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###
### Running command:
###
###   rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.15.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R netboost.buildbin-libdir
###
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=netboost.buildbin-libdir netboost_2.15.0.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 x86_64
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 x86_64 accepts -g... yes
checking for clang -arch x86_64 option to accept ISO C89... none needed
checking whether clang -arch x86_64 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 x86_64... none
checking how to run the C preprocessor... clang -arch x86_64 -E
checking build system type... x86_64-apple-darwin21.6.0
checking host system type... x86_64-apple-darwin21.6.0
checking for x86 cpuid  output... unknown
checking for x86-AVX xgetbv  output... unknown
checking for x86 cpuid 0x00000000 output... 16:756e6547:6c65746e:49656e69
checking for x86 cpuid 0x80000000 output... 80000008:0:0:0
checking for x86 cpuid 0x00000001 output... 50657:38400800:7ffefbff:bfebfbff
checking for x86 cpuid 0x00000007 output... 0:d39ff7eb:808:bc000400
checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800
checking for x86-AVX xgetbv 0x00000000 output... 7:0
checking whether RDRND is supported by the processor... yes
checking whether RDRND is supported by the processor and OS... yes
checking whether C compiler accepts -mrdrnd... yes
checking whether BMI1 is supported by the processor... yes
checking whether BMI1 is supported by the processor and OS... yes
checking whether C compiler accepts -mbmi... yes
checking whether BMI2 is supported by the processor... yes
checking whether BMI2 is supported by the processor and OS... yes
checking whether C compiler accepts -mbmi2... yes
checking whether ADX is supported by the processor... yes
checking whether ADX is supported by the processor and OS... yes
checking whether C compiler accepts -madx... yes
checking whether MPX is supported by the processor... yes
checking whether MPX is supported by the processor and OS... yes
checking whether C compiler accepts -mmpx... yes
checking whether PREFETCHWT1 is supported by the processor... no
checking whether ABM is supported by the processor... yes
checking whether ABM is supported by the processor and OS... yes
checking whether C compiler accepts -mabm... no
configure: WARNING: Your processor and OS supports ABM instructions but not your compiler, can you try another compiler?
checking whether MMX is supported by the processor... yes
checking whether MMX is supported by the processor and OS... yes
checking whether C compiler accepts -mmmx... yes
checking whether SSE is supported by the processor... yes
checking whether SSE is supported by the processor and OS... yes
checking whether C compiler accepts -msse... yes
checking whether SSE2 is supported by the processor... yes
checking whether SSE2 is supported by the processor and OS... yes
checking whether C compiler accepts -msse2... yes
checking whether SSE3 is supported by the processor... yes
checking whether SSE3 is supported by the processor and OS... yes
checking whether C compiler accepts -msse3... yes
checking whether SSSE3 is supported by the processor... yes
checking whether SSSE3 is supported by the processor and OS... yes
checking whether C compiler accepts -mssse3... yes
checking whether SSE4.1 is supported by the processor... yes
checking whether SSE4.1 is supported by the processor and OS... yes
checking whether C compiler accepts -msse4.1... yes
checking whether SSE4.2 is supported by the processor... yes
checking whether SSE4.2 is supported by the processor and OS... yes
checking whether C compiler accepts -msse4.2... yes
checking whether SSE4a is supported by the processor... no
checking whether SHA is supported by the processor... no
checking whether AES is supported by the processor... yes
checking whether AES is supported by the processor and OS... yes
checking whether C compiler accepts -maes... yes
checking whether AVX is supported by the processor... yes
checking whether AVX is supported by the processor and OS... yes
checking whether C compiler accepts -mavx... yes
checking whether FMA3 is supported by the processor... yes
checking whether FMA3 is supported by the processor and OS... yes
checking whether C compiler accepts -mfma... yes
checking whether FMA4 is supported by the processor... no
checking whether XOP is supported by the processor... no
checking whether AVX2 is supported by the processor... yes
checking whether AVX2 is supported by the processor and OS... yes
checking whether C compiler accepts -mavx2... yes
checking whether AVX512-F is supported by the processor... yes
checking whether AVX512-F is supported by the processor and OS... no
configure: WARNING: Your processor supports AVX512-F, but your OS doesn't
checking whether AVX512-CD is supported by the processor... yes
checking whether AVX512-CD is supported by the processor and OS... no
configure: WARNING: Your processor supports AVX512-CD, but your OS doesn't
checking whether AVX512-PF is supported by the processor... no
checking whether AVX512-ER is supported by the processor... no
checking whether AVX512-VL is supported by the processor... yes
checking whether AVX512-VL is supported by the processor and OS... no
configure: WARNING: Your processor supports AVX512-VL, but your OS doesn't
checking whether AVX512-BW is supported by the processor... yes
checking whether AVX512-BW is supported by the processor and OS... no
configure: WARNING: Your processor supports AVX512-BW, but your OS doesn't
checking whether AVX512-DQ is supported by the processor... yes
checking whether AVX512-DQ is supported by the processor and OS... no
configure: WARNING: Your processor supports AVX512-DQ, but your OS doesn't
checking whether AVX512-IFMA is supported by the processor... no
checking whether AVX512-VBMI is supported by the processor... no
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 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c boosting.cpp -o boosting.o
boosting.cpp:418:18: warning: format specifies type 'int' but the argument has type '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 '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 '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);
                  ^
4 warnings generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c dist_tom.cpp -o dist_tom.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -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/RcppParallel/include' -I/opt/R/x86_64/include   `/Library/Frameworks/R.framework/Resources/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c tree_sort.cpp -o tree_sort.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-3.21-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /tmp/RtmpY8SSD9/R.INSTALL74c82a68311b/netboost"
[1] "R_PACKAGE_DIR:  /Users/biocbuild/bbs-3.21-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /tmp/RtmpY8SSD9/R.INSTALL74c82a68311b/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.x86_64_Darwin
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/ClusteringUtil.o ClusteringUtil.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/Tree.o Tree.cpp
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG   -o bin/edges2valid_clusters HashingMergerMain.cpp obj.x86_64_Darwin/HashingMergerMain.cmdline.o obj.x86_64_Darwin/ClusteringUtil.o obj.x86_64_Darwin/Tree.o 
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Darwin/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
c++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -o bin/edge_collator EdgeCollatorMain.cpp obj.x86_64_Darwin/EdgeCollatorMain.cmdline.o obj.x86_64_Darwin/ClusteringUtil.o obj.x86_64_Darwin/Tree.o 
==== compiling  sources using external Makefile (clustering_round/Makefile) recursively 
make -C clustering_round  -f Makefile
mkdir -p dep.x86_64_Darwin 
test -d dep.x86_64_Darwin && c++ -MM -MT 'dep.x86_64_Darwin/test_heap.d  obj.x86_64_Darwin/test_heap.o  obj.x86_64_Darwin.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.x86_64_Darwin/test_heap.d
test -d dep.x86_64_Darwin && c++ -MM -MT 'dep.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.d  obj.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.o  obj.x86_64_Darwin.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.d
test -d dep.x86_64_Darwin && c++ -MM -MT 'dep.x86_64_Darwin/HierarchicalClustering_main.d  obj.x86_64_Darwin/HierarchicalClustering_main.o  obj.x86_64_Darwin.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.x86_64_Darwin/HierarchicalClustering_main.d
mkdir -p obj.x86_64_Darwin 
mkdir -p bin
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.x86_64_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.x86_64_Darwin/HierarchicalClustering_main.cmdline.o
c++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.x86_64_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.x86_64_Darwin/HierarchicalClustering_main.o obj.x86_64_Darwin/HierarchicalClustering_main.cmdline.o obj.x86_64_Darwin/HierarchicalClustering_with_unknown_edges.o  -o bin/hierarchical_clustering  -O3
c++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.x86_64_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.x86_64_Darwin/test_heap.cmdline.o
c++ obj.x86_64_Darwin/test_heap.o obj.x86_64_Darwin/test_heap.cmdline.o  -o bin/test_heap  -O3
[1] "SRC:  /tmp/RtmpY8SSD9/R.INSTALL74c82a68311b/netboost/src/mcupgma"
[1] "DEST: /Users/biocbuild/bbs-3.21-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/RtmpY8SSD9/R.INSTALL74c82a68311b/netboost/src/mcupgma/clustering_round/bin TO: /Users/biocbuild/bbs-3.21-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/RtmpY8SSD9/R.INSTALL74c82a68311b/netboost/src/mcupgma/clustering_util/bin TO: /Users/biocbuild/bbs-3.21-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /tmp/RtmpY8SSD9/R.INSTALL74c82a68311b/netboost/src/mcupgma/scripts TO: /Users/biocbuild/bbs-3.21-bioc/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/4.5-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" "netboost.buildbin-libdir/netboost/libs/netboost.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" "netboost.buildbin-libdir/netboost/libs/netboost.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" "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/4.5-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)