The last commit didn't really fix the bug. This one seems to do a better job :)

setup.py

@@ -256,7 +256,6 @@ _ON_POSIX = 'posix' in sys.builtin_module_names
 def enqueue_output(out, queue):
     for line in iter(out.readline, b''):
         queue.put(line)
-    out.close()
 
 
 def _log_buf(buf):
@@ -269,21 +268,70 @@ def _log_buf(buf):
         log.info(line)
 
 
-def run_process(cmds):
-    """run a process 
+def run_process(cmds, timeout=None):
+    """run a process asynchronously
     :param cmds: list of commands to invoke on a shell e.g. ['make', 'install']
+    :param timeout: timeout in seconds (optional)
     """
 
-    # Run the process
+    # open process as its own session, and with no stdout buffering
     p = Popen(cmds,
               stdout=PIPE, stderr=STDOUT,
               bufsize=1,
               close_fds=_ON_POSIX, preexec_fn=os.setsid if _ON_POSIX else None)
-    # And send it's output to the console. 
-    for line in p.stdout:
-        _log_buf(line)
-    p.wait()
 
+    q = Queue()
+    t = Thread(target=enqueue_output, args=(p.stdout, q))
+    t.daemon = True  # thread dies with the program
+    t.start()
+
+    _time = time.time()
+    e = None
+    try:
+        while t.isAlive():
+            try:
+                buf = q.get(timeout=.1)
+            except Empty:
+                buf = b''
+            _log_buf(buf)
+            elapsed = time.time() - _time
+            if timeout and elapsed > timeout:
+                break
+        # Make sure we print all the output from the process.
+        if p.stdout:
+            for line in p.stdout:
+                _log_buf(line)
+            p.wait()
+    except (KeyboardInterrupt, SystemExit) as e:
+        # if user interrupted
+        pass
+
+    # noinspection PyBroadException
+    try:
+        os.kill(p.pid, signal.SIGINT)
+    except (KeyboardInterrupt, SystemExit) as e:
+        pass
+    except:
+        pass
+
+    # noinspection PyBroadException
+    try:
+        if e:
+            os.kill(p.pid, signal.SIGKILL)
+        else:
+            p.wait()
+    except (KeyboardInterrupt, SystemExit) as e:
+        # noinspection PyBroadException
+        try:
+            os.kill(p.pid, signal.SIGKILL)
+        except:
+            pass
+    except:
+        pass
+
+    t.join(timeout=0.1)
+    if e:
+        raise e
 
     return p.returncode