############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL netboost ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘netboost’ ... ** this is package ‘netboost’ version ‘2.19.0’ ** using staged installation 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 -std=gnu2x 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 -std=gnu2x accepts -g... yes checking for clang -arch arm64 -std=gnu2x option to accept ISO C89... unsupported checking whether clang -arch arm64 -std=gnu2x 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 -std=gnu2x... none checking how to run the C preprocessor... clang -arch arm64 -std=gnu2x -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-1500.1.0.2.5)’ using C++11 using SDK: ‘MacOSX11.3.1.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. In file included from dist_tom.cpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/RcppCommon.h:30: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages] #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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 'CxxFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. In file included from tree_sort.cpp:12: In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/RcppCommon.h:30: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include/Rcpp/r/check_r_headers.h:27:13: warning: R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410 [-W#pragma-messages] #pragma message "R.h has been included before any Rcpp headers. This can lead to hard-to-debug errors, and is not necessary. See https://github.com/RcppCore/Rcpp/issues/1410" ^ 1 warning generated. 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 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 'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. 'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'. strip -S netboost.so installing via 'install.libs.R' to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-netboost/00new/netboost [1] "R_PACKAGE_SRC: /Users/biocbuild/bbs-3.23-bioc/meat/netboost" [1] "R_PACKAGE_DIR: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-netboost/00new/netboost" [1] "R_ARCH: " [1] "SHLIB_EXT: .so" [1] "INSTALL PATH: /Users/biocbuild/bbs-3.23-bioc/meat/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: /Users/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma" [1] "DEST: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /Users/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /Users/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /Users/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/scripts TO: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/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)