diff --git a/fdroidserver/build.py b/fdroidserver/build.py
index f80fb933..e44dd5bb 100644
--- a/fdroidserver/build.py
+++ b/fdroidserver/build.py
@@ -434,6 +434,8 @@ def adapt_gradle(build_dir):
             if not filename.endswith('.gradle'):
                 continue
             path = os.path.join(root, filename)
+            if not os.path.isfile(path):
+                continue
             logging.debug("Adapting %s at %s" % (filename, path))
 
             FDroidPopen(['sed', '-i',
diff --git a/fdroidserver/common.py b/fdroidserver/common.py
index 810cf729..ec4a6eea 100644
--- a/fdroidserver/common.py
+++ b/fdroidserver/common.py
@@ -1312,6 +1312,8 @@ def prepare_source(vcs, app, build, build_dir, srclib_dir, extlib_dir, onserver=
                 if not filename.endswith('.gradle'):
                     continue
                 path = os.path.join(dir_path, filename)
+                if not os.path.isfile(path):
+                    continue
                 for line in file(path):
                     match = version_regex.match(line)
                     if match:
@@ -1588,6 +1590,8 @@ def scan_source(build_dir, root_dir, thisbuild):
                     warnproblem('unknown compressed or binary file', fd)
 
             elif has_extension(fp, 'java') and os.path.isfile(fp):
+                if not os.path.isfile(fp):
+                    continue
                 for line in file(fp):
                     if 'DexClassLoader' in line:
                         count += handleproblem('DexClassLoader', fd, fp)