############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL netboost ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘netboost’ ... ** 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... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu 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: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4.1/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4.1/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c boosting.cpp -o boosting.o boosting.cpp: In constructor 'Boosting::Boosting(const Rcpp::NumericMatrix&, unsigned int, double)': boosting.cpp:415:71: warning: format '%d' expects argument of type 'int', but argument 4 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 415 | Rprintf( " DATA POINTER REAL LENGTH: %li / %li dbl (matrix: %d -- max %d)\n", | ~^ | | | int | %ld ...... 418 | (col+1) * nrow, | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} boosting.cpp:415:81: warning: format '%d' expects argument of type 'int', but argument 5 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 415 | Rprintf( " DATA POINTER REAL LENGTH: %li / %li dbl (matrix: %d -- max %d)\n", | ~^ | | | int | %ld ...... 419 | (col+1) * (nrow + 256/sizeof(double)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} boosting.cpp: In instantiation of 'Rcpp::IntegerVector Boosting::filter_column_gen(size_t) [with bool AVX = true; bool FMA = false; bool ALIGNED = true; Rcpp::IntegerVector = Rcpp::Vector<13>; size_t = long unsigned int]': boosting.cpp:729:53: required from here 729 | return boost->filter_column_gen(col_y-1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ boosting.cpp:645:44: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 645 | Rprintf( "C STEP: %d (ACTUAL_SEL: %d, UPDATE: %f)\n ", | ~^ | | | int | %ld 646 | bstep + 1, actual_sel + 1, actual_update); | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} boosting.cpp: In instantiation of 'Rcpp::IntegerVector Boosting::filter_column_gen(size_t) [with bool AVX = false; bool FMA = false; bool ALIGNED = true; Rcpp::IntegerVector = Rcpp::Vector<13>; size_t = long unsigned int]': boosting.cpp:732:54: required from here 732 | return boost->filter_column_gen(col_y-1); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ boosting.cpp:645:44: warning: format '%d' expects argument of type 'int', but argument 3 has type 'size_t' {aka 'long unsigned int'} [-Wformat=] 645 | Rprintf( "C STEP: %d (ACTUAL_SEL: %d, UPDATE: %f)\n ", | ~^ | | | int | %ld 646 | bstep + 1, actual_sel + 1, actual_update); | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4.1/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c dist_tom.cpp -o dist_tom.o In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb.h:32, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel/TBB.h:10, from /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/RcppParallel.h:24, from dist_tom.cpp:16: /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = long unsigned int]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/tbb_thread.h:251:29: required from here 251 | return as_atomic(location.my_id).compare_and_swap(value.my_id, comparand.my_id); | ~~~~~~~~~^~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'long unsigned int' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(long unsigned int)' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]': /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/concurrent_hash_map.h:291:31: required from here 291 | && as_atomic(my_table[new_seg]).compare_and_swap(is_allocating, NULL) == NULL ) | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting 'tbb::interface5::internal::hash_map_base::bucket*' to 'tbb::atomic&' does not use 'constexpr tbb::atomic::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]' [-Wcast-user-defined] 544 | return (atomic&)t; | ^~~~~~~~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/include/R.h:73, from dist_tom.cpp:14: /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function 'void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]': /home/biocbuild/R/R-4.4.1/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion] 69 | #define warning Rf_warning | ^~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro 'warning' 46 | inline void warning(const char* fmt, Args&&... args ) { | ^~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions.h:180, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:130, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27, from dist_tom.cpp:15: /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call 47 | Rf_warning("%s", tfm::format(fmt, std::forward(args)... ).c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppParallel/include' -I/usr/local/include `/home/biocbuild/R/R-4.4.1/bin/Rscript -e "Rcpp:::CxxFlags()"` -fPIC -g -O2 -Wall -c tree_sort.cpp -o tree_sort.o In file included from /home/biocbuild/R/R-4.4.1/include/R.h:73, from tree_sort.cpp:11: /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h: In function 'void Rcpp::Rf_warning(const char*, Args&& ...) [with Args = {const char*}]': /home/biocbuild/R/R-4.4.1/include/R_ext/Error.h:69:17: warning: infinite recursion detected [-Winfinite-recursion] 69 | #define warning Rf_warning | ^~~~~~~~~~ /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:46:13: note: in expansion of macro 'warning' 46 | inline void warning(const char* fmt, Args&&... args ) { | ^~~~~~~ In file included from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions.h:180, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/RcppCommon.h:130, from /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp.h:27, from tree_sort.cpp:12: /home/biocbuild/R/R-4.4.1/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call 47 | Rf_warning("%s", tfm::format(fmt, std::forward(args)... ).c_str()); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -L/home/biocbuild/R/R-4.4.1/lib -lR strip -S netboost.so installing via 'install.libs.R' to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-netboost/00new/netboost [1] "R_PACKAGE_SRC: /home/biocbuild/bbs-3.20-bioc/meat/netboost" [1] "R_PACKAGE_DIR: /home/biocbuild/R/R-4.4.1/site-library/00LOCK-netboost/00new/netboost" [1] "R_ARCH: " [1] "SHLIB_EXT: .so" [1] "INSTALL PATH: /home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/scripts/install_path.mk" make: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma' Clean build. make: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma' make: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma' ==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively make -C clustering_util -f Makefile mcupgma_install make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_util' mkdir -p bin mkdir -p obj.aarch64_Linux g++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c g++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/ClusteringUtil.o ClusteringUtil.cpp g++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/Tree.o Tree.cpp g++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edges2valid_clusters HashingMergerMain.cpp obj.aarch64_Linux/HashingMergerMain.cmdline.o obj.aarch64_Linux/ClusteringUtil.o obj.aarch64_Linux/Tree.o g++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.aarch64_Linux/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c g++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edge_collator EdgeCollatorMain.cpp obj.aarch64_Linux/EdgeCollatorMain.cmdline.o obj.aarch64_Linux/ClusteringUtil.o obj.aarch64_Linux/Tree.o make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_util' ==== compiling sources using external Makefile (clustering_round/Makefile) recursively make -C clustering_round -f Makefile make[1]: Entering directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_round' mkdir -p dep.aarch64_Linux test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/test_heap.d obj.aarch64_Linux/test_heap.o obj.aarch64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.aarch64_Linux/test_heap.d test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o obj.aarch64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_main.d obj.aarch64_Linux/HierarchicalClustering_main.o obj.aarch64_Linux.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.aarch64_Linux/HierarchicalClustering_main.d test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/test_heap.d obj.aarch64_Linux/test_heap.o obj.aarch64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.aarch64_Linux/test_heap.d test -d dep.aarch64_Linux && g++ -MM -MT 'dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o obj.aarch64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.aarch64_Linux/HierarchicalClustering_with_unknown_edges.d mkdir -p obj.aarch64_Linux mkdir -p bin g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.aarch64_Linux/HierarchicalClustering_main.o In file included from HierarchicalClustering_main.cpp:96: HierarchicalClustering_with_unknown_edges.hpp:150:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 150 | struct fCompareEdgesByLowerBound : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/refwrap.h:39, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/vector:68, from HierarchicalClustering_with_unknown_edges.hpp:40: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 177 | struct fCompareEdgesByUpperBound : public binary_function { | ^~~~~~~~~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 259 | struct fIsClusterInvalid : unary_function { | ^~~~~~~~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.aarch64_Linux/HierarchicalClustering_main.cmdline.o g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o In file included from HierarchicalClustering_with_unknown_edges.cpp:28: HierarchicalClustering_with_unknown_edges.hpp:150:47: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 150 | struct fCompareEdgesByLowerBound : public binary_function { | ^~~~~~~~~~~~~~~ In file included from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/refwrap.h:39, from /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/vector:68, from HierarchicalClustering_with_unknown_edges.hpp:40: /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 177 | struct fCompareEdgesByUpperBound : public binary_function { | ^~~~~~~~~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: 'template struct std::unary_function' is deprecated [-Wdeprecated-declarations] 259 | struct fIsClusterInvalid : unary_function { | ^~~~~~~~~~~~~~ /home/biocbuild/miniforge3/lib/gcc/aarch64-conda-linux-gnu/14.2.0/include/c++/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ obj.aarch64_Linux/HierarchicalClustering_main.o obj.aarch64_Linux/HierarchicalClustering_main.cmdline.o obj.aarch64_Linux/HierarchicalClustering_with_unknown_edges.o -o bin/hierarchical_clustering -O3 g++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.aarch64_Linux/test_heap.o cc -O3 -I./ -c test_heap.cmdline.c -o obj.aarch64_Linux/test_heap.cmdline.o g++ obj.aarch64_Linux/test_heap.o obj.aarch64_Linux/test_heap.cmdline.o -o bin/test_heap -O3 make[1]: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_round' make: Leaving directory '/home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma' [1] "SRC: /home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma" [1] "DEST: /home/biocbuild/R/R-4.4.1/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /home/biocbuild/R/R-4.4.1/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /home/biocbuild/R/R-4.4.1/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /home/biocbuild/bbs-3.20-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/R/R-4.4.1/site-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)