diff --git a/dvc/output.py b/dvc/output.py
index d32a334f1..95d3f2dea 100644
--- a/dvc/output.py
+++ b/dvc/output.py
@@ -98,6 +98,10 @@ class Dependency(object):
         if not os.path.isfile(self.path) and not os.path.isdir(self.path):
             raise CmdOutputIsNotFileOrDirError(self.rel_path)
 
+        if (os.path.isfile(self.path) and os.path.getsize(self.path) == 0) or \
+           (os.path.isdir(self.path) and len(os.listdir(self.path)) == 0):
+            self.project.logger.warn("File/directory '{}' is empty.".format(self.rel_path))
+
         self.md5 = self.project.state.update(self.path)
 
     @staticmethod
diff --git a/dvc/scm.py b/dvc/scm.py
index 79a7572c7..46a95ff9c 100644
--- a/dvc/scm.py
+++ b/dvc/scm.py
@@ -87,7 +87,7 @@ class Git(Base):
         gitignore = os.path.abspath(os.path.realpath(gitignore))
 
         if not gitignore.startswith(self.root_dir):
-            raise FileNotInRepoError()
+            raise FileNotInRepoError(path)
 
         return entry, gitignore