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.
- 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)
- 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!)
- 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)
- 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
- 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:
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.
Download and extract the installation file from https://bio7.org.
For Linux you have to install R and Rserve (see Rserve installation below!).
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:
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
A plethora of Bio7 videotutorials can be found on YouTube.