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.
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)!
Play Video
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.