##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf plier.buildbin-libdir && mkdir plier.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh plier_1.68.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R plier.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=plier.buildbin-libdir plier_1.68.0.tar.gz'
>>>>>>> 

* installing *source* package ‘plier’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c affyplier.cpp -o affyplier.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c plier_impl.cpp -o plier_impl.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c plieralg.cpp -o plieralg.o
plieralg.cpp:905:14: warning: variable 'icount' set but not used [-Wunused-but-set-variable]
        long count, icount;
                    ^
plieralg.cpp:49:12: warning: unused variable 'g_ErrorCode' [-Wunused-variable]
static int g_ErrorCode=NoError;
           ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c rwrapper.cpp -o rwrapper.o
rwrapper.cpp:192:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete pm_ptr;  
    ^
          []
rwrapper.cpp:151:23: note: allocated with 'new[]' here
    double **pm_ptr = new double *[*num_exp];
                      ^
rwrapper.cpp:193:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete mm_ptr;
    ^
          []
rwrapper.cpp:152:23: note: allocated with 'new[]' here
    double **mm_ptr = new double *[*num_exp];
                      ^
rwrapper.cpp:194:5: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
    delete rpct;
    ^
          []
rwrapper.cpp:159:21: note: allocated with 'new[]' here
    long    *rpct = new long [*num_exp]; /* the API expects a long array that it wants to delete itself (replicate). We have an int array that R owns so we need to create the long one here, but let the API handle the clean up. Which is nice. */
                    ^
3 warnings generated.
clang++ -arch arm64 -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/opt/R/arm64/lib -o plier.so affyplier.o plier_impl.o plieralg.o rwrapper.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/plier.buildbin-libdir/00LOCK-plier/00new/plier/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (plier)


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

install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "plier.buildbin-libdir/plier/libs/plier.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "plier.buildbin-libdir/plier/libs/plier.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "plier.buildbin-libdir/plier/libs/plier.so"