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(I think the Gem error is unrelated, so I'm better opening another thread)
with the pd~-help i am experiencing the problem, that I can't move the objects in edit mode, clicked message boxes will keep their highlighted border permanently. That's only in the child process. Audio and Messages however can be sent from and to the subprocess.
SOLUTION
before sending the mail I found the problem, It may be useful as a future reference, so I am sending it anyways:
I suspect that when trying to install the current Pd, I re-set the path settings.
So in verbose mode I noticed that pd~ was found in /usr/local/lib/pd/extra I removed that path from the path settings and now pd~ is found somewhere else. It is the same (v0.3) but it works now.
tried /usr/lib/puredata/tcl/../extra/pd~/pd~.pd_linux and succeeded