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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL netboost
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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 /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc accepts -g... yes
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc option to accept ISO C89... none needed
checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc... none
checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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<true,false,true>(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<false,false,true>(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}
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c dist_tom.cpp -o dist_tom.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/RcppParallel.h:24,
                 from dist_tom.cpp:16:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘long unsigned int’ to ‘tbb::atomic<long unsigned int>&’ does not use ‘constexpr tbb::atomic<long unsigned int>::atomic(long unsigned int)’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/tbb/atomic.h: In instantiation of ‘tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = tbb::interface5::internal::hash_map_base::bucket*]’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/RcppParallel/include/tbb/atomic.h:544:12: warning: casting ‘tbb::interface5::internal::hash_map_base::bucket*’ to ‘tbb::atomic<tbb::interface5::internal::hash_map_base::bucket*>&’ does not use ‘constexpr tbb::atomic<T*>::atomic(T*) [with T = tbb::interface5::internal::hash_map_base::bucket]’ [-Wcast-user-defined]
  544 |     return (atomic<T>&)t;
      |            ^~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c tree_sort.cpp -o tree_sort.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -L/home/biocbuild/R/R/lib -lR
strip -S netboost.so
installing via 'install.libs.R' to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /home/biocbuild/bbs-3.21-bioc/meat/netboost"
[1] "R_PACKAGE_DIR:  /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/scripts/install_path.mk"
make: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma'
Clean build.
make: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma'
make: Entering directory '/home/biocbuild/bbs-3.21-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-3.21-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-3.21-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-3.21-bioc/meat/netboost/src/mcupgma/clustering_round'
mkdir -p dep.aarch64_Linux 
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/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/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_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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  150 |     struct fCompareEdgesByLowerBound : public binary_function<tEdge, tEdge, bool> {
      |                                               ^~~~~~~~~~~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/refwrap.h:39,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/vector:68,
                 from HierarchicalClustering_with_unknown_edges.hpp:40:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  177 |   struct fCompareEdgesByUpperBound : public binary_function<tEdge, tEdge, bool> {
      |                                             ^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  259 |    struct fIsClusterInvalid : unary_function<tClusterId, bool> {
      |                               ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  150 |     struct fCompareEdgesByLowerBound : public binary_function<tEdge, tEdge, bool> {
      |                                               ^~~~~~~~~~~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/refwrap.h:39,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/vector:68,
                 from HierarchicalClustering_with_unknown_edges.hpp:40:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  177 |   struct fCompareEdgesByUpperBound : public binary_function<tEdge, tEdge, bool> {
      |                                             ^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  259 |    struct fIsClusterInvalid : unary_function<tClusterId, bool> {
      |                               ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/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-3.21-bioc/meat/netboost/src/mcupgma/clustering_round'
make: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma'
[1] "SRC:  /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma"
[1] "DEST: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)