Proposed fix for Mojave build errors related to location of cstring h…

…eaders
gtDMMB · Feb 24, 2021 · d3718be · d3718be
1 parent 9ac4197
commit d3718be
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Showing 10 changed files with 22 additions and 14 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -122,18 +122,17 @@ else()
      set(RHEL_LINKER_APPENDS "")
 endif()
 if(APPLE)
-    #"${CMAKE_CXX_FLAGS} -Wall -std=c++14 -stdlib=libc++ -fPIC -fopenmp -g -O2 -fno-lto
     set(CMAKE_CXX_FLAGS
-        "${CMAKE_CXX_FLAGS} -Wall -mlinker-version=450 -std=c++14 -fPIC -fopenmp -g -O2 -fno-lto \
+        "${CMAKE_CXX_FLAGS} -Wall -mlinker-version=450 -isystem /usr/local/opt/llvm/include \
+        -std=c++14 -fPIC -fopenmp -g -O2 -fno-lto \
         -I/usr/local/include -I/usr/local/opt/llvm/include -Igtfold-mfe/include/ \
         -DGTFOLD_PACKAGE_VERSION=\"${GTFOLD_PACKAGE_VERSION}\"" #${PC_GMP_INCLUDE_DIRS} ${PC_GMPXX_INCLUDE_DIRS}
     )
     # NOTE: Providing the explicit LLVM linker path seems to fix the problems on Mojave.
     set(CMAKE_EXE_LINKER_FLAGS
         "${CMAKE_CXX_FLAGS} ${CMAKE_EXE_LINKER_FLAGS} \
          -mlinker-version=450 -L/usr/local/lib -lm -lpthread \
-        -L/usr/local/opt/llvm/lib \
-        ${PC_GMP_LIBRARIES} ${PC_GMPXX_LIBRARIES}"
+        -L/usr/local/opt/llvm/lib ${PC_GMP_LIBRARIES} ${PC_GMPXX_LIBRARIES}"
     )
 elseif(UNIX AND NOT APPLE) # Primary target: Linux (typically RHEL)
     set(CMAKE_CXX_FLAGS

diff --git a/gtfold-mfe/include/partition-func-d2.h b/gtfold-mfe/include/partition-func-d2.h
@@ -3,7 +3,8 @@
 #include <iostream>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 #include <math.h>
 
 //#include "MyDouble.cc"
@@ -106,7 +107,7 @@ class PartitionFunctionD2{
 #include "algorithms-partition.h"
 #include "global.h"
 #include "utils.h"
-#include<omp.h>
+#include <omp.h>
 #include <assert.h>
 #define MEMORY_OPTIMIZATION_ENABLED false
 #define PAIRABLE_POINTS_GATHER_OPTIMIZATION_DISABLED true

diff --git a/gtfold-mfe/include/stochastic-sampling-d2.h b/gtfold-mfe/include/stochastic-sampling-d2.h
@@ -129,7 +129,8 @@ class StochasticTracebackD2{
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 #include <stack>
 #include <map>
 #include<sstream>

diff --git a/gtfold-mfe/src/binexe-utils/calc_pnum.cc b/gtfold-mfe/src/binexe-utils/calc_pnum.cc
@@ -4,7 +4,8 @@
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 #include <stack>
 #include <map>
 #include<sstream>

diff --git a/gtfold-mfe/src/binexe-utils/limitCDboltzmanntest.cc b/gtfold-mfe/src/binexe-utils/limitCDboltzmanntest.cc
@@ -3,7 +3,8 @@
 #include<sstream>
 #include <stdio.h>
 #include <stdlib.h>
-#include<string.h>
+//#include<string.h>
+#include <cstring>
 #include <stack>
 using namespace std;
 

diff --git a/gtfold-mfe/src/binexe-utils/main.cc b/gtfold-mfe/src/binexe-utils/main.cc
@@ -27,7 +27,8 @@
 #include <sstream>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 
 #include "main.h"
 #include "mfe_main.h"

diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc
@@ -1,5 +1,6 @@
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 #include <stdio.h>
 #include <iostream>
 #include <fstream>

diff --git a/gtfold-mfe/src/mfe_main.cc b/gtfold-mfe/src/mfe_main.cc
@@ -26,7 +26,8 @@
 #include <sstream>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 #include <cassert>
 
 #include "main.h"

diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc
@@ -1,6 +1,7 @@
 #include<iostream>
 #include<fstream>
-#include<string.h>
+//#include<string.h>
+#include <cstring>
 #include<stdio.h>
 #include <stdlib.h>
 #include <math.h>

diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc
@@ -4,7 +4,8 @@
 #include <assert.h>
 #include <stdio.h>
 #include <stdlib.h>
-#include <string.h>
+//#include <string.h>
+#include <cstring>
 #include <stack>
 #include <map>
 #include<sstream>