actually compare file contents in case of permissions error

easybuild/tools/filetools.py

@@ -42,6 +42,7 @@
 """
 import datetime
 import difflib
+import filecmp
 import glob
 import hashlib
 import inspect
@@ -2448,7 +2449,7 @@ def copy_file(path, target_path, force_in_dry_run=False):
                             if not isinstance(err, PermissionError):
                                 raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
                         # double-check whether the copy actually succeeded
-                        if not os.path.exists(target_path) or not os.path.samefile(path, target_path):
+                        if not os.path.exists(target_path) or not filecmp.cmp(path, target_path, shallow=False):
                             raise EasyBuildError("Failed to copy file %s to %s: %s", path, target_path, err)
                         _log.info("%s copied to %s, ignoring permissions error: %s", path, target_path, err)
                 elif os.path.islink(path):