diff --git a/test/fs/test_fs_enotdir.c b/test/fs/test_fs_enotdir.c
index e221ed8e59304..0e776a732a248 100644
--- a/test/fs/test_fs_enotdir.c
+++ b/test/fs/test_fs_enotdir.c
@@ -17,7 +17,7 @@ int main() {
     assert(errno == ENOTDIR);
   }
   {
-    assert(open("./does-not-exist/", O_CREAT) == -1);
+    assert(open("./does-not-exist/", O_CREAT, 0777) == -1);
     assert(errno == EISDIR);
   }
   printf("success\n");
diff --git a/test/fs/test_fs_readdir_ino_matches_stat_ino.c b/test/fs/test_fs_readdir_ino_matches_stat_ino.c
index 68e1f1da4e55d..3d231eb7a60e7 100644
--- a/test/fs/test_fs_readdir_ino_matches_stat_ino.c
+++ b/test/fs/test_fs_readdir_ino_matches_stat_ino.c
@@ -58,5 +58,6 @@ int main() {
   assert(a_ino == sta.st_ino);
   assert(b_ino == stb.st_ino);
   printf("success\n");
+  closedir(dirp);
   return 0;
 }
diff --git a/test/test_core.py b/test/test_core.py
index 6846074f2dfa2..8075a42ade9bd 100644
--- a/test/test_core.py
+++ b/test/test_core.py
@@ -19,7 +19,7 @@
 
 from tools.shared import PIPE
 from tools.shared import EMCC, EMAR, FILE_PACKAGER
-from tools.utils import WINDOWS, MACOS, write_file, delete_file
+from tools.utils import WINDOWS, MACOS, LINUX, write_file, delete_file
 from tools import shared, building, config, utils, webassembly
 import common
 from common import RunnerCore, path_from_root, requires_native_clang, test_file, create_file
@@ -5546,8 +5546,8 @@ def test_fcntl(self):
   @also_with_nodefs_both
   @crossplatform
   def test_fcntl_open(self):
-    if '-DNODERAWFS' in self.emcc_args and WINDOWS:
-      self.skipTest('currently failing under windows and noderawfs')
+    if '-DNODERAWFS' in self.emcc_args and not LINUX:
+      self.skipTest('noderawfs fails here under non-linux')
     self.do_run_in_out_file_test('fcntl/test_fcntl_open.c')
 
   @also_with_wasm_bigint
diff --git a/tools/system_libs.py b/tools/system_libs.py
index 3b01a85fbf651..ef896f6ec96ac 100644
--- a/tools/system_libs.py
+++ b/tools/system_libs.py
@@ -471,14 +471,9 @@ def get_files(self):
   def generate_ninja(self, build_dir, libname):
     ensure_sysroot()
     utils.safe_ensure_dirs(build_dir)
+    self.build_dir = build_dir
 
     cflags = self.get_cflags()
-    if self.deterministic_paths:
-      source_dir = utils.path_from_root()
-      relative_source_dir = os.path.relpath(source_dir, build_dir)
-      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
-                 f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}',
-                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     asflags = get_base_cflags(preprocess=False)
     input_files = self.get_files()
     ninja_file = os.path.join(build_dir, 'build.ninja')
@@ -492,17 +487,11 @@ def build_objects(self, build_dir):
     with the `cflags` returned by `self.get_cflags()`.
     """
     batch_inputs = int(os.environ.get('EMCC_BATCH_BUILD', '1'))
+    self.build_dir = build_dir
     batches = {}
     commands = []
     objects = set()
     cflags = self.get_cflags()
-    if self.deterministic_paths:
-      source_dir = utils.path_from_root()
-      if batch_inputs:
-        relative_source_dir = os.path.relpath(source_dir, build_dir)
-        cflags += [f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}']
-      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
-                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     case_insensitive = is_case_insensitive(build_dir)
     for src in self.get_files():
       ext = shared.suffix(src)
@@ -611,6 +600,12 @@ def get_cflags(self):
     if self.includes:
       cflags += ['-I' + utils.path_from_root(i) for i in self._inherit_list('includes')]
 
+    if self.deterministic_paths:
+      source_dir = utils.path_from_root()
+      relative_source_dir = os.path.relpath(source_dir, self.build_dir)
+      cflags += [f'-ffile-prefix-map={relative_source_dir}={DETERMINISITIC_PREFIX}']
+      cflags += [f'-ffile-prefix-map={source_dir}={DETERMINISITIC_PREFIX}',
+                 f'-fdebug-compilation-dir={DETERMINISITIC_PREFIX}']
     return cflags
 
   def get_base_name_prefix(self):