##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL XDE
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’
* installing *source* package ‘XDE’ ...
** this is package ‘XDE’ version ‘2.57.0’
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Cholesky.cpp -o Cholesky.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Matrix_v2.cpp -o Matrix_v2.o
In file included from Matrix_v2.cpp:1:
./Matrix_v2.h:4:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
Matrix_v2.cpp:148:7: warning: variable 'signDet' set but not used [-Wunused-but-set-variable]
  int signDet = 1;
      ^
Matrix_v2.cpp:244:7: warning: unused variable 'k' [-Wunused-variable]
  int k = 1;
      ^
Matrix_v2.cpp:246:9: warning: unused variable 'j' [-Wunused-variable]
  int i,j,r;
        ^
4 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp:374:34: warning: equality comparison result unused [-Wunused-comparison]
        if (theGene[k][i] == 1) include == 1;
                                ~~~~~~~~^~~~
Potential_v2.cpp:374:34: note: use '=' to turn this equality comparison into an assignment
        if (theGene[k][i] == 1) include == 1;
                                        ^~
                                        =
1 warning generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp:12:16: warning: variable 'temp' set but not used [-Wunused-but-set-variable]
  unsigned int temp = UINT_MAX - 1;
               ^
Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable]
  double x,y,tt,sum;
         ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Rinterface_v2.cpp -o Rinterface_v2.o
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Structure.cpp -o Structure.o
Structure.cpp:528:8: warning: unused variable 'c' [-Wunused-variable]
  char c;
       ^
Structure.cpp:1642:8: warning: unused variable 'nRead' [-Wunused-variable]
          int nRead = sscanf(var1,"%d",&value);
              ^
Structure.cpp:1668:12: warning: unused variable 'nRead' [-Wunused-variable]
              int nRead = sscanf(var2,"%le",&value);
                  ^
Structure.cpp:1579:12: warning: unused variable 'c' [-Wunused-variable]
      char c;
           ^
Structure.cpp:1728:12: warning: unused variable 'c' [-Wunused-variable]
      char c;
           ^
Structure.cpp:1971:4: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
          filename.empty();
          ^~~~~~~~~~~~~~
Structure.cpp:1983:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:1990:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:1996:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2002:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2008:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2014:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2020:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2026:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2032:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2038:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2044:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2050:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2056:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2062:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2068:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2074:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2080:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2086:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2092:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2098:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2104:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
Structure.cpp:2110:7: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result]
      filename.empty();
      ^~~~~~~~~~~~~~
28 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp:2314:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
    int nOn = 0;
        ^
Update_v2.cpp:2464:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
    int nOn = 0;
        ^
Update_v2.cpp:3293:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
    int nOn = 0;
        ^
Update_v2.cpp:3404:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
    int nOn = 0;
        ^
Update_v2.cpp:3919:10: warning: unused variable 'pot' [-Wunused-variable]
  double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta,
         ^
Update_v2.cpp:3973:10: warning: unused variable 'pot' [-Wunused-variable]
  double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues,
         ^
Update_v2.cpp:4526:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
    int nOn = 0;
        ^
Update_v2.cpp:4657:9: warning: variable 'nOn' set but not used [-Wunused-but-set-variable]
    int nOn = 0;
        ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp:221:12: warning: unused variable 'detPrior' [-Wunused-variable]
    double detPrior = inverse(var,varInv);
           ^
Utility_v2.cpp:228:12: warning: unused variable 'detPosterior' [-Wunused-variable]
    double detPosterior = 1.0 /inverse(varInv,var);
           ^
Utility_v2.cpp:303:9: warning: unused variable 's' [-Wunused-variable]
    int s;
        ^
Utility_v2.cpp:328:12: warning: unused variable 'detPrior' [-Wunused-variable]
    double detPrior = inverse(var,varInv);
           ^
Utility_v2.cpp:334:12: warning: unused variable 'detPosterior' [-Wunused-variable]
    double detPosterior = 1.0 / inverse(varInv,var);
           ^
Utility_v2.cpp:764:6: warning: unused variable 'ngg' [-Wunused-variable]
        int ngg = neighbour[gg].size();
            ^
Utility_v2.cpp:954:8: warning: unused variable 'ngg' [-Wunused-variable]
          int ngg = neighbour[gg].size();
              ^
Utility_v2.cpp:1463:33: warning: unused variable 'itextra' [-Wunused-variable]
      map<int,double>::iterator itextra = VinvSparse[k].end();
                                ^
8 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:38:
./UpdateGamma2Gibbs.h:112:14: warning: variable 'pot' set but not used [-Wunused-but-set-variable]
      double pot = - model->potential(ran);
             ^
In file included from diffExpressed_main.cpp:42:
./UpdateXiGibbs.h:95:11: warning: variable 'pot' set but not used [-Wunused-but-set-variable]
          double pot = - model->potential(ran);
                 ^
./UpdateXiGibbs.h:162:15: warning: variable 'pot' set but not used [-Wunused-but-set-variable]
              double pot = - model->potential(ran);
                     ^
3 warnings generated.
clang -arch arm64 -std=gnu23 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
error: invalid value 'gnu23' in '-std=gnu23'
note: use 'c89', 'c90', or 'iso9899:1990' for 'ISO C 1990' standard
note: use 'iso9899:199409' for 'ISO C 1990 with amendment 1' standard
note: use 'gnu89' or 'gnu90' for 'ISO C 1990 with GNU extensions' standard
note: use 'c99' or 'iso9899:1999' for 'ISO C 1999' standard
note: use 'gnu99' for 'ISO C 1999 with GNU extensions' standard
note: use 'c11' or 'iso9899:2011' for 'ISO C 2011' standard
note: use 'gnu11' for 'ISO C 2011 with GNU extensions' standard
note: use 'c17', 'iso9899:2017', 'c18', or 'iso9899:2018' for 'ISO C 2017' standard
note: use 'gnu17' or 'gnu18' for 'ISO C 2017 with GNU extensions' standard
note: use 'c2x' for 'Working Draft for ISO C2x' standard
note: use 'gnu2x' for 'Working Draft for ISO C2x with GNU extensions' standard
make: *** [registerDynamicSymbol.o] Error 1
ERROR: compilation failed for package ‘XDE’
* removing ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library/XDE’