I’ve noticed that the latest version of CellProfiler seems to change system environment variables, specifically those pertaining to Java. This is causing issues with Java-dependent applications, such as FIJI. Is this related to the fact that CellProfiler seems to now ship with it’s own local Java installation?
So, for example, I’m inclined to keep a single Java installation on my machines, for use by all installed applications. When I do so with FIJI, no problems are encountered. Following installation of the latest Cell Profiler however, FIJI throws an error on startup telling me it cannot locate jvm.dll.
Is this a known issue? Is there a reason why CellProfiler cannot just use whatever version of Java is preinstalled on the machine?