diff --git a/CMakeLists.txt b/CMakeLists.txt
index a2f5dec2bd..3c778af8e8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -53,10 +53,8 @@ if(ENABLE_RAPIDJSON)
     include(FetchContent)
     FetchContent_Declare(
       rapidjson
-      GIT_REPOSITORY https://github.com/Tencent/rapidjson.git
-      GIT_TAG "origin/master"
-      GIT_SHALLOW TRUE
-      GIT_PROGRESS TRUE)
+      URL https://codeload.github.com/Tencent/rapidjson/tar.gz/24b5e7a8b27f42fa16b96fc70aade9106cf7102f
+    )
     set(RAPIDJSON_BUILD_TESTS
         OFF
         CACHE INTERNAL "")
diff --git a/cmake/FindCereal.cmake b/cmake/FindCereal.cmake
index e32f94711a..f6c5f39877 100644
--- a/cmake/FindCereal.cmake
+++ b/cmake/FindCereal.cmake
@@ -15,7 +15,7 @@ if(NOT CEREAL_INCLUDE_DIR)
     include(FetchContent)
     FetchContent_Declare(
         cereal
-        URL https://github.com/USCiLab/cereal/archive/refs/tags/v1.3.0.tar.gz
+        URL https://codeload.github.com/USCiLab/cereal/tar.gz/22a1b369f39be918ca79206a83c4facd759f9105
     )
     FetchContent_Populate(cereal)
     set(CEREAL_INCLUDE_DIR ${cereal_SOURCE_DIR}/include)
diff --git a/cmake/FindLibComm.cmake b/cmake/FindLibComm.cmake
index 9921badb93..28016bfaa7 100644
--- a/cmake/FindLibComm.cmake
+++ b/cmake/FindLibComm.cmake
@@ -16,7 +16,7 @@ if(NOT LIBCOMM_DIR)
     include(FetchContent)
     FetchContent_Declare(
         LibComm
-        URL https://github.com/abacusmodeling/LibComm/archive/refs/tags/v0.1.1.tar.gz
+        URL https://codeload.github.com/abacusmodeling/LibComm/tar.gz/965bf90713ce5598bae4fd957d417065f77ceb42
     )
     FetchContent_Populate(LibComm)
     set(LIBCOMM_DIR ${libcomm_SOURCE_DIR})
diff --git a/cmake/FindLibRI.cmake b/cmake/FindLibRI.cmake
index b8f060a483..3208a86219 100644
--- a/cmake/FindLibRI.cmake
+++ b/cmake/FindLibRI.cmake
@@ -16,7 +16,7 @@ if(NOT LIBRI_DIR)
     include(FetchContent)
     FetchContent_Declare(
         LibRI
-        URL https://github.com/abacusmodeling/LibRI/archive/refs/tags/v0.2.1.1.tar.gz
+        URL https://codeload.github.com/abacusmodeling/LibRI/tar.gz/e6d78e0504693d2a464c72b87d3240ce183fd881
     )
     FetchContent_Populate(LibRI)
     set(LIBRI_DIR ${libri_SOURCE_DIR})
diff --git a/toolchain/scripts/package_versions.sh b/toolchain/scripts/package_versions.sh
index b8e689c367..3ef4bf08dd 100644
--- a/toolchain/scripts/package_versions.sh
+++ b/toolchain/scripts/package_versions.sh
@@ -99,22 +99,22 @@ libnpy_main_sha256="43452a4db1e8c1df606c64376ea1e32789124051d7640e7e4e8518ab4f0f
 libnpy_alt_ver="1.0.1"
 libnpy_alt_sha256="43452a4db1e8c1df606c64376ea1e32789124051d7640e7e4e8518ab4f0fba44"
 
-# Master branch packages (no fixed versions)
-cereal_ver="master"
-cereal_sha256="--no-checksum"
+# Branch packages cut with specific commits
+cereal_ver="22a1b369f39be918ca79206a83c4facd759f9105"
+cereal_sha256="ca3d544456f93ea3176eab85e2e7892063af45b20467bb4ad9c1c51068e521c6"
 
-libcomm_ver="master"
-libcomm_sha256="--no-checksum"
+libcomm_ver="965bf90713ce5598bae4fd957d417065f77ceb42"
+libcomm_sha256="1d1626b833c51efa7ab844af140e022e063ea64389c9e47b168c24fcc05b7323"
 
-libri_ver="master"
-libri_sha256="--no-checksum"
+libri_ver="e6d78e0504693d2a464c72b87d3240ce183fd881"
+libri_sha256="ead14f05b645f3d028e09f715abaa0e8fca3d1d6d61804239c4858b33397286a"
 
-rapidjson_ver="master"
-rapidjson_sha256="--no-checksum"
+rapidjson_ver="24b5e7a8b27f42fa16b96fc70aade9106cf7102f"
+rapidjson_sha256="2d2601a82d2d3b7e143a3c8d43ef616671391034bc46891a9816b79cf2d3e7a8"
 
 # NEP (Neural Evolution Potential) - CPU version
-nep_ver="main"
-nep_sha256="--no-checksum"
+nep_ver="629ec5dda3127e046fde3f8082aedfca8deb915e"
+nep_sha256="57803d2e98ca5c8ced09e3e8d21ac1a0dbd61dda1977997864195f8c54b9b1f9"
 
 # =============================================================================
 # Package Variable Loading Function
@@ -265,4 +265,4 @@ load_package_vars() {
             return 1
             ;;
     esac
-}
\ No newline at end of file
+}
diff --git a/toolchain/scripts/patches/6190.patch b/toolchain/scripts/patches/6190.patch
deleted file mode 100644
index 5d4d3f3f30..0000000000
--- a/toolchain/scripts/patches/6190.patch
+++ /dev/null
@@ -1,41 +0,0 @@
-From 409db5e910279224bd7e78f8188450c7e7d34d87 Mon Sep 17 00:00:00 2001
-From: Khem Raj <raj.khem@gmail.com>
-Date: Tue, 10 Sep 2024 18:11:40 -0700
-Subject: [PATCH] Fix instances of
- -Wmissing-template-arg-list-after-template-kw.
-
-Clang has a new warning that requires a template argument list after using
-the template keyword. Remove uses of the template keyword when we're not
-specifying types.
-
-See https://github.com/llvm/llvm-project/issues/94194 for the upstream
-clang changes
-
-Signed-off-by: Khem Raj <raj.khem@gmail.com>
----
- include/cereal/types/tuple.hpp | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/include/cereal/types/tuple.hpp b/include/cereal/types/tuple.hpp
-index 80c68075..5c79eca9 100644
---- a/include/cereal/types/tuple.hpp
-+++ b/include/cereal/types/tuple.hpp
-@@ -95,7 +95,7 @@ namespace cereal
-       template <class Archive, class ... Types> inline
-       static void apply( Archive & ar, std::tuple<Types...> & tuple )
-       {
--        serialize<Height - 1>::template apply( ar, tuple );
-+        serialize<Height - 1>::apply( ar, tuple );
-         ar( CEREAL_NVP_(tuple_element_name<Height - 1>::c_str(),
-             std::get<Height - 1>( tuple )) );
-       }
-@@ -116,7 +116,7 @@ namespace cereal
-   template <class Archive, class ... Types> inline
-   void CEREAL_SERIALIZE_FUNCTION_NAME( Archive & ar, std::tuple<Types...> & tuple )
-   {
--    tuple_detail::serialize<std::tuple_size<std::tuple<Types...>>::value>::template apply( ar, tuple );
-+    tuple_detail::serialize<std::tuple_size<std::tuple<Types...>>::value>::apply( ar, tuple );
-   }
- } // namespace cereal
-
- 
\ No newline at end of file
diff --git a/toolchain/scripts/stage4/install_cereal.sh b/toolchain/scripts/stage4/install_cereal.sh
index 5d5852a337..eeb3492960 100755
--- a/toolchain/scripts/stage4/install_cereal.sh
+++ b/toolchain/scripts/stage4/install_cereal.sh
@@ -48,9 +48,9 @@ case "$with_cereal" in
         #pkg_install_dir="${HOME}/lib/cereal/${cereal_ver}"
         install_lock_file="$pkg_install_dir/install_successful"
         # url construction rules:
-        # - Branch names (master, main, develop) without v prefix
+        # - Commit hash (40 hex chars) without v prefix
         # - Version tags (e.g., 1.0.0) with v prefix
-        if [[ "${cereal_ver}" =~ ^(master|main|develop)$ ]]; then
+        if [[ "${cereal_ver}" =~ ^[0-9a-f]{40}$ ]]; then
             url="https://codeload.github.com/USCiLab/cereal/tar.gz/${cereal_ver}"
         else
             url="https://codeload.github.com/USCiLab/cereal/tar.gz/v${cereal_ver}"
@@ -72,10 +72,6 @@ case "$with_cereal" in
             echo "Installing from scratch into ${pkg_install_dir}"
             [ -d $dirname ] && rm -rf $dirname
             tar -xzf $filename
-            #unzip -q $filename
-            # apply patch files for libri installation in issue #6190, Kai Luo
-            # echo ${SCRIPT_DIR}
-            cd $dirname && pwd && patch -p1 < ${SCRIPT_DIR}/patches/6190.patch
             cd "${BUILDDIR}"
             # 
             mkdir -p "${pkg_install_dir}"
diff --git a/toolchain/scripts/stage4/install_libcomm.sh b/toolchain/scripts/stage4/install_libcomm.sh
index f5b0c22715..ba779b88be 100755
--- a/toolchain/scripts/stage4/install_libcomm.sh
+++ b/toolchain/scripts/stage4/install_libcomm.sh
@@ -55,7 +55,7 @@ case "$with_libcomm" in
         # url construction rules:
         # - Branch names (master, main, develop) without v prefix
         # - Version tags (e.g., 1.0.0) with v prefix
-        if [[ "${libcomm_ver}" =~ ^(master|main|develop)$ ]]; then
+        if [[ "${libcomm_ver}" =~ ^[0-9a-f]{40}$ ]]; then
             url="https://codeload.github.com/abacusmodeling/LibComm/tar.gz/${libcomm_ver}"
         else
             url="https://codeload.github.com/abacusmodeling/LibComm/tar.gz/v${libcomm_ver}"
diff --git a/toolchain/scripts/stage4/install_libri.sh b/toolchain/scripts/stage4/install_libri.sh
index ba0ee25c46..186a7572ea 100755
--- a/toolchain/scripts/stage4/install_libri.sh
+++ b/toolchain/scripts/stage4/install_libri.sh
@@ -53,7 +53,7 @@ case "$with_libri" in
         # url construction rules:
         # - Branch names (master, main, develop) without v prefix
         # - Version tags (e.g., 1.0.0) with v prefix
-        if [[ "${libri_ver}" =~ ^(master|main|develop)$ ]]; then
+        if [[ "${libri_ver}" =~ ^[0-9a-f]{40}$ ]]; then
             url="https://codeload.github.com/abacusmodeling/LibRI/tar.gz/${libri_ver}"
         else
             url="https://codeload.github.com/abacusmodeling/LibRI/tar.gz/v${libri_ver}"
diff --git a/toolchain/scripts/stage4/install_rapidjson.sh b/toolchain/scripts/stage4/install_rapidjson.sh
index da6727ac40..480f8d6177 100755
--- a/toolchain/scripts/stage4/install_rapidjson.sh
+++ b/toolchain/scripts/stage4/install_rapidjson.sh
@@ -51,7 +51,7 @@ case "$with_rapidjson" in
         # url construction rules:
         # - Branch names (master, main, develop) without v prefix
         # - Version tags (e.g., 1.0.0) with v prefix
-        if [[ "${rapidjson_ver}" =~ ^(master|main|develop)$ ]]; then
+        if [[ "${rapidjson_ver}" =~ ^[0-9a-f]{40}$ ]]; then
             url="https://codeload.github.com/Tencent/rapidjson/tar.gz/${rapidjson_ver}"
         else
             url="https://codeload.github.com/Tencent/rapidjson/tar.gz/v${rapidjson_ver}"