diff --git a/bisect.c b/bisect.c
index f5b1368128..3b763dab6b 100644
--- a/bisect.c
+++ b/bisect.c
@@ -1090,7 +1090,7 @@ enum bisect_error bisect_next_all(struct repository *r, const char *prefix)
 		  nr), nr, steps_msg);
 	free(steps_msg);
 	/* Clean up objects used, as they will be reused. */
-	clear_commit_marks_all(ALL_REV_FLAGS);
+	repo_clear_commit_marks(the_repository, ALL_REV_FLAGS);
 
 	return bisect_checkout(bisect_rev, no_checkout);
 }
diff --git a/builtin/checkout.c b/builtin/checkout.c
index 0951f8fee5..e6f801464d 100644
--- a/builtin/checkout.c
+++ b/builtin/checkout.c
@@ -1029,7 +1029,7 @@ static void orphaned_commit_warning(struct commit *old_commit, struct commit *ne
 		describe_detached_head(_("Previous HEAD position was"), old_commit);
 
 	/* Clean up objects used, as they will be reused. */
-	clear_commit_marks_all(ALL_REV_FLAGS);
+	repo_clear_commit_marks(the_repository, ALL_REV_FLAGS);
 }
 
 static int switch_branches(const struct checkout_opts *opts,
diff --git a/builtin/gc.c b/builtin/gc.c
index 090959350e..e7932f0480 100644
--- a/builtin/gc.c
+++ b/builtin/gc.c
@@ -786,7 +786,7 @@ static int should_write_commit_graph(void)
 
 	result = for_each_ref(dfs_on_ref, &data);
 
-	clear_commit_marks_all(SEEN);
+	repo_clear_commit_marks(the_repository, SEEN);
 
 	return result;
 }
diff --git a/object.c b/object.c
index 3257518656..05544bc92b 100644
--- a/object.c
+++ b/object.c
@@ -453,12 +453,12 @@ void clear_object_flags(unsigned flags)
 	}
 }
 
-void clear_commit_marks_all(unsigned int flags)
+void repo_clear_commit_marks(struct repository *r, unsigned int flags)
 {
 	int i;
 
-	for (i = 0; i < the_repository->parsed_objects->obj_hash_size; i++) {
-		struct object *obj = the_repository->parsed_objects->obj_hash[i];
+	for (i = 0; i < r->parsed_objects->obj_hash_size; i++) {
+		struct object *obj = r->parsed_objects->obj_hash[i];
 		if (obj && obj->type == OBJ_COMMIT)
 			obj->flags &= ~flags;
 	}
diff --git a/object.h b/object.h
index 20b18805f0..59daadce21 100644
--- a/object.h
+++ b/object.h
@@ -191,8 +191,9 @@ void object_array_clear(struct object_array *array);
 void clear_object_flags(unsigned flags);
 
 /*
- * Clear the specified object flags from all in-core commit objects.
+ * Clear the specified object flags from all in-core commit objects from
+ * the specified repository.
  */
-void clear_commit_marks_all(unsigned int flags);
+void repo_clear_commit_marks(struct repository *r, unsigned int flags);
 
 #endif /* OBJECT_H */