Fix nested dynamic library loading

See upstream PR:
emscripten-core/emscripten#25694

This fixes shapely.

Author: hoodmane

emsdk/patches/0001-Add-useful-error-when-symbol-resolution-fails.patch

@@ -1,7 +1,7 @@
-From 4aa8434d294dea2c98225a6a36f4300f279ec2bd Mon Sep 17 00:00:00 2001
+From bbfcf45d1a257b4cb69356d48bdeed93430b60a5 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <roberthoodchatham@gmail.com>
 Date: Fri, 19 May 2023 12:19:00 -0700
-Subject: [PATCH 1/4] Add useful error when symbol resolution fails
+Subject: [PATCH 1/3] Add useful error when symbol resolution fails
 
 Currently if symbol resolution fails, we get:
 ```js
@@ -19,7 +19,7 @@ symbol.
  1 file changed, 3 insertions(+)
 
 diff --git a/src/lib/libdylink.js b/src/lib/libdylink.js
-index 491b62735..3e6839be9 100644
+index fdfe2e608..737a9773e 100644
 --- a/src/lib/libdylink.js
 +++ b/src/lib/libdylink.js
 @@ -736,6 +736,9 @@ var LibraryDylink = {

emsdk/patches/0002-Don-t-check-exports-for-being-valid-C-C-identifiers-.patch

@@ -1,7 +1,7 @@
-From e16f400d460cfd921192b5d32a52329bfe037f96 Mon Sep 17 00:00:00 2001
+From 3db1a0fe9d6d6697b6af78f178aedc58c7a280b8 Mon Sep 17 00:00:00 2001
 From: Hood Chatham <roberthoodchatham@gmail.com>
 Date: Sat, 17 May 2025 15:15:02 -0400
-Subject: [PATCH 2/4] Don't check exports for being valid C/C++ identifiers in
+Subject: [PATCH 2/3] Don't check exports for being valid C/C++ identifiers in
  side modules
 
 This unbreaks Rust side modules, which have been broken since

emsdk/patches/0003-Fix-nested-dynamic-library-loading-via-RPATH.patch

@@ -0,0 +1,126 @@
+From 1a07b14227c65ae49d933584bb8760f3980edfed Mon Sep 17 00:00:00 2001
+From: Hood Chatham <roberthoodchatham@gmail.com>
+Date: Fri, 31 Oct 2025 15:29:33 -0700
+Subject: [PATCH 3/3] Fix nested dynamic library loading via RPATH
+
+There is a bug with dynamic library loading. Suppose
+liba.so is on LD_LIBRARY_PATH and it has an RPATH of `$ORIGIN/other_dir`
+and loads `libb.so` from other_dir. Then suppose `libb.so` has an RPATH of
+`$ORIGIN` and wants to load `libc.so` also from `other_dir`.
+
+Before this PR this doesn't work. The problem is that `flags.rpath.parentLibPath`
+is set to `libb.so` and we replace $ORIGIN with `PATH.dirname(parentLibName)`
+which is `.`. So unless `other_dir` is on the `LD_LIBRARY_PATH` or is the
+current working directory, loading will fail.
+
+The fix: if `findLibraryFS()` returns a value that is not `undefined`, replace
+`libName` with the returned value.
+---
+ src/lib/libdylink.js |  4 ++-
+ test/test_other.py   | 61 ++++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 64 insertions(+), 1 deletion(-)
+
+diff --git a/src/lib/libdylink.js b/src/lib/libdylink.js
+index 737a9773e..c1d2c72d9 100644
+--- a/src/lib/libdylink.js
++++ b/src/lib/libdylink.js
+@@ -990,7 +990,7 @@ var LibraryDylink = {
+ #endif
+     }
+     var rpathResolved = (rpath?.paths || []).map((p) => replaceORIGIN(rpath?.parentLibPath, p));
+-    return withStackSave(() => {
++    var result = withStackSave(() => {
+       // In dylink.c we use: `char buf[2*NAME_MAX+2];` and NAME_MAX is 255.
+       // So we use the same size here.
+       var bufSize = 2*255 + 2;
+@@ -1000,6 +1000,7 @@ var LibraryDylink = {
+       var resLibNameC = __emscripten_find_dylib(buf, rpathC, libNameC, bufSize);
+       return resLibNameC ? UTF8ToString(resLibNameC) : undefined;
+     });
++    return FS.lookupPath(result).path;
+   },
+ #endif // FILESYSTEM
+ 
+@@ -1107,6 +1108,7 @@ var LibraryDylink = {
+       dbg(`checking filesystem: ${libName}: ${f ? 'found' : 'not found'}`);
+ #endif
+       if (f) {
++        libName = f;
+         var libData = FS.readFile(f, {encoding: 'binary'});
+         return flags.loadAsync ? Promise.resolve(libData) : libData;
+       }
+diff --git a/test/test_other.py b/test/test_other.py
+index 57ceb9f09..1baca1251 100644
+--- a/test/test_other.py
++++ b/test/test_other.py
+@@ -2381,6 +2381,67 @@ Module['postRun'] = () => {
+     self.assertEqual(get_runtime_paths('libside1.so'), ['$ORIGIN'])
+     self.assertEqual(get_runtime_paths('a.out.wasm'), ['$ORIGIN'])
+ 
++  def test_dylink_dependencies_rpath_nested(self):
++    create_file('pre.js', r'''
++      Module.preRun.push(() => {
++        Module.ENV.LD_LIBRARY_PATH = "/lib1";
++      });
++    ''')
++    create_file('side1.c', r'''
++    #include <stdio.h>
++
++    void side2();
++
++    void side1() {
++        printf("side1\n");
++        side2();
++    }
++    ''')
++    create_file('side2.c', r'''
++    #include <stdio.h>
++    void side3();
++
++    void side2() {
++        printf("side2\n");
++        side3();
++    }
++    ''')
++    create_file('side3.c', r'''
++    #include <stdio.h>
++
++    void side3() {
++        printf("side3\n");
++    }
++    ''')
++    create_file('main.c', r'''
++    #include <dlfcn.h>
++    #include <stdio.h>
++
++    typedef void (*F)(void);
++
++    int main() {
++        void* handle = dlopen("libside1.so", RTLD_NOW);
++        F side1 = (F)dlsym(handle, "side1");
++
++        printf("main\n");
++        side1();
++        return 0;
++    }
++    ''')
++    os.mkdir('libs')
++    os.mkdir('lib1')
++    self.emcc('side3.c', ['-fPIC', '-sSIDE_MODULE', '-olibs/libside3.so'])
++    self.emcc('side2.c', ['-fPIC', '-sSIDE_MODULE', '-olibs/libside2.so', '-Wl,-rpath,$ORIGIN', 'libs/libside3.so'])
++    self.emcc('side1.c', ['-fPIC', '-sSIDE_MODULE', '-Wl,-rpath,$ORIGIN/../libs', '-olib1/libside1.so', 'libs/libside2.so'])
++    settings = ['-sMAIN_MODULE=2', '-sDYLINK_DEBUG', "-sEXPORTED_FUNCTIONS=[_printf,_main]", "-sEXPORTED_RUNTIME_METHODS=ENV"]
++    preloads = []
++    for file in ['lib1/libside1.so', 'libs/libside2.so', 'libs/libside3.so']:
++      preloads += ['--preload-file', file]
++    cmd = [EMCC, 'main.c', '-fPIC', '--pre-js', 'pre.js'] + settings + preloads
++    self.run_process(cmd)
++
++    self.run_js('a.out.js')
++
+   def test_dylink_LEGACY_GL_EMULATION(self):
+     # LEGACY_GL_EMULATION wraps JS library functions. This test ensure that when it does
+     # so it preserves the `.sig` attributes needed by dynamic linking.
+-- 
+2.34.1
+