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###
### Running command:
###
###   rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DeMixT_1.16.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DeMixT.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DeMixT.buildbin-libdir DeMixT_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DeMixT’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c DeMixT.c -o DeMixT.o
DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable]
  double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                            ^
DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable]
  double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                     ^
DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable]
  double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
                                ^
DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable]
  double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
          ^
DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
                    ^
DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
           ^
DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
           ^
DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
                    ^
DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
        double obj_old, obj_new;
                        ^
DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
        double obj_old, obj_new;
               ^
DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
                    ^
DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable]
    double obj_old, obj_new;
           ^
12 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Profile_2D.cpp -o Profile_2D.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c init.c -o init.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’
Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’
Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’
** testing if installed package keeps a record of temporary installation path
* DONE (DeMixT)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so
>>>>>>> 

>>>>>>> Paths before fix:
DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so:
	DeMixT.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so"

>>>>>>> Paths after fix:

DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so:
	DeMixT.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)