macro)<br>
</span></li>
<li><span>JavaScript can be executed in the current opened browser if enabled in the preferences</span></li>
<li><span>Added JavaScript support to the console</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/v9TFfw3bv9g"></iframe></p>
<ul>
<li><span>Custom views are now entitled with the id of the view</span></li>
<li><span>A</span><span>dded a new „Document“ perspective </span><span>for LaTeX, Sweave, knitr and rmarkdown documents</span></li>
<li><span>Added a new PDF viewer in the JavaFX browser to display PDF’s from LaTeX, knitr, rmarkdown and R plots („Display“)</span></li>
</ul>
<p><img sizes="(max-width: 1914px) 100vw, 1914px" alt="" class="wp-image-2871" src="https://i1.wp.com/bio7.org/wp-content/uploads/2017/04/screen2_5_1.jpg?w=450" data-recalc-dims="1"></p>
<ul>
<li><span>Added options and actions to fullscreen a PDF on different monitors (press the key ‘t’ and the PDF will be centered and the toolbar will be removed)<br>
</span></li>
<li><span>Added several PDF options (scroll to selected page, etc.)<br>
</span></li>
<li><span>Added a new JavaFX browser for *.html and *.pdf files based on PDF.js</span></li>
<li><span>PDF files can be opened within the Navigator view with a double-click of the mouse device (also popular image types with ImageJ).</span></li>
<li><span>Added drag and drop support for the browser for *.html and *.pdf files</span></li>
<li><span>All editor fonts can now be scaled with the key combination ‘Ctlr +’</span></li>
<li><span>Added new global preferences for the editor fonts</span></li>
<li><span>Added preferences links for an improved navigation</span></li>
<li><span>Updated the default scientific Java libraries<br>
</span></li>
<li><span>Implemented a reload of the JavaFX Browser to avoid a cached display<br>
</span></li>
<li><span>Improved the resizing of the Quadgrid (Hexgrid) view<br>
</span></li>
<li><span>Added a new preference to disable the scrollbars of the Quadgrid (Hexgrid) view</span></li>
</ul>
<h2><span><b>R</b></span></h2>
<ul>
<li><span>Updated R to 3.3.3 on Windows<br>
</span></li>
<li><span>Added an action to download and install ‘Rserve cooperative mode’  for Linux and MacOSX</span></li>
<li><span>Improved the speed of the „Load packages“ dialog</span></li>
<li><span>Improved the speed of the „Install packages“ dialog.<br>
</span></li>
<li><span>Improved the speed of the refresh action in the R-Shell view</span></li>
<li><span>Added browser preferences to select the browser and the display</span></li>
<li><span>Added a new toolbar action for Sweave</span></li>
<li><span>Added an extra view for plots</span></li>
<li><span>Added the package install dialog as an view</span></li>
<li><span>Added an option to open a HTML package info for a selected package in the package install view (see video below).</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/di05Obs1Qcc"></iframe></p>
<ul>
<li><span>Added a preference for a custom Rserve client connection port if you start the Rserve server with a different port<br>
</span></li>
<li><span>Added code completion in the R-Shell view for s3 and s4 methods (see video below)<br>
</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/SZY8zrV00Po"></iframe></p>
<ul>
<li><span>Added an option to automatically open code completion when typing in the R-Shell</span></li>
<li><span>R-Shell R help now recognizes the selected browser</span></li>
<li><span>Added several actions to create, built, and test R packages to the context menu of the Navigator view (using the ‘devtools’ package)<br>
</span></li>
<li><span>Added a Shiny test action in the context menu of the Navigator view which opens a browser with the running shiny application (select a project folder with the server and ui files – to stop the server use the interrupt action in the R-Shell console or press ‘Strg c’ in the Console).</span></li>
<li><span>Improved the transfer of variables and sheet names from the Table view and LibreOffice<br>
</span></li>
<li><span>Improved the display of the R preferences (opening the default preferences structure)<br>
</span></li>
</ul>
<h2><strong><span>R editor</span></strong></h2>
<ul>
<li><span>Improved the code completion in general</span></li>
<li><span>Code completion dialogs are now synchronized with the other dialogs<br>
</span></li>
<li><span>Added code completion for</span>
<ul>
<li><span>S3 objects (after <em>$</em>)</span></li>
<li><span>S4 object slots (after <em>@</em>)</span></li>
<li><span>the library function (<em>library()</em>)</span></li>
<li><span>the data function (<em>data()</em>)</span></li>
</ul>
</li>
<li><span>Added new individual images to the code completion</span></li>
<li><span>Improved the close parentheses functions</span></li>
<li><span>Improved the visual appearence of the hoover dialog</span></li>
<li><span>Corrected the code completion images to match the Outline view images</span></li>
<li><span>Improved the display of markers</span></li>
<li><span>Added a popup display for the ‚str‘ function when hoovering over a workspace variable</span></li>
<li><span>Fonts can now be scaled with the key shortcuts ‘Strg +’</span></li>
<li><span>Added automatic indention after parentheses (loops, function, etc.)</span></li>
<li><span>Added preferences for the formatR package</span></li>
<li><span>Added an formatR action to format editor selections only<br>
</span></li>
<li><span>Added a refactor rename method for a selected scope<br>
</span></li>
<li><span>Added roxygen code completion in comments</span></li>
</ul>
<p><img sizes="(max-width: 346px) 100vw, 346px" alt="" class="wp-image-2901" src="https://i1.wp.com/bio7.org/wp-content/uploads/2017/04/roxygencompletion.jpg?resize=346%2C197" data-recalc-dims="1"></p>
<ul>
<li><span>Added an action to create roxygen templates from selected function, S3, S4, Reference and R6 classes (see video below)</span><span><br>
</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/2zdbPtI-3Fw"></iframe></p>
<ul>
<li><span>In the popup menu added several actions of the devtools package to create, test and install R packages (select a project or regular folder)</span></li>
<li><span>Added plot preferences to open plot images individually and an option to execute an ImageJ macro after plot creation (e.g. to scale a plot after creation, etc.)</span></li>
<li><span>Added an ‘Open File’ and ‘Save File’ dialog to create file templates with selected files in the R editor and the R-Shell view (see video)<br>
</span></li>
<li><span>Added a new shortcut to create an assign operator (‘ALT   _’)</span></li>
<li><span>Added a new shortcut to create a pipe operator (‘CTRL SHIFT M’)</span></li>
<li><span>Added simple editor templates for S3, S4, Reference and R6 classes</span></li>
<li><span>Improved the preferences navigation</span></li>
<li><span>Reorganized some preferences</span></li>
<li><span>Updated the parser to ANTLR 4.6</span></li>
</ul>
<h2><strong><span>R Markdown</span></strong></h2>
<ul>
<li><span>Improved the R markdown editor</span></li>
<li><span>Header and R chunks are now displayed in the Outline view<br>
</span></li>
<li><span>Added spell checking to the rmarkdown editor</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/r08-PVwf3N8"></iframe></p>
<ul>
<li><span>Compiled documents are now displayed in a special custom view of Bio7 if enabled (by default enabled)<br>
</span></li>
<li><span>Added font and color preferences to the editor<br>
</span></li>
<li><span>Added new browser preferences (use of JavaFX webkit browser or system browser) and additional preferences for the control of the output</span></li>
<li><span>Added preferences to compile the document automatically after a specific time intervall (adjustable in the preferences – see video below)<br>
</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/pIaTGHwX5Zg"></iframe></p>
<ul>
<li><span>Added code templates for popular markdown commands<br>
</span></li>
<li><span>Added an option to open word documents embedded in a custom view with Word (Windows only)</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/QrtboAOe3Fs"></iframe></p>
<ul>
<li><span>Added a key shortcut for the action to compile markdown documents</span></li>
</ul>
<h2><strong><span>LaTeX</span></strong></h2>
<ul>
<li><span>Improved the compile actions in the Bio7 toolbar (new icon) and removed the popup actions in the Navigator view<br>
</span></li>
<li><span>Added a key shortcut for the compilation</span></li>
<li><span>By default Latex documents are opened in the new PDF viewer (custom view)</span></li>
<li><span>Added new Bio7 LaTeX preferences to compile documents easily (without the need to create a LaTeX project with <a target="_blank" rel="nofollow" href="http://texlipse.sourceforge.net/">Texclipse</a>)</span></li>
<li><span>Added new preferences to optional use <a target="_blank" rel="nofollow" href="http://tex.stackexchange.com/questions/2984/frequently-loaded-packages-differences-between-pdflatex-and-xelatex">XeLaTex</a> and cleanup auxiliary files in the project folder</span></li>
<li><span>Added an option to compile BibTeX along with the *.tex file (several compilation iterations are performed)</span></li>
</ul>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/1PyNTUYg43o"></iframe></p>
<h2><strong><span>ImageJ</span></strong></h2>
<ul>
<li><span>Updated ImageJ to version1.51m</span></li>
<li><span>Improved the ImageJ menus to display all ImageJ menus correctly and nested (with key shortcuts and seperators)</span></li>
<li><span>ImageJ plugins now extend the respective SWT menu analogue to the ImageJ AWT menu.</span></li>
<li><span>Plugins, scripts and macros are now displayed in their defined menus or submenus.</span></li>
<li><span>Some popular image types can now be opened (double-click) directly from a Navigator folder (registered as a fake editor type)</span></li>
<li><span>Added two preferences to define the install location of plugins and macros (e.g external locations for teams).</span></li>
<li><span>Plugins now contribute to all ImageJ menus (SWT) like it is known from ImageJ</span></li>
<li><span>Dramatically improved the compatibility for ImageJ plugins (partially AWT)</span></li>
<li><span>Added a menu option to open images in a nested JavaFX panel (fullscreen on different monitors possible)</span></li>
<li><span>Addded JavaScript support for ImageJ (default editor is the text editor but a advanced Eclipse JavaScript editor can easily be installed)</span></li>
<li><span>Added a ImageJ macro wizard action to create ImageJ macros</span></li>
<li><span>Added an JavaScript wizard action to create a JavaScript file</span></li>
<li><span>JavaScript and ImageJ macros can now be executed with a toolbar (JavaScript) action.</span></li>
</ul>
<p><strong><span>WorldWind</span></strong></p>
<ul>
<li><span>Updated WorldWind to version 2.1</span></li>
<li><span>Made improvements for the dark theme<br>
</span></li>
</ul>
<h1><strong>Installation:</strong></h1>
<h2><strong>Windows:</strong></h2>
<p><span>Just download the *.zip distribution file from <a target="_blank" rel="nofollow" href="http://bio7.org/">http://bio7.org</a> and unzip it in your preferred location. Bio7 comes bundled with the latest Java Runtime Environment, R and Rserve distribution and works out of the box.</span></p>
<h2><strong>Linux:</strong></h2>
<p><span>Download and extract the installation file from <a target="_blank" rel="nofollow" href="http://bio7.org/">http://bio7.org</a>.<br>
</span></p>
<p><span>For Linux you have to install R and Rserve.</span></p>
<p><span>To install Rserve open the R shell and then execute the menu action “Options->Install Rserve (coop. mode)”. This will download an install Rserve in your default R library location, see video below (please make sure that your default Linux R library install location has <a target="_blank" rel="nofollow" href="http://stackoverflow.com/questions/32540919/library-is-not-writable">writing permissions</a>!).</span></p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/tF7HbRBRIFQ"></iframe></p>
<p><span>The special version of Rserve can also be downloaded here:<br>
<a target="_blank" rel="nofollow" href="https://bitbucket.org/maustenfeld/bio7-new/downloads">https://bitbucket.org/maustenfeld/bio7-new/downloads</a></span></p>
<p><span>For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):</span></p>
<blockquote><p><span><em>install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)</em></span></p>
</blockquote>
<p><span>For more information please consult the <a target="_blank" rel="nofollow" href="http://bio7.org/manual/Main.html">Bio7 User Guide</a>.</span></p>
<p> </p>
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