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###
### Running command:
###
###   rm -rf VegaMC.buildbin-libdir && mkdir VegaMC.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh VegaMC_3.44.0.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_3.44.0.tar.gz'
>>>>>>> 

* installing *source* package ‘VegaMC’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
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:144:62: warning: data argument not used by format string [-Wformat-extra-args]
    Rprintf("\tAberration Matrices Successfully Computed\n", num_seg_regions);
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  ^
run_vegaMC.c:150:13: warning: data argument not used by format string [-Wformat-extra-args]
            num_seg_regions);
            ^
run_vegaMC.c:317:17: warning: variable 'tot_baf' set but not used [-Wunused-but-set-variable]
            int tot_baf = 0;
                ^
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;
                 ^
6 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 -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
installing to /Users/biocbuild/bbs-3.20-bioc/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 PATHS TO DYNAMIC LIBRARIES FOR VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so
>>>>>>> 

>>>>>>> Paths before fix:
VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so:
	VegaMC.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so"

>>>>>>> Paths after fix:
VegaMC.buildbin-libdir/VegaMC/libs/VegaMC.so:
	VegaMC.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)