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###
### Running command:
###
###   rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.40.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R XDE.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XDE.buildbin-libdir XDE_2.40.0.tar.gz'
>>>>>>> 

* installing *source* package ‘XDE’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Cholesky.cpp -o Cholesky.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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: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;
        ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp:1847:10: warning: unused variable 'x' [-Wunused-variable]
  double x,y,tt,sum;
         ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Rinterface_v2.cpp:2:
In file included from ./Update_v2.h:8:
./Random.h:19:9: warning: 'PI' macro redefined [-Wmacro-redefined]
#define PI         3.14159265
        ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:39:9: note: previous definition is here
#define PI             M_PI
        ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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;
           ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c Update_v2.cpp -o Update_v2.o
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,
         ^
2 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
./Random.h:19:9: warning: 'PI' macro redefined [-Wmacro-redefined]
#define PI         3.14159265
        ^
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:39:9: note: previous definition is here
#define PI             M_PI
        ^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/XDE.buildbin-libdir/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘qqplot’ in package ‘XDE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XDE)


>>>>>>> 
>>>>>>> FIXING LINKS FOR XDE.buildbin-libdir/XDE/libs/XDE.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "XDE.buildbin-libdir/XDE/libs/XDE.so"