The test case from below hangs when executed with

  emacs -Q --batch -l apo-tests.el -f ert-run-tests-batch-and-exit

It's not 100% reproducible, but it seems to hang 80% of the time.

The test is fairly complicated and involves a TLS connection, a
sub-process and a background thread.  The background thread starts a
sub-process and reads all its output until the process terminates.  Then
the main thread opens a TLS connection, sends a HTTP request and tries
to read the response.  At this point, accept-process-output hangs even
though there is output available.

I think the reason for this problem is that the sub-process uses a file
descriptor (usually number 6) and sets
fd_callback_info[6].waiting_thread to the background thread (in
compute_non_keyboard_wait_mask) .  Later, the TLS connection receives a
file descriptor with the same number (6) because the sub-process closed
it already.  That would be fine, however
fd_callback_info[6].waiting_thread is still set to the background
thread.  So this time compute_non_keyboard_wait_mask doesn't include 6
in the wait mask.  Because 6 is not in the wait mask,
emacs_gnutls_record_check_pending will not be called and Emacs doesn't
notice the buffered output.

The intention in the code seems to be that clear_waiting_thread_info
resets fd_callback_info[6].waiting_thread to NULL, however by the time
that clear_waiting_thread_info is called, max_desc was reduced to 4,
because somebody closed file descriptors 5 and 6.  So
clear_waiting_thread_info doesn't touch fd_callback_info[6].

A possible solution would be to reset the .waiting_thread field in
delete_read_fd, like so:

diff --git a/src/process.c b/src/process.c
index 08cb810ec13..74d0bf252ab 100644
--- a/src/process.c
+++ b/src/process.c
@@ -513,6 +513,9 @@ delete_read_fd (int fd)
     {
       fd_callback_info[fd].func = 0;
       fd_callback_info[fd].data = 0;
+
+      if (fd_callback_info[fd].waiting_thread == current_thread)
+	fd_callback_info[fd].waiting_thread = NULL;
     }
 }


With this change, the test doesn't hang.

Helmut