##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf beachmat.tiledb.buildbin-libdir && mkdir beachmat.tiledb.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beachmat.tiledb_0.99.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R beachmat.tiledb.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=beachmat.tiledb.buildbin-libdir beachmat.tiledb_0.99.1.tar.gz'
>>>>>>> 

* installing *source* package ‘beachmat.tiledb’ ...
** this is package ‘beachmat.tiledb’ version ‘0.99.1’
** using staged installation
checking if tiledb-R downloaded its own TileDB... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c initialize.cpp -o initialize.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c load_dense.cpp -o load_dense.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/tiledb/tiledb/include -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/assorthead/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/beachmat/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c load_sparse.cpp -o load_sparse.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o beachmat.tiledb.so RcppExports.o initialize.o load_dense.o load_sparse.o -ltiledb -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/tiledb/lib -L/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/tiledb/tiledb/lib -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.21-bioc/meat/beachmat.tiledb.buildbin-libdir/00LOCK-beachmat.tiledb/00new/beachmat.tiledb/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 (beachmat.tiledb)


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

>>>>>>> Paths before fix:
beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so:
	beachmat.tiledb.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtiledb.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-x86_64/Resources/lib/libgcc_s.1.1.dylib" "beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libgfortran.5.dylib" "beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libquadmath.0.dylib" "beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so"

>>>>>>> Paths after fix:
beachmat.tiledb.buildbin-libdir/beachmat.tiledb/libs/beachmat.tiledb.so:
	beachmat.tiledb.so (compatibility version 0.0.0, current version 0.0.0)
	@rpath/libtiledb.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)