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diff --git a/mesonbuild/scripts/depfixer.py b/mesonbuild/scripts/depfixer.py
index 77ac03d66..d12f77592 100644
--- a/mesonbuild/scripts/depfixer.py
+++ b/mesonbuild/scripts/depfixer.py
@@ -337,6 +337,15 @@ class Elf(DataSizes):
if not new_rpath:
self.remove_rpath_entry(entrynum)
else:
+ # Clear old rpath to avoid stale references,
+ # not heeding the warning above about de-duplication
+ # since it does not seem to cause issues for us
+ # and not doing so trips up Nix’s reference checker.
+ # See https://github.com/NixOS/nixpkgs/pull/46020
+ # and https://github.com/NixOS/nixpkgs/issues/95163
+ self.bf.seek(rp_off)
+ self.bf.write(b'\0'*len(old_rpath))
+
self.bf.seek(rp_off)
self.bf.write(new_rpath)
self.bf.write(b'\0')
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