diff -aruN PEAR.orig/Builder.php PEAR/Builder.php
--- a/PEAR/Builder.php	2014-07-12 08:25:32.000000000 -0400
+++ b/PEAR/Builder.php	2015-01-16 13:43:14.927894013 -0500
@@ -340,6 +340,11 @@
         }
         // }}} end of interactive part
 
+        if (file_exists('aclocal.m4')) {
+                $this->_runCommand('rm aclocal.m4');
+                $this->_runCommand('autoreconf');
+        }
+
         // FIXME make configurable
         if (!$user=getenv('USER')) {
             $user='defaultuser';