16.08.2018

A new release of Bio7 is available. The new Bio7 2.9 release comes with a plethora of new R features and bugfixes.

Screenshot MacOSX with dark theme and opened ‘R ImageJ Analysis’ perspective

Screenshot ‘R’ perspective Windows and opened R-Shell code completion

Release Notes:

General:

• Based on Eclipse 4.8
• Improved the dark theme and the layout of the dark theme in many places
  
• All editor font colors are now changed automatically to default optimized colors when using the dark theme
  
• New ‘Switch Theme’ action available to easily switch to the dark theme or back to the default theme
• Java updated to 1.8.181
• New Fullscreen/Hide Menu action available (Main menu “Window” – Key: Strg+Shift+ 4)
• New Hide and Show main menu actions available (useful to hide added plugin menus again)
• Added pdf reader option “Okular” to open a R pdf plot with the okular application (used when the SWT browser + open external preference is selected)
• Added a new Table API method to transfer a matrix array form Java more efficiently
• Improved the WorldWind search function (using the photon geocoding API)
• Improved the default font size for Swing components on Retina displays (e.g., ImageJ components)

R:

• Updated R for Windows to version 3.5.1
• 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!)

ImageJ

• ImageJ Updated to 1.52f18
• ImageJ toolbar improved for the dark theme (see screenshots)
• Added a new ImageJ detach image menu in the ‘Window’ menu of the ImageJ-Canvas view

R Markdown:

• Added syntax coloring of R markdown snippets
• Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)
• Added a new context menu action to toggle word wrap, etc.
  

R editor:

• Added a new warning and quickfix for possibly wrong comparisons of NULL, NA, NaN

• Added a new option in the preferences for the new warning
• Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)
• Improved the display for quickfix suggestion, warning and errors when the font is resized dynamically (especially for MacOSX)
  
• The help browser for code completion popups now display help sites in dark mode if the Bio7 dark theme is enabled.

ImageJ Macro Editor

• Added a general rename method to rename selected word occurences
  
• Added new context menu actions in menu “Text” (Find and replace, Toggle Block Selection, To Upper Case, To Lower Case)
• Added latest macro code completion function definitions

Download and Installation:

Windows:

Just download the *.zip distribution file from https://bio7.org 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.

Linux:

Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).

MacOSX:

Download and extract the installation file from https://bio7.org.

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:

OS X Yosemite: Open an app from an unidentified developer

macOS Sierra: Open an app from an unidentified developer

If you have still problems with Sierra see this solution!

In addition for MacOSX you have to install R and Rserve (see below!).

Linux and MacOSX Rserve (compiled for cooperative mode) installation:

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 writing permissions!). 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)!

Installation of Useful R Packages

R packages which are useful in combination with Bio7 can easily be installed with the R-Shell context menu “Packages” action:

R-Shell context menu->Packages->Install_Default_R_Packages

Bio7 Documentation

For more information about Bio7 please consult the soon updated Bio7 User Guide.

A plethora of Bio7 videotutorials for an introduction can be found on YouTube.