FAQ

Is Bio7 an OpenSource application?
Yes, Bio7 is licensed under the EPL which is an OSI approved OpenSource license.

How can i update R for Bio7 on Windows?
See this post for details how you can use the latest R version with Bio7.

How can i update R for Bio7 on Linux and MacOSX?
See this post for details how you can use the latest R version with Bio7.

How can i update the default JRE for Bio7 on Windows?
Simply rename the subfolder of the bundled JRE in Bio7 (“/jre”) to e.g. “jre_old”. After a restart of Bio7 the systems default JRE is used instead of the bundled JRE.

How can i increase the available RAM for Bio7?

Windows and Linux:
For an increased Java heap space open the Bio7.ini file in the install directory of Bio7. In the file you can change the default memory settings e.g. the initial heap size -Xms and the maximum heap space -Xmx.
MacOSX:
For an increased Java heap space open the Bio7 package (context menu if you click on the icon) then go to Contents->MacOS and open the Bio7.ini file with a texteditor. In the file you can change the default memory settings e.g. the initial heap size -Xms and the maximum heap space -Xmx

Sometimes my application freezes if i work with big data. Is this a bug?
Often times this error is related to the available RAM of the Virtual Maschine. As a solution increase the heap space of the Bio7 application.

If i use Bio7 in combination with R for image analysis my application freezes. How can i avoid this error?
If you use Bio7 in combination with R please note if you have transferred images or data to the R workspace the data exists twice, in the Virtual Maschine and in the R workspace (which can be displayed in the R console). If you need more memory (e.g. for analysis on 32-bit systems with less memory) if possible delete the data on the Java or R side to free resources for the underlying OS.

Can i interrupt a running R script execution?

If you start Rserve on Windows with an open shell window (see R preferences->Start with shell) select the shell and press the key combination Strg+Break to send an interrupt signal. This only works if the applied functions catch the interrupt signal.
For Linux and Mac open the embedded shell in Bio7 (in the Console view) and type:
killall -INT Rserve
This work also with an external shell!

How can i install ImageJ plugins?

You will find the typical ImageJ folder structure in the Bio7 ImageJ plugin:
Path: Bio7/plugins/com.eco.bio7.image_x.xx.x/
As known from ImageJ put the extensions in the /plugins folder.

The “WorldWind” view and the “3d” view are flickering under Windos Vista and Windows 7 if i open or resize them.

The 3d effects under Windows Vista and Windows 7 are interfering with the OpenGl panels of Bio7. Switch off the Aero effects (e.g. switch to Windows 7-Basis) if the flickering disturbs you (besides it consumes less cpu power for the OpenGL drawing).

If i compile Java source with the Bio7 Java compiler i can find no Java *.class file (classbody compilation only!).

Bio7 uses the ClassBodyCompiler of the Java Janino compiler. In the compilation process the imports are parsed heuristically and from the class body and the parsed (and default) imports a regular Java class is constructed before a regular compilation process is started. No class file will be produced in the compilation process because everything is stored in memory. Each time after a compilation the same class is reloaded into the running Java Virtual Maschine.

The Java compilation errors are not in accordance with the line numbers of the Java editor (classbody compilation only!).

Please write the Java imports at the beginning of a Bio7 Java file. Because of the parsing process the line numbers of the compilation errors can differ from the line numbers (error) occuring in the editor. If the imports in the Java source occur at first the line numbers of error messages of the compiler should be found exactly at the line numbers in the Bio7 Java editor.

If i try to use Sweave i get the error message that the*.pdf file can’t be opened.

Please avoid empty spaces in the path to your document. With a correct path you will get detailed error messages in the Bio7 console from the e.g. Latex environment. The Sweave action executes Sweave then the Latex environment and finally tries to open the created *.pdf file with the default *.pdf Reader (*.pdf will be opened automatically only under Windows). If no *pdf document is created in a Latex compilation process the pdf error message will be thrown.