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###
### Running command:
###
###   rm -rf densvis.buildbin-libdir && mkdir densvis.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh densvis_1.00.6.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R densvis.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=densvis.buildbin-libdir densvis_1.00.6.tar.gz'
>>>>>>> 

* installing *source* package ‘densvis’ ...
** using non-staged installation via StagedInstall field
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c densne.cpp -o densne.o
In file included from densne.cpp:62:
In file included from ./vptree.h:43:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
densne.cpp:181:24: warning: variable 'row_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:33: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:35: note: initialize the variable 'row_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                  ^
                                   = nullptr
densne.cpp:181:24: warning: variable 'col_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:40: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                       ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:56: note: initialize the variable 'col_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                       ^
                                                        = nullptr
densne.cpp:181:24: warning: variable 'val_P' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:47: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                              ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:71: note: initialize the variable 'val_P' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                                      ^
                                                                       = nullptr
densne.cpp:181:24: warning: variable 'val_D' is used uninitialized whenever 'for' loop exits because its condition is false [-Wsometimes-uninitialized]
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:201:54: note: uninitialized use occurs here
    computeExpectedLogDist(&ro, row_P, col_P, val_P, val_D, N, logdist_shift);
                                                     ^~~~~
densne.cpp:181:24: note: remove the condition if it is always true
        for(int i = 0; i < N * N; i++) P[i] /= sum_P;
                       ^~~~~~~~~
densne.cpp:154:86: note: initialize the variable 'val_D' to silence this warning
    double* P; unsigned int* row_P; unsigned int* col_P; double* val_P; double* val_D;
                                                                                     ^
                                                                                      = nullptr
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c densvis.cpp -o densvis.o
In file included from densvis.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c sptree.cpp -o sptree.o
In file included from sptree.cpp:63:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
            SEXP data = Parent::get__();
                 ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 densvis.so RcppExports.o densne.o densvis.o sptree.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/densvis.buildbin-libdir/densvis/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (densvis)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "densvis.buildbin-libdir/densvis/libs/densvis.so"