From: Michael R. Crusoe <crusoe@debian.org>
Subject: use packaged libraries
Forwarded: not-needed
--- iqtree.orig/CMakeLists.txt
+++ iqtree/CMakeLists.txt
@@ -132,7 +132,6 @@
 endif()
 
 include_directories("${PROJECT_SOURCE_DIR}")
-include_directories("${PROJECT_SOURCE_DIR}/yaml-cpp/include")
 include_directories(after system "/usr/local/include")
 
 ##################################################################
@@ -758,7 +757,7 @@
 option(YAML_CPP_BUILD_TOOLS "Enable parse tools" OFF)
 option(YAML_CPP_BUILD_CONTRIB "Enable contrib stuff in library" OFF)
 option(YAML_CPP_INSTALL "Enable generation of install target" OFF)
-add_subdirectory(yaml-cpp)
+find_package(yaml-cpp)
 add_subdirectory(phylo-yaml)
 
 if (USE_TERRAPHAST)
@@ -821,9 +820,9 @@
 
 if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
     if (NOT IQTREE_FLAGS MATCHES "nosse")
-        set_target_properties(iqtree2 ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main ${TARGET_CMAPLE} PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+        set_target_properties(iqtree2 ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator phyloYAML main ${TARGET_CMAPLE} PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
         if (USE_CMAPLE_AA STREQUAL "ON")
-        	set_target_properties(iqtree2-aa ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main-aa maple-aa PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+        	set_target_properties(iqtree2-aa ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator phyloYAML main-aa maple-aa PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
         endif()
         if (USE_TERRAPHAST)
             set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
@@ -875,11 +874,11 @@
 
 # basic linking librararies
 target_link_libraries(iqtree2 pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model
-    gsl alignment tree simulator terrace yaml-cpp phyloYAML main ${TARGET_CMAPLE} ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
+    gsl alignment tree simulator terrace phyloYAML main ${TARGET_CMAPLE} ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
 
 if (USE_CMAPLE_AA STREQUAL "ON")
 	target_link_libraries(iqtree2-aa pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model
-    	gsl alignment tree simulator terrace yaml-cpp phyloYAML main-aa maple-aa ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
+    	gsl alignment tree simulator terrace phyloYAML main-aa maple-aa ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
 endif()
 	
 if (USE_TERRAPHAST)
--- iqtree.orig/cmaple/CMakeLists.txt
+++ iqtree/cmaple/CMakeLists.txt
@@ -274,7 +274,8 @@
 )
 # For Windows: Prevent overriding the parent project's compiler/linker settings
 set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
-FetchContent_MakeAvailable(googletest)
+add_subdirectory(/usr/src/googletest googletest EXCLUDE_FROM_ALL)
+include_directories(/usr/share/googletest)
 
 ##################################################################
 # subdirectories containing necessary libraries for the build
@@ -287,8 +288,6 @@
     add_subdirectory(libraries/nclextra)
 endif()
 add_subdirectory(utils)
-add_subdirectory(libraries/SIMDe)
-target_include_directories(cmaple_utils PUBLIC ${SIMDE_INCLUDE_DIRECTORY})
 add_subdirectory(model)
 add_subdirectory(alignment)
 add_subdirectory(tree)
