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I have code that launches Java from C to run a jar file, and creates a socket to communicate between the calling program and the jar file. It works in OS X, Linux, and MinGW on Windows, but not on Cygwin.
One can definitely spawn Java from C, but every JVM I know of is a *Windows* application, which mean that it wants *Windows paths*, not cygwin-style paths. You may find the cygpath utility useful in scripts run under cygwin, to convert between different styles of path.
Java, in particular, wants things like its classpath as a *semicolon*-separate list of *Windows* path names. These generally require suitable quoting if being used in scripts or with bash, since bash interprets semicolcon as separating bash commands, etc.
As for the particular errors, I am personally less familiar with using cygrunsrv ...
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