############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf netboost.buildbin-libdir && mkdir netboost.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh netboost_2.14.0.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_2.14.0.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' requested here return boost->filter_column_gen(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' requested here return boost->filter_column_gen(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/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost [1] "R_PACKAGE_SRC: /tmp/RtmpHpn5ZI/R.INSTALL42944eedbc10/netboost" [1] "R_PACKAGE_DIR: /Users/biocbuild/bbs-3.20-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost" [1] "R_ARCH: " [1] "SHLIB_EXT: .so" [1] "INSTALL PATH: /tmp/RtmpHpn5ZI/R.INSTALL42944eedbc10/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/RtmpHpn5ZI/R.INSTALL42944eedbc10/netboost/src/mcupgma" [1] "DEST: /Users/biocbuild/bbs-3.20-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /tmp/RtmpHpn5ZI/R.INSTALL42944eedbc10/netboost/src/mcupgma/clustering_round/bin TO: /Users/biocbuild/bbs-3.20-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /tmp/RtmpHpn5ZI/R.INSTALL42944eedbc10/netboost/src/mcupgma/clustering_util/bin TO: /Users/biocbuild/bbs-3.20-bioc/meat/netboost.buildbin-libdir/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /tmp/RtmpHpn5ZI/R.INSTALL42944eedbc10/netboost/src/mcupgma/scripts TO: /Users/biocbuild/bbs-3.20-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/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.2) /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 4.4.2) /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)