gpkg: on error, close stdin before killing external programs

Otherwise, this may trigger a BrokenPipeError.  Sensitive to buffer
fullness, this was observed on 64k page size system immediately after
triggering E2BIG error from kernel.

Signed-off-by: Matoro Mahri <matoro_gentoo@matoro.tk>
Signed-off-by: Sam James <sam@gentoo.org>

lib/portage/gpkg.py

@@ -149,9 +149,9 @@ def kill(self):
         kill external program if any error happened in python
         """
         if self.proc is not None:
-            self.killed = True
-            self.proc.kill()
             self.proc.stdin.close()
+            self.proc.kill()
+            self.killed = True
             self.close()
 
     def _cmd_read_thread(self):
@@ -347,9 +347,9 @@ def kill(self):
         kill external program if any error happened in python
         """
         if self.proc is not None:
-            self.killed = True
-            self.proc.kill()
             self.proc.stdin.close()
+            self.proc.kill()
+            self.killed = True
             self.close()
 
     def read(self, bufsize=-1):