diff --git a/script/bootstrap b/script/bootstrap
index 489187a37..8e53ffd33 100755
--- a/script/bootstrap
+++ b/script/bootstrap
@@ -91,6 +91,7 @@ function bootstrap() {
     moduleInstallCommand += ' --loglevel error';
     dedupeApmCommand     += ' --quiet';
 
+    apmDedupeOptions.ignoreStderr = true;
     apmDedupeOptions.ignoreStdout = true;
     buildInstallOptions.ignoreStdout = true;
     apmInstallOptions.ignoreStdout = true;
diff --git a/script/utils/child-process-wrapper.js b/script/utils/child-process-wrapper.js
index 2afc57934..3a05973d5 100644
--- a/script/utils/child-process-wrapper.js
+++ b/script/utils/child-process-wrapper.js
@@ -15,7 +15,7 @@ exports.safeExec = function(command, options, callback) {
   options.maxBuffer = 1024 * 1024;
 
   var child = childProcess.exec(command, options, function(error, stdout, stderr) {
-    if (error)
+    if (error && !options.ignoreStderr)
       process.exit(error.code || 1);
     else
       callback(null);