This issue is related and probably the reason for asciidoctor/asciidoctorj#409

I have the following test ruby script that pipes a string to a graphviz process.
(So to retest graphviz should be installed on the machine.)
I experienced the issue with JRuby 9.0.4.0, with JRuby 1.7.+ everything works fine.

If you start this script it simply hangs:

args = ['C:\Tools\graphviz\bin\dot.exe', '-oimage.png', '-Tpng']
input = <<EOS
digraph G {
    A -> B
}
EOS

IO.popen(args, 'w') { |io|
    io.write input
}

I think the reason is that JRuby thinks that the stream is already closed in https://github.com/jruby/jruby/blob/master/core/src/main/java/org/jruby/RubyIO.java#L3900 and does not close the stream.
Then the following process.waitFor() hangs until the end of days.