<p><div><div><div><div data-show-faces="false" data-height="21" data-width="100" data-layout="button_count" data-send="true" data-href="https://www.r-bloggers.com/bio7-2-9-released/"></div></div><div></div></div><div></div></div>
<div>
(This article was first published on <strong><a href="https://bio7.org/bio7-2-9-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>16.08.2018</strong></p>
<p>A new release of <a rel="nofollow" href="https://bio7.org/" target="_blank">Bio7</a> is available. The new Bio7 2.9 release comes with a plethora of new R features and bugfixes.</p>
<div class="wp-caption"><img sizes="(max-width: 2880px) 100vw, 2880px" src="https://i0.wp.com/bio7.org/wp-content/uploads/2018/08/Bildschirmfoto-2018-07-07-um-22.42.27.png?w=450&ssl=1" alt="" class="wp-image-3361" data-recalc-dims="1">
<p class="wp-caption-text">Screenshot MacOSX with dark theme and opened ‘R ImageJ Analysis’ perspective</p>
</div>
<div class="wp-caption"><img sizes="(max-width: 1918px) 100vw, 1918px" src="https://i0.wp.com/bio7.org/wp-content/uploads/2018/08/screenwin.jpg?w=450&ssl=1" alt="" class="wp-image-3368" data-recalc-dims="1">
<p class="wp-caption-text">Screenshot ‘R’ perspective Windows and opened R-Shell code completion</p>
</div>
<h2><strong>Release Notes:</strong></h2>
<p><span lang="en-US"><b>General:</b></span></p>
<ul>
<li><span lang="en-US">Based on Eclipse 4.8</span></li>
<li><span lang="en-US">Improved the dark theme and the layout of the dark theme in many places<br>
</span></li>
<li><span lang="en-US">All editor font colors are now changed automatically </span><span lang="en-US">to default optimized colors </span><span lang="en-US">when using the dark theme<br>
</span></li>
<li><span lang="en-US">New ‘Switch Theme’ action available to easily switch to the dark theme or back to the default theme</span></li>
<li><span lang="en-US">Java updated to 1.8.181</span></li>
<li><span lang="en-US">New Fullscreen/Hide Menu action available (Main menu “Window” – Key: Strg+Shift+ 4)</span></li>
<li><span lang="en-US">New Hide and Show main menu actions available (useful to hide added plugin menus again)</span></li>
<li><span lang="en-US">Added pdf reader option “<a rel="nofollow" href="https://okular.kde.org/" target="_blank">Okular</a>” to open a R pdf plot with the okular application (used when the SWT browser + open external preference is selected)</span></li>
<li><span lang="en-US">Added a new Table API method to transfer a matrix array form Java more efficiently</span></li>
<li><span lang="en-US">Improved the WorldWind search function (using the <a rel="nofollow" href="https://photon.komoot.de/" target="_blank">photon</a> geocoding API)</span></li>
<li>Improved the default font size for Swing components on Retina displays (e.g., ImageJ components)</li>
</ul>
<p><strong><span lang="en-US">R:</span></strong></p>
<ul>
<li><span lang="en-US">Updated R for Windows to version 3.5.1</span></li>
<li><span lang="en-US">Added a new plot option to plot huge plots in a temporary folder and open them in ImageJ virtually (disk resident). The folder will automatically be opened after plotting (plot images have to be deleted manually!)</span></li>
</ul>
<p><strong>ImageJ</strong></p>
<ul>
<li><span lang="en-US">ImageJ Updated to 1.52f18</span></li>
<li>ImageJ toolbar improved for the dark theme (see screenshots)</li>
<li><span lang="en-US">Added a new ImageJ detach image menu in the ‘Window’ menu of the ImageJ-Canvas view</span></li>
</ul>
<p><strong><span lang="en-US">R Markdown:</span></strong></p>
<ul>
<li><span lang="en-US">Added syntax coloring of R markdown snippets</span></li>
<li><span lang="en-US">Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)</span></li>
<li><span lang="en-US">Added a new context menu action to toggle word wrap, etc.<br>
</span></li>
</ul>
<p><strong><span lang="en-US">R editor:</span></strong></p>
<ul>
<li><span lang="en-US">Added a new warning and quickfix for possibly wrong comparisons of NULL, NA, NaN</span></li>
</ul>
<p><img alt="" src="https://i1.wp.com/bio7.org/wp-content/uploads/2018/08/comparison-1.gif?w=450&ssl=1" class="wp-image-3366" data-recalc-dims="1"></p>
<ul>
<li><span lang="en-US">Added a new option in the preferences for the new warning</span></li>
<li><span lang="en-US">Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)</span></li>
<li><span lang="en-US">Improved the display for quickfix suggestion, warning and errors when the font is resized dynamically (especially for MacOSX)<br>
</span></li>
<li><span lang="en-US">The help browser for code completion popups now display help sites in dark mode if the Bio7 dark theme is enabled.</span></li>
</ul>
<p><strong><span lang="en-US">ImageJ Macro Editor</span></strong></p>
<ul>
<li><span lang="en-US">Added a general rename method to rename selected word occurences<br>
</span></li>
<li><span lang="en-US">Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)</span></li>
<li><span lang="en-US">Added latest macro code completion function definitions</span></li>
</ul>
<h2></h2>
<h2><strong>Download and Installation:</strong></h2>
<h3><strong>Windows:</strong></h3>
<p>Just download the *.zip distribution file from <a rel="nofollow" href="https://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>
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<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> for an introduction can be found on YouTube.</p>
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