From e91130e69a4dfbc4aa75ace6e70b0e77598e5666 Mon Sep 17 00:00:00 2001
From: Brian Ward <bward@flatironinstitute.org>
Date: Wed, 17 Jun 2026 10:44:35 -0400
Subject: [PATCH 1/2] Use -isystem for libraries

---
 make/compiler_flags | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/make/compiler_flags b/make/compiler_flags
index 177bebca39b..34f578ae991 100644
--- a/make/compiler_flags
+++ b/make/compiler_flags
@@ -118,10 +118,13 @@ endif
 ##
 O ?= 3
 
+## Replace with -I if running into system conflicts
+INC_FLAG ?= -isystem
+
 ## setup includes
-INC ?= $(INC_FIRST) -I $(if $(MATH),$(MATH),.) -I $(EIGEN) -I $(BOOST) $(INC_SUNDIALS)
-INC_SUNDIALS ?= -I $(SUNDIALS)/include -I $(SUNDIALS)/src/sundials
-INC_GTEST ?= -I $(GTEST)/include -I $(GTEST)
+INC ?= $(INC_FIRST) -I $(if $(MATH),$(MATH),.) $(INC_FLAG) $(EIGEN) $(INC_FLAG) $(BOOST) $(INC_SUNDIALS)
+INC_SUNDIALS ?= $(INC_FLAG) $(SUNDIALS)/include $(INC_FLAG) $(SUNDIALS)/src/sundials
+INC_GTEST ?= $(INC_FLAG) $(GTEST)/include $(INC_FLAG) $(GTEST)
 
 ## setup precompiler options
 CPPFLAGS_BOOST ?= -DBOOST_DISABLE_ASSERTS
@@ -254,7 +257,7 @@ ifdef STAN_OPENCL
   CPPFLAGS_OPENCL ?= -DSTAN_OPENCL -DOPENCL_DEVICE_ID=$(OPENCL_DEVICE_ID) -DOPENCL_PLATFORM_ID=$(OPENCL_PLATFORM_ID)
   CPPFLAGS_OPENCL += -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120
   CPPFLAGS_OPENCL += -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes
-  CXXFLAGS_OPENCL ?= -I $(OPENCL)
+  CXXFLAGS_OPENCL ?= $(INC_FLAG) $(OPENCL)
 
 	ifdef INTEGRATED_OPENCL
 		CPPFLAGS_OPENCL += -DINTEGRATED_OPENCL=1
@@ -288,9 +291,9 @@ endif
 ifdef TBB_LIB
 
 ifdef TBB_INC
-CXXFLAGS_TBB ?= -I $(TBB_INC)
+CXXFLAGS_TBB ?= $(INC_FLAG) $(TBB_INC)
 else
-CXXFLAGS_TBB ?= -I $(TBB)/include
+CXXFLAGS_TBB ?= $(INC_FLAG) $(TBB)/include
 endif
 
 # MacOS ld does not support --disable-new-dtags
@@ -321,7 +324,7 @@ ifeq ($(OS),Linux)
   TBB_TARGETS ?= $(addprefix $(TBB_BIN)/lib,$(addsuffix $(LIBRARY_SUFFIX).2,$(TBB_LIBRARIES)))
 endif
 
-CXXFLAGS_TBB ?= -I $(TBB)/include
+CXXFLAGS_TBB ?= $(INC_FLAG) $(TBB)/include
 LDFLAGS_TBB ?= -Wl,-L,"$(TBB_BIN_ABSOLUTE_PATH)" $(LDFLAGS_FLTO_FLTO) $(LDFLAGS_OPTIM_TBB)
 
 # Windows LLVM/Clang does not support -rpath, but is not needed on Windows anyway

From 12fe63f8dd3e3957cd3227127b0a8055dd6351b4 Mon Sep 17 00:00:00 2001
From: Brian Ward <bward@flatironinstitute.org>
Date: Thu, 18 Jun 2026 09:47:20 -0400
Subject: [PATCH 2/2] Rename to INC_DIR_OPT

---
 make/compiler_flags | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/make/compiler_flags b/make/compiler_flags
index 34f578ae991..a78e8ccd9b4 100644
--- a/make/compiler_flags
+++ b/make/compiler_flags
@@ -119,12 +119,12 @@ endif
 O ?= 3
 
 ## Replace with -I if running into system conflicts
-INC_FLAG ?= -isystem
+INC_DIR_OPT ?= -isystem
 
 ## setup includes
-INC ?= $(INC_FIRST) -I $(if $(MATH),$(MATH),.) $(INC_FLAG) $(EIGEN) $(INC_FLAG) $(BOOST) $(INC_SUNDIALS)
-INC_SUNDIALS ?= $(INC_FLAG) $(SUNDIALS)/include $(INC_FLAG) $(SUNDIALS)/src/sundials
-INC_GTEST ?= $(INC_FLAG) $(GTEST)/include $(INC_FLAG) $(GTEST)
+INC ?= $(INC_FIRST) -I $(if $(MATH),$(MATH),.) $(INC_DIR_OPT) $(EIGEN) $(INC_DIR_OPT) $(BOOST) $(INC_SUNDIALS)
+INC_SUNDIALS ?= $(INC_DIR_OPT) $(SUNDIALS)/include $(INC_DIR_OPT) $(SUNDIALS)/src/sundials
+INC_GTEST ?= $(INC_DIR_OPT) $(GTEST)/include $(INC_DIR_OPT) $(GTEST)
 
 ## setup precompiler options
 CPPFLAGS_BOOST ?= -DBOOST_DISABLE_ASSERTS
@@ -257,7 +257,7 @@ ifdef STAN_OPENCL
   CPPFLAGS_OPENCL ?= -DSTAN_OPENCL -DOPENCL_DEVICE_ID=$(OPENCL_DEVICE_ID) -DOPENCL_PLATFORM_ID=$(OPENCL_PLATFORM_ID)
   CPPFLAGS_OPENCL += -DCL_HPP_TARGET_OPENCL_VERSION=120 -DCL_HPP_MINIMUM_OPENCL_VERSION=120
   CPPFLAGS_OPENCL += -DCL_HPP_ENABLE_EXCEPTIONS -Wno-ignored-attributes
-  CXXFLAGS_OPENCL ?= $(INC_FLAG) $(OPENCL)
+  CXXFLAGS_OPENCL ?= $(INC_DIR_OPT) $(OPENCL)
 
 	ifdef INTEGRATED_OPENCL
 		CPPFLAGS_OPENCL += -DINTEGRATED_OPENCL=1
@@ -291,9 +291,9 @@ endif
 ifdef TBB_LIB
 
 ifdef TBB_INC
-CXXFLAGS_TBB ?= $(INC_FLAG) $(TBB_INC)
+CXXFLAGS_TBB ?= $(INC_DIR_OPT) $(TBB_INC)
 else
-CXXFLAGS_TBB ?= $(INC_FLAG) $(TBB)/include
+CXXFLAGS_TBB ?= $(INC_DIR_OPT) $(TBB)/include
 endif
 
 # MacOS ld does not support --disable-new-dtags
@@ -324,7 +324,7 @@ ifeq ($(OS),Linux)
   TBB_TARGETS ?= $(addprefix $(TBB_BIN)/lib,$(addsuffix $(LIBRARY_SUFFIX).2,$(TBB_LIBRARIES)))
 endif
 
-CXXFLAGS_TBB ?= $(INC_FLAG) $(TBB)/include
+CXXFLAGS_TBB ?= $(INC_DIR_OPT) $(TBB)/include
 LDFLAGS_TBB ?= -Wl,-L,"$(TBB_BIN_ABSOLUTE_PATH)" $(LDFLAGS_FLTO_FLTO) $(LDFLAGS_OPTIM_TBB)
 
 # Windows LLVM/Clang does not support -rpath, but is not needed on Windows anyway