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###
### Running command:
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###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL netboost
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/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... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
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... 50657:8400800:7ffefbff:bfebfbff
checking for x86 cpuid 0x00000007 output... 0:d39ff7eb:818:bc000400
checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800
checking for x86-AVX xgetbv 0x00000000 output... 2ff: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... yes
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... yes
checking whether C compiler accepts -mavx512f... yes
checking whether AVX512-CD is supported by the processor... yes
checking whether AVX512-CD is supported by the processor and OS... yes
checking whether C compiler accepts -mavx512cd... yes
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... yes
checking whether C compiler accepts -mavx512vl... yes
checking whether AVX512-BW is supported by the processor... yes
checking whether AVX512-BW is supported by the processor and OS... yes
checking whether C compiler accepts -mavx512bw... yes
checking whether AVX512-DQ is supported by the processor... yes
checking whether AVX512-DQ is supported by the processor and OS... yes
checking whether C compiler accepts -mavx512dq... yes
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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic  -g -O2  -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic  -g -O2  -Wall -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
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
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/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic  -g -O2  -Wall -DR_NO_REMAP -c dist_tom.cpp -o dist_tom.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include  -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic  -g -O2  -Wall -DR_NO_REMAP -c tree_sort.cpp -o tree_sort.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
strip -S netboost.so
installing via 'install.libs.R' to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /home/biocbuild/bbs-3.21-bioc/meat/netboost"
[1] "R_PACKAGE_DIR:  /home/biocbuild/bbs-3.21-bioc/R/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.x86_64_Linux
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/ClusteringUtil.o ClusteringUtil.cpp
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/Tree.o Tree.cpp
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG   -o bin/edges2valid_clusters HashingMergerMain.cpp obj.x86_64_Linux/HashingMergerMain.cmdline.o obj.x86_64_Linux/ClusteringUtil.o obj.x86_64_Linux/Tree.o 
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c
g++ -Wall  -Wno-deprecated -O3 -DNDEBUG  -o bin/edge_collator EdgeCollatorMain.cpp obj.x86_64_Linux/EdgeCollatorMain.cmdline.o obj.x86_64_Linux/ClusteringUtil.o obj.x86_64_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.x86_64_Linux 
test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/test_heap.d  obj.x86_64_Linux/test_heap.o  obj.x86_64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.x86_64_Linux/test_heap.d
test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d  obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o  obj.x86_64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d
test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/HierarchicalClustering_main.d  obj.x86_64_Linux/HierarchicalClustering_main.o  obj.x86_64_Linux.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.x86_64_Linux/HierarchicalClustering_main.d
test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/test_heap.d  obj.x86_64_Linux/test_heap.o  obj.x86_64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.x86_64_Linux/test_heap.d
test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d  obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o  obj.x86_64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d
mkdir -p obj.x86_64_Linux 
mkdir -p bin
g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.x86_64_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 /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from HierarchicalClustering_with_unknown_edges.hpp:40:
/usr/include/c++/13/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> {
      |                                             ^~~~~~~~~~~~~~~
/usr/include/c++/13/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> {
      |                               ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.x86_64_Linux/HierarchicalClustering_main.cmdline.o
g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.x86_64_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 /usr/include/c++/13/bits/refwrap.h:39,
                 from /usr/include/c++/13/vector:68,
                 from HierarchicalClustering_with_unknown_edges.hpp:40:
/usr/include/c++/13/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> {
      |                                             ^~~~~~~~~~~~~~~
/usr/include/c++/13/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> {
      |                               ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
g++ obj.x86_64_Linux/HierarchicalClustering_main.o obj.x86_64_Linux/HierarchicalClustering_main.cmdline.o obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o  -o bin/hierarchical_clustering  -O3
g++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.x86_64_Linux/test_heap.o
cc -O3 -I./ -c test_heap.cmdline.c -o obj.x86_64_Linux/test_heap.cmdline.o
g++ obj.x86_64_Linux/test_heap.o obj.x86_64_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/bbs-3.21-bioc/R/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/bbs-3.21-bioc/R/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/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/bbs-3.21-bioc/R/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)