diff --git a/readthedocs/vcs_support/base.py b/readthedocs/vcs_support/base.py
index 1b7da2017d0..b482f0796d5 100644
--- a/readthedocs/vcs_support/base.py
+++ b/readthedocs/vcs_support/base.py
@@ -1,10 +1,11 @@
-# -*- coding: utf-8 -*-
-
 """Base classes for VCS backends."""
 import logging
 import os
 import shutil
 
+from readthedocs.doc_builder.exceptions import BuildEnvironmentWarning
+from readthedocs.projects.exceptions import RepositoryError
+
 
 log = logging.getLogger(__name__)
 
@@ -102,7 +103,13 @@ def run(self, *cmd, **kwargs):
             'shell': False,
         })
 
-        build_cmd = self.environment.run(*cmd, **kwargs)
+        try:
+            build_cmd = self.environment.run(*cmd, **kwargs)
+        except BuildEnvironmentWarning as e:
+            # Re raise as RepositoryError,
+            # so isn't logged as ERROR.
+            raise RepositoryError(str(e))
+
         # Return a tuple to keep compatibility
         return (build_cmd.exit_code, build_cmd.output, build_cmd.error)