##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.13.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netboost.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netboost.buildbin-libdir netboost_2.13.0.tar.gz'
>>>>>>> 

* installing *source* package ‘netboost’ ...
** using staged installation
CLEANUP cleanup
Clean build.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking whether clang -arch arm64 understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of clang -arch arm64... none
checking how to run the C preprocessor... clang -arch arm64 -E
checking build system type... arm-apple-darwin22.6.0
checking host system type... arm-apple-darwin22.6.0
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking whether C compiler accepts -Wno-deprecated... yes
checking for strip... strip
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/mcupgma/clustering_util/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c boosting.cpp -o boosting.o
boosting.cpp:418:18: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                 (col+1) * nrow,
                 ^~~~~~~~~~~~~~
boosting.cpp:419:18: warning: format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]
                 (col+1) * (nrow + 256/sizeof(double))
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                 bstep + 1, actual_sel + 1, actual_update);
                            ^~~~~~~~~~~~~~
boosting.cpp:729:19: note: in instantiation of function template specialization 'Boosting::filter_column_gen<true, false, true>' requested here
    return boost->filter_column_gen<true,false,true>(col_y-1);
                  ^
boosting.cpp:646:29: warning: format specifies type 'int' but the argument has type 'size_t' (aka 'unsigned long') [-Wformat]
                 bstep + 1, actual_sel + 1, actual_update);
                            ^~~~~~~~~~~~~~
boosting.cpp:732:19: note: in instantiation of function template specialization 'Boosting::filter_column_gen<false, false, true>' requested here
    return boost->filter_column_gen<false,false,true>(col_y-1);
                  ^
boosting.cpp:79:15: warning: unused variable 'AVX_UNROLL' [-Wunused-const-variable]
constexpr int AVX_UNROLL = 4;
              ^
5 warnings generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c dist_tom.cpp -o dist_tom.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -falign-functions=64 -Wall -g -O2   -c tree_sort.cpp -o tree_sort.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
strip -S netboost.so
installing via 'install.libs.R' to /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /tmp/Rtmpb5eJWE/R.INSTALLbbfee83f1f3/netboost"
[1] "R_PACKAGE_DIR:  /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /tmp/Rtmpb5eJWE/R.INSTALLbbfee83f1f3/netboost/src/mcupgma/scripts/install_path.mk"
Clean build.
==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively 
make -C clustering_util  -f Makefile mcupgma_install
mkdir -p bin
mkdir -p obj.arm64_Darwin
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/ClusteringUtil.o ClusteringUtil.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/Tree.o Tree.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG   -o bin/edges2valid_clusters HashingMergerMain.cpp obj.arm64_Darwin/HashingMergerMain.cmdline.o obj.arm64_Darwin/ClusteringUtil.o obj.arm64_Darwin/Tree.o 
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.arm64_Darwin/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -o bin/edge_collator EdgeCollatorMain.cpp obj.arm64_Darwin/EdgeCollatorMain.cmdline.o obj.arm64_Darwin/ClusteringUtil.o obj.arm64_Darwin/Tree.o 
==== compiling  sources using external Makefile (clustering_round/Makefile) recursively 
make -C clustering_round  -f Makefile
mkdir -p dep.arm64_Darwin 
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/test_heap.d  obj.arm64_Darwin/test_heap.o  obj.arm64_Darwin.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.arm64_Darwin/test_heap.d
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/HierarchicalClustering_with_unknown_edges.d  obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o  obj.arm64_Darwin.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.arm64_Darwin/HierarchicalClustering_with_unknown_edges.d
test -d dep.arm64_Darwin && c++ -MM -MT 'dep.arm64_Darwin/HierarchicalClustering_main.d  obj.arm64_Darwin/HierarchicalClustering_main.o  obj.arm64_Darwin.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.arm64_Darwin/HierarchicalClustering_main.d
mkdir -p obj.arm64_Darwin 
mkdir -p bin
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.arm64_Darwin/HierarchicalClustering_main.o
HierarchicalClustering_main.cpp:79:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.arm64_Darwin/HierarchicalClustering_main.cmdline.o
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o
HierarchicalClustering_with_unknown_edges.cpp:26:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
HierarchicalClustering_with_unknown_edges.cpp:85:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
  ubEdgeHeap(edges.begin(), edges.size(), CompareEdgesByUpperBound(isLeftGreater)),
                                                                   ^
HierarchicalClustering_with_unknown_edges.cpp:86:68: warning: field 'isLeftGreater' is uninitialized when used here [-Wuninitialized]
  lbEdgeHeap(edges.begin(), edges.size(), CompareEdgesByLowerBound(isLeftGreater)),
                                                                   ^
3 warnings generated.
c++ obj.arm64_Darwin/HierarchicalClustering_main.o obj.arm64_Darwin/HierarchicalClustering_main.cmdline.o obj.arm64_Darwin/HierarchicalClustering_with_unknown_edges.o  -o bin/hierarchical_clustering  -O3
c++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.arm64_Darwin/test_heap.o
test_heap.cpp:20:17: warning: using directive refers to implicitly-defined namespace 'std'
using namespace std;
                ^
1 warning generated.
cc -O3 -I./ -c test_heap.cmdline.c -o obj.arm64_Darwin/test_heap.cmdline.o
c++ obj.arm64_Darwin/test_heap.o obj.arm64_Darwin/test_heap.cmdline.o  -o bin/test_heap  -O3
[1] "SRC:  /tmp/Rtmpb5eJWE/R.INSTALLbbfee83f1f3/netboost/src/mcupgma"
[1] "DEST: /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/Rtmpb5eJWE/R.INSTALLbbfee83f1f3/netboost/src/mcupgma/clustering_round/bin TO: /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/Rtmpb5eJWE/R.INSTALLbbfee83f1f3/netboost/src/mcupgma/clustering_util/bin TO: /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/Rtmpb5eJWE/R.INSTALLbbfee83f1f3/netboost/src/mcupgma/scripts TO: /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "netboost.so"
** R
** data
*** moving datasets to lazyload DB
** 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 (netboost)


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

>>>>>>> Paths before fix:
netboost.buildbin-libdir/netboost/libs/netboost.so:
	netboost.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 4.4.0)
	/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/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "netboost.buildbin-libdir/netboost/libs/netboost.so"

>>>>>>> Paths after fix:
netboost.buildbin-libdir/netboost/libs/netboost.so:
	netboost.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 4.4.0)
	/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)