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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL HIBAG
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘HIBAG’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c HIBAG.cpp -o HIBAG.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA.cpp -o LibHLA.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_avx.cpp -o LibHLA_ext_avx.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_avx2.cpp -o LibHLA_ext_avx2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_avx512bw.cpp -o LibHLA_ext_avx512bw.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_avx512f.cpp -o LibHLA_ext_avx512f.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_avx512vpopcnt.cpp -o LibHLA_ext_avx512vpopcnt.o
LibHLA_ext_avx512vpopcnt.cpp: In static member function ‘static HLA_LIB::THLAType HLA_LIB::CAlg_Prediction::_BestGuess_avx512vpopcnt(const HLA_LIB::CHaplotypeList&, const HLA_LIB::TGenotype&)’:
LibHLA_ext_avx512vpopcnt.cpp:239:81: warning: ‘GS.TGenoStruct_512vpopcnt::S2_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  239 |                         __m512i va_1 = (H1_1_8 ^ S1_1) & MASK_1, vb_1 = (H2_1_8 ^ S2_1) & MASK_1;
      |                                                                         ~~~~~~~~^~~~~~~
LibHLA_ext_avx512vpopcnt.cpp:358:38: note: ‘GS.TGenoStruct_512vpopcnt::S2_1’ was declared here
  358 |         const TGenoStruct_512vpopcnt GS(Haplo, Geno);
      |                                      ^~
LibHLA_ext_avx512vpopcnt.cpp:237:90: warning: ‘GS.TGenoStruct_512vpopcnt::S1_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  237 |                         __m512i MASK_1 = SIMD_ANDNOT_I512(M_1, (H1_1_8 ^ S2_1) | (H2_1_8 ^ S1_1));
      |                                                                                          ^
LibHLA_ext_avx512vpopcnt.cpp:358:38: note: ‘GS.TGenoStruct_512vpopcnt::S1_1’ was declared here
  358 |         const TGenoStruct_512vpopcnt GS(Haplo, Geno);
      |                                      ^~
LibHLA_ext_avx512vpopcnt.cpp: In static member function ‘static double HLA_LIB::CAlg_Prediction::_PostProb_avx512vpopcnt(const HLA_LIB::CHaplotypeList&, const HLA_LIB::TGenotype&, const HLA_LIB::THLAType&)’:
LibHLA_ext_avx512vpopcnt.cpp:239:81: warning: ‘GS.TGenoStruct_512vpopcnt::S2_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  239 |                         __m512i va_1 = (H1_1_8 ^ S1_1) & MASK_1, vb_1 = (H2_1_8 ^ S2_1) & MASK_1;
      |                                                                         ~~~~~~~~^~~~~~~
LibHLA_ext_avx512vpopcnt.cpp:431:38: note: ‘GS.TGenoStruct_512vpopcnt::S2_1’ was declared here
  431 |         const TGenoStruct_512vpopcnt GS(Haplo, Geno);
      |                                      ^~
LibHLA_ext_avx512vpopcnt.cpp:237:90: warning: ‘GS.TGenoStruct_512vpopcnt::S1_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  237 |                         __m512i MASK_1 = SIMD_ANDNOT_I512(M_1, (H1_1_8 ^ S2_1) | (H2_1_8 ^ S1_1));
      |                                                                                          ^
LibHLA_ext_avx512vpopcnt.cpp:431:38: note: ‘GS.TGenoStruct_512vpopcnt::S1_1’ was declared here
  431 |         const TGenoStruct_512vpopcnt GS(Haplo, Geno);
      |                                      ^~
LibHLA_ext_avx512vpopcnt.cpp: In static member function ‘static double HLA_LIB::CAlg_Prediction::_PostProb2_avx512vpopcnt(const HLA_LIB::CHaplotypeList&, const HLA_LIB::TGenotype&, double*)’:
LibHLA_ext_avx512vpopcnt.cpp:239:81: warning: ‘GS.TGenoStruct_512vpopcnt::S2_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  239 |                         __m512i va_1 = (H1_1_8 ^ S1_1) & MASK_1, vb_1 = (H2_1_8 ^ S2_1) & MASK_1;
      |                                                                         ~~~~~~~~^~~~~~~
LibHLA_ext_avx512vpopcnt.cpp:500:38: note: ‘GS.TGenoStruct_512vpopcnt::S2_1’ was declared here
  500 |         const TGenoStruct_512vpopcnt GS(Haplo, Geno);
      |                                      ^~
LibHLA_ext_avx512vpopcnt.cpp:237:90: warning: ‘GS.TGenoStruct_512vpopcnt::S1_1’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  237 |                         __m512i MASK_1 = SIMD_ANDNOT_I512(M_1, (H1_1_8 ^ S2_1) | (H2_1_8 ^ S1_1));
      |                                                                                          ^
LibHLA_ext_avx512vpopcnt.cpp:500:38: note: ‘GS.TGenoStruct_512vpopcnt::S1_1’ was declared here
  500 |         const TGenoStruct_512vpopcnt GS(Haplo, Geno);
      |                                      ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_sse2.cpp -o LibHLA_ext_sse2.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c LibHLA_ext_sse4_2.cpp -o LibHLA_ext_sse4_2.o
gcc -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppParallel/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.19-bioc/R/lib -L/usr/local/lib -o HIBAG.so 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 -lgcc -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/site-library/00LOCK-HIBAG/00new/HIBAG/libs
** 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 (HIBAG)