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###
### Running command:
###
###   rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.36.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R VegaMC.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=VegaMC.buildbin-libdir VegaMC_3.36.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c run_vegaMC.c -o run_vegaMC.o
run_vegaMC.c:491:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
run_vegaMC.c:526:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
run_vegaMC.c:618:18: warning: unused variable 'brkt' [-Wunused-variable]
    char *elem, *brkt;
                 ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c sort_data.c -o sort_data.o
sort_data.c:131:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
sort_data.c:180:27: warning: expression which evaluates to zero treated as a null pointer constant of type 'char *' [-Wnon-literal-null-conversion]
            elem = strtok('\0', sep);
                          ^~~~
2 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c vegaMC.c -o vegaMC.o
vegaMC.c:235:10: warning: variable 'deleted' set but not used [-Wunused-but-set-variable]
    node deleted;
         ^
vegaMC.c:458:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
    lambda_gradient = abs(lambda);
                      ^
vegaMC.c:458:23: note: use function 'fabsf' instead
    lambda_gradient = abs(lambda);
                      ^~~
                      fabsf
vegaMC.c:592:15: warning: variable 'index' set but not used [-Wunused-but-set-variable]
    int i, j, index;
              ^
3 warnings generated.
clang -arch arm64 -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 VegaMC.so run_vegaMC.o sort_data.o vegaMC.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/VegaMC.buildbin-libdir/00LOCK-VegaMC/00new/VegaMC/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 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 (VegaMC)


>>>>>>> 
>>>>>>> FIXING LINKS FOR VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.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" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"