Is Bio7 an OpenSource application?
Yes, Bio7 is licensed under the EPL which is an OSI approved OpenSource license.
On MacOSX I can’t import or create Java projects. A deadlock (GUI freezes) occurs.
Solution: Install a Java JDK or OpenJDK for MacOSX. Unfortunately this Eclipse bug workaround seems to be necessary for JDT (Java Development Tools) if no JDK/OpenJDK is installed by default. Bio7 already comes shipped with a JRE (Bio7 <=2.9) or OpenJDK (with Bio7 > 3.0) but JDT seems to search in the default Java MacOSX location and blocks infinite the UI if empty !
On MacOSX I can’t start Bio7. An error message occurs.
Solution: Allow apps which are downloaded from anywhere (this can be deactivated later after Bio7 was started once):
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!
On MacOSX I can’t start R
R is not on the OS system PATH. Please adjust the path to R in the Bio7 preferences:
Bio7->Preferences->Preferences Bio7->Path to R
The default R installation path on MacOSX is (version number can differ):
/Library/Frameworks/R.framework/Resources
or:
/Library/Frameworks/R.framework/Versions/3.2/Resources
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 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.
If I want to transfer a huge image to R the following warning message about buffer size occurs: “WARNING: discarding buffer because too big (awaiting……”
Solution: Increase the size of the input buffer in the Rserve preferences. Open the Rserve preferences Preferences->Preferences Bio7->Preferences R.
In the Field “Rserve startup arguments” copy the following startup argument:
maxinbuf=”4194304″
The max. packet size from the client to Rserve is set to 4GB in this example (maxinbuf argument in kb). Use the example size only if necessary and if you have the memory available!
Can i interrupt a running R script execution?
Yes, there is a new interrupt action for Windows, Linux and MacOSX available in the R-Shell view. In addition the key combination Strg+c in the Bio7 console (R interpreter selected) works, too.
Another way (Linux and Mac) is to open an external shell and type:
killall -INT Rserve
If you start Rserve (not in native mode) 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.
Please note that an interrupt only works if the applied functions catch the interrupt signal.
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 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.
Under Ubuntu 16.x, 17.x the help browser is not available.
Install the libwebkit package form the Ubuntu repositories to make the SWT browser available:
$ sudo apt-get install libwebkitgtk-1.0-0