Multiple platform build/check report for BioC 3.8 - BUILD BIN report for methimpute on merida1

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### Running command:
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###   rm -rf methimpute.buildbin-libdir && mkdir methimpute.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh methimpute_1.4.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R methimpute.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=methimpute.buildbin-libdir methimpute_1.4.1.tar.gz'
>>>>>>> 

* installing *source* package ‘methimpute’ ...
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c densities.cpp -o densities.o
In file included from densities.cpp:1:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(int test, int total);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
                virtual double getLogDensityAt(int) { return(0); };
                               ^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(double x);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
                virtual double getLogDensityAt(int) { return(0); };
                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c fitHMM.cpp -o fitHMM.o
In file included from fitHMM.cpp:2:
In file included from ./scalehmm.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(int test, int total);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
                virtual double getLogDensityAt(int) { return(0); };
                               ^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(double x);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
                virtual double getLogDensityAt(int) { return(0); };
                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c fitHMM_context.cpp -o fitHMM_context.o
In file included from fitHMM_context.cpp:2:
In file included from ./hmm_context.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(int test, int total);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
                virtual double getLogDensityAt(int) { return(0); };
                               ^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(double x);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
                virtual double getLogDensityAt(int) { return(0); };
                               ^
2 warnings generated.
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c hmm_context.cpp -o hmm_context.o
In file included from hmm_context.cpp:1:
In file included from ./hmm_context.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(int test, int total);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
                virtual double getLogDensityAt(int) { return(0); };
                               ^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(double x);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
                virtual double getLogDensityAt(int) { return(0); };
                               ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c methimpute_init.c -o methimpute_init.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include  -fopenmp -fPIC  -Wall -g -O2 -c scalehmm.cpp -o scalehmm.o
In file included from scalehmm.cpp:1:
In file included from ./scalehmm.h:4:
./densities.h:98:10: warning: 'BinomialTest::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(int test, int total);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: different number of parameters (1 vs 2)
                virtual double getLogDensityAt(int) { return(0); };
                               ^
./densities.h:224:10: warning: 'Beta::getLogDensityAt' hides overloaded virtual function [-Woverloaded-virtual]
                double getLogDensityAt(double x);
                       ^
./densities.h:31:18: note: hidden overloaded virtual function 'Density::getLogDensityAt' declared here: type mismatch at 1st parameter ('int' vs 'double')
                virtual double getLogDensityAt(int) { return(0); };
                               ^
2 warnings generated.
clang++ -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 methimpute.so RcppExports.o densities.o fitHMM.o fitHMM_context.o hmm_context.o methimpute_init.o scalehmm.o -fopenmp -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/methimpute.buildbin-libdir/methimpute/libs
** R
** data
** 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 (methimpute)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "methimpute.buildbin-libdir/methimpute/libs//methimpute.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "methimpute.buildbin-libdir/methimpute/libs//methimpute.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "methimpute.buildbin-libdir/methimpute/libs//methimpute.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "methimpute.buildbin-libdir/methimpute/libs//methimpute.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "methimpute.buildbin-libdir/methimpute/libs//methimpute.so"
BUILD BIN report for methimpute on merida1

Summary

Command output
