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(This article was first published on <strong><a href="http://bio7.org/bio7-2-7-released/"> R – Bio7 Website</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p><strong>02.01.2018</strong></p>
<p>A new version of Bio7 is available. The application Bio7 is an integrated development environment for ecological modeling scientific image analysis and statistical analysis. Over the years Bio7 evolved to a platform useful for a broad scientific context.</p>
<p><img sizes="(max-width: 1919px) 100vw, 1919px" src="https://i2.wp.com/bio7.org/wp-content/uploads/2017/12/bio7_27_r_pdf.png?w=450" alt="" class="wp-image-3051" data-recalc-dims="1"></p>
<p>This release includes a plethora of new features and improvements for the R editor, RShell, RMarkdown editor and the ImageJ plugin.</p>
<h2>Release Notes:</h2>
<h3>General:</h3>
<ul>
<li>Bundled with Java 1.8.52</li>
<li>Updated bundled R to version 3.4.3 (Windows)</li>
<li>Improved PDF rendering (<a rel="nofollow" href="https://mozilla.github.io/pdf.js/" target="_blank">PDF.js</a>) with Java 1.8.52 (<a rel="nofollow" href="https://bugs.openjdk.java.net/browse/JDK-8180825" target="_blank">fixed rendering</a>)</li>
<li>Updated the<a rel="nofollow" href="https://github.com/PowerShell/Win32-OpenSSH/releases.html" target="_blank"> Windows SSH client</a></li>
<li>Simplified the dynamic java compilation</li>
<li>Updated the Java compiler infrastructure</li>
</ul>
<h3>R</h3>
<ul>
<li>Improved the context information when opening code completion (R-Shell and R editor)</li>
<li>Added an improved context information when openening code completion in the R-Shell</li>
<li>Context information of a function is shown when using code completion inside function calls</li>
<li>Added code completion for function arguments in the R-Shell</li>
<li>Added code completion help for ‘library’, ‘require’, ‘data’,’::’ and ‘:::’ functions in the R-Shell and in the R editor</li>
</ul>
<p>Screencast code completion:</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/tbh1URVwTo0" data-mce-fragment="1"></iframe></p>
<p>Screencast code completion with particle analysis:</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/qYyNLH1RZTY" data-mce-fragment="1"></iframe></p>
<ul>
<li>Improved code completion for S3 and S4 nested attributes (e.g., x@y$z) also in function calls when cursor is set inside of a composite call</li>
<li>Implemented a code completion filter (when typing)</li>
<li>Added an option to select different key combinations for the R-Shell code completion (Strg+Space can already be occupied on MacOSX)</li>
<li>Added dark theme support for the help browser when opened from the R-Shell help (?)</li>
<li>Added a matching brackets selection action to the R-Shell view (Key+Mouse-click before opening or closing bracket)</li>
<li>Added an action to transfer the R-Shell history to an opened R editor (see R-Shell help (?))</li>
<li>The R-Shell and code completion fonts can now be changed and the size increased</li>
<li>The R-Shell is now faster if long text is printed (removed automatic text wrapping)</li>
<li>Added the Eclipse Spell Checking infrastructure to the R editor (can be enabled in the preferences)</li>
</ul>
<p>Screencast spell checking:</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/kbY1nJG5fig" data-mce-fragment="1"></iframe></p>
<ul>
<li>Spell checking errors can now be fixed in the R editor (hoover action available)</li>
<li>Added a preference to enable/disable spell checking</li>
<li>Added a ‘Load packages tab’ in the ‘Packages’ view as an UI replacement for the Load packages dialog (improved usability)</li>
<li>Added an action to update the display list of installed packages (also triggered if you activate the tab)</li>
<li>Added an ‘Attached Packages’ tab to the ‘Packages’ view</li>
<li>Added an action to update all packages (‘Load Packages’ tab)</li>
</ul>
<p>Screencast R Packages view:</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/rbEOFSnFNwI" data-mce-fragment="1"></iframe></p>
<ul>
<li>Improved the R-Shell code completion in general</li>
<li>Improved the hoover display layout (for warnings and errors)</li>
<li>Fixed several bugs (Reenabled loop parsing and fixed a bug to restore code folding after using code completion in the R editor!)</li>
<li>Updated ANTLR parser to version 4.7</li>
<li>Added „require“ for package code completion</li>
<li>Reduced the memory footprint of the R editor (OS handles)</li>
<li>Added missing roxygen tags for code completion of the R editor</li>
<li>Created a wizard to support a project template (default folders and files) for reproducible projects</li>
<li>Changed key binding of ‘&lt;-‘ and ‘%>%’ operators to make them available in the R-Shell, too (see help in R-Shell)</li>
<li>Improved the “Evaluate Selected Line” Action for Rserve (Evaluated when successfully parsed!)</li>
</ul>
<h3>R Markdown editor</h3>
<ul>
<li>Spell checking errors in the R markdown editor can now be fixed with a hoover action</li>
<li>Added a decent markdown parser (<a rel="nofollow" href="https://github.com/vsch/flexmark-java" target="_blank">flexmark</a>) to the editor which fixes some minor display problems</li>
<li>Added a format action for selected text to the markdown editor</li>
</ul>
<p>Screencast format markdown selection:<br>
<iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/Kgw9If8hx44" data-mce-fragment="1"></iframe></p>
<h3>ImageJ:</h3>
<ul>
<li>Updated ImageJ plugin to version 1.51.t16</li>
<li>Code completion (template) action now displays the macro documentation when typing</li>
<li>Code completion context information improved</li>
<li>Images from macros are now opened fast (before had a 2s delay because of a missing ImageJ attribute)</li>
<li>Cluttered MACOSX menus are now closed (added from opened application windows and frames). Some default added menus are disabled in the Bio7 preferences by default</li>
<li>Macros can now be executed within an external ImageJ instance in a separate Java process (if enabled in the preferences). Windows only!</li>
<li>Added Macro debugging context menus to the macro editor</li>
</ul>
<p>Screencast ImageJ macro debugging:</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/TqbnFnazxyw" data-mce-fragment="1"></iframe></p>
<ul>
<li>Added an context actions to copy the Macro Recorder code to the current editor</li>
<li>Added an „Evaluate Line“ action</li>
<li>Reenabled CTRL+X as default „Cut“ text action.</li>
</ul>
<h2><strong>Download and Installation:</strong></h2>
<h3><strong>Windows:</strong></h3>
<p>Just download the *.zip distribution file from <a rel="nofollow" href="http://bio7.org/" target="_blank">http://bio7.org</a> and unzip it in your preferred location. Bio7 comes bundled with a Java Runtime Environment, R and Rserve distribution and works out of the box.</p>
<h3><strong>Linux:</strong></h3>
<p>Download and extract the installation file from <a rel="nofollow" href="http://bio7.org/" target="_blank">http://bio7.org</a>.<br>
For Linux you have to install R and Rserve (see Rserve installation below!).</p>
<h3>MacOSX:</h3>
<p>Download and extract the installation file from <a rel="nofollow" href="http://bio7.org/" target="_blank">http://bio7.org</a>.</p>
<p><strong>If you start Bio7 a warning or error can occur because of the changes how Apple treats signatures! To allow Bio7 to start see this instructions for Yosemite and Sierra:<br>
</strong></p>
<p><a rel="nofollow" href="https://support.apple.com/kb/PH18657?locale=en_US" target="_blank">OS X Yosemite: Open an app from an unidentified developer</a></p>
<p><a rel="nofollow" href="https://support.apple.com/kb/PH25088?locale=en_US" target="_blank">macOS Sierra: Open an app from an unidentified developer</a></p>
<p>If you have still problems with Sierra <a rel="nofollow" href="http://osxdaily.com/2016/09/27/allow-apps-from-anywhere-macos-gatekeeper/" target="_blank">see this solution</a>!</p>
<p>In addition For MacOSX you have to install R and Rserve (see below!).</p>
<h3>Linux and MacOSX Rserve installation:</h3>
<p>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 rel="nofollow" href="http://stackoverflow.com/questions/32540919/library-is-not-writable" target="_blank">writing permissions</a>!).</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/tF7HbRBRIFQ" data-mce-fragment="1"></iframe></p>
<p>The special version of Rserve can also be downloaded here:</p>
<p><a rel="nofollow" href="https://bitbucket.org/maustenfeld/bio7-new/downloads" target="_blank">https://bitbucket.org/maustenfeld/bio7-new/downloads</a></p>
<p>For a manual installation in the R prompt type the following command to install the compiled package (replace with your file path!):</p>
<p><em>install.packages(“Users/yourName/Downloads/Rserve_1.8-4_Mac_cooperative.tgz”, repos=NULL)</em></p>
<h2>Installation of Useful R Packages</h2>
<p>R packages which are useful in combination with Bio7 can easily be installed with the main menu “Scripts” action:</p>
<p><em>Scripts->R-Scripts->InstallDefaultRPackages</em></p>
<h2>Bio7 Documentation</h2>
<p>For more information about <a rel="nofollow" href="http://bio7.org/" target="_blank">Bio7</a> please consult the soon updated <a rel="nofollow" href="http://bio7.org/manual/Main.html" target="_blank">Bio7 User Guide</a>.</p>
<p>A plethora of <a rel="nofollow" href="https://www.youtube.com/channel/UCFY-w-tMbVzhrLro4Q2KbFg/" target="_blank">Bio7 videotutorials</a> can be found on YouTube.</p>
	<p>
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