flushing stdout and stderr causes BrokenPipeError

[goodmami]

In 8bd5e99 I started flushing stdout and stderr to synchronize warnings from --check with graphs on stdout, but it turns out this breaks the pipe. See https://stackoverflow.com/questions/26692284/how-to-prevent-brokenpipeerror-when-doing-a-flush-in-python

I can catch the errors and close stderr as described in https://stackoverflow.com/a/26738736/1441112, or do something else, like put the graph number or identifier on stderr before the error messages and not flush at all.

[goodmami]

I'm having trouble reproducing now, and besides #65 will make this issue mostly irrelevant as the errors can be put in metadata and not on stderr, which is probably more useful anyway.

This bug can still be closed when the flush calls are removed.