The output window (Ctrl+4) is not displaying stdout and stderr in the order of calls to System.out.println() and System.err.println().

System.{out,err}.flush() has no effect on the displayed content.

Test program:

  public class Main {
    public static void main(String[] args) {
      for(int i=0; i<2; i++) System.out.println("stdout");
      for(int i=0; i<2; i++) System.err.println("stderr");
    }
  }

Content displayed in the output window:

  run:
  stdout
  stderr
  stdout
  stderr
  BUILD SUCCESSFUL (total time: 0 seconds)

Expected content of the output window:

  run:
  stdout
  stdout
  stderr
  stderr
  BUILD SUCCESSFUL (total time: 0 seconds)

Suggested solution:

Netbeans should use a single Linux file to read the program's outputs. In C/C++ world, this would mean that read(1, stdout_buf, size) and read(2, stderr_buf, size) read from the same underlying file. Linux man pages: dup2.

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Related bugs: bug 202545 - not a duplicate of this bug because it targets the BlueJ component and because it is old