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### Running command:
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###   F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL HIBAG
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* installing to library 'F:/biocbuild/bbs-3.22-bioc/R/library'
* installing *source* package 'HIBAG' ...
** this is package 'HIBAG' version '1.45.0'
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 14.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c HIBAG.cpp -o HIBAG.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24,
                 from HIBAG.cpp:32:
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
F:/biocbuild/bbs-3.22-bioc/R/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);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/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;
      |            ^~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/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*]':
F:/biocbuild/bbs-3.22-bioc/R/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 )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/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;
      |            ^~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c LibHLA.cpp -o LibHLA.o
In file included from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/tbb.h:32,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel/TBB.h:10,
                 from F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/RcppParallel.h:24,
                 from LibHLA.cpp:49:
F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include/tbb/atomic.h: In instantiation of 'tbb::atomic<T>& tbb::internal::as_atomic(T&) [with T = long unsigned int]':
F:/biocbuild/bbs-3.22-bioc/R/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);
      |                    ~~~~~~~~~^~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/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;
      |            ^~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/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*]':
F:/biocbuild/bbs-3.22-bioc/R/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 )
      |                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~
F:/biocbuild/bbs-3.22-bioc/R/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;
      |            ^~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512bw.cpp -c -o LibHLA_ext_avx512bw.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512f.cpp -c -o LibHLA_ext_avx512f.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -ffixed-xmm16 -ffixed-xmm17 -ffixed-xmm18 -ffixed-xmm19 -ffixed-xmm20 -ffixed-xmm21 -ffixed-xmm22 -ffixed-xmm23 -ffixed-xmm24 -ffixed-xmm25 -ffixed-xmm26 -ffixed-xmm27 -ffixed-xmm28 -ffixed-xmm29 -ffixed-xmm30 -ffixed-xmm31 LibHLA_ext_avx512vpopcnt.cpp -c -o LibHLA_ext_avx512vpopcnt.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"   -DRCPP_PARALLEL_USE_TBB=1 -I../inst/include   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
gcc  -I"F:/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall -std=gnu2x  -mfpmath=sse -msse2 -mstackrealign   -c samtools_ext.c -o samtools_ext.o
g++ -shared -s -static-libgcc -o HIBAG.dll tmp.def HIBAG.o LibHLA.o LibHLA_ext_avx.o LibHLA_ext_avx2.o LibHLA_ext_avx512bw.o LibHLA_ext_avx512f.o LibHLA_ext_avx512vpopcnt.o LibHLA_ext_sse2.o LibHLA_ext_sse4_2.o samtools_ext.o -LF:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/libs/x64 -lRcppParallel -LF:/biocbuild/bbs-3.22-bioc/R/library/RcppParallel/lib/x64 -ltbb -ltbbmalloc -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.22-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.22-bioc/R/library/00LOCK-HIBAG/00new/HIBAG/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HIBAG)