Same problem with gstreamer libs.
After looking into code I found next problems. Here we define rpath=$ORIGIN for any shared lib:

linuxdeploy/src/core/appdir.cpp

Lines 830 to 838 in 63d2fa5

    
           for (const auto& sharedLibrary : listSharedLibraries()) { 
        
               if (bf::is_symlink(sharedLibrary)) 
        
                   continue; 
        
               if (!d->deployElfDependencies(sharedLibrary)) 
        
                   return false; 
        
               d->setElfRPathOperations[sharedLibrary] = "$ORIGIN"; 
        
           }

Here we set $ORIGIN as rpath:

linuxdeploy/src/core/appdir.cpp

Lines 289 to 294 in 63d2fa5

    
           } else { 
        
               ldLog() << "Setting rpath in ELF file" << filePath << "to" << rpath << std::endl; 
        
               if (!elf_file::ElfFile(filePath).setRPath(rpath)) { 
        
                   ldLog() << LD_ERROR << "Failed to set rpath in ELF file:" << filePath << std::endl; 
        
                   success = false; 
        
               }

As result, linuxdeploy ignore any rpath, that sets manually.

	for (const auto& sharedLibrary : listSharedLibraries()) {
	if (bf::is_symlink(sharedLibrary))
	continue;

	if (!d->deployElfDependencies(sharedLibrary))
	return false;

	d->setElfRPathOperations[sharedLibrary] = "$ORIGIN";
	}

	} else {
	ldLog() << "Setting rpath in ELF file" << filePath << "to" << rpath << std::endl;
	if (!elf_file::ElfFile(filePath).setRPath(rpath)) {
	ldLog() << LD_ERROR << "Failed to set rpath in ELF file:" << filePath << std::endl;
	success = false;
	}

Skip changing rpaths #149

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