diff --git a/hgext/eol.py b/hgext/eol.py
--- a/hgext/eol.py
+++ b/hgext/eol.py
@@ -318,7 +318,10 @@ def reposetup(ui, repo):
             for f in sorted(ctx.added() + ctx.modified()):
                 if not self._eolfile(f):
                     continue
-                data = ctx[f].data()
+                try:
+                    data = ctx[f].data()
+                except IOError:
+                    continue
                 if util.binary(data):
                     # We should not abort here, since the user should
                     # be able to say "** = native" to automatically