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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-devel_2025-02-19/site-library’
* installing *source* package ‘netboost’ ...
** this is package ‘netboost’ version ‘2.19.3’
** 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 -std=gnu23
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 -std=gnu23 accepts -g... yes
checking for /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 option to accept ISO C89... none needed
checking whether /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 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 -std=gnu23... none
checking how to run the C preprocessor... /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security  -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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security  -c boosting.cpp -o boosting.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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security  -c dist_tom.cpp -o dist_tom.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/tbb/tbb.h:32,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include/RcppParallel.h:24,
                 from dist_tom.cpp:16:
/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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-devel_2025-02-19/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;
      |            ^~~~~~~~~~~~~
In file included from /home/biocbuild/R/R/include/R.h:73,
                 from dist_tom.cpp:14:
/home/biocbuild/R/R-devel_2025-02-19/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/include/R_ext/Error.h:114:17: warning: infinite recursion detected [-Winfinite-recursion]
  114 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include/Rcpp/exceptions.h:180,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/RcppCommon.h:130,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp.h:27,
                 from dist_tom.cpp:15:
/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
   47 |     Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppParallel/include' -I/usr/local/include   `/home/biocbuild/R/R/bin/Rscript -e "Rcpp:::CxxFlags()"`  -fPIC  -g -O2  -Wall -Werror=format-security  -c tree_sort.cpp -o tree_sort.o
In file included from /home/biocbuild/R/R/include/R.h:73,
                 from tree_sort.cpp:11:
/home/biocbuild/R/R-devel_2025-02-19/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/include/R_ext/Error.h:114:17: warning: infinite recursion detected [-Winfinite-recursion]
  114 | #define warning Rf_warning
      |                 ^~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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-devel_2025-02-19/site-library/Rcpp/include/Rcpp/exceptions.h:180,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/RcppCommon.h:130,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp.h:27,
                 from tree_sort.cpp:12:
/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include/Rcpp/exceptions/cpp11/exceptions.h:47:15: note: recursive call
   47 |     Rf_warning("%s", tfm::format(fmt, std::forward<Args>(args)... ).c_str());
      |     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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-devel_2025-02-19/site-library/00LOCK-netboost/00new/netboost
[1] "R_PACKAGE_SRC:  /home/biocbuild/bbs-3.23-bioc/meat/netboost"
[1] "R_PACKAGE_DIR:  /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-netboost/00new/netboost"
[1] "R_ARCH:         "
[1] "SHLIB_EXT:      .so"
[1] "INSTALL PATH:  /home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/scripts/install_path.mk"
make: Entering directory '/home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma'
Clean build.
make: Leaving directory '/home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma'
make: Entering directory '/home/biocbuild/bbs-3.23-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-3.23-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-3.23-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-3.23-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
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
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-3.23-bioc/meat/netboost/src/mcupgma/clustering_round'
make: Leaving directory '/home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma'
[1] "SRC:  /home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma"
[1] "DEST: /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-netboost/00new/netboost/mcupgma"
[1] "INSTALL FROM: /home/biocbuild/bbs-3.23-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/R/R-devel_2025-02-19/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
Error: package or namespace load failed for ‘netboost’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘Biostrings’
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/netboost’
* restoring previous ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/netboost’