From 20a249a428d0f980e2e9503daa8b46df97076824 Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Fri, 9 May 2025 17:18:11 +0800
Subject: [PATCH 01/24] determinestic is good

---
 src/auditwheel/lddtree.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 07326341..ba5f9c12 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -13,6 +13,7 @@
 
 from __future__ import annotations
 
+from collections import OrderedDict
 import errno
 import functools
 import glob
@@ -441,7 +442,7 @@ def ldd(
     """
     _first = _all_libs is None
     if _all_libs is None:
-        _all_libs = {}
+        _all_libs = OrderedDict()
 
     log.debug("ldd(%s)", path)
 
@@ -554,7 +555,7 @@ def ldd(
         + ldpaths["interp"]
     )
     _excluded_libs: set[str] = set()
-    for soname in needed:
+    for soname in sorted(needed):
         if soname in _all_libs:
             continue
         if soname in _excluded_libs:

From 87148d310af9714939a9e09bb3371feca596e9af Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Fri, 9 May 2025 17:38:27 +0800
Subject: [PATCH 02/24] fix

---
 src/auditwheel/lddtree.py | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index ba5f9c12..66aeb9fb 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -556,7 +556,7 @@ def ldd(
     )
     _excluded_libs: set[str] = set()
     for soname in sorted(needed):
-        if soname in _all_libs:
+        if soname in _all_libs and _all_libs[soname].realpath is not None:
             continue
         if soname in _excluded_libs:
             continue
@@ -565,13 +565,15 @@ def ldd(
             _excluded_libs.add(soname)
             continue
         realpath, fullpath = find_lib(platform, soname, all_ldpaths, root)
+        if realpath is None:
+            log.info("Could not locate %s, skipping.", soname)
+            continue
         if realpath is not None and any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
             continue
-        _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
-        if realpath is None or fullpath is None:
-            continue
+        if soname not in _all_libs:
+            _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(
             soname,

From e9ade2be5f19cf09e18eb95bda60425b145b761c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 9 May 2025 09:40:03 +0000
Subject: [PATCH 03/24] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/auditwheel/lddtree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 66aeb9fb..4664fd60 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -13,12 +13,12 @@
 
 from __future__ import annotations
 
-from collections import OrderedDict
 import errno
 import functools
 import glob
 import logging
 import os
+from collections import OrderedDict
 from dataclasses import dataclass
 from fnmatch import fnmatch
 from pathlib import Path

From ef347fcdf92ce39d0a51bc7112bee361ecf5e15c Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Fri, 9 May 2025 17:43:29 +0800
Subject: [PATCH 04/24] fmt

---
 src/auditwheel/lddtree.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 66aeb9fb..cc8b1049 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -13,12 +13,12 @@
 
 from __future__ import annotations
 
-from collections import OrderedDict
 import errno
 import functools
 import glob
 import logging
 import os
+from collections import OrderedDict
 from dataclasses import dataclass
 from fnmatch import fnmatch
 from pathlib import Path
@@ -568,7 +568,7 @@ def ldd(
         if realpath is None:
             log.info("Could not locate %s, skipping.", soname)
             continue
-        if realpath is not None and any(fnmatch(str(realpath), e) for e in exclude):
+        if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
             continue

From 8b5df9525520403e780f16bdb3d72f77dc90deda Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Fri, 9 May 2025 18:46:58 +0800
Subject: [PATCH 05/24] Update lddtree.py

---
 src/auditwheel/lddtree.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index cc8b1049..291905b3 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -565,6 +565,8 @@ def ldd(
             _excluded_libs.add(soname)
             continue
         realpath, fullpath = find_lib(platform, soname, all_ldpaths, root)
+        if soname not in _all_libs:
+            _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
         if realpath is None:
             log.info("Could not locate %s, skipping.", soname)
             continue
@@ -572,8 +574,6 @@ def ldd(
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
             continue
-        if soname not in _all_libs:
-            _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(
             soname,

From cb6498a1d13af41b3b8a8c681ebe7dba9dce4dd5 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 07:27:13 +0800
Subject: [PATCH 06/24] update

---
 src/auditwheel/lddtree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 291905b3..b9053a68 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -570,7 +570,7 @@ def ldd(
         if realpath is None:
             log.info("Could not locate %s, skipping.", soname)
             continue
-        if any(fnmatch(str(realpath), e) for e in exclude):
+        elif any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
             continue

From 78dcfe02975eb5cd4659c56e003befb8572f3d82 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 9 May 2025 23:27:27 +0000
Subject: [PATCH 07/24] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/auditwheel/lddtree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index b9053a68..291905b3 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -570,7 +570,7 @@ def ldd(
         if realpath is None:
             log.info("Could not locate %s, skipping.", soname)
             continue
-        elif any(fnmatch(str(realpath), e) for e in exclude):
+        if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
             continue

From 70e94a1b710e9b104ba8af913c0d73b2f1ed3df8 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 20:38:13 +0800
Subject: [PATCH 08/24] Start test

---
 tests/integration/test_manylinux.py  | 7 +++++++
 tests/integration/testrpath/a/a.c    | 4 ++--
 tests/integration/testrpath/c/c.c    | 3 +++
 tests/integration/testrpath/c/c.h    | 1 +
 tests/integration/testrpath/setup.py | 8 +++++---
 5 files changed, 18 insertions(+), 5 deletions(-)
 create mode 100644 tests/integration/testrpath/c/c.c
 create mode 100644 tests/integration/testrpath/c/c.h

diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index e3097db4..0ce64b16 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -636,6 +636,13 @@ def test_rpath(
                         ]
                         assert len(rpath_tags) == 1
                         assert rpath_tags[0].rpath == "$ORIGIN"
+    
+    def test_dependency_order(self, anylinux: AnyLinuxContainer, python: PythonContainer) -> None:
+        policy = anylinux.policy
+
+        test_path = "/auditwheel_src/tests/integration/testrpath"
+
+        pass
 
     def test_multiple_top_level(
         self, anylinux: AnyLinuxContainer, python: PythonContainer
diff --git a/tests/integration/testrpath/a/a.c b/tests/integration/testrpath/a/a.c
index 0a4ec831..0d0a0923 100644
--- a/tests/integration/testrpath/a/a.c
+++ b/tests/integration/testrpath/a/a.c
@@ -1,6 +1,6 @@
 #include "b.h"
-
+#include "c.h"
 
 int fa(void) {
-    return 1 + fb();
+    return 1 + fb() + fc();
 }
diff --git a/tests/integration/testrpath/c/c.c b/tests/integration/testrpath/c/c.c
new file mode 100644
index 00000000..97968f2d
--- /dev/null
+++ b/tests/integration/testrpath/c/c.c
@@ -0,0 +1,3 @@
+int fc(void) {
+    return 11;
+}
diff --git a/tests/integration/testrpath/c/c.h b/tests/integration/testrpath/c/c.h
new file mode 100644
index 00000000..9593d7d5
--- /dev/null
+++ b/tests/integration/testrpath/c/c.h
@@ -0,0 +1 @@
+int fb(void);
diff --git a/tests/integration/testrpath/setup.py b/tests/integration/testrpath/setup.py
index 75b92674..ea32d218 100644
--- a/tests/integration/testrpath/setup.py
+++ b/tests/integration/testrpath/setup.py
@@ -9,12 +9,14 @@
 
 class BuildExt(build_ext):
     def run(self) -> None:
-        cmd = "gcc -fPIC -shared -o b/libb.so b/b.c"
+        cmd = "gcc -fPIC -shared -o c/libc.so c/c.c"
+        subprocess.check_call(cmd.split())
+        cmd = "gcc -fPIC -shared -o b/libb.so b/b.c -Wl,-rpath=$ORIGIN/../c -Ic -Lc -lc"
         subprocess.check_call(cmd.split())
         cmd = (
-            "gcc -fPIC -shared -o a/liba.so "
+            "gcc -fPIC -shared -o a/liba.so a/a.c "
             "-Wl,{dtags_flag} -Wl,-rpath=$ORIGIN/../b "
-            "-Ib a/a.c -Lb -lb"
+            "-Ib -Lb -lb -Ic -Lc -lc"
         ).format(
             dtags_flag=(
                 "--enable-new-dtags"

From 4272b5303f518b1c232a3fb25fcf328aeb0850fd Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 20:40:27 +0800
Subject: [PATCH 09/24] fix

---
 tests/integration/test_manylinux.py  | 8 ++++----
 tests/integration/testrpath/c/c.h    | 2 +-
 tests/integration/testrpath/setup.py | 4 ++--
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index 0ce64b16..1ff09f54 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -636,14 +636,14 @@ def test_rpath(
                         ]
                         assert len(rpath_tags) == 1
                         assert rpath_tags[0].rpath == "$ORIGIN"
-    
-    def test_dependency_order(self, anylinux: AnyLinuxContainer, python: PythonContainer) -> None:
+
+    def test_dependency_order(
+        self, anylinux: AnyLinuxContainer, python: PythonContainer
+    ) -> None:
         policy = anylinux.policy
 
         test_path = "/auditwheel_src/tests/integration/testrpath"
 
-        pass
-
     def test_multiple_top_level(
         self, anylinux: AnyLinuxContainer, python: PythonContainer
     ) -> None:
diff --git a/tests/integration/testrpath/c/c.h b/tests/integration/testrpath/c/c.h
index 9593d7d5..018d9d29 100644
--- a/tests/integration/testrpath/c/c.h
+++ b/tests/integration/testrpath/c/c.h
@@ -1 +1 @@
-int fb(void);
+int fc(void);
diff --git a/tests/integration/testrpath/setup.py b/tests/integration/testrpath/setup.py
index ea32d218..fd0aec05 100644
--- a/tests/integration/testrpath/setup.py
+++ b/tests/integration/testrpath/setup.py
@@ -11,11 +11,11 @@ class BuildExt(build_ext):
     def run(self) -> None:
         cmd = "gcc -fPIC -shared -o c/libc.so c/c.c"
         subprocess.check_call(cmd.split())
-        cmd = "gcc -fPIC -shared -o b/libb.so b/b.c -Wl,-rpath=$ORIGIN/../c -Ic -Lc -lc"
+        cmd = "gcc -fPIC -shared -o b/libb.so b/b.c -Ic -Lc -lc"
         subprocess.check_call(cmd.split())
         cmd = (
             "gcc -fPIC -shared -o a/liba.so a/a.c "
-            "-Wl,{dtags_flag} -Wl,-rpath=$ORIGIN/../b "
+            "-Wl,{dtags_flag} -Wl,-rpath=$ORIGIN/../b -Wl,-rpath=$ORIGIN/../c "
             "-Ib -Lb -lb -Ic -Lc -lc"
         ).format(
             dtags_flag=(

From 315f12a6f0128506e388e3fa87afd17309d23992 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 22:03:26 +0800
Subject: [PATCH 10/24] finish test

---
 src/auditwheel/lddtree.py                    |  2 +-
 tests/integration/test_manylinux.py          | 10 +++++++++-
 tests/integration/testrpath/a/a.c            |  4 ++--
 tests/integration/testrpath/b/b.c            |  4 +++-
 tests/integration/testrpath/c/c.h            |  1 -
 tests/integration/testrpath/{c/c.c => d/d.c} |  2 +-
 tests/integration/testrpath/d/d.h            |  1 +
 tests/integration/testrpath/setup.py         | 10 ++++++----
 8 files changed, 23 insertions(+), 11 deletions(-)
 delete mode 100644 tests/integration/testrpath/c/c.h
 rename tests/integration/testrpath/{c/c.c => d/d.c} (53%)
 create mode 100644 tests/integration/testrpath/d/d.h

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 291905b3..edf6e2e3 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -568,7 +568,7 @@ def ldd(
         if soname not in _all_libs:
             _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
         if realpath is None:
-            log.info("Could not locate %s, skipping.", soname)
+            log.debug("Could not locate %s, skipping.", soname)
             continue
         if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index 1ff09f54..500e5cfa 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -161,13 +161,17 @@ def repair(
         strip: bool = False,
         library_paths: list[str] | None = None,
         excludes: list[str] | None = None,
+        verbose: int = 0,
     ) -> str:
         plat = plat or self._policy
         args = []
         if library_paths:
             ld_library_path = ":".join([*library_paths, "$LD_LIBRARY_PATH"])
             args.append(f"LD_LIBRARY_PATH={ld_library_path}")
-        args.extend(["auditwheel", "repair", "-w", "/io", "--plat", plat])
+        args.append("auditwheel")
+        if verbose:
+            args.append(f"-{'v' * verbose}")
+        args.extend(["repair", "-w", "/io", "--plat", plat])
         if only_plat:
             args.append("--only-plat")
         if not isa_ext_check:
@@ -643,6 +647,10 @@ def test_dependency_order(
         policy = anylinux.policy
 
         test_path = "/auditwheel_src/tests/integration/testrpath"
+        orig_wheel = anylinux.build_wheel(test_path)
+
+        repair_output = anylinux.repair(orig_wheel, library_paths=[f"{test_path}/a"], verbose=3)
+        assert 'lddtree:Could not locate libd.so, skipping' in repair_output
 
     def test_multiple_top_level(
         self, anylinux: AnyLinuxContainer, python: PythonContainer
diff --git a/tests/integration/testrpath/a/a.c b/tests/integration/testrpath/a/a.c
index 0d0a0923..2dd8e414 100644
--- a/tests/integration/testrpath/a/a.c
+++ b/tests/integration/testrpath/a/a.c
@@ -1,6 +1,6 @@
 #include "b.h"
-#include "c.h"
+#include "d.h"
 
 int fa(void) {
-    return 1 + fb() + fc();
+    return 1 + fb() + fd();
 }
diff --git a/tests/integration/testrpath/b/b.c b/tests/integration/testrpath/b/b.c
index d1b58fac..15202ee3 100644
--- a/tests/integration/testrpath/b/b.c
+++ b/tests/integration/testrpath/b/b.c
@@ -1,3 +1,5 @@
+#include "d.h"
+
 int fb(void) {
-    return 10;
+    return 10 + fd();
 }
diff --git a/tests/integration/testrpath/c/c.h b/tests/integration/testrpath/c/c.h
deleted file mode 100644
index 018d9d29..00000000
--- a/tests/integration/testrpath/c/c.h
+++ /dev/null
@@ -1 +0,0 @@
-int fc(void);
diff --git a/tests/integration/testrpath/c/c.c b/tests/integration/testrpath/d/d.c
similarity index 53%
rename from tests/integration/testrpath/c/c.c
rename to tests/integration/testrpath/d/d.c
index 97968f2d..2647917e 100644
--- a/tests/integration/testrpath/c/c.c
+++ b/tests/integration/testrpath/d/d.c
@@ -1,3 +1,3 @@
-int fc(void) {
+int fd(void) {
     return 11;
 }
diff --git a/tests/integration/testrpath/d/d.h b/tests/integration/testrpath/d/d.h
new file mode 100644
index 00000000..15aace72
--- /dev/null
+++ b/tests/integration/testrpath/d/d.h
@@ -0,0 +1 @@
+int fd(void);
diff --git a/tests/integration/testrpath/setup.py b/tests/integration/testrpath/setup.py
index fd0aec05..9ebe7ec9 100644
--- a/tests/integration/testrpath/setup.py
+++ b/tests/integration/testrpath/setup.py
@@ -9,14 +9,16 @@
 
 class BuildExt(build_ext):
     def run(self) -> None:
-        cmd = "gcc -fPIC -shared -o c/libc.so c/c.c"
+        cmd = "gcc -fPIC -shared -o d/libd.so d/d.c"
         subprocess.check_call(cmd.split())
-        cmd = "gcc -fPIC -shared -o b/libb.so b/b.c -Ic -Lc -lc"
+        cmd = "gcc -fPIC -shared -o b/libb.so b/b.c -Id"
+        subprocess.check_call(cmd.split())
+        cmd = "patchelf --add-needed libd.so b/libb.so"
         subprocess.check_call(cmd.split())
         cmd = (
             "gcc -fPIC -shared -o a/liba.so a/a.c "
-            "-Wl,{dtags_flag} -Wl,-rpath=$ORIGIN/../b -Wl,-rpath=$ORIGIN/../c "
-            "-Ib -Lb -lb -Ic -Lc -lc"
+            "-Wl,{dtags_flag} -Wl,-rpath=$ORIGIN/../b -Wl,-rpath=$ORIGIN/../d "
+            "-Ib -Lb -lb -Id -Ld -ld"
         ).format(
             dtags_flag=(
                 "--enable-new-dtags"

From a7560b383045ae1c184c78fb78804a2ce076d392 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 10 May 2025 14:03:46 +0000
Subject: [PATCH 11/24] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 tests/integration/test_manylinux.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index 500e5cfa..23dd6a8c 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -649,8 +649,10 @@ def test_dependency_order(
         test_path = "/auditwheel_src/tests/integration/testrpath"
         orig_wheel = anylinux.build_wheel(test_path)
 
-        repair_output = anylinux.repair(orig_wheel, library_paths=[f"{test_path}/a"], verbose=3)
-        assert 'lddtree:Could not locate libd.so, skipping' in repair_output
+        repair_output = anylinux.repair(
+            orig_wheel, library_paths=[f"{test_path}/a"], verbose=3
+        )
+        assert "lddtree:Could not locate libd.so, skipping" in repair_output
 
     def test_multiple_top_level(
         self, anylinux: AnyLinuxContainer, python: PythonContainer

From 51e3c2e30e8de0039b01e1f50966d77ab533b424 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 22:08:51 +0800
Subject: [PATCH 12/24] merge tests and fmt

---
 tests/integration/test_manylinux.py | 21 +++++++--------------
 1 file changed, 7 insertions(+), 14 deletions(-)

diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index 23dd6a8c..7e7b5135 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -592,6 +592,7 @@ def test_rpath(
         # - check if RUNPATH is replaced by RPATH
         # - check if RPATH location is correct, i.e. it is inside .libs directory
         #   where all gathered libraries are put
+        # - check if the order of dependencies affects if library is found
 
         policy = anylinux.policy
 
@@ -605,7 +606,12 @@ def test_rpath(
             assert f"DT_{dtag.upper()}" in tags
 
         # Repair the wheel using the appropriate manylinux container
-        anylinux.repair(orig_wheel, library_paths=[f"{test_path}/a"])
+        repair_output = anylinux.repair(
+            orig_wheel, library_paths=[f"{test_path}/a"], verbose=3
+        )
+        assert "lddtree:Could not locate libd.so, skipping" in repair_output, (
+            repair_output
+        )
         repaired_wheel = anylinux.check_wheel("testrpath")
         assert_show_output(anylinux, repaired_wheel, policy, False)
 
@@ -641,19 +647,6 @@ def test_rpath(
                         assert len(rpath_tags) == 1
                         assert rpath_tags[0].rpath == "$ORIGIN"
 
-    def test_dependency_order(
-        self, anylinux: AnyLinuxContainer, python: PythonContainer
-    ) -> None:
-        policy = anylinux.policy
-
-        test_path = "/auditwheel_src/tests/integration/testrpath"
-        orig_wheel = anylinux.build_wheel(test_path)
-
-        repair_output = anylinux.repair(
-            orig_wheel, library_paths=[f"{test_path}/a"], verbose=3
-        )
-        assert "lddtree:Could not locate libd.so, skipping" in repair_output
-
     def test_multiple_top_level(
         self, anylinux: AnyLinuxContainer, python: PythonContainer
     ) -> None:

From c8cdf8f1d37bc541d3974617d6f3700f7b77a512 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 22:21:36 +0800
Subject: [PATCH 13/24] fix result

---
 tests/integration/test_manylinux.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index 7e7b5135..affe1c4a 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -617,7 +617,7 @@ def test_rpath(
 
         python.install_wheel(repaired_wheel)
         output = python.run("from testrpath import testrpath; print(testrpath.func())")
-        assert output.strip() == "11"
+        assert output.strip() == "33"
         with zipfile.ZipFile(anylinux.io_folder / repaired_wheel) as w:
             libraries = tuple(
                 name for name in w.namelist() if "testrpath.libs/lib" in name

From 40c9b98eda6a7e38c4ebc3230628e67c986a1396 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 22:49:56 +0800
Subject: [PATCH 14/24] fix result

---
 tests/integration/test_manylinux.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index affe1c4a..0b3f5f22 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -622,8 +622,11 @@ def test_rpath(
             libraries = tuple(
                 name for name in w.namelist() if "testrpath.libs/lib" in name
             )
-            assert len(libraries) == 2
-            assert any(".libs/liba" in name for name in libraries)
+            assert len(libraries) == 3
+            assert all(
+                (any(f".libs/lib{lib}" in name for name in libraries))
+                for lib in ["a", "b", "d"]
+            )
             for name in libraries:
                 with w.open(name) as f:
                     elf = ELFFile(io.BytesIO(f.read()))

From 806646dcdf80394c5efa5dbd79fcea702ab75056 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 10 May 2025 23:32:01 +0800
Subject: [PATCH 15/24] workaround 3.9 failure

---
 tests/integration/sample_extension/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/integration/sample_extension/pyproject.toml b/tests/integration/sample_extension/pyproject.toml
index 9307927e..5cc7636a 100644
--- a/tests/integration/sample_extension/pyproject.toml
+++ b/tests/integration/sample_extension/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools >= 45.0.0", "cython"]
+requires = ["setuptools >= 45.0.0", "cython < 3.1.0"]
 build-backend = "setuptools.build_meta"

From 3296f332883743aff55ec020add103f9b8223808 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sun, 11 May 2025 00:04:12 +0800
Subject: [PATCH 16/24] more cython workaround

---
 tests/integration/internal_rpath/pyproject.toml     | 2 +-
 tests/integration/multiple_top_level/pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/integration/internal_rpath/pyproject.toml b/tests/integration/internal_rpath/pyproject.toml
index 745445f4..6b494fb1 100644
--- a/tests/integration/internal_rpath/pyproject.toml
+++ b/tests/integration/internal_rpath/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["cython", "setuptools"]
+requires = ["cython < 3.1.0", "setuptools"]
 build-backend = "setuptools.build_meta"
diff --git a/tests/integration/multiple_top_level/pyproject.toml b/tests/integration/multiple_top_level/pyproject.toml
index 745445f4..6b494fb1 100644
--- a/tests/integration/multiple_top_level/pyproject.toml
+++ b/tests/integration/multiple_top_level/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["cython", "setuptools"]
+requires = ["cython < 3.1.0", "setuptools"]
 build-backend = "setuptools.build_meta"

From 7993e1d950b403c3b680879e0a0a79f94b5f393d Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sun, 11 May 2025 09:29:07 +0800
Subject: [PATCH 17/24] revert hard-code cython version and use env as
 workaround

---
 tests/integration/internal_rpath/pyproject.toml     | 2 +-
 tests/integration/multiple_top_level/pyproject.toml | 2 +-
 tests/integration/sample_extension/pyproject.toml   | 2 +-
 tests/integration/test_manylinux.py                 | 4 ++++
 4 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/tests/integration/internal_rpath/pyproject.toml b/tests/integration/internal_rpath/pyproject.toml
index 6b494fb1..745445f4 100644
--- a/tests/integration/internal_rpath/pyproject.toml
+++ b/tests/integration/internal_rpath/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["cython < 3.1.0", "setuptools"]
+requires = ["cython", "setuptools"]
 build-backend = "setuptools.build_meta"
diff --git a/tests/integration/multiple_top_level/pyproject.toml b/tests/integration/multiple_top_level/pyproject.toml
index 6b494fb1..745445f4 100644
--- a/tests/integration/multiple_top_level/pyproject.toml
+++ b/tests/integration/multiple_top_level/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["cython < 3.1.0", "setuptools"]
+requires = ["cython", "setuptools"]
 build-backend = "setuptools.build_meta"
diff --git a/tests/integration/sample_extension/pyproject.toml b/tests/integration/sample_extension/pyproject.toml
index 5cc7636a..9307927e 100644
--- a/tests/integration/sample_extension/pyproject.toml
+++ b/tests/integration/sample_extension/pyproject.toml
@@ -1,3 +1,3 @@
 [build-system]
-requires = ["setuptools >= 45.0.0", "cython < 3.1.0"]
+requires = ["setuptools >= 45.0.0", "cython"]
 build-backend = "setuptools.build_meta"
diff --git a/tests/integration/test_manylinux.py b/tests/integration/test_manylinux.py
index 0b3f5f22..c6321079 100644
--- a/tests/integration/test_manylinux.py
+++ b/tests/integration/test_manylinux.py
@@ -458,6 +458,10 @@ def anylinux(
         for key in os.environ:
             if key.startswith("COV_CORE_"):
                 env[key] = os.environ[key]
+        # cython 3.1.0+ requires a C99 compiler,
+        # where manylinux_2_5 uses gcc 4.8 which is not C99 compliant by default.
+        if policy == "manylinux_2_5":
+            env["CFLAGS"] = "-std=c99"
 
         with docker_container_ctx(manylinux_img, io_folder, env) as container:
             platform_tag = ".".join(

From eb8773aa97ba5fa676390502c7b8c128ae2e7273 Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Wed, 14 May 2025 11:07:14 +0800
Subject: [PATCH 18/24] Also remove excluded libs from
 `DynamicExecutable.libraries` when exclude based on path

---
 src/auditwheel/lddtree.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index edf6e2e3..c6ba704d 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -592,5 +592,5 @@ def ldd(
         frozenset(needed - _excluded_libs),
         tuple(rpaths),
         tuple(runpaths),
-        _all_libs,
+        {k: v for k, v in _all_libs.items() if k not in _excluded_libs},
     )

From 76b78ac041dbfeb9293a3a27a99fc5497d26319e Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Wed, 14 May 2025 15:38:46 +0800
Subject: [PATCH 19/24] Keep order for libraries

---
 src/auditwheel/lddtree.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index c6ba704d..c934943b 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -573,6 +573,7 @@ def ldd(
         if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
+            _all_libs.pop(soname)
             continue
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(
@@ -592,5 +593,5 @@ def ldd(
         frozenset(needed - _excluded_libs),
         tuple(rpaths),
         tuple(runpaths),
-        {k: v for k, v in _all_libs.items() if k not in _excluded_libs},
+        _all_libs,
     )

From 0732b99fe2615f200fe71e30717972f1b7ad8699 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sat, 24 May 2025 08:49:07 +0800
Subject: [PATCH 20/24] same order with main

---
 src/auditwheel/lddtree.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 930f8129..f9439aaa 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -18,7 +18,6 @@
 import glob
 import logging
 import os
-from collections import OrderedDict
 from dataclasses import dataclass
 from fnmatch import fnmatch
 from pathlib import Path
@@ -442,7 +441,7 @@ def ldd(
     """
     _first = _all_libs is None
     if _all_libs is None:
-        _all_libs = OrderedDict()
+        _all_libs = {}
 
     log.debug("ldd(%s)", path)
 
@@ -555,7 +554,7 @@ def ldd(
         + ldpaths["interp"]
     )
     _excluded_libs: set[str] = set()
-    for soname in sorted(needed):
+    for soname in needed:
         if soname in _all_libs and _all_libs[soname].realpath is not None:
             continue
         if soname in _excluded_libs:

From 0deaf39687e2cc839f73e30cb4386da77ff00d25 Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sun, 25 May 2025 13:04:48 +0800
Subject: [PATCH 21/24] update

---
 src/auditwheel/lddtree.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index f9439aaa..0a7679e1 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -572,7 +572,6 @@ def ldd(
         if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
-            _all_libs.pop(soname)
             continue
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(
@@ -592,5 +591,9 @@ def ldd(
         tuple(soname for soname in needed if soname not in _excluded_libs),
         tuple(rpaths),
         tuple(runpaths),
-        _all_libs,
+        {
+            soname: lib
+            for soname, lib in _all_libs.items()
+            if soname not in _excluded_libs
+        },
     )

From 719797a4e3a56539e2d8091b86b09f4a6f6e828a Mon Sep 17 00:00:00 2001
From: Yichen Yan <oraluben@outlook.com>
Date: Sun, 25 May 2025 14:09:31 +0800
Subject: [PATCH 22/24] Revert "update"

This reverts commit 0deaf39687e2cc839f73e30cb4386da77ff00d25.
---
 src/auditwheel/lddtree.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 0a7679e1..f9439aaa 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -572,6 +572,7 @@ def ldd(
         if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
+            _all_libs.pop(soname)
             continue
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(
@@ -591,9 +592,5 @@ def ldd(
         tuple(soname for soname in needed if soname not in _excluded_libs),
         tuple(rpaths),
         tuple(runpaths),
-        {
-            soname: lib
-            for soname, lib in _all_libs.items()
-            if soname not in _excluded_libs
-        },
+        _all_libs,
     )

From fd10d3721af22a4bec3cd23f53037a4d1781feb1 Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Tue, 27 May 2025 06:58:31 +0800
Subject: [PATCH 23/24] test: revert changed logic

---
 src/auditwheel/lddtree.py | 13 +++++--------
 1 file changed, 5 insertions(+), 8 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 87a97148..44785791 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -559,7 +559,7 @@ def ldd(
     )
     _excluded_libs: set[str] = set()
     for soname in needed:
-        if soname in _all_libs and _all_libs[soname].realpath is not None:
+        if soname in _all_libs:
             continue
         if soname in _excluded_libs:
             continue
@@ -578,15 +578,12 @@ def ldd(
             continue
 
         realpath, fullpath = find_lib(platform, soname, all_ldpaths, root)
-        if soname not in _all_libs:
-            _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
-        if realpath is None:
-            log.debug("Could not locate %s, skipping.", soname)
-            continue
-        if any(fnmatch(str(realpath), e) for e in exclude):
+        if realpath is not None and any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
-            _all_libs.pop(soname)
+            continue
+        _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
+        if realpath is None or fullpath is None:
             continue
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(

From ef63c60af5ea7e4f50564669de596128717aea70 Mon Sep 17 00:00:00 2001
From: Yichen Yan <wenji.yyc@alibaba-inc.com>
Date: Tue, 27 May 2025 07:46:36 +0800
Subject: [PATCH 24/24] Revert "test: revert changed logic"

This reverts commit fd10d3721af22a4bec3cd23f53037a4d1781feb1.
---
 src/auditwheel/lddtree.py | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/auditwheel/lddtree.py b/src/auditwheel/lddtree.py
index 44785791..87a97148 100644
--- a/src/auditwheel/lddtree.py
+++ b/src/auditwheel/lddtree.py
@@ -559,7 +559,7 @@ def ldd(
     )
     _excluded_libs: set[str] = set()
     for soname in needed:
-        if soname in _all_libs:
+        if soname in _all_libs and _all_libs[soname].realpath is not None:
             continue
         if soname in _excluded_libs:
             continue
@@ -578,12 +578,15 @@ def ldd(
             continue
 
         realpath, fullpath = find_lib(platform, soname, all_ldpaths, root)
-        if realpath is not None and any(fnmatch(str(realpath), e) for e in exclude):
+        if soname not in _all_libs:
+            _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
+        if realpath is None:
+            log.debug("Could not locate %s, skipping.", soname)
+            continue
+        if any(fnmatch(str(realpath), e) for e in exclude):
             log.info("Excluding %s", realpath)
             _excluded_libs.add(soname)
-            continue
-        _all_libs[soname] = DynamicLibrary(soname, fullpath, realpath)
-        if realpath is None or fullpath is None:
+            _all_libs.pop(soname)
             continue
         dependency = ldd(realpath, root, prefix, ldpaths, fullpath, exclude, _all_libs)
         _all_libs[soname] = DynamicLibrary(