Bio7 2.8 Released

30.05.2018

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.

Release Notes:

General:

• Updated Eclipse RCP to 4.7.3
• Windows R update to version 3.5.0
• ImageJ plugin updated to version 1.52d7
• Added the ImageJ Edit perspective to the default opened perspectives
• The R perspective is now selected as the opened perspective after startup of Bio7
• Added an option to save all editors on close (default enabled on MacOSX)
• Improved the main ‘Scripts’ menu to allow nested custom scripts in folders and subfolders which form new submenus
• Improved the Table and R-Shell context scripts menu
• Added some example scripts to the new scripts menu
• Added an script to open the default script location in the OS file explorer
• Simplified the different script locations (reduced to four locations in the Bio7 preferences)
• Spatial import, export scripts moved to the main ‘Scripts’ and R-Shell script context menu (Deleted import, export script locations)

R:

• Simplified the Bio7 R-Shell interface
• Added a new view for some R templates
• Code completion from loaded R packages can now be imported from the R-Shell or the R editor (both completions will be updated!)
• Improved the reload code completion by only considering R functions (cleaner seperation of functions and datasets)
• The updated R-Shell context menu can now dynamically be extended with custom scripts (updated dynamically). Folder and subfolders form new submenus.
• Improved, bugfixed and extended the ‚Evaluate Line‘ action which was renamed to ‚Evaluate Line or Selection‘  action which now interprets selected R code, too.
• Improved MacOSX ImageJ interaction (editor hoover focus)
• 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.)
• Added a new menu to install Rserve for R > 3.5.0
• 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!)
• Improved the general error messages of the R-Shell view and the R editor evaluation. Now much simpler and printed cleaner!
• 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!)
• Fixed a bug with the shiny execution (removed annoying dialog)
• Fixed many other bugs (unnecessary error messages, execution errors, MacOSX bugs, etc.)
• R-Shell code completion improved (see editor code completion improvements below)
• Removed the use of temporary files of the R-Shell and R editor code completion
• Added an preference option to add arguments to the source command
• 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!)

R Editor:

• 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

• Added a quickfix to add a library definition when an unknown function is called (not defined and loaded but package with function is installed)
• Added support for the the magrittr piping operator in code completion to autocomplete a given dataframe in the workspace (column completion)

• Added code completion support for dataframes columns and rows, named list elements and named arrays (of arbitrary dimension)

• Improved code completion to display current workspace variables
• Classes of R objects are now displayed in the code completion context dialog
• Editor variables and functions are now emphazised in code completion, too
• Added a directory dialog to easily create a directory string for the editor file
• Created new submenus for the organization of the context menu
• Improved the hoover dialog (improved offset)
• Improved the completion context of R objects (current workspace objects)
• The styler package can now be used for an improved code formatting (requires UTF-8 Bio7 workspace on Windows – see preferences!)
• Improved code completion for S3 and S4 objects (correctly display current cursor completion)

ImageJ:

• Updated ImageJ plugin to version 1.52d7
• Updated ImageJ2 libraries
• Added new ImageJ macro functions to the code completion of the macro editor
• Added the ImageJ Edit perspective to the default openend perspectives
• Improved the editor hoover activation on MacOSX
• Improved the ImageJ MacOSX touchpad resizing of the ImageJ panel

Java:

• Updated JRE to 1.8.71
• Improved the creation of Java projects and project imports (no annoying dialog anymore)
• Improved the ‘Add Selected Libraries’ preference to add multiple Java libraries for dynamic compilation (e.g., to compile more embedded Eclipse library functions)
• Now ImageJ2 libs have to be added to the dynamic compilation libraries for compilation (removed as default libraries)
• Added a key shortcut (STRG + ‚+‘) to increase the SceneBuilder panel (2x)

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 can be found on YouTube.