##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.32.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HDF5Array.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HDF5Array.buildbin-libdir HDF5Array_1.32.0.tar.gz'
>>>>>>> 

* installing *source* package ‘HDF5Array’ ...
** 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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c H5File.c -o H5File.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c global_errmsg_buf.c -o global_errmsg_buf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c H5DSetDescriptor.c -o H5DSetDescriptor.o
H5DSetDescriptor.c:720:45: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat]
        Rprintf("%s  * h5type_id = %ld\n", margin, h5type->h5type_id);
                                   ~~~             ^~~~~~~~~~~~~~~~~
                                   %lld
H5DSetDescriptor.c:1204:31: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat]
        Rprintf("- dset_id = %ld\n", h5dset->dset_id);
                             ~~~     ^~~~~~~~~~~~~~~
                             %lld
H5DSetDescriptor.c:1222:34: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat]
        Rprintf("- h5space_id = %ld\n", h5dset->h5space_id);
                                ~~~     ^~~~~~~~~~~~~~~~~~
                                %lld
H5DSetDescriptor.c:1226:34: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat]
        Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id);
                                ~~~     ^~~~~~~~~~~~~~~~~~
                                %lld
4 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5dimscales.c -o h5dimscales.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c uaselection.c -o uaselection.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_helpers.c -o h5mread_helpers.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_startscounts.c -o h5mread_startscounts.o
h5mread_startscounts.c:300:16: warning: variable 'num_hyperslabs' set but not used [-Wunused-but-set-variable]
        long long int num_hyperslabs;
                      ^
1 warning generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c ChunkIterator.c -o ChunkIterator.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_index.c -o h5mread_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:123:13: warning: unused function 'NOT_USED_make_nzindex_from_buf' [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
            ^
h5mread_sparse.c:179:13: warning: unused function 'NOT_USED_make_nzdata_from_IntAE_bufs' [-Wunused-function]
static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
            ^
h5mread_sparse.c:206:13: warning: unused function 'NOT_USED_make_nzindex_from_bufs' [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
            ^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5mread.c -o h5mread.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c h5summarize.c -o h5summarize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c R_init_HDF5Array.c -o R_init_HDF5Array.o
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 HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib/libhdf5_hl.a /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/HDF5Array.buildbin-libdir/00LOCK-HDF5Array/00new/HDF5Array/libs
** R
** inst
** 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 (HDF5Array)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so
>>>>>>> 

>>>>>>> Paths before fix:
HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so:
	HDF5Array.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)

>>>>>>> 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" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so"

>>>>>>> Paths after fix:
HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so:
	HDF5Array.so (compatibility version 0.0.0, current version 0.0.0)
	/usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0)
	/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)