Bio7 3.3 on MacBook Pro M1

26.01.2022

Recently I tested Bio7 3.3 on MacBook Pro M1. The application runs fine with Rosetta (you will be asked for if not installed).

Important note for R:

To run R with Bio7 interestingly you have to install R for Intel (again runs on Rosetta) and then Rserve from Github (as explained in the manual).

With this setup I experienced no problem so far.

R Editor and ImageJ Plugin Update

22.05.21

Two new plugin updates are available for Bio7.

R Editor update:

The R editor plugin has been updated for the new R 4.1 grammar (shorthand function notation, native pipe operators). The new grammar is also considered in the code completion of the editor and in the R-Shell (e.g., function calls, pipes with piped dataframes).

Annonymous shorthand functions are also displayed as ‘aFunc’ in the Outline view.

ImageJ Plugin update:

  1. Improved the ‘Detach Images’ menu action
  2. Added an post activation action for detached views (‘Open All Images as Views’ action bugfix for Windows)
  3. Improved the layout action for orthogonal stack views (in detached views)
  4. Added an API method to invoke the ‘Open All Images as Views’ action
  5. The ImageJ macro action ‘setLocation’ will now change the size and location of detached views if available
  6. Fixed some minor bugs

For the R editor update add the following URL site to the Update Manager:
https://bio7.github.io/reditor

For ImageJ (if not already available) add:
https://bio7.github.io/imagej/

 

Fixed OpenJDK Path for MacOSX – Allow Bio7 on Big Sur

02.05.2021

Uploaded MacOSX version with corrected OpenJDK path

In the latest MacOSX release the path to the embedded Java OpenJDK was wrong (not a relative path). I uploaded a corrected version to sourceforge.

If you have already downloaded Bio7 you can simply correct the path in the Bio7.ini file (right-click, “Show Package Contents”, Path: “Contents/Eclipse”. Replace the vm path argument with the relative path to the embedded OpenJDK:

-vm
../MacOS/jdk/Contents/Home/lib/libjli.dylib

Fix – can’t run app because of permission in Big Sur

If you can’t open Bio7 after download even after the changes of the security settings try the following command-line recipe:

https://stackoverflow.com/questions/64842819/cant-run-app-because-of-permission-in-big-sur

Solution which worked in the Terminal:

> sudo chmod -R 755 /Applications/Bio7.app

> sudo xattr -dr com.apple.quarantine /Applications/Bio7.app

There is also a utility app available on Github to help with the MacOSX security settings, see:

https://github.com/wynioux/macOS-GateKeeper-Helper