<p><div><div><div><div data-width="100" data-show-faces="false" data-send="true" data-layout="button_count" data-height="21" data-href="http://www.r-bloggers.com/bio7-2-4-for-windows-and-mac-released/"></div></div><div><a data-url="http://www.r-bloggers.com/bio7-2-4-for-windows-and-mac-released/" data-counturl="http://www.r-bloggers.com/bio7-2-4-for-windows-and-mac-released/" data-count="horizontal" data-text="Bio7 2.4 for Windows and Mac Released" class="twitter-share-button" data-via="rbloggers" href="https://twitter.com/share"></a></div><div></div></div><div></div></div>
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(This article was first published on <strong><a href="http://bio7.org/?p=2737"> R</a></strong>, and kindly contributed to <a rel="nofollow" href="http://www.r-bloggers.com/">R-bloggers)</a> </div>
<p>A new release of Bio7 is available for Windows and MacOSX. The Linux version will be released soon, too. This release comes with a plethora of new functions, especially for the R editor.</p>
<p>Download at: <a target="_blank" href="http://bio7.org/">http://bio7.org</a></p>
<h2><strong>Release notes:</strong></h2>
<p><strong>General</strong></p>
<ul>
<li>Updated Bio7 to use Eclipse 4.6 (Neon) as RCP basis</li>
<li>Updated the embedded Java Runtime Environment to version 1.8.92</li>
<li>Updated embedded R for Windows to R 3.3.1</li>
<li>Improved the toolbar layout and action alignments (CSS can be edited!)</li>
<li>Added a new ImageJ R analysis perspective</li>
</ul>
<p><img sizes="(max-width: 1370px) 100vw, 1370px" srcset="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/rimagejpersp.jpg?resize=456%2C310 1370w, http://bio7.org/wp-content/uploads/2016/07/rimagejpersp-300x204.jpg 300w, http://bio7.org/wp-content/uploads/2016/07/rimagejpersp-768x521.jpg 768w, http://bio7.org/wp-content/uploads/2016/07/rimagejpersp-1024x695.jpg 1024w, http://bio7.org/wp-content/uploads/2016/07/rimagejpersp-624x424.jpg 624w" alt="rimagejpersp" class="wp-image-2752" src="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/rimagejpersp.jpg?resize=456%2C310" data-recalc-dims="1"></p>
<ul>
<li>Added a new R debug perspective</li>
<li>Added a new and easy to use text preference field to execute Groovy script commands at startup (beside any scripts in the startup folder!) to open, e.g., a custom perspective, or startup R  if enabled.</li>
</ul>
<p><img sizes="(max-width: 904px) 100vw, 904px" srcset="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/preferencestartup.jpg?resize=456%2C292 904w, http://bio7.org/wp-content/uploads/2016/07/preferencestartup-300x192.jpg 300w, http://bio7.org/wp-content/uploads/2016/07/preferencestartup-768x491.jpg 768w, http://bio7.org/wp-content/uploads/2016/07/preferencestartup-624x399.jpg 624w" alt="preferencestartup" class="wp-image-2753" src="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/preferencestartup.jpg?resize=456%2C292" data-recalc-dims="1"></p>
<ul>
<li>The Quadgrid, Linechart, Piechart and the Points view are now embedded in a Swt JavaFX panel and can be fullscreened (F1, F2, F3, F4, F5 – F1 key is Windows only!)</li>
<li>Added a terminate (Java controlled) and kill R process (OS controlled) action to the main toolbar of Bio7.</li>
</ul>
<p><img alt="terninatetoolbar" class="wp-image-2754" src="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/terninatetoolbar.jpg?resize=289%2C150" data-recalc-dims="1"></p>
<ul>
<li>At R/Rserve startup a new check for a running R instance is executed with an option to kill all running R instances (to avoid a wrong connection to a running instance from an crashed Bio7 R session).</li>
<li>Added  many new Bio7 R command key shortcuts</li>
<li>Added an install R packages script to install some useful default R packages for Bio7</li>
</ul>
<p><strong>R editor:</strong></p>
<ul>
<li>The R editor has been transferred to it’s own Github repository and can be updated as a plugin</li>
<li>Improved and formatted the display of the error messages</li>
<li>Improved massively the speed for parsing and marker creation</li>
<li>Added many new R editor key shortcuts to speed up editing</li>
<li>Added an action to the context menu to open the plot preferences</li>
<li>Added an action to the context menu to open the font preferences</li>
<li>Added a RServe formatR action to the context menu</li>
<li>Added a Profile script action for the profvis package to the context menu</li>
<li>Added a Profile script selection action for the profvis package to the context menu</li>
<li>Added a color dialog to the context menu. A selected R,G,B color will be displayed and set in the editor</li>
<li>Added an “Reload Package Completion” action to the context menu to load completion help for loaded packages (decrease warnings by known methods, increase available code completion templates – The same action is available in the R-Shell view evaluation textfield).</li>
</ul>
<p><img sizes="(max-width: 248px) 100vw, 248px" srcset="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/contextRmenu.jpg?resize=248%2C427 451w, http://bio7.org/wp-content/uploads/2016/07/contextRmenu-174x300.jpg 174w" alt="contextRmenu" class="wp-image-2756" src="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/contextRmenu.jpg?resize=248%2C427" data-recalc-dims="1"></p>
<ul>
<li>The Load/Remove packages(s) dialog has a new action to transfer available selected package names to the R editor (as ‘library(package)’)</li>
<li>Now warnings and errors are displayed more consistently. If a quick fix is available it will be indicated with a warning/error quick fix icon instead of a default warning/error icon</li>
<li>Added new quick fixes to the R editor</li>
<li>Quick fixes and warning messages can now be displayed and fixed by hoovering over the underlined editor marker</li>
<li>Added the automatic close of {braces}, (parentheses), [brackets], “strings” and ‘strings’. It can be disabled in the preferences</li>
<li>Improved the speed of the ‘Mark selected word’ action (scope independant) which can be enabled in the preferences</li>
</ul>
<p>R editor refactoring</p>
<ul>
<li>Added an ‘Extract Method’ action which parses and extract a method from a selected text if valid</li>
</ul>
<p><img sizes="(max-width: 331px) 100vw, 331px" srcset="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/refactordialog.jpg?resize=331%2C351 538w, http://bio7.org/wp-content/uploads/2016/07/refactordialog-283x300.jpg 283w" alt="refactordialog" class="wp-image-2757" src="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/refactordialog.jpg?resize=331%2C351" data-recalc-dims="1"></p>
<ul>
<li>Added an ‘Extract Variable’ action which parses and extracts a variable from a selected text if valid</li>
<li>Added a ‘Create new File from Clipboard’ action which parses and creates a new file from the clipboard text if valid in the project folder and opens the R file for editing</li>
<li>Added an ‘Extract Editor Selection to File’ action which parses and creates a new file from a selection if valid in the project folder and opens the R file for editing</li>
</ul>
<p>R editor code analysis:</p>
<ul>
<li>Added an analysis function to detect Unused Functions</li>
<li>Added an analysis function to detect if a function is available</li>
<li>Added an analysis function to detect if a variable is used</li>
<li>Added an analysis function to detect if a variable is available</li>
<li>Added an analysis function to check for wrong constants (na, true, false, null)</li>
<li>Added an analysis function to check for functions if a function (or variable) with that name is already defined</li>
<li>Added an analysis function to check for variables if a variable (or function) with that name is already defined</li>
<li>Added an analysis function to check if a function call argument is missing</li>
<li>Added an analysis function to check if a function call has to many arguments</li>
<li>Added an analysis function to check if the name of a variable assignment in a function call is wrong</li>
<li>Added an analysis function to check a function call with parameter on a parameterless function</li>
<li>Added an analysis function to check variables in function calls and square brackets</li>
<li>Added options in the preferences to enable/disable the code analysis functions</li>
</ul>
<p><img sizes="(max-width: 444px) 100vw, 444px" srcset="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/warningscodeanalysis.jpg?resize=444%2C239 609w, http://bio7.org/wp-content/uploads/2016/07/warningscodeanalysis-300x162.jpg 300w" alt="warningscodeanalysis" class="wp-image-2759" src="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/warningscodeanalysis.jpg?resize=444%2C239" data-recalc-dims="1"></p>
<p>R Outline View</p>
<ul>
<li>Added the display of loop variables to the outline view</li>
<li>Added the display of function call variable assignments to the outline view</li>
<li>Added the display of S3,S4, References and R6 classes to the outline view (S3 classes are only detected with class(x), References classes and R6 classes functions are not displayed nested!)</li>
</ul>
<p><img sizes="(max-width: 954px) 100vw, 954px" srcset="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/classesoutline.jpg?resize=456%2C216 954w, http://bio7.org/wp-content/uploads/2016/07/classesoutline-300x142.jpg 300w, http://bio7.org/wp-content/uploads/2016/07/classesoutline-768x363.jpg 768w, http://bio7.org/wp-content/uploads/2016/07/classesoutline-624x295.jpg 624w" alt="classesoutline" class="wp-image-2760" src="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/classesoutline.jpg?resize=456%2C216" data-recalc-dims="1"></p>
<p>R editor code completion</p>
<ul>
<li>The sorting of the code completion dialog has been improved</li>
<li>The code completion dialog now displays local defined variables and methods available in the current scope</li>
<li>Added a new function in the code completion popup dialog to open the template preferences faster</li>
</ul>
<p><img sizes="(max-width: 479px) 100vw, 479px" srcset="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/codecompletionvar.jpg?resize=456%2C190 732w, http://bio7.org/wp-content/uploads/2016/07/codecompletionvar-300x125.jpg 300w, http://bio7.org/wp-content/uploads/2016/07/codecompletionvar-624x261.jpg 624w" alt="codecompletionvar" class="wp-image-2762" src="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/codecompletionvar.jpg?resize=456%2C190" data-recalc-dims="1"></p>
<ul>
<li>If the code completion is opened in a method call the arguments of the function will be displayed in a new table dialog. However if an function or variable is started within the method call the regular code completion is shown (for nested functions or variables call)</li>
</ul>
<p><img sizes="(max-width: 304px) 100vw, 304px" srcset="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/codecompletioninfun-1.jpg?resize=304%2C348 478w, http://bio7.org/wp-content/uploads/2016/07/codecompletioninfun-1-262x300.jpg 262w" alt="codecompletioninfun" class="wp-image-2765" src="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/codecompletioninfun-1.jpg?resize=304%2C348" data-recalc-dims="1"></p>
<ul>
<li>Added two actions in the hoover help dialog to open the help browser (?) or search in the Rdocumentation website</li>
</ul>
<p><img sizes="(max-width: 393px) 100vw, 393px" srcset="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/hooveractions.jpg?resize=393%2C215 516w, http://bio7.org/wp-content/uploads/2016/07/hooveractions-300x164.jpg 300w" alt="hooveractions" class="wp-image-2764" src="http://i2.wp.com/bio7.org/wp-content/uploads/2016/07/hooveractions.jpg?resize=393%2C215" data-recalc-dims="1"></p>
<ul>
<li>The code completion dialog can now be configured in the preferences to open automatically on key typing  (number of typed chars and chars can be configured, too).</li>
</ul>
<p><strong>R-Shell view</strong></p>
<ul>
<li>The R text is now validated with the Bio7 default R code parser</li>
<li>Added an error marker to the textfield if a parsing error occurs</li>
<li>Added code completions to the evaluate expression textfield (Ctrl+Space). Code completion is only available in nested calls after open parentheses</li>
</ul>
<p><img sizes="(max-width: 500px) 100vw, 500px" srcset="http://i1.wp.com/bio7.org/wp-content/uploads/2016/07/rshellparse.jpg?resize=456%2C168 860w, http://bio7.org/wp-content/uploads/2016/07/rshellparse-300x110.jpg 300w, http://bio7.org/wp-content/uploads/2016/07/rshellparse-768x282.jpg 768w, http://bio7.org/wp-content/uploads/2016/07/rshellparse-624x229.jpg 624w" alt="rshellparse" class="wp-image-2767" src="http://i1.wp.com/bio7.org/wp-content/uploads/2016/07/rshellparse.jpg?resize=456%2C168" data-recalc-dims="1"></p>
<ul>
<li>A help file browser can now be opened from selected text (e.g., nested function).</li>
<li>Native connection commands can now be executed in the evaluate expression textfield</li>
</ul>
<p><strong>R Markdown</strong></p>
<ul>
<li>Now JavaScript is enabled for the HTML-Browser by default</li>
<li>Added a new option to scale the JavaFX browser content if enabled  (handy for R markdown presentations). The JavaFX  browser can be fullscreened (F1,F2,F3 – secondary monitor…..)</li>
</ul>
<p><strong>Table view</strong></p>
<ul>
<li>Improved massively the speed of the close operation of a table sheet</li>
<li>Improved the CSV importer with more options to import data with a dynamic preview</li>
<li>The CSV importer now accepts clipboard data if selected</li>
<li>The preview table is now updated dynamically if changes occur</li>
</ul>
<p><img sizes="(max-width: 310px) 100vw, 310px" srcset="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/csvimportdialog.jpg?resize=310%2C495 504w, http://bio7.org/wp-content/uploads/2016/07/csvimportdialog-188x300.jpg 188w" alt="csvimportdialog" class="wp-image-2768" src="http://i0.wp.com/bio7.org/wp-content/uploads/2016/07/csvimportdialog.jpg?resize=310%2C495" data-recalc-dims="1"></p>
<p><strong>ImageJ</strong></p>
<ul>
<li>Updated ImageJ to version 1.51d</li>
<li>Added a subset of ImageJ2 libraries in a new ImageJ2 Eclipse plugin</li>
<li>Improved the ROI image pixel data transfer methods. Now selected ROI’s pixels are transferred. If no selection is available all ROI‘s will be transferred!</li>
<li>The ROI transfer methods now also accept points and lines (please note that line pixels are interpolated in the ImageJ results table by default)</li>
<li>The Bio7 ImageJ plugin can now be updated or installed individually</li>
<li>ImageJ panels can now be opened in a JavaFX panel embedded in SWT (experimental) if enabled in the preferences</li>
</ul>
<p><strong>Other</strong></p>
<ul>
<li>Updated all Java libraries</li>
<li>Update the JavaFX SceneBuilder to version 2.2</li>
<li>The JavaFX SceneBuilder controller class created variables and methods are now ‘public’ by default.</li>
<li>Added support for LibreOffice 5. Now the Bio7 LibreOffice functions work again with LibreOffice 5.</li>
</ul>
<p><strong>Eclipse Neon features<br>
</strong></p>
<ul>
<li>Toogle fullscreen available (Alt+F11)</li>
<li>Toggle toolbar visibility (You have to define the key in the key preferences)</li>
<li>Autosave is available for all editors (enable in the preferences)</li>
<li>Word wrap is available for all editors (Alt+Shift+Y)</li>
<li><a target="_blank" href="https://www.eclipse.org/eclipse/news/4.6/jdt.php">New Eclipse Neon Java features</a></li>
<li><a target="_blank" href="https://www.eclipse.org/eclipse/news/4.6/platform.php">New Eclipse Neon Platform features</a></li>
</ul>
<h2><strong>Installation:</strong></h2>
<p><strong>Windows:</strong></p>
<p>Just download the *.zip distribution file from <a target="_blank" 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.</p>
<p><strong>MacOSX:</strong></p>
<p>Just download and execute the *.dmg installation file from <a target="_blank" href="http://bio7.org/">http://bio7.org</a>.</p>
<p>To use R and Rserve you have to install R for MacOSX.</p>
<p>In addition you have to install Rserve configured to use ‘cooperative mode’ (shared workspace in Rserve and R mode) which can be downloaded here:</p>
<p><a target="_blank" href="https://bitbucket.org/maustenfeld/bio7-new/downloads">https://bitbucket.org/maustenfeld/bio7-new/downloads</a></p>
<p>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)<br>
</em><br>
You can also compile Rserve by yourself. For an HowTo please consult the Bio7 documentation <a target="_blank" href="http://bio7.org/manual/Main.html#toc-Subsubsection-2.1.2.1">here</a>.</p>
<p><strong> Miscellaneous:</strong></p>
<p>Added a tiny script to install useful default R packages for Bio7 to use all available GUI functionalities (e.g. rmarkdown, rgdal, spatstat, formatR, knitr, etc.). To install the scripts start Rserve and execute the action <strong>Scripts->RScripts->Install_R_Packages.</strong></p>
<p>The script will install the R packages.</p>
<p>For<strong> MacOSX</strong> it could be that you have to select a mirror in the Bio7 Console (shell). Type in a number (1- …) and press return to start the installation if no shell message is displayed. The R installation script can be edited in /plugins/com.eco.bio7_2.4.0/r_scripts. Suggestions for improvements are welcome.</p>
<p> </p>
<p> </p>
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