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(This article was first published on <strong><a href="https://bio7.org/bio7-2-8-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>30.05.2018</strong></p>
<p>A new and improved release of Bio7 is available. The new Bio7 2.8 release comes with a plethora of new R features and bugfixes.</p>
<p><img sizes="(max-width: 1921px) 100vw, 1921px" src="https://i0.wp.com/bio7.org/wp-content/uploads/2018/05/rperspnew.jpg?w=450" alt="" class="wp-image-3158" data-recalc-dims="1"></p>
<h2><strong>Release Notes:</strong></h2>
<p><strong>General:</strong></p>
<ul>
<li>Updated Eclipse <a rel="nofollow" href="https://wiki.eclipse.org/Rich_Client_Platform" target="_blank">RCP</a> to 4.7.3</li>
<li>Windows R update to version 3.5.0</li>
<li><a rel="nofollow" href="https://github.com/Bio7/EclipseImageJ1Plugin" target="_blank">ImageJ plugin</a> updated to version 1.52d7</li>
<li>Added the ImageJ Edit perspective to the default opened perspectives</li>
<li>The R perspective is now selected as the opened perspective after startup of Bio7</li>
<li>Added an option to save all editors on close (default enabled on MacOSX)</li>
<li>Improved the main ‘Scripts’ menu to allow nested custom scripts in folders and subfolders which form new submenus</li>
<li>Improved the Table and R-Shell context scripts menu</li>
<li>Added some example scripts to the new scripts menu</li>
<li>Added an script to open the default script location in the OS file explorer</li>
<li>Simplified the different script locations (reduced to four locations in the Bio7 preferences)</li>
<li>Spatial import, export scripts moved to the main ‘Scripts’ and R-Shell script context menu (Deleted import, export script locations)</li>
</ul>
<p><strong>R:</strong></p>
<ul>
<li>Simplified the Bio7 R-Shell interface</li>
<li>Added a new view for some R templates</li>
<li>Code completion from loaded R packages can now be imported from the R-Shell or the R editor (both completions will be updated!)</li>
<li>Improved the reload code completion by only considering R functions (cleaner seperation of functions and datasets)</li>
<li>The updated R-Shell context menu can now dynamically be extended with custom scripts (updated dynamically). Folder and subfolders form new submenus.</li>
<li>Improved, bugfixed and extended the ‚Evaluate Line‘ action which was renamed to ‚Evaluate Line or Selection‘  action which now interprets selected R code, too.</li>
<li>Improved MacOSX ImageJ interaction (editor hoover focus)</li>
<li>Improved the call of the default plot device (quartz) in a native R connection on MacOSX (now default opened when, e.g., plotting, debugging, etc.)</li>
<li>Added a new menu to install Rserve for R > 3.5.0</li>
<li>New shutdown option to execute R code at shutdown (e.g., to save the current R workspace – a reload with the already existing startup option is possible, too!)</li>
<li>Improved the general error messages of the R-Shell view and the R editor evaluation. Now much simpler and printed cleaner!</li>
<li>Added an option to print the error stream of the Bio7 console to the R-Shell view (to the right output panel to get an output if the console is hidden!)</li>
<li>Fixed a bug with the shiny execution (removed annoying dialog)</li>
<li>Fixed many other bugs (unnecessary error messages, execution errors, MacOSX bugs, etc.)</li>
<li>R-Shell code completion improved (see editor code completion improvements below)</li>
<li>Removed the use of temporary files of the R-Shell and R editor code completion</li>
<li>Added an preference option to add arguments to the source command</li>
<li>Multiple selected R-Shell variables are now available in the R workspace (‘.r_shell_vars’ – a character vector) for the use in custom R scripts (e.g., to extend the R-Shell script context menu!)</li>
</ul>
<p><strong>R Editor:</strong></p>
<ul>
<li>Added a detection/quickfix function to install missing packages when a package load definition is in the editor file but the package is not installed</li>
</ul>
<p><img alt="" src="https://i2.wp.com/bio7.org/wp-content/uploads/2018/05/packageinstall-1.gif?w=450" class="wp-image-3218" data-recalc-dims="1"></p>
<ul>
<li>Added a quickfix to add a library definition when an unknown function is called (not defined and loaded but package with function is installed)</li>
<li>Added support for the the <a rel="nofollow" href="http://magrittr.tidyverse.org/" target="_blank">magrittr</a> piping operator in code completion to autocomplete a given dataframe in the workspace (column completion)</li>
</ul>
<p><img alt="" src="https://i2.wp.com/bio7.org/wp-content/uploads/2018/05/dplycode-1.gif?w=456" class="wp-image-3171" data-recalc-dims="1"></p>
<ul>
<li>Added code completion support for dataframes columns and rows, named list elements and named arrays (of arbitrary dimension)</li>
</ul>
<p><img alt="" src="https://i2.wp.com/bio7.org/wp-content/uploads/2018/05/arrayc.gif?w=456" class="wp-image-3179" data-recalc-dims="1"></p>
<ul>
<li>Improved code completion to display current workspace variables</li>
<li>Classes of R objects are now displayed in the code completion context dialog</li>
<li>Editor variables and functions are now emphazised in code completion, too</li>
<li>Added a directory dialog to easily create a directory string for the editor file</li>
<li>Created new submenus for the organization of the context menu</li>
<li>Improved the hoover dialog (improved offset)</li>
<li>Improved the completion context of R objects (current workspace objects)</li>
<li>The styler package can now be used for an improved code formatting (requires UTF-8 Bio7 workspace on Windows – see preferences!)</li>
<li>Improved code completion for S3 and S4 objects (correctly display current cursor completion)</li>
</ul>
<p><strong>ImageJ:</strong></p>
<ul>
<li>Updated ImageJ plugin to version 1.52d7</li>
<li>Updated ImageJ2 libraries</li>
<li>Added new ImageJ macro functions to the code completion of the macro editor</li>
<li>Added the ImageJ Edit perspective to the default openend perspectives</li>
<li>Improved the editor hoover activation on MacOSX</li>
<li>Improved the ImageJ MacOSX touchpad resizing of the ImageJ panel</li>
</ul>
<p><strong>Java:</strong></p>
<ul>
<li>Updated JRE to 1.8.71</li>
<li>Improved the creation of Java projects and project imports (no annoying dialog anymore)</li>
<li>Improved the ‘Add Selected Libraries’ preference to add multiple Java libraries for dynamic compilation (e.g., to compile more embedded Eclipse library functions)</li>
<li>Now ImageJ2 libs have to be added to the dynamic compilation libraries for compilation (removed as default libraries)</li>
<li>Added a key shortcut (STRG + ‚+‘) to increase the SceneBuilder panel (2x)</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">https://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="https://bio7.org/" target="_blank">https://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="https://bio7.org/" target="_blank">https://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 (compiled for cooperative mode) installation:</h3>
<p>To install Rserve open the R shell and then execute the menu action “Options -> Install Rserve (coop. mode) for R …” for different R versions. 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>!). In cooperative mode only one connection at a time is allowed (which we want for this Desktop appl.) and all subsequent connections share the same namespace (default on Windows)!</p>
<p><iframe width="450" allowfullscreen="allowfullscreen" src="https://www.youtube.com/embed/tF7HbRBRIFQ" data-mce-fragment="1"></iframe></p>
<h2>Installation of Useful R Packages</h2>
<p>R packages which are useful in combination with Bio7 can easily be installed with the R-Shell context menu “Packages” action:</p>
<p><em>R-Shell context menu->Packages->Install_Default_R_Packages</em></p>
<h2>Bio7 Documentation</h2>
<p>For more information about <a rel="nofollow" href="https://bio7.org/" target="_blank">Bio7</a> please consult the soon updated <a rel="nofollow" href="https://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> </p>
	<p>
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