Author: Michael R. Crusoe <crusoe@debian.org>
Description: Use packaged system libs
Forwarded: not-needed
--- iqtree3.orig/CMakeLists.txt
+++ iqtree3/CMakeLists.txt
@@ -153,7 +153,6 @@
 endif()
 
 include_directories("${PROJECT_SOURCE_DIR}")
-include_directories("${PROJECT_SOURCE_DIR}/yaml-cpp/include")
 include_directories(AFTER SYSTEM "/usr/local/include")
 
 ##################################################################
@@ -846,7 +845,6 @@
 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)
 add_subdirectory(phylo-yaml)
 
 if (USE_TERRAPHAST)
@@ -915,9 +913,9 @@
 
 if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
     if (NOT IQTREE_FLAGS MATCHES "nosse")
-        set_target_properties(iqtree3 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(iqtree3 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(iqtree3-aa ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main-aa maple-aa PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+        	set_target_properties(iqtree3-aa ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator phyloYAML main-aa maple-aa PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
         endif()
         if (USE_TERRAPHAST)
             set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
--- iqtree3.orig/cmaple/CMakeLists.txt
+++ iqtree3/cmaple/CMakeLists.txt
@@ -280,7 +280,7 @@
 )
 # 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)
 
 ##################################################################
 # subdirectories containing necessary libraries for the build
@@ -293,8 +293,7 @@
     add_subdirectory(libraries/nclextra)
 endif()
 add_subdirectory(utils)
-add_subdirectory(libraries/SIMDe)
-target_include_directories(cmaple_utils PUBLIC ${SIMDE_INCLUDE_DIRECTORY})
+target_include_directories(cmaple_utils PUBLIC)
 add_subdirectory(model)
 add_subdirectory(alignment)
 add_subdirectory(tree)
--- iqtree3.orig/cmaple/libraries/nclextra/modelsblock.h
+++ iqtree3/cmaple/libraries/nclextra/modelsblock.h
@@ -8,7 +8,7 @@
 #ifndef MODELSBLOCK_H_
 #define MODELSBLOCK_H_
 
-#include "../../libraries/ncl/ncl.h"
+#include "ncl/ncl.h"
 #include "../../utils/tools.h"
 
 const int NM_ATOMIC  = 1; // NxsModel is not mixture or +G etc. model
--- iqtree3.orig/cmaple/libraries/nclextra/myreader.h
+++ iqtree3/cmaple/libraries/nclextra/myreader.h
@@ -24,7 +24,7 @@
 #include <iostream>
 #include <fstream>
 //#include "node.h"
-#include "../../libraries/ncl/ncl.h"
+#include "ncl/ncl.h"
 
 /**
 	MyReader class to make more informative message
--- iqtree3.orig/cmaple/model/modelbase.cpp
+++ iqtree3/cmaple/model/modelbase.cpp
@@ -1,7 +1,7 @@
 #include "../alignment/seqregions.h"
 
 using namespace std;
-#include "../libraries/ncl/ncl.h"
+#include "ncl/ncl.h"
 #include "../libraries/nclextra/modelsblock.h"
 #include "../libraries/nclextra/myreader.h"
 #include "modelbase.h"
