diff --git a/layerindex/update.py b/layerindex/update.py
index 855878f..b724a25 100755
--- a/layerindex/update.py
+++ b/layerindex/update.py
@@ -369,7 +369,9 @@ def main():
                     urldir = layer.get_fetch_dir()
                     repodir = os.path.join(fetchdir, urldir)
                     repo = git.Repo(repodir)
-                    assert repo.bare == False
+                    if repo.bare:
+                        logger.error('Repository %s is bare, not supported' % repodir)
+                        continue
                     try:
                         # Always get origin/branchname, so it raises error when branch doesn't exist when nocheckout
                         topcommit = repo.commit('origin/%s' % branchname)
diff --git a/layerindex/update_layer.py b/layerindex/update_layer.py
index fac914c..cad9393 100644
--- a/layerindex/update_layer.py
+++ b/layerindex/update_layer.py
@@ -371,7 +371,9 @@ def main():
 
     # Collect repo info
     repo = git.Repo(repodir)
-    assert repo.bare == False
+    if repo.bare:
+        logger.error('Repository %s is bare, not supported' % repodir)
+        sys.exit(1)
     topcommit = repo.commit('origin/%s' % branchname)
     if options.nocheckout:
         topcommit = repo.commit('HEAD')
diff --git a/layerindex/utils.py b/layerindex/utils.py
index 814dee8..6ec80fb 100644
--- a/layerindex/utils.py
+++ b/layerindex/utils.py
@@ -259,7 +259,8 @@ def is_branch_valid(layerdir, branch):
     import git
 
     g = git.cmd.Git(layerdir)
-    assert g.rev_parse('--is-bare-repository') == 'false'
+    if g.rev_parse('--is-bare-repository') != 'false':
+        raise Exception('is_branch_valid: git repository is a bare repository')
     try:
         g.rev_parse('--verify', 'origin/%s' % branch)
     except git.exc.GitCommandError:
diff --git a/rrs/tools/rrs_upgrade_history.py b/rrs/tools/rrs_upgrade_history.py
index f39e5c6..38a6b68 100755
--- a/rrs/tools/rrs_upgrade_history.py
+++ b/rrs/tools/rrs_upgrade_history.py
@@ -139,7 +139,9 @@ def upgrade_history(options, logger):
                     since_option = '--since="%s" origin/master' % since
 
                 repo = git.Repo(repodir)
-                assert repo.bare == False
+                if repo.bare:
+                    logger.error('Repository %s is bare, not supported' % repodir)
+                    continue
 
                 commits = utils.runcmd("git log %s --format='%%H %%ct' --reverse" % since_option,
                                     repodir,