##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf alabaster.base.buildbin-libdir && mkdir alabaster.base.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh alabaster.base_1.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R alabaster.base.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=alabaster.base.buildbin-libdir alabaster.base_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘alabaster.base’ ...
** using staged installation
** 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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c check_csv.cpp -o check_csv.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c check_list.cpp -o check_list.o
In file included from check_list.cpp:3:
In file included from ../inst/include/uzuki2/uzuki2.hpp:15:
In file included from ../inst/include/uzuki2/parse_json.hpp:15:
In file included from ../inst/include/byteme/SomeBufferReader.hpp:6:
../inst/include/byteme/ZlibBufferReader.hpp:47:24: warning: variable 'ret' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                       ^~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:51:17: note: uninitialized use occurs here
            if (ret != Z_OK) {
                ^~~
../inst/include/byteme/ZlibBufferReader.hpp:47:20: note: remove the 'if' if its condition is always true
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                   ^~~~~~~~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:40:20: note: initialize the variable 'ret' to silence this warning
            int ret;
                   ^
                    = 0
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c load_csv.cpp -o load_csv.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c load_list.cpp -o load_list.o
In file included from load_list.cpp:3:
In file included from ../inst/include/uzuki2/uzuki2.hpp:15:
In file included from ../inst/include/uzuki2/parse_json.hpp:15:
In file included from ../inst/include/byteme/SomeBufferReader.hpp:6:
../inst/include/byteme/ZlibBufferReader.hpp:47:24: warning: variable 'ret' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                       ^~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:51:17: note: uninitialized use occurs here
            if (ret != Z_OK) {
                ^~~
../inst/include/byteme/ZlibBufferReader.hpp:47:20: note: remove the 'if' if its condition is always true
            } else if (mode == 3) { // Gzip/Zlib auto-detected
                   ^~~~~~~~~~~~~~~
../inst/include/byteme/ZlibBufferReader.hpp:40:20: note: initialize the variable 'ret' to silence this warning
            int ret;
                   ^
                    = 0
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c write_scalar.cpp -o write_scalar.o
clang++ -arch arm64 -std=gnu++17 -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 alabaster.base.so RcppExports.o check_csv.o check_list.o load_csv.o load_list.o write_scalar.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/alabaster.base.buildbin-libdir/00LOCK-alabaster.base/00new/alabaster.base/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 (alabaster.base)


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

>>>>>>> Paths before fix:
alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so:
	alabaster.base.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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so"

>>>>>>> Paths after fix:

alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so:
	alabaster.base.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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1)
	/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)